US20210047654A1 - Rna-targeting fusion protein compositions and methods for use - Google Patents

Rna-targeting fusion protein compositions and methods for use Download PDF

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US20210047654A1
US20210047654A1 US17/001,318 US202017001318A US2021047654A1 US 20210047654 A1 US20210047654 A1 US 20210047654A1 US 202017001318 A US202017001318 A US 202017001318A US 2021047654 A1 US2021047654 A1 US 2021047654A1
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rna
sequence
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David A. Nelles
Ranjan Batra
Eugene Yeo
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Locanabio Inc
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    • C12N2750/14011—Parvoviridae
    • C12N2750/14111—Dependovirus, e.g. adenoassociated viruses
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    • C12N2830/008—Vector systems having a special element relevant for transcription cell type or tissue specific enhancer/promoter combination

Definitions

  • the disclosure is directed to molecular biology, and more, specifically, to compositions and methods for modifying expression and activity of RNA molecules.
  • compositions and methods for specifically targeting RNA molecules in sequence-specific manner that further precludes modification of DNA sequences There has been a long-felt but unmet need in the art for a method of specifically binding target RNA molecules for modification of expression or activity of the RNA molecule or a protein encoded by the RNA molecule.
  • the disclosure provides compositions and methods for specifically targeting RNA molecules in sequence-specific manner that further precludes modification of DNA sequences.
  • composition comprising (a) a sequence comprising a guide RNA (gRNA) that specifically binds a target sequence within an RNA molecule and (b) a sequence encoding a fusion protein, the sequence comprising a sequence encoding a first RNA-binding polypeptide and a sequence encoding a second RNA-binding polypeptide, wherein neither the first RNA-binding polypeptide nor the second RNA-binding polypeptide comprises a significant DNA-nuclease activity, wherein the first RNA-binding polypeptide and the second RNA-binding polypeptide are not identical, and wherein the second RNA-binding polypeptide comprises an RNA-nuclease activity wherein the first RNA-binding polypeptide and the second RNA-binding polypeptide are not identical, and wherein the second RNA-binding polypeptide comprises an RNA-nuclease activity.
  • gRNA guide RNA
  • the disclosure also provides a composition comprising a sequence encoding an RNA-guided target RNA-binding fusion protein comprising (a) a sequence encoding a first RNA-binding polypeptide or portion thereof; and (b) a sequence encoding a second RNA-binding polypeptide, wherein the first RNA-binding polypeptide binds a target RNA guided by a gRNA sequence, and wherein the second RNA-binding polypeptide comprises RNA-nuclease activity.
  • the disclosure additionally provides a composition comprising a sequence encoding a target RNA-binding fusion protein comprising (a) a sequence encoding a first RNA-binding polypeptide or portion thereof; and (b) a sequence encoding a second RNA-binding polypeptide, wherein the first RNA-binding polypeptide binds a target RNA without a gRNA sequence, and wherein the second RNA-binding polypeptide comprises RNA-nuclease activity.
  • the target sequence comprises at least one repeated sequence.
  • the sequence comprising the gRNA further comprises a sequence encoding a promoter capable of expressing the gRNA in a eukaryotic cell.
  • the eukaryotic cell is an animal cell.
  • the animal cell is a mammalian cell. In some embodiments, the animal cell is a human cell.
  • the promoter is a constitutively active promoter.
  • the promoter sequence is isolated or derived from a promoter capable of driving expression of an RNA polymerase.
  • the promoter sequence is isolated or derived from a U6 promoter.
  • the promoter is a sequence isolated or derived from a promoter capable of driving expression of a transfer RNA (tRNA).
  • tRNA transfer RNA
  • the promoter is isolated or derived from an alanine tRNA promoter, an arginine tRNA promoter, an asparagine tRNA promoter, an aspartic acid tRNA promoter, a cysteine tRNA promoter, a glutamine tRNA promoter, a glutamic acid tRNA promoter, a glycine tRNA promoter, a histidine tRNA promoter, an isoleucine tRNA promoter, a leucine tRNA promoter, a lysine tRNA promoter, a methionine tRNA promoter, a phenylalanine tRNA promoter, a proline tRNA promoter, a serine tRNA promoter, a threonine tRNA promoter, a tryptophan tRNA promoter, a tyrosine tRNA promoter, or a valine tRNA promoter. In some embodiments, the promoter is isolated or
  • the sequence comprising the gRNA further comprises a spacer sequence that specifically binds to the target RNA sequence.
  • the spacer sequence has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 87%, 90%, 95%, 97%, 99% or any percentage in between of complementarity to the target RNA sequence.
  • the spacer sequence has 100% complementarity to the target RNA sequence.
  • the spacer sequence comprises or consists of 20 nucleotides.
  • the spacer sequence comprises or consists of 21 nucleotides.
  • the spacer sequence comprises or consists of the sequence
  • the sequence comprising the gRNA further comprises a spacer sequence that specifically binds to the target RNA sequence.
  • the spacer sequence has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 87%, 90%, 95%, 97%, 99% or any percentage in between of complementarity to the target RNA sequence.
  • the spacer sequence has 100% complementarity to the target RNA sequence. In some embodiments, the spacer sequence comprises or consists of 20 nucleotides. In some embodiments, the spacer sequence comprises or consists of 21 nucleotides. In some embodiments, the spacer sequence comprises or consists of the sequence
  • the sequence comprising the gRNA further comprises a spacer sequence that specifically binds to the target RNA sequence.
  • the spacer sequence has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 87%, 90%, 95%, 97%, 99% or any percentage in between of complementarity to the target RNA sequence.
  • the spacer sequence has 100% complementarity to the target RNA sequence.
  • the spacer sequence comprises or consists of 20 nucleotides. In some embodiments, the spacer sequence comprises or consists of 21 nucleotides.
  • the spacer sequence comprises or consists of a sequence comprising at least 1, 2, 3, 4, 5, 6, or 7 repeats of the sequence CUG (SEQ ID NO: 18), CCUG (SEQ ID NO: 19), CAG (SEQ ID NO: 80), GGGGCC (SEQ ID NO: 81) or any combination thereof.
  • the sequence comprising the gRNA further comprises a scaffold sequence that specifically binds to the first RNA binding protein.
  • the scaffold sequence comprises a stem-loop structure.
  • the scaffold sequence comprises or consists of 90 nucleotides.
  • the scaffold sequence comprises or consists of 93 nucleotides.
  • the scaffold sequence comprises or consists of the sequence GUUUAAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUCCGUU AUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUUU (SEQ ID NO: 13).
  • the scaffold sequence comprises or consists of the sequence GGACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGG CACCGAGUCGGUGCUUUUU (SEQ ID NO: 17). In some embodiments, the scaffold sequence comprises or consists of the sequence
  • the gRNA does not bind or does not selectively bind to a second sequence within the RNA molecule.
  • an RNA genome or an RNA transcriptome comprises the RNA molecule.
  • the first RNA binding protein comprises a CRISPR-Cas protein.
  • the CRISPR-Cas protein is a Type II CRISPR-Cas protein.
  • the first RNA binding protein comprises a Cas9 polypeptide or an RNA-binding portion thereof.
  • the CRISPR-Cas protein comprises a native RNA nuclease activity.
  • the native RNA nuclease activity is reduced or inhibited.
  • the native RNA nuclease activity is increased or induced.
  • the CRISPR-Cas protein comprises a native DNA nuclease activity and the native DNA nuclease activity is inhibited.
  • the CRISPR-Cas protein comprises a mutation.
  • a nuclease domain of the CRISPR-Cas protein comprises the mutation.
  • the mutation occurs in a nucleic acid encoding the CRISPR-Cas protein.
  • the mutation occurs in an amino acid encoding the CRISPR-Cas protein.
  • the mutation comprises a substitution, an insertion, a deletion, a frameshift, an inversion, or a transposition.
  • the mutation comprises a deletion of a nuclease domain, a binding site within the nuclease domain, an active site within the nuclease domain, or at least one essential amino acid residue within the nuclease domain.
  • the first RNA binding protein comprises a CRISPR-Cas protein.
  • the CRISPR-Cas protein is a Type V CRISPR-Cas protein.
  • the first RNA binding protein comprises a Cpf1 polypeptide or an RNA-binding portion thereof.
  • the CRISPR-Cas protein comprises a native RNA nuclease activity.
  • the native RNA nuclease activity is reduced or inhibited.
  • the native RNA nuclease activity is increased or induced.
  • the CRISPR-Cas protein comprises a native DNA nuclease activity and the native DNA nuclease activity is inhibited.
  • the CRISPR-Cas protein comprises a mutation.
  • a nuclease domain of the CRISPR-Cas protein comprises the mutation.
  • the mutation occurs in a nucleic acid encoding the CRISPR-Cas protein.
  • the mutation occurs in an amino acid encoding the CRISPR-Cas protein.
  • the mutation comprises a substitution, an insertion, a deletion, a frameshift, an inversion, or a transposition.
  • the mutation comprises a deletion of a nuclease domain, a binding site within the nuclease domain, an active site within the nuclease domain, or at least one essential amino acid residue within the nuclease domain.
  • the first RNA binding protein comprises a CRISPR-Cas protein.
  • the CRISPR-Cas protein is a Type VI CRISPR-Cas protein.
  • the first RNA binding protein comprises a Cas13 polypeptide or an RNA-binding portion thereof.
  • the first RNA binding protein comprises a CasRx/Cas13d polypeptide or an RNA-binding portion thereof.
  • the CRISPR-Cas protein comprises a native RNA nuclease activity. In some embodiments, the native RNA nuclease activity is reduced or inhibited.
  • the native RNA nuclease activity is increased or induced.
  • the CRISPR-Cas protein comprises a native DNA nuclease activity and the native DNA nuclease activity is inhibited.
  • the CRISPR-Cas protein comprises a mutation.
  • a nuclease domain of the CRISPR-Cas protein comprises the mutation.
  • the mutation occurs in a nucleic acid encoding the CRISPR-Cas protein.
  • the mutation occurs in an amino acid encoding the CRISPR-Cas protein.
  • the mutation comprises a substitution, an insertion, a deletion, a frameshift, an inversion, or a transposition. In some embodiments, the mutation comprises a deletion of a nuclease domain, a binding site within the nuclease domain, an active site within the nuclease domain, or at least one essential amino acid residue within the nuclease domain.
  • the first RNA binding protein comprises a Pumilio and FBF (PUF) protein or an RNA binding portion thereof. In some embodiments, the first RNA binding protein comprises a Pumilio-based assembly (PUMBY) protein or an RNA binding portion thereof.
  • PAF Pumilio and FBF
  • PUMBY Pumilio-based assembly
  • the first RNA binding protein does not require multimerization for RNA-binding activity. In some embodiments, the first RNA binding protein is not a monomer of a multimer complex. In some embodiments, a multimer protein complex does not comprise the first RNA binding protein.
  • the first RNA binding protein selectively binds to a target sequence within the RNA molecule. In some embodiments, the first RNA binding protein does not comprise an affinity for a second sequence within the RNA molecule. In some embodiments, the first RNA binding protein does not comprise a high affinity for or selectively bind a second sequence within the RNA molecule.
  • an RNA genome or an RNA transcriptome comprises the RNA molecule.
  • the first RNA binding protein comprises between 2 and 1300 amino acids, inclusive of the endpoints.
  • the sequence encoding the first RNA binding protein further comprises a sequence encoding a nuclear localization signal (NLS), a nuclear export signal (NES) or tag.
  • the sequence encoding a nuclear localization signal (NLS) is positioned 3′ to the sequence encoding the first RNA binding protein.
  • the first RNA binding protein comprises an NLS at a C-terminus of the protein.
  • the sequence encoding the first RNA binding protein further comprises a first sequence encoding a first NLS and a second sequence encoding a second NLS. In some embodiments, the sequence encoding the first NLS or the second NLS is positioned 3′ to the sequence encoding the first RNA binding protein. In some embodiments, the first RNA binding protein comprises the first NLS or the second NLS at a C-terminus of the protein.
  • the second RNA binding protein comprises or consists of a nuclease domain. In some embodiments, the second RNA binding protein binds RNA in a manner in which it associates with RNA. In some embodiments, the second RNA binding protein associates with RNA in a manner in which it cleaves RNA.
  • the sequence encoding the second RNA binding protein comprises or consists of an RNAse.
  • the second RNA binding protein comprises or consists of an RNAse1.
  • the RNAse1 comprises or consists of SEQ ID NO: 20.
  • the second RNA binding protein comprises or consists of an RNAse4.
  • the RNAse4 comprises or consists of SEQ ID NO: 21.
  • the second RNA binding protein comprises or consists of an RNAse6.
  • the RNAse6 comprises or consists of SEQ ID NO: 22.
  • the second RNA binding protein comprises or consists of an RNAse7. In some embodiments, the RNAse7 comprises or consists of SEQ ID NO: 23. In some embodiments, the second RNA binding protein comprises or consists of an RNAse8. In some embodiments, the RNAse8 protein comprises or consists of SEQ ID NO: 24. In some embodiments, the second RNA binding protein comprises or consists of an RNAse2. In some embodiments, the RNAse2 protein comprises or consists of SEQ ID NO: 25. In some embodiments, the second RNA binding protein comprises or consists of an RNAse6PL. In some embodiments, the RNAse6PL protein comprises or consists of SEQ ID NO: 26.
  • the second RNA binding protein comprises or consists of an RNAseL. In some embodiments the RNAseL protein comprises or consists of SEQ ID NO: 27. In some embodiments, the second RNA binding protein comprises or consists of an RNAseT2. In some embodiments, the RNAseT2 protein comprises or consists of SEQ ID NO: 28. In some embodiments, the second RNA binding protein comprises or consists of an RNAse11. In some embodiments, the RNAse11 protein comprises or consists of SEQ ID NO: 29. In some embodiments, the second RNA binding protein comprises or consists of an RNAseT2-like. In some embodiments, the RNAseT2-like protein comprises or consists of SEQ ID NO: 30.
  • the second RNA binding protein comprises or consists of a mutated RNAse.
  • the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(K41R)) polypeptide.
  • the Rnase1 (K41R) polypeptide comprises or consists of SEQ ID NO: 116.
  • the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(K41R, D121E)) polypeptide.
  • the Rnase1 (Rnase1(K41R, D121E)) polypeptide comprises or consists of SEQ ID NO: 66.
  • the second RNA binding protein comprises or consists of a mutated Rnase1(Rnase1(K41R, D121E, H119N)) polypeptide.
  • the Rnase1(Rnase1(K41R, D121E, H119N)) polypeptide comprises or consists of SEQ ID NO: 118.
  • the second RNA binding protein comprises or consists of a mutated Rnase1.
  • the second RNA binding protein comprises or consists of a mutated Rnase1(Rnase1(H119N)) polypeptide.
  • the Rnase1(Rnase1(H119N)) polypeptide comprises or consists SEQ ID NO: 119.
  • the second RNA binding protein comprises or consists of a mutated Rnase1(Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide.
  • the Rnase1(Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide comprises or consists of SEQ ID NO: 120.
  • the second RNA binding protein comprises or consists of a mutated Rnase1(Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide.
  • the Rnase1(Rnase1(R39D, N67D, N88A, G89D, R91D, H119N, K41R, D121E)) polypeptide comprises or consists of SEQ ID NO: 121.
  • the second RNA binding protein comprises or consists of a mutated Rnase1(Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide.
  • the Rnase1(Rnase1(R39D, N67D, N88A, G89D, R91D)) polypeptide comprises or consists of SEQ ID NO: 122.
  • the second RNA binding protein comprises or consists of a NOB1 polypeptide.
  • the NOB1 polypeptide comprises or consists of SEQ ID NO: 31.
  • the second RNA binding protein comprises or consists of an endonuclease. In some embodiments, the second RNA binding protein comprises or consists of an endonuclease V (ENDOV). In some embodiments, the ENDOV protein comprises or consists of SEQ ID NO: 32. In some embodiments, the second RNA binding protein comprises or consists of an endonuclease G (ENDOG). In some embodiments, the ENDOG protein comprises or consists of SEQ ID NO: 33. In some embodiments, the second RNA binding protein comprises or consists of an endonuclease D1 (ENDOD1). In some embodiments, the ENDOD1 protein comprises or consists of SEQ ID NO: 34.
  • ENDOV endonuclease V
  • ENDOG endonuclease G
  • ENDOG protein endonuclease G
  • the ENDOG protein comprises or consists of SEQ ID NO: 33.
  • the second RNA binding protein comprises or consists of an endonucleas
  • the second RNA binding protein comprises or consists of a Human flap endonuclease-1 (hFEN1).
  • the hFEN1 protein comprises or consists of SEQ ID NO: 35.
  • the second RNA binding protein comprises or consists of a DNA repair endonuclease XPF (ERCC4) polypeptide.
  • the ERCC4 protein comprises or consists of SEQ ID NO: 64.
  • the second RNA binding protein comprises or consists of an Endonuclease III-like protein 1 (NTHL) polypeptide.
  • NTHL polypeptide comprises or consists of SEQ ID NO: 123.
  • the second RNA binding protein comprises or consists of a human Schlafen 14 (hSLFN14) polypeptide.
  • hSLFN14 polypeptide comprises or consists of SEQ ID NO: 36.
  • the second RNA binding protein comprises or consists of a human beta-lactamase-like protein 2 (hLACTB2) polypeptide.
  • hLACTB2 polypeptide comprises or consists of SEQ ID NO: 37.
  • the second RNA binding protein comprises or consists of an apurinic/apyrimidinic (AP) endodeoxyribonuclease (APEX) polypeptide.
  • the second RNA binding protein comprises or consists of an apurinic/apyrimidinic (AP) endodeoxyribonuclease (APEX2) polypeptide.
  • the APEX2 polypeptide comprises or consists of SEQ ID NO: 38.
  • the APEX2 polypeptide comprises or consists of SEQ ID NO: 39.
  • the second RNA binding protein comprises or consists of an apurinic or apyrimidinic site lyase (APEX1) polypeptide.
  • APEX1 polypeptide comprises or consists of SEQ ID NO: 125.
  • the second RNA binding protein comprises or consists of an angiogenin (ANG) polypeptide.
  • ANG polypeptide comprises or consists SEQ ID NO: 40.
  • the second RNA binding protein comprises or consists of a heat responsive protein 12 (HRSP12) polypeptide.
  • HRSP12 heat responsive protein 12
  • the HRSP12 polypeptide comprises or consists of SEQ ID NO: 41.
  • the second RNA binding protein comprises or consists of a Zinc Finger CCCH-Type Containing 12A (ZC3H12A) polypeptide.
  • ZC3H12A polypeptide comprises or consists of SEQ ID NO: 42.
  • the ZC3H12A polypeptide comprises or consists of SEQ ID NO: 43.
  • the second RNA binding protein comprises or consists of a Reactive Intermediate Imine Deaminase A (RIDA) polypeptide.
  • RIDA Reactive Intermediate Imine Deaminase A
  • the RIDA polypeptide comprises or consists of SEQ ID NO: 44.
  • the second RNA binding protein comprises or consists of a Phospholipase D Family Member 6 (PDL6) polypeptide.
  • PDL6 polypeptide comprises or consists of SEQ ID NO: 126.
  • the second RNA binding protein comprises or consists of a mitochondrial ribonuclease P catalytic subunit (KIAA0391) polypeptide.
  • the KIAA0391 polypeptide comprises or consists of SEQ ID NO: 127.
  • the second RNA binding protein comprises or consists of an argonaute 2 (AGO2) polypeptide.
  • the AGO2 polypeptide comprises or consists of SEQ ID NO: 128.
  • the second RNA binding protein comprises or consists of a mitochondrial nuclease EXOG (EXOG) polypeptide.
  • EXOG mitochondrial nuclease EXOG
  • the EXOG polypeptide comprises or consists of SEQ ID NO: 129.
  • the second RNA binding protein comprises or consists of a Zinc Finger CCCH-Type Containing 12D (ZC3H12D) polypeptide.
  • ZC3H12D polypeptide comprises or consists of SEQ ID NO: 130.
  • the second RNA binding protein comprises or consists of an endoplasmic reticulum to nucleus signaling 2 (ERN2) polypeptide.
  • ERN2 polypeptide comprises or consists of SEQ ID NO: 131.
  • the second RNA binding protein comprises or consists of a pelota mRNA surveillance and ribosome rescue factor (PELO) polypeptide.
  • the PELO polypeptide comprises or consists of SEQ ID NO: 132.
  • the second RNA binding protein comprises or consists of a YBEY metallopeptidase (YBEY) polypeptide.
  • YBEY YBEY metallopeptidase
  • the YBEY polypeptide comprises or consists of SEQ ID NO: 133.
  • the second RNA binding protein comprises or consists of a cleavage and polyadenylation specific factor 4 like (CPSF4L) polypeptide.
  • CPSF4L polypeptide comprises or consists of SEQ ID NO: 134.
  • the second RNA binding protein comprises or consists of an hCG_2002731 polypeptide.
  • the hCG_2002731 comprises or consists of SEQ ID NO: 135.
  • the hCG_2002731 polypeptide comprises or consists of SEQ ID NO: 136.
  • the second RNA binding protein comprises or consists of an Excision Repair Cross-Complementation Group 1 (ERCC1) polypeptide.
  • ERCC1 polypeptide comprises or consists of SEQ ID NO: 137.
  • the second RNA binding protein comprises or consists of a ras-related C3 botulinum toxin substrate 1 isoform (RAC1) polypeptide.
  • RAC1 polypeptide comprises or consists of SEQ ID NO: 138.
  • the second RNA binding protein comprises or consists of a Ribonuclease A A1 (RAA1) polypeptide.
  • RAA1 polypeptide comprises or consists of SEQ ID NO: 139.
  • the second RNA binding protein comprises or consists of a Ras Related Protein (RAB1) polypeptide.
  • RAB1 polypeptide comprises or consists of SEQ ID NO: 140.
  • the second RNA binding protein comprises or consists of a DNA Replication Helicase/Nuclease 2 (DNA2) polypeptide.
  • the DNA2 polypeptide comprises or consists of SEQ ID NO: 141.
  • the second RNA binding protein comprises or consists of a FLJ35220 polypeptide.
  • the FLJ35220 polypeptide comprises or consists of SEQ ID NO: 142.
  • the second RNA binding protein comprises or consists of a FLJ13173 polypeptide.
  • the FLJ13173 polypeptide comprises or consists of SEQ ID NO: 143.
  • the second RNA binding protein comprises or consists of Teneurin Transmembrane Protein (TENM) polypeptide.
  • the second RNA binding protein comprises or consists of Teneurin Transmembrane Protein 1 (TENM1) polypeptide.
  • the TENM1 polypeptide comprises or consists of SEQ ID NO: 144.
  • the second RNA binding protein comprises or consists of Teneurin Transmembrane Protein 2 (TENM2) polypeptide.
  • the TENM2 polypeptide comprises or consists of SEQ ID NO: 145.
  • the second RNA binding protein comprises or consists of a Ribonuclease Kappa (RNAseK) polypeptide.
  • RNAseK Ribonuclease Kappa
  • the RNAseK polypeptide comprises or consists of SEQ ID NO: 204.
  • the fusion proteins of the disclosure are used in methods for treating a subject in need thereof, the methods comprising contacting a target RNA with a fusion protein or the sequence encoding the fusion protein.
  • FIGS. 1A-B is a schematic diagram of an exemplary embodiment of a composition of the disclosure.
  • FIG. 1A An RNA-targeting Cas9 system fused to an endonuclease targets and cleaves a disease-causing RNA.
  • FIG. 1B Depicts an application of (A) in the context of myotonic dystrophy type 1, wherein an RNA-targeting Cas9 system fused to an endonuclease targets and cleaves a repetitive RNA composed of repeating CUG units.
  • the repetitive RNA composed of repeating CUG units binds to a splicing factor MBNL and causes pathology via dysfunctional RNA splicing. Cleavage of this repetitive RNA ameliorates disease.
  • FIG. 2 is a schematic diagram depicting an exemplary modular therapeutic platform for treating genetic disease by targeting RNA molecules.
  • FIGS. 3A-B is a pair of schematic diagrams depicting ( FIG. 3A ) a “high expression” control system (also referred to as “pos control”) comprising a two plasmid system comprising a cytomegalovirus promoter driving expression of the RNA endonuclease/Cas9 fusion and ( FIG. 3B ) a “low expression” control system (also referred to as “P13”) comprising a single plasmid system comprising a lower-expression promoter (pEFS) driving expression of the RNA endonuclease/Cas9 fusion.
  • a “high expression” control system also referred to as “pos control”
  • a cytomegalovirus promoter driving expression of the RNA endonuclease/Cas9 fusion
  • P13 lower expression promoter
  • FIG. 4A is a pair of schematic diagrams depicting an exemplary RNA Endonuclease- C. jejuni Cas9 fusion protein (left) and a vector comprising an exemplary RNA Endonuclease- S. pyogenes Cas9 fusion protein (right)
  • FIG. 4B is a graph depicting the ability of a variety of fusion proteins comprising either C. jejuni Cas9 or S. pyogenes Cas9, as shown in FIG. 4A , to cleave repetitive RNA molecules.
  • FIG. 5A is a pair of schematic diagrams depicting an exemplary RNA Endonuclease- C. jejuni Cas9 fusion protein (left) and a vector comprising an exemplary RNA Endonuclease- S. pyogenes Cas9 fusion protein (right)
  • FIG. 5B is a graph depicting the ability of a variety of fusion proteins comprising either C. jejuni Cas9 or S. pyogenes Cas9, as shown in FIG. 5A , to cleave mRNA molecules encoding a luciferase protein.
  • FIG. 6 is a table providing a key to the endonucleases shown in FIGS. 4B, 5B, and 9 .
  • FIG. 7A is a schematic diagram depicting an exemplary RNA Endonuclease- C. jejuni Cas9 fusion protein.
  • FIG. 7B is a graph depicting changes in expression levels of Zika NS5 in the presence of both E43 and E67 CjeCas9-endonuclease fusions with sgRNAs containing the various NS5-targeting spacer sequences as indicated in Table 2.
  • Zika NS5 expression is displayed as fold change relative to the endonuclease loaded with an sgRNA containing a control (Lambda) spacer sequence.
  • FIG. 8A is a fluorescence microscopy image of cells transfected with CjeCas9-endonuclease fusions loaded with an sgRNA containing a Zika NS5-targeting spacer sequence.
  • FIG. 8B is a graph depicting changes of expression of Zika NS5 in the presence of CjeCas9-endonuclease fusions loaded with the appropriate Zika NS5-targeting sgRNA as compared to a CjeCas9-endonuclease fusions loaded with a non-Zika NS5 targeting sgRNA.
  • FIG. 9 is a graph depicting the cleavage efficiencies of a variety of exemplary fusion proteins (SpyCas9 fused to the annotated endonuclease).
  • the disclosure provides an RNA-guided fusion protein that selectively binds and, optionally, cleaves RNA molecules.
  • the disclosure provides vectors, compositions and cells comprising the RNA-guided fusion protein.
  • the disclosure provides methods of using the RNA-guided fusion protein, vectors, compositions and cells of the disclosure to treat a disease or disorder.
  • gRNA guide RNA
  • sgRNA single guide RNA
  • gRNAs Guide RNAs of the disclosure may comprise of a spacer sequence and a scaffolding sequence.
  • a guide RNA is a single guide RNA (sgRNA) comprising a contiguous spacer sequence and scaffolding sequence.
  • the spacer sequence and the scaffolding sequence are not contiguous.
  • a scaffold sequence comprises a “direct repeat” (DR) sequence.
  • DR sequences refer to the repetitive sequences in the CRISPR locus (naturally-occurring in a bacterial genome or plasmid) that are interspersed with the spacer sequences.
  • a sequence encoding a guide RNA or single guide RNA of the disclosure comprises or consists of a spacer sequence and a scaffolding sequence, that are separated by a linker sequence.
  • the linker sequence may comprise or consist of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or any number of nucleotides in between.
  • the linker sequence may comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or any number of nucleotides in between.
  • RNAs Guide RNAs (gRNAs) of the disclosure may comprise non-naturally occurring nucleotides.
  • a guide RNA of the disclosure or a sequence encoding the guide RNA comprises or consists of modified or synthetic RNA nucleotides.
  • modified RNA nucleotides include, but are not limited to, pseudouridine ( ⁇ ), dihydrouridine (D), inosine (I), and 7-methylguanosine (m7G), hypoxanthine, xanthine, xanthosine, 7-methylguanine, 5, 6-Dihydrouracil, 5-methylcytosine, 5-methylcytidine, 5-hydropxymethylcytosine, isoguanine, and isocytosine.
  • Guide RNAs (gRNAs) of the disclosure may bind modified RNA within a target sequence.
  • guide RNAs (gRNAs) of the disclosure may bind modified RNA.
  • Exemplary epigenetically or post-transcriptionally modified RNA include, but are not limited to, 2′-O-Methylation (2′-OMe) (2′-O-methylation occurs on the oxygen of the free 2′-OH of the ribose moiety), N6-methyladenosine (m6A), and 5-methylcytosine (m5C).
  • a guide RNA of the disclosure comprises at least one sequence encoding a non-coding C/D box small nucleolar RNA (snoRNA) sequence.
  • the snoRNA sequence comprises at least one sequence that is complementary to the target RNA, wherein the target sequence of the RNA molecule comprises at least one 2′-OMe.
  • the snoRNA sequence comprises at least one sequence that is complementary to the target RNA, wherein the at least one sequence that is complementary to the target RNA comprises a box C motif (RUGAUGA) and a box D motif (CUGA).
  • Spacer sequences of the disclosure bind to the target sequence of an RNA molecule.
  • Spacer sequences of the disclosure may comprise a CRISPR RNA (crRNA).
  • Spacer sequences of the disclosure comprise or consist of a sequence having sufficient complementarity to a target sequence of an RNA molecule to bind selectively to the target sequence.
  • the spacer sequence may guide one or more of a scaffolding sequence and a fusion protein to the RNA molecule.
  • a sequence having sufficient complementarity to a target sequence of an RNA molecule to bind selectively to the target sequence has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96, 97%, 98%, 99%, or any percentage identity in between to the target sequence. In some embodiments, a sequence having sufficient complementarity to a target sequence of an RNA molecule to bind selectively to the target sequence has 100% identity the target sequence.
  • Scaffolding sequences of the disclosure bind the first RNA-binding polypeptide of the disclosure.
  • Scaffolding sequences of the disclosure may comprise a trans acting RNA (tracrRNA).
  • Scaffolding sequences of the disclosure comprise or consist of a sequence having sufficient complementarity to a target sequence of an RNA molecule to bind selectively to the target sequence.
  • the scaffolding sequence may guide a fusion protein to the RNA molecule.
  • a sequence having sufficient complementarity to a target sequence of an RNA molecule to bind selectively to the target sequence has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96, 97%, 98%, 99%, or any percentage identity in between to the target sequence.
  • a sequence having sufficient complementarity to a target sequence of an RNA molecule to bind selectively to the target sequence has 100% identity the target sequence.
  • scaffolding sequences of the disclosure comprise or consist of a sequence that binds to a first RNA binding protein or a second RNA binding protein of a fusion protein of the disclosure.
  • scaffolding sequences of the disclosure comprise a secondary structure or a tertiary structure.
  • Exemplary secondary structures include, but are not limited to, a helix, a stem loop, a bulge, a tetraloop and a pseudoknot.
  • Exemplary tertiary structures include, but are not limited to, an A-form of a helix, a B-form of a helix, and a Z-form of a helix.
  • Exemplary tertiary structures include, but are not limited to, a twisted or helicized stem loop.
  • Exemplary tertiary structures include, but are not limited to, a twisted or helicized pseudoknot.
  • scaffolding sequences of the disclosure comprise at least one secondary structure or at least one tertiary structure.
  • scaffolding sequences of the disclosure comprise one or more secondary structure(s) or one or more tertiary structure(s).
  • a guide RNA or a portion thereof selectively binds to a tetraloop motif in an RNA molecule of the disclosure.
  • a target sequence of an RNA molecule comprises a tetraloop motif.
  • the tetraloop motif is a “GRNA” motif comprising or consisting of one or more of the sequences of GAAA, GUGA, GCAA or GAGA.
  • a guide RNA or a portion thereof that binds to a target sequence of an RNA molecule hybridizes to the target sequence of the RNA molecule.
  • a guide RNA or a portion thereof that binds to a first RNA binding protein or to a second RNA binding protein covalently binds to the first RNA binding protein or to the second RNA binding protein.
  • a guide RNA or a portion thereof that binds to a first RNA binding protein or to a second RNA binding protein non-covalently binds to the first RNA binding protein or to the second RNA binding protein.
  • a guide RNA or a portion thereof comprises or consists of between 10 and 100 nucleotides, inclusive of the endpoints.
  • a spacer sequence of the disclosure comprises or consists of between 10 and 30 nucleotides, inclusive of the endpoints.
  • a spacer sequence of the disclosure comprises or consists of 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 nucleotides.
  • the spacer sequence of the disclosure comprises or consists of 20 nucleotides.
  • the spacer sequence of the disclosure comprises or consists of 21 nucleotides.
  • a scaffold sequence of the disclosure comprises or consists of between 10 and 100 nucleotides, inclusive of the endpoints. In some embodiments, a scaffold sequence of the disclosure comprises or consists of 30, 35, 40, 45, 50, 55, 60, 65, 70, 76, 80, 87, 90, 95, 100 or any number of nucleotides in between. In some embodiments, the scaffold sequence of the disclosure comprises or consists of between 85 and 95 nucleotides, inclusive of the endpoints. In some embodiments, the scaffold sequence of the disclosure comprises or consists of 85 nucleotides. In some embodiments, the scaffold sequence of the disclosure comprises or consists of 90 nucleotides. In some embodiments, the scaffold sequence of the disclosure comprises or consists of 93 nucleotides.
  • a guide RNA or a portion thereof does not comprise a nuclear localization sequence (NLS).
  • NLS nuclear localization sequence
  • a guide RNA or a portion thereof does not comprise a sequence complementary to a protospacer adjacent motif (PAM).
  • PAM protospacer adjacent motif
  • compositions of the disclosure do not comprise a PAMmer oligonucleotide.
  • non-therapeutic or non-pharmaceutical compositions may comprise a PAMmer oligonucleotide.
  • PAMmer refers to an oligonucleotide comprising a PAM sequence that is capable of interacting with a guide nucleotide sequence-programmable RNA binding protein.
  • Non-limiting examples of PAMmers are described in O'Connell et al. Nature 516, pages 263-266 (2014), incorporated herein by reference.
  • a PAM sequence refers to a protospacer adjacent motif comprising about 2 to about 10 nucleotides.
  • PAM sequences are specific to the guide nucleotide sequence-programmable RNA binding protein with which they interact and are known in the art.
  • Streptococcus pyogenes PAM has the sequence 5′-NGG-3′, where “N” is any nucleobase followed by two guanine (“G”) nucleobases.
  • Cas9 of Francisella novicida recognizes the canonical PAM sequence 5′-NGG-3′, but has been engineered to recognize the PAM 5′-YG-3′ (where “Y” is a pyrimidine), thus adding to the range of possible Cas9 targets.
  • the Cpf1 nuclease of Francisella novicida recognizes the PAM 5′-TTTN-3′ or 5′-YTN-3′.
  • a guide RNA or a portion thereof comprises a sequence complementary to a protospacer flanking sequence (PFS).
  • PFS protospacer flanking sequence
  • the first RNA binding protein may comprise a sequence isolated or derived from a Cas13 protein.
  • the first RNA binding protein may comprise a sequence encoding a Cas13 protein or an RNA-binding portion thereof.
  • the guide RNA or a portion thereof does not comprise a sequence complementary to a PFS.
  • guide RNA sequence of the disclosure comprises a promoter sequence to drive expression of the guide RNA.
  • a vector comprising a guide RNA sequence of the disclosure comprises a promoter sequence to drive expression of the guide RNA.
  • the promoter to drive expression of the guide RNA is a constitutive promoter.
  • the promoter sequence is an inducible promoter.
  • the promoter is a sequence is a tissue-specific and/or cell-type specific promoter.
  • the promoter is a hybrid or a recombinant promoter.
  • the promoter is a promoter capable of expressing the guide RNA in a mammalian cell.
  • the promoter is a promoter capable of expressing the guide RNA in a human cell. In some embodiments, the promoter is a promoter capable of expressing the guide RNA and restricting the guide RNA to the nucleus of the cell. In some embodiments, the promoter is a human RNA polymerase promoter or a sequence isolated or derived from a sequence encoding a human RNA polymerase promoter. In some embodiments, the promoter is a U6 promoter or a sequence isolated or derived from a sequence encoding a U6 promoter. In some embodiments, the promoter is a human tRNA promoter or a sequence isolated or derived from a sequence encoding a human tRNA promoter. In some embodiments, the promoter is a human valine tRNA promoter or a sequence isolated or derived from a sequence encoding a human valine tRNA promoter.
  • a promoter to drive expression of the guide RNA further comprises a regulatory element.
  • a vector comprising a promoter sequence to drive expression of the guide RNA further comprises a regulatory element.
  • a regulatory element enhances expression of the guide RNA.
  • Exemplary regulatory elements include, but are not limited to, an enhancer element, an intron, an exon, or a combination thereof.
  • a vector of the disclosure comprises one or more of a sequence encoding a guide RNA, a promoter sequence to drive expression of the guide RNA and a sequence encoding a regulatory element. In some embodiments of the compositions of the disclosure, the vector further comprises a sequence encoding a fusion protein of the disclosure.
  • Fusion proteins of the disclosure comprise a first RNA binding protein and a second RNA binding protein.
  • the sequence encoding the first RNA binding protein is positioned 5′ of the sequence encoding the second RNA binding protein.
  • the sequence encoding the first RNA binding protein is positioned 3′ of the sequence encoding the second RNA binding protein.
  • the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein capable of binding an RNA molecule. In some embodiments, the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein capable of selectively binding an RNA molecule and not binding a DNA molecule, a mammalian DNA molecule or any DNA molecule. In some embodiments, the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein capable of binding an RNA molecule and inducing a break in the RNA molecule.
  • the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein capable of binding an RNA molecule, inducing a break in the RNA molecule, and not binding a DNA molecule, a mammalian DNA molecule or any DNA molecule. In some embodiments, the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein capable of binding an RNA molecule, inducing a break in the RNA molecule, and neither binding nor inducing a break in a DNA molecule, a mammalian DNA molecule or any DNA molecule.
  • the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein with no DNA nuclease activity.
  • the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein having DNA nuclease activity, wherein the DNA nuclease activity does not induce a break in a DNA molecule, a mammalian DNA molecule or any DNA molecule when a composition of the disclosure is contacted to an RNA molecule or introduced into a cell or into a subject of the disclosure.
  • the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein having DNA nuclease activity, wherein the DNA nuclease activity is inactivated and wherein the DNA nuclease activity does not induce a break in a DNA molecule, a mammalian DNA molecule or any DNA molecule when a composition of the disclosure is contacted to an RNA molecule or introduced into a cell or into a subject of the disclosure.
  • the sequence encoding the first RNA binding protein comprises a mutation that inactivates or decreases the DNA nuclease activity to a level at which the DNA nuclease activity does not induce a break in a DNA molecule, a mammalian DNA molecule or any DNA molecule when a composition of the disclosure is contacted to an RNA molecule or introduced into a cell or into a subject of the disclosure.
  • the sequence encoding the first RNA binding protein comprises a mutation that inactivates or decreases the DNA nuclease activity and the mutation comprises one or more of a substitution, inversion, transposition, insertion, deletion, or any combination thereof to a nucleic acid sequence or amino acid sequence encoding the first RNA binding protein or a nuclease domain thereof.
  • the sequence encoding the first RNA binding protein of an RNA-guided fusion protein disclosed herein comprises a sequence isolated or derived from a CRISPR Cas protein.
  • the CRISPR Cas protein comprises a Type II CRISPR Cas protein.
  • the Type II CRISPR Cas protein comprises a Cas9 protein.
  • Exemplary Cas9 proteins of the disclosure may be isolated or derived from any species, including, but not limited to, a bacteria or an archaea.
  • Exemplary Cas9 proteins of the disclosure may be isolated or derived from any species, including, but not limited to, Streptococcus pyogenes, Haloferax mediteranii, Mycobacterium tuberculosis, Francisella tularensis subsp. novicida, Pasteurella multocida, Neisseria meningitidis, Campylobacter jejune, Streptococcus thermophilus, Campylobacter lari CF89-12, Mycoplasma gallisepticum str. F, Nitratifractor salsuginis str.
  • DSM 16511 Parvibaculum lavamentivorans, Roseburia intestinalis, Neisseria cinerea , a Gluconacetobacter diazotrophicus , an Azospirillum B510, a Sphaerochaeta globus str. Buddy, Flavobacterium columnare, Fluviicola taffensis, Bacteroides coprophilus, Mycoplasma mobile, Lactobacillus farciminis, Streptococcus pasteurianus, Lactobacillus johnsonii, Staphylococcus pseudintermedius, Filifactor alocis, Treponema denticola, Legionella pneumophila str. Paris, Sutterella wadsworthensis, Corynebacter diphtherias, Streptococcus aureus , and Francisella novicida.
  • Exemplary wild type S. pyogenes Cas9 proteins of the disclosure may comprise or consist of the amino acid sequence:
  • Nuclease inactivated S. pyogenes Cas9 proteins may comprise a substitution of an Alanine (A) for an Aspartic Acid (D) at position 10 and an alanine (A) for a Histidine (H) at position 840.
  • Exemplary nuclease inactivated S. pyogenes Cas9 proteins of the disclosure may comprise or consist of the amino acid sequence (D10A and H840A bolded and underlined):
  • Nuclease inactivated S. pyogenes Cas9 proteins may comprise deletion of a RuvC nuclease domain or a portion thereof, an HNH domain, a DNAse active site, a ⁇ -metal fold or a portion thereof comprising a DNAse active site or any combination thereof.
  • exemplary Cas9 proteins or portions thereof may comprise or consist of the following amino acid sequences.
  • the Cas9 protein can be S. pyogenes Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be S. aureus Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be S. thermophiles CRISPR1 Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be N. meningitidis Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be Parvibaculum.
  • lavamentivorans Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be Corynebacter diphtheria Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be Streptococcus pasteurianus Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be Neisseria cinerea Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be Campylobacter lari Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be T. denticola Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be S. mutans Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be S. thermophilus CRISPR 3 Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be C. jejuni Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be P. multocida Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be F. novicida Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be Lactobacillus buchneri Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be Listeria innocua Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be L. pneumophilia Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be N. lactamica Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be N. meningitides Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be B. longum Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be A. muciniphila Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be O. laneus Cas9 and may comprise or consist of the amino acid sequence:
  • the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a CRISPR Cas protein or portion thereof.
  • the CRISPR Cas protein comprises a Type V CRISPR Cas protein.
  • the Type V CRISPR Cas protein comprises a Cpf1 protein.
  • Exemplary Cpf1 proteins of the disclosure may be isolated or derived from any species, including, but not limited to, a bacteria or an archaea.
  • Exemplary Cpf1 proteins of the disclosure may be isolated or derived from any species, including, but not limited to, Francisella tularensis subsp. novicida, Acidaminococcus sp. BV3L6 and Lachnospiraceae bacterium sp. ND2006.
  • Exemplary Cpf1 proteins of the disclosure may be nuclease inactivated.
  • Novicida Cpf1 (FnCpf1) proteins of the disclosure may comprise or consist of the amino acid sequence:
  • Exemplary wild type Lachnospiraceae bacterium sp. ND2006 Cpf1 (LbCpf1) proteins of the disclosure may comprise or consist of the amino acid sequence:
  • Exemplary wild type Acidaminococcus sp. BV3L6 Cpf1 (AsCpf1) proteins of the disclosure may comprise or consist of the amino acid sequence:
  • the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a CRISPR Cas protein.
  • the CRISPR Cas protein comprises a Type VI CRISPR Cas protein or portion thereof.
  • the Type VI CRISPR Cas protein comprises a Cas13 protein or portion thereof.
  • Exemplary Cas13 proteins of the disclosure may be isolated or derived from any species, including, but not limited to, a bacteria or an archaea.
  • Exemplary Cas13 proteins of the disclosure may be isolated or derived from any species, including, but not limited to, Leptotrichia wadei, Listeria seeligeri serovar 1/2b (strain ATCC 35967/DSM 20751/CIP 100100/SLCC 3954), Lachnospiraceae bacterium, Clostridium aminophilum DSM 10710 , Carnobacterium gallinarum DSM 4847 , Paludibacter propionicigenes WB4 , Listeria weihenstephanensis FSL R9-0317 , Listeria weihenstephanensis FSL R9-0317, bacterium FSL M6-0635 ( Listeria newyorkensis ), Leptotrichia wadei F0279 , Rhodobacter capsulatus SB 1003 , Rhodobacter capsulatus R121 , Rhodobacter capsulatus DE442 and Corynebacterium ulcerans .
  • Exemplary Cas13 proteins of the disclosure may be DNA nuclease inactivated.
  • Exemplary Cas13 proteins of the disclosure include, but are not limited to, Cas13a, Cas13b, Cas13c, Cas13d and orthologs thereof.
  • Exemplary Cas13b proteins of the disclosure include, but are not limited to, subtypes 1 and 2 referred to herein as Csx27 and Csx28, respectively.
  • Exemplary Cas13a proteins include, but are not limited to:
  • Exemplary wild type Cas13a proteins of the disclosure may comprise or consist of the amino acid sequence:
  • Exemplary Cas13b proteins include, but are not limited to:
  • Flavobacterium column is ATCC 49512 WP_014165541.1 1180 Flavobacterium columnare WP_060381855.1 1214 Flavobacterium columnare WP_063744070.1 1214 Flavobacterium columnare WP_065213424.1 1215 Chryseobacterium sp.
  • Exemplary wild type Bergeyella zoohelcum ATCC 43767 Cas13b (BzCas13b) proteins of the disclosure may comprise or consist of the amino acid sequence:
  • the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a CasRX/Cas13d protein.
  • CasRX/Cas13d is an effector of the type VI-D CRISPR-Cas systems.
  • the CasRX/Cas13d protein is an RNA-guided RNA endonuclease enzyme that can cut or bind RNA.
  • the CasRX/Cas13d protein can include one or more higher eukaryotes and prokaryotes nucleotide-binding (HEPN) domains.
  • HEPN prokaryotes nucleotide-binding
  • the CasRX/Cas13d protein can include either a wild-type or mutated HEPN domain. In some embodiments, the CasRX/Cas13d protein includes a mutated HEPN domain that cannot cut RNA but can process guide RNA. In some embodiments, the CasRX/Cas13d protein does not require a protospacer flanking sequence. Also see WO Publication No.
  • CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig6049000251:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig546000275:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig4114000374:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig721000619:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig2002000411:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig13552000311:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig10037000527:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig238000329:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig2643000492:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig874000057:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig4781000489:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig12144000352:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig5590000448:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig525000349:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig7229000302:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig3227000343:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig7030000469:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d gut_metagenome_P17E0k2120140920, c87000043:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig tpg
  • An exemplary direct repeat sequence of CasRX/Cas13d Metagenomic hit (no protein accession): contig tpg
  • CasRX/Cas13dDR (SEQ ID NO: 96) caactacaac cccgtaaaaa tacggggttc tgaaac. 36
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig OGZC01000639.1 (human gut metagenome assembly):
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): from contig emb
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig OIZX01000427.1:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig OCTWO11587266.1:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig e-k87_11092736:
  • An exemplary direct repeat sequence of CasRX/Cas13d Metagenomic hit (no protein accession): contig e-k87_11092736 (SEQ ID NO: 107) comprises or consists of the nucleic acid sequence:
  • CasRX/Cas13d Direct repeat 1 (SEQ ID NO: 108) gtgagaagtc tccttatggg gagatgctac.
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Ga0129306_1000735:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Ga0129317_1008067:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Ga0224415_10048792:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence CasRX/Cas13d 160582958_gene49834:
  • An exemplary direct repeat sequence of CasRX/Cas13d proteins may comprise or consist of the sequence CasRX/Cas13d 160582958_gene49834 (SEQ ID NO: 112) comprises or consists of the nucleic acid sequence: CasRX/Cas13d DR:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d 250twins_35838_GL0110300:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d 250twins_36050_GL0158985:
  • Exemplary wild type Cas13d proteins of the disclosure may comprise or consist of the amino acid sequence:
  • Exemplary wild type Cas13d proteins of the disclosure may comprise or consist of the amino acid sequence:
  • An exemplary direct repeat sequence of Cas13d (contig e-k87_11092736) (SEQ ID NO: 46) comprises or consists of the nucleic acid sequence:Cas13d (contig e-k87_11092736) Direct Repeat Sequence): GTGAGAAGTCTCCTTATGGGGAGATGCTAC (SEQ ID NO: 47).
  • Exemplary wild type Cas13d proteins of the disclosure may comprise or consist of the amino acid sequence:
  • An exemplary direct repeat sequence of Cas13d (160582958_gene49834) (SEQ ID NO: 48) comprises or consists of the nucleic acid sequence:
  • Exemplary wild type Cas13d proteins of the disclosure may comprise or consist of the amino acid sequence:
  • An exemplary direct repeat sequence of Cas13d (contig tpg
  • a target sequence of an RNA molecule comprises a sequence motif corresponding to the first RNA binding protein and/or the second RNA binding protein.
  • the sequence motif is a signature of a disease or disorder.
  • a sequence motif of the disclosure may be isolated or derived from a sequence of foreign or exogenous sequence found in a genomic sequence, and therefore translated into an mRNA molecule of the disclosure or a sequence of foreign or exogenous sequence found in an RNA sequence of the disclosure.
  • a sequence motif of the disclosure may comprise or consist of a mutation in an endogenous sequence that causes a disease or disorder.
  • the mutation may comprise or consist of a sequence substitution, inversion, deletion, insertion, transposition, or any combination thereof.
  • a sequence motif of the disclosure may comprise or consist of a repeated sequence.
  • the repeated sequence may be associated with a microsatellite instability (MSI). MSI at one or more loci results from impaired DNA mismatch repair mechanisms of a cell of the disclosure.
  • MSI microsatellite instability
  • a hypervariable sequence of DNA may be transcribed into an mRNA of the disclosure comprising a target sequence comprising or consisting of the hypervariable sequence.
  • a sequence motif of the disclosure may comprise or consist of a biomarker.
  • the biomarker may indicate a risk of developing a disease or disorder.
  • the biomarker may indicate a healthy gene (low or no determinable risk of developing a disease or disorder.
  • the biomarker may indicate an edited gene.
  • Exemplary biomarkers include, but are not limited to, single nucleotide polymorphisms (SNPs), sequence variations or mutations, epigenetic marks, splice acceptor sites, exogenous sequences, heterologous sequences, and any combination thereof.
  • a sequence motif of the disclosure may comprise or consist of a secondary, tertiary or quaternary structure.
  • the secondary, tertiary or quaternary structure may be endogenous or naturally occurring.
  • the secondary, tertiary or quaternary structure may be induced or non-naturally occurring.
  • the secondary, tertiary or quaternary structure may be encoded by an endogenous, exogenous, or heterologous sequence.
  • a target sequence of an RNA molecule comprises or consists of between 2 and 100 nucleotides or nucleic acid bases, inclusive of the endpoints. In some embodiments, the target sequence of an RNA molecule comprises or consists of between 2 and 50 nucleotides or nucleic acid bases, inclusive of the endpoints. In some embodiments, the target sequence of an RNA molecule comprises or consists of between 2 and 20 nucleotides or nucleic acid bases, inclusive of the endpoints.
  • a target sequence of an RNA molecule is continuous.
  • the target sequence of an RNA molecule is discontinuous.
  • the target sequence of an RNA molecule may comprise or consist of one or more nucleotides or nucleic acid bases that are not contiguous because one or more intermittent nucleotides are positioned in between the nucleotides of the target sequence.
  • a target sequence of an RNA molecule is naturally occurring.
  • the target sequence of an RNA molecule is non-naturally occurring.
  • Exemplary non-naturally occurring target sequences may comprise or consist of sequence variations or mutations, chimeric sequences, exogenous sequences, heterologous sequences, chimeric sequences, recombinant sequences, sequences comprising a modified or synthetic nucleotide or any combination thereof.
  • a target sequence of an RNA molecule binds to a guide RNA of the disclosure.
  • a target sequence of an RNA molecule binds to a first RNA binding protein of the disclosure.
  • a target sequence of an RNA molecule binds to a second RNA binding protein of the disclosure.
  • an RNA molecule of the disclosure comprises a target sequence. In some embodiments, the RNA molecule of the disclosure comprises at least one target sequence. In some embodiments, the RNA molecule of the disclosure comprises one or more target sequence(s). In some embodiments, the RNA molecule of the disclosure comprises two or more target sequences.
  • an RNA molecule of the disclosure is a naturally occurring RNA molecule.
  • the RNA molecule of the disclosure is a non-naturally occurring molecule.
  • Exemplary non-naturally occurring RNA molecules may comprise or consist of sequence variations or mutations, chimeric sequences, exogenous sequences, heterologous sequences, chimeric sequences, recombinant sequences, sequences comprising a modified or synthetic nucleotide or any combination thereof.
  • an RNA molecule of the disclosure comprises or consists of a sequence isolated or derived from a virus.
  • an RNA molecule of the disclosure comprises or consists of a sequence isolated or derived from a prokaryotic organism. In some embodiments, an RNA molecule of the disclosure comprises or consists of a sequence isolated or derived from a species or strain of archaea or a species or strain of bacteria.
  • the RNA molecule of the disclosure comprises or consists of a sequence isolated or derived from a eukaryotic organism.
  • an RNA molecule of the disclosure comprises or consists of a sequence isolated or derived from a species of protozoa, parasite, protist, algae, fungi, yeast, amoeba, worm, microorganism, invertebrate, vertebrate, insect, rodent, mouse, rat, mammal, or a primate.
  • an RNA molecule of the disclosure comprises or consists of a sequence isolated or derived from a human.
  • the RNA molecule of the disclosure comprises or consists of a sequence derived from a coding sequence from a genome of an organism or a virus.
  • the RNA molecule of the disclosure comprises or consists of a primary RNA transcript, a precursor messenger RNA (pre-mRNA) or messenger RNA (mRNA).
  • pre-mRNA precursor messenger RNA
  • mRNA messenger RNA
  • the RNA molecule of the disclosure comprises or consists of a gene product that has not been processed (e.g. a transcript).
  • the RNA molecule of the disclosure comprises or consists of a gene product that has been subject to post-transcriptional processing (e.g. a transcript comprising a 5′ cap and a 3′ polyadenylation signal).
  • the RNA molecule of the disclosure comprises or consists of a gene product that has been subject to alternative splicing (e.g. a splice variant). In some embodiments, the RNA molecule of the disclosure comprises or consists of a gene product that has been subject to removal of non-coding and/or intronic sequences (e.g. a messenger RNA (mRNA)).
  • alternative splicing e.g. a splice variant
  • the RNA molecule of the disclosure comprises or consists of a gene product that has been subject to removal of non-coding and/or intronic sequences (e.g. a messenger RNA (mRNA)).
  • mRNA messenger RNA
  • the RNA molecule of the disclosure comprises or consists of a sequence derived from a non-coding sequence (e.g. a non-coding RNA (ncRNA)).
  • a non-coding RNA e.g. a non-coding RNA (ncRNA)
  • the RNA molecule of the disclosure comprises or consists of a ribosomal RNA.
  • the RNA molecule of the disclosure comprises or consists of a small ncRNA molecule.
  • RNA molecules of the disclosure include, but are not limited to, microRNAs (miRNAs), small interfering (siRNAs), piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs), extracellular or exosomal RNAs (exRNAs), and small Cajal body-specific RNAs (scaRNAs).
  • miRNAs microRNAs
  • siRNAs small interfering
  • piRNAs piwi-interacting RNAs
  • small nucleolar RNAs small nucleolar RNAs
  • snRNAs small nuclear RNAs
  • exRNAs extracellular or exosomal RNAs
  • scaRNAs small Cajal body-specific RNAs
  • the RNA molecule of the disclosure comprises or consists of a long ncRNA molecule.
  • Exemplary long RNA molecules of the disclosure include, but are not limited to, X-inactive specific transcript (Xist) and HO
  • the RNA molecule of the disclosure contacted by a composition of the disclosure in an intracellular space. In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in a cytosolic space. In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in a nucleus. In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in a vesicle, membrane-bound compartment of a cell, or an organelle.
  • the RNA molecule of the disclosure contacted by a composition of the disclosure in an extracellular space. In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in an exosome. In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in a liposome, a polymersome, a micelle or a nanoparticle. In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in an extracellular matrix. In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in a droplet. In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in a microfluidic droplet.
  • a RNA molecule of the disclosure comprises or consists of a single-stranded sequence. In some embodiments, the RNA molecule of the disclosure comprises or consists of a double-stranded sequence. In some embodiments, the double-stranded sequence comprises two RNA molecules. In some embodiments, the double-stranded sequence comprises one RNA molecule and one DNA molecule. In some embodiments, including those wherein the double-stranded sequence comprises one RNA molecule and one DNA molecule, compositions of the disclosure selectively bind and, optionally, selectively cut the RNA molecule.
  • the second RNA binding protein comprises or consists of a nuclease domain. In some embodiments, the second RNA binding protein binds RNA in a manner in which it associates with RNA. In some embodiments, the second RNA binding protein associates with RNA in a manner in which it cleaves RNA.
  • the second RNA binding protein comprises or consists of an RNAse.
  • the second RNA binding protein comprises or consists of an RNAse1.
  • the RNAse1 protein comprises or consists of:
  • the second RNA binding protein comprises or consists of an RNAse4.
  • the RNAse4 protein comprises or consists of:
  • the second RNA binding protein comprises or consists of an RNAse6.
  • the RNAse6 protein comprises or consists of:
  • the second RNA binding protein comprises or consists of an RNAse7.
  • the RNAse7 protein comprises or consists of:
  • the second RNA binding protein comprises or consists of an RNAse8.
  • the RNAse8 protein comprises or consists of:
  • the second RNA binding protein comprises or consists of an RNAse2.
  • the RNAse2 protein comprises or consists of:
  • the second RNA binding protein comprises or consists of an RNAse6PL.
  • the RNAse6PL protein comprises or consists of:
  • the second RNA binding protein comprises or consists of an RNAseL.
  • the RNAseL protein comprises or consists of:
  • the second RNA binding protein comprises or consists of an RNAseT2.
  • the RNAseT2 protein comprises or consists of:
  • the second RNA binding protein comprises or consists of an RNAse11.
  • the RNAse11 protein comprises or consists of:
  • the second RNA binding protein comprises or consists of an RNAseT2-like.
  • the RNAseT2-like protein comprises or consists of:
  • the second RNA binding protein comprises or consists of a mutated RNAse.
  • the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(K41R)) polypeptide.
  • Rnase1(K41R) polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(K41R, D121E)) polypeptide.
  • the Rnase1 (Rnase1(K41R, D121E)) polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(K41R, D121E, H119N)) polypeptide.
  • Rnase1 (Rnase1(K41R, D121E, H119N)) polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a mutated Rnase1. In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(H119N)) polypeptide. In some embodiments, the Rnase1 (Rnase1(H119N)) polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide.
  • the Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide comprises or consists of: KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGDCKPVNTFVHEPLVDVQNV CFQEKVTCKDGQGNCYKSNSSMHITDCRLTADSDYPNCAYRTSPKERHIIVACEGSPYV PVNFDASVEDST (SEQ ID NO: 120).
  • the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide.
  • Rnase1 Rnase1(R39D, N67D, N88A, G89D, R91D, H119N, K41R, D121E)
  • polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1 (R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide.
  • Rnase1 (Rnase1 (R39D, N67D, N88A, G89D, R91D)) polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1 (R39D, N67D, N88A, G89D, R91D, H119N, K41R, D121E)) polypeptide that comprises or consists of:
  • the second RNA binding protein comprises or consists of a NOB1 polypeptide.
  • the NOB1 polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of an endonuclease. In some embodiments, the second RNA binding protein comprises or consists of an endonuclease V (ENDOV). In some embodiments, the ENDOV protein comprises or consists of:
  • the second RNA binding protein comprises or consists of an endonuclease G (ENDOG).
  • ENDOG endonuclease G
  • the ENDOG protein comprises or consists of:
  • the second RNA binding protein comprises or consists of an endonuclease D1 (ENDOD1).
  • ENDOD1 protein comprises or consists of:
  • the second RNA binding protein comprises or consists of a Human flap endonuclease-1 (hFEN1).
  • hFEN1 polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a DNA repair endonuclease XPF (ERCC4) polypeptide.
  • ERCC4 polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of an Endonuclease III-like protein 1 (NTHL) polypeptide.
  • NTHL Endonuclease III-like protein 1
  • the NTHL polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a human Schlafen 14 (hSLFN14) polypeptide.
  • hSLFN14 polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a human beta-lactamase-like protein 2 (hLACTB2) polypeptide.
  • the hLACTB2 polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of an apurinic/apyrimidinic (AP) endodeoxyribonuclease (APEX) polypeptide.
  • the second RNA binding protein comprises or consists of an apurinic/apyrimidinic (AP) endodeoxyribonuclease (APEX2) polypeptide.
  • the APEX2 polypeptide comprises or consists of:
  • the APEX2 polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of an apurinic or apyrimidinic site lyase (APEX1) polypeptide.
  • APEX1 polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of an angiogenin (ANG) polypeptide.
  • ANG polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a heat responsive protein 12 (HRSP12) polypeptide.
  • HRSP12 heat responsive protein 12
  • the HRSP12 polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a Zinc Finger CCCH-Type Containing 12A (ZC3H12A) polypeptide.
  • ZC3H12A polypeptide comprises or consists of:
  • the ZC3H12A polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a Reactive Intermediate Imine Deaminase A (RIDA) polypeptide.
  • RIDA Reactive Intermediate Imine Deaminase A
  • the RIDA polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a Phospholipase D Family Member 6 (PDL6) polypeptide.
  • PDL6 polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a mitochondrial ribonuclease P catalytic subunit (KIAA0391) polypeptide.
  • the KIAA0391 polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of an argonaute 2 (AGO2) polypeptide.
  • the AGO2 polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a mitochondrial nuclease EXOG (EXOG) polypeptide.
  • EXOG mitochondrial nuclease EXOG
  • the EXOG polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a Zinc Finger CCCH-Type Containing 12D (ZC3H12D) polypeptide.
  • ZC3H12D polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of an endoplasmic reticulum to nucleus signaling 2 (ERN2) polypeptide.
  • ERN2 polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a pelota mRNA surveillance and ribosome rescue factor (PELO) polypeptide.
  • PELO ribosome rescue factor
  • the PELO polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a YBEY metallopeptidase (YBEY) polypeptide.
  • YBEY YBEY metallopeptidase
  • the YBEY polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a cleavage and polyadenylation specific factor 4 like (CPSF4L) polypeptide.
  • CPSF4L polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of an hCG_2002731 polypeptide.
  • the hCG_2002731 polypeptide comprises or consists of:
  • the hCG_2002731 polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of an Excision Repair Cross-Complementation Group 1 (ERCC1) polypeptide.
  • ERCC1 polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a ras-related C3 botulinum toxin substrate 1 isoform (RAC1) polypeptide.
  • RAC1 polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a Ribonuclease A A1 (RAA1) polypeptide.
  • RAA1 polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a Ras Related Protein (RAB1) polypeptide.
  • RAB1 polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a DNA Replication Helicase/Nuclease 2 (DNA2) polypeptide.
  • DNA2 polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a FLJ35220 polypeptide.
  • the FLJ35220 polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a FLJ13173 polypeptide.
  • the FLJ13173 polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of Teneurin Transmembrane Protein (TENM) polypeptide. In some embodiments, the second RNA binding protein comprises or consists of Teneurin Transmembrane Protein 1 (TENM1) polypeptide. In some embodiments, the TENM1 polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of Teneurin Transmembrane Protein 2 (TENM2) polypeptide.
  • the TENM2 polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a Ribonuclease Kappa (RNAseK) polypeptide.
  • RNAseK Ribonuclease Kappa
  • the RNAseK polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a transcription activator-like effector nuclease (TALEN) polypeptide or a nuclease domain thereof.
  • TALEN transcription activator-like effector nuclease
  • the TALEN polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists a zinc finger nuclease polypeptide or a nuclease domain thereof. In some embodiments, the second RNA binding protein comprises or consists of a ZNF638 polypeptide or a nuclease domain thereof. In some embodiments, the ZNF638 polypeptide polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a PIN domain derived from the human SMG6 protein, also commonly known as telomerase-binding protein EST1A isoform 3, NCBI Reference Sequence: NP_001243756.1.
  • the PIN from hSMG6 is used herein in the form of a Cas fusion protein and as an internal control, for example, and without limitation, see FIG. 9 , which shows PIN-dSauCas9, PIN-dSauCas9dHNH, PIN-dSPCas9, and dcjeCas9-PIN.
  • the composition further comprises (a) a sequence comprising a gRNA that specifically binds within an RNA molecule and (b) a sequence encoding a nuclease.
  • a nuclease comprises a sequence isolated or derived from a CRISPR/Cas protein.
  • the CRISPR/Cas protein is isolated or derived from any one of a type I, a type IA, a type IB, a type IC, a type ID, a type IE, a type IF, a type IU, a type III, a type IIIA, a type IIIB, a type IIIC, a type IIID, a type IV, a type IVA, a type IVB, a type II, a type IIA, a type IIB, a type ITC, a type V, or a type VI CRISPR/Cas protein.
  • a nuclease comprises a sequence isolated or derived from a TALEN or a nuclease domain thereof. In some embodiments, a nuclease comprises a sequence isolated or derived from a zinc finger nuclease or a nuclease domain thereof.
  • the composition comprises a sequence encoding a target RNA-binding fusion protein comprising (a) a sequence encoding a first RNA-binding polypeptide or portion thereof; and (b) a sequence encoding a second RNA-binding polypeptide, wherein the first RNA-biding polypeptide binds a target RNA, and wherein the second RNA-binding polypeptide comprises RNA-nuclease activity.
  • a target RNA-binding fusion protein is an RNA-guided target RNA-binding fusion protein.
  • RNA-guided target RNA-binding fusion proteins comprise at least one RNA-binding polypeptide which corresponds to a gRNA which guides the RNA-binding polypeptide to target RNA.
  • RNA-guided target RNA-binding fusion proteins include without limitation, RNA-binding polypeptides which are CRISPR/Cas-based RNA-binding polypeptides or portions thereof.
  • a target RNA-binding fusion protein is not an RNA-guided target RNA-binding fusion protein and as such comprises at least one RNA-binding polypeptide which is capable of binding a target RNA without a corresponding gRNA sequence.
  • Such non-guided RNA-binding polypeptides include, without limitation, at least one RNA-binding protein or RNA-binding portion thereof which is a PUF (Pumilio and FBF homology family). This type RNA-binding polypeptide can be used in place of a gRNA-guided RNA binding protein such as CRISPR/Cas.
  • the unique RNA recognition mode of PUF proteins (named for Drosophila Pumilio and C.
  • the PUF domain of human Pumiliol also known in the art, binds tightly to cognate RNA sequences and its specificity can be modified. It contains eight PUF repeats that recognize eight consecutive RNA bases with each repeat recognizing a single base. Since two amino acid side chains in each repeat recognize the Watson-Crick edge of the corresponding base and determine the specificity of that repeat, a PUF domain can be designed to specifically bind most 8-nt RNA. Wang et al., Nat Methods. 2009; 6(11): 825-830. See also WO2012/068627 which is incorporated by reference herein in its entirety.
  • the fusion protein comprises at least one RNA-binding protein or RNA-binding portion thereof which is a PUMBY (Pumilio-based assembly) protein.
  • RNA-binding protein PumHD Pano homology domain, a member of the PUF family
  • Pumby for Pumilio-based assembly
  • these modules can be concatenated in chains of varying composition and length, to bind desired target RNAs.
  • the first RNA binding protein comprises a Pumilio and FBF (PUF) protein. In some embodiments, the first RNA binding protein comprises a Pumilio-based assembly (PUMBY) protein. In some embodiments, a PUF1 protein of the disclosure comprises or consists of the amino acid sequence of
  • RNA-binding proteins or RNA-binding portions thereof is a PPR protein.
  • PPR proteins proteins with pentatricopeptide repeat (PPR) motifs derived from plants
  • PPR proteins are nuclear-encoded and exclusively controlled at the RNA level organelles (chloroplasts and mitochondria), cutting, translation, splicing, RNA editing, genes specifically acting on RNA stability.
  • PPR proteins are typically a motif of 35 amino acids and have a structure in which a PPR motif is about 10 contiguous amino acids.
  • the combination of PPR motifs can be used for sequence-selective binding to RNA.
  • PPR proteins are often comprised of PPR motifs of about 10 repeat domains.
  • PPR domains or RNA-binding domains may be configured to be catalytically inactive. WO 2013/058404 incorporated herein by reference in its entirety.
  • the fusion protein disclosed herein comprises a linker between the at least two RNA-binding polypeptides.
  • the linker is a peptide linker.
  • the peptide linker comprises one or more repeats of the tri-peptide GGS. In other embodiments, the linker is a non-peptide linker.
  • the non-peptide linker comprises polyethylene glycol (PEG), polypropylene glycol (PPG), co-poly(ethylene/propylene) glycol, polyoxyethylene (POE), polyurethane, polyphosphazene, polysaccharides, dextran, polyvinyl alcohol, polyvinylpyrrolidones, polyvinyl ethyl ether, polyacryl amide, polyacrylate, polycyanoacrylates, lipid polymers, chitins, hyaluronic acid, heparin, or an alkyl linker.
  • PEG polyethylene glycol
  • PPG polypropylene glycol
  • POE polyoxyethylene
  • polyurethane polyphosphazene
  • polysaccharides dextran
  • polyvinyl alcohol polyvinylpyrrolidones
  • polyvinyl ethyl ether polyacryl amide
  • polyacrylate polycyanoacrylates
  • lipid polymers chitins, hyaluronic
  • the at least one RNA-binding protein does not require multimerization for RNA-binding activity. In some embodiments, the at least one RNA-binding protein is not a monomer of a multimer complex. In some embodiments, a multimer protein complex does not comprise the RNA binding protein. In some embodiments, the at least one of RNA-binding protein selectively binds to a target sequence within the RNA molecule. In some embodiments, the at least one RNA-binding protein does not comprise an affinity for a second sequence within the RNA molecule. In some embodiments, the at least one RNA-binding protein does not comprise a high affinity for or selectively bind a second sequence within the RNA molecule. In some embodiments, the at least one RNA-binding protein comprises between 2 and 1300 amino acids, inclusive of the endpoints.
  • the at least one RNA-binding protein of the fusion proteins disclosed herein further comprises a sequence encoding a nuclear localization signal (NLS).
  • a nuclear localization signal (NLS) is positioned 3′ to the RNA binding protein.
  • the at least one RNA-binding protein comprises an NLS at a C-terminus of the protein.
  • the at least one RNA-binding protein further comprises a first sequence encoding a first NLS and a second sequence encoding a second NLS.
  • the first NLS or the second NLS is positioned 3′ to the RNA-binding protein.
  • the at least one RNA-binding protein comprises the first NLS or the second NLS at a C-terminus of the protein. In some embodiments, the at least one RNA-binding protein further comprises an NES (nuclear export signal) or other peptide tag or secretory signal.
  • NES nuclear export signal
  • a fusion protein disclosed herein comprises the at least one RNA-binding protein as a first RNA-binding protein together with a second RNA-binding protein comprising or consisting of a nuclease domain.
  • the second RNA-binding polypeptide is operably configured to the first RNA-binding polypeptide at the C-terminus of the first RNA-binding polypeptide. In some embodiments, the second RNA-binding polypeptide is operably configured to the first RNA-binding polypeptide at the N-terminus of the first RNA-binding polypeptide.
  • one such exemplary fusion protein is E99 which is configured so that RNAse1(R39D, N67D, N88A, G89D, R19D, H119N, K41R) is located at the N-terminus of SpyCas9 whereas another exemplary fusion protein, E100, is configured so that RNAse1(R39D, N67D, N88A, G89D, R19D, H119N, K41R) is located at the C-terminus of SpyCas9. See FIG. 6 .
  • a vector comprises a guide RNA of the disclosure. In some embodiments, the vector comprises at least one guide RNA of the disclosure. In some embodiments, the vector comprises one or more guide RNA(s) of the disclosure. In some embodiments, the vector comprises two or more guide RNAs of the disclosure. In some embodiments, the vector further comprises a fusion protein of the disclosure. In some embodiments, the fusion protein comprises a first RNA binding protein and a second RNA binding protein.
  • a first vector comprises a guide RNA of the disclosure and a second vector comprises a fusion protein of the disclosure.
  • the first vector comprises at least one guide RNA of the disclosure.
  • the first vector comprises one or more guide RNA(s) of the disclosure.
  • the first vector comprises two or more guide RNA(s) of the disclosure.
  • the fusion protein comprises a first RNA binding protein and a second RNA binding protein.
  • the first vector and the second vector are identical. In some embodiments, the first vector and the second vector are not identical.
  • the vector is or comprises a component of a “2-component RNA targeting system” comprising (a) nucleic acid sequence encoding a RNA-targeted fusion protein of the disclosure; and (b) a single guide RNA (sgRNA) sequence comprising: on its 5′ end, an RNA sequence (or spacer sequence) that hybridizes to or binds to a target RNA sequence; and on its 3′ end, an RNA sequence (or scaffold sequence) capable of binding to or associating with the CRISPR/Cas protein of the fusion protein; and wherein the 2-component RNA targeting system recognizes and alters the target RNA in a cell in the absence of a PAMmer.
  • sgRNA single guide RNA
  • sequences of the 2-component system are in a single vector.
  • the spacer sequence of the 2-component system targets a repeat sequence selected from the group consisting of CUG, CCUG, CAG, and GGGGCC.
  • a vector of the disclosure is a viral vector.
  • the viral vector comprises a sequence isolated or derived from a retrovirus.
  • the viral vector comprises a sequence isolated or derived from a lentivirus.
  • the viral vector comprises a sequence isolated or derived from an adenovirus.
  • the viral vector comprises a sequence isolated or derived from an adeno-associated virus (AAV).
  • AAV adeno-associated virus
  • the viral vector is replication incompetent.
  • the viral vector is isolated or recombinant.
  • the viral vector is self-complementary.
  • the viral vector comprises a sequence isolated or derived from an adeno-associated virus (AAV).
  • AAV adeno-associated virus
  • the viral vector comprises an inverted terminal repeat sequence or a capsid sequence that is isolated or derived from an AAV of serotype AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11 or AAV12.
  • the viral vector is replication incompetent.
  • the viral vector is isolated or recombinant (rAAV).
  • the viral vector is self-complementary (scAAV).
  • a vector of the disclosure is a non-viral vector.
  • the vector comprises or consists of a nanoparticle, a micelle, a liposome or lipoplex, a polymersome, a polyplex or a dendrimer.
  • the vector is an expression vector or recombinant expression system.
  • the term “recombinant expression system” refers to a genetic construct for the expression of certain genetic material formed by recombination.
  • an expression vector, viral vector or non-viral vector provided herein includes without limitation, an expression control element.
  • An “expression control element” as used herein refers to any sequence that regulates the expression of a coding sequence, such as a gene.
  • Exemplary expression control elements include but are not limited to promoters, enhancers, microRNAs, post-transcriptional regulatory elements, polyadenylation signal sequences, and introns. Expression control elements may be constitutive, inducible, repressible, or tissue-specific, for example.
  • a “promoter” is a control sequence that is a region of a polynucleotide sequence at which initiation and rate of transcription are controlled.
  • Non-limiting exemplary promoters include CMV, CBA, CAG, Cbh, EF-1a, PGK, UBC, GUSB, UCOE, hAAT, TBG, Desmin, MCK, C5-12, NSE, Synapsin, PDGF, MecP2, CaMKII, mGluR2, NFL, NFH, n ⁇ 2, PPE, ENK, EAAT2, GFAP, MBP, and U6 promoters.
  • An “enhancer” is a region of DNA that can be bound by activating proteins to increase the likelihood or frequency of transcription.
  • Non-limiting exemplary enhancers and posttranscriptional regulatory elements include the CMV enhancer and WPRE.
  • an expression vector, viral vector or non-viral vector includes without limitation, vector elements such as an IRES or 2A peptide sites for configuration of “multicistronic” or “polycistronic” or “bicistronic” or tricistronic” constructs, i.e., having double or triple or multiple coding areas or exons, and as such will have the capability to express from mRNA two or more proteins from a single construct.
  • Multicistronic vectors simultaneously express two or more separate proteins from the same mRNA.
  • the two strategies most widely used for constructing multicistronic configurations are through the use of an IRES or a 2A self-cleaving site.
  • an “IRES” refers to an internal ribosome entry site or portion thereof of viral, prokaryotic, or eukaryotic origin which are used within polycistronic vector constructs.
  • an IRES is an RNA element that allows for translation initiation in a cap-independent manner.
  • self-cleaving peptides or “sequences encoding self-cleaving peptides” or “2A self-cleaving site” refer to linking sequences which are used within vector constructs to incorporate sites to promote ribosomal skipping and thus to generate two polypeptides from a single promoter, such self-cleaving peptides include without limitation, T2A, and P2A peptides or sequences encoding the self-cleaving peptides.
  • the vector is a viral vector.
  • the vector is an adenoviral vector, an adeno-associated viral (AAV) vector, or a lentiviral vector.
  • the vector is a retroviral vector, an adenoviral/retroviral chimera vector, a herpes simplex viral I or II vector, a parvoviral vector, a reticuloendotheliosis viral vector, a polioviral vector, a papillomaviral vector, a vaccinia viral vector, or any hybrid or chimeric vector incorporating favorable aspects of two or more viral vectors.
  • the vector further comprises one or more expression control elements operably linked to the polynucleotide. In some embodiments, the vector further comprises one or more selectable markers. In some embodiments, the AAV vector has low toxicity. In some embodiments, the AAV vector does not incorporate into the host genome, thereby having a low probability of causing insertional mutagenesis. In some embodiments, the AAV vector can encode a range of total polynucleotides from 4.5 kb to 4.75 kb.
  • exemplary AAV vectors that may be used in any of the herein described compositions, systems, methods, and kits can include an AAV1 vector, a modified AAV1 vector, an AAV2 vector, a modified AAV2 vector, an AAV3 vector, a modified AAV3 vector, an AAV4 vector, a modified AAV4 vector, an AAV5 vector, a modified AAV5 vector, an AAV6 vector, a modified AAV6 vector, an AAV7 vector, a modified AAV7 vector, an AAV8 vector, an AAV9 vector, an AAV.rh10 vector, a modified AAV.rh10 vector, an AAV.rh32/33 vector, a modified AAV.rh32/33 vector, an AAV.rh43 vector, a modified AAV.rh43 vector, an AAV.rh64R1 vector, and a modified AAV.rh64R1 vector and any combinations or equivalents thereof.
  • the lentiviral vector is an integrase-competent lentiviral vector (ICLV).
  • the lentiviral vector can refer to the transgene plasmid vector as well as the transgene plasmid vector in conjunction with related plasmids (e.g., a packaging plasmid, a rev expressing plasmid, an envelope plasmid) as well as a lentiviral-based particle capable of introducing exogenous nucleic acid into a cell through a viral or viral-like entry mechanism.
  • Lentiviral vectors are well-known in the art (see, e.g., Trono D.
  • exemplary lentiviral vectors that may be used in any of the herein described compositions, systems, methods, and kits can include a human immunodeficiency virus (HIV) 1 vector, a modified human immunodeficiency virus (HIV) 1 vector, a human immunodeficiency virus (HIV) 2 vector, a modified human immunodeficiency virus (HIV) 2 vector, a sooty mangabey simian immunodeficiency virus (SIVsM) vector, a modified sooty mangabey simian immunodeficiency virus (SIVsM) vector, a African green monkey simian immunodeficiency virus (SIVAGm) vector, a modified African green monkey simian immunodeficiency virus (SIVAGm) vector, an equine
  • nucleic acid sequences encoding the fusion proteins disclosed herein for use in gene transfer and expression techniques described herein. It should be understood, although not always explicitly stated that the sequences provided herein can be used to provide the expression product as well as substantially identical sequences that produce a protein that has the same biological properties. These “biologically equivalent” or “biologically active” or “equivalent” polypeptides are encoded by equivalent polynucleotides as described herein.
  • They may possess at least 60%, or alternatively, at least 65%, or alternatively, at least 70%, or alternatively, at least 75%, or alternatively, at least 80%, or alternatively at least 85%, or alternatively at least 90%, or alternatively at least 95% or alternatively at least 98%, identical primary amino acid sequence to the reference polypeptide when compared using sequence identity methods run under default conditions.
  • Specific polypeptide sequences are provided as examples of particular embodiments. Modifications to the sequences to amino acids with alternate amino acids that have similar charge.
  • an equivalent polynucleotide is one that hybridizes under stringent conditions to the reference polynucleotide or its complement or in reference to a polypeptide, a polypeptide encoded by a polynucleotide that hybridizes to the reference encoding polynucleotide under stringent conditions or its complementary strand.
  • an equivalent polypeptide or protein is one that is expressed from an equivalent polynucleotide.
  • nucleic acid sequences e.g., polynucleotide sequences
  • exemplary Cas sequences such as e.g., SEQ ID NO: 46 (Cas13d) are codon optimized for expression in human cells. Codon optimization refers to the fact that different cells differ in their usage of particular codons. This codon bias corresponds to a bias in the relative abundance of particular tRNAs in the cell type. By altering the codons in the sequence to match with the relative abundance of corresponding tRNAs, it is possible to increase expression.
  • nucleic acid sequences coding for, e.g., a Cas protein can be generated.
  • such a sequence is optimized for expression in a host or target cell, such as a host cell used to express the Cas protein or a cell in which the disclosed methods are practiced (such as in a mammalian cell, e.g., a human cell).
  • Codon preferences and codon usage tables for a particular species can be used to engineer isolated nucleic acid molecules encoding a Cas protein (such as one encoding a protein having at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to its corresponding wild-type protein) that takes advantage of the codon usage preferences of that particular species.
  • the Cas proteins disclosed herein can be designed to have codons that are preferentially used by a particular organism of interest.
  • an Cas nucleic acid sequence is optimized for expression in human cells, such as one having at least 70%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 98%, or at least 99% sequence identity to its corresponding wild-type or originating nucleic acid sequence.
  • an isolated nucleic acid molecule encoding at least one Cas protein (which can be part of a vector) includes at least one Cas protein coding sequence that is codon optimized for expression in a eukaryotic cell, or at least one Cas protein coding sequence codon optimized for expression in a human cell.
  • such a codon optimized Cas coding sequence has at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to its corresponding wild-type or originating sequence.
  • a eukaryotic cell codon optimized nucleic acid sequence encodes a Cas protein having at least 85%, at least 90%, at least 92%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to its corresponding wild-type or originating protein.
  • clones containing functionally equivalent nucleic acids may be routinely generated, such as nucleic acids which differ in sequence but which encode the same Cas protein sequence.
  • Silent mutations in the coding sequence result from the degeneracy (i.e., redundancy) of the genetic code, whereby more than one codon can encode the same amino acid residue.
  • leucine can be encoded by CTT, CTC, CTA, CTG, TTA, or TTG; serine can be encoded by TCT, TCC, TCA, TCG, AGT, or AGC; asparagine can be encoded by AAT or AAC; aspartic acid can be encoded by GAT or GAC; cysteine can be encoded by TGT or TGC; alanine can be encoded by GCT, GCC, GCA, or GCG; glutamine can be encoded by CAA or CAG; tyrosine can be encoded by TAT or TAC; and isoleucine can be encoded by ATT, ATC, or ATA. Tables showing the standard genetic code can be found in various sources (see, for example, Stryer, 1988, Biochemistry, 3.sup.rd Edition, W.H. 5 Freeman and Co., NY).
  • Hybridization refers to a reaction in which one or more polynucleotides react to form a complex that is stabilized via hydrogen bonding between the bases of the nucleotide residues.
  • the hydrogen bonding may occur by Watson-Crick base pairing, Hoogstein binding, or in any other sequence-specific manner.
  • the complex may comprise two strands forming a duplex structure, three or more strands forming a multi-stranded complex, a single self-hybridizing strand, or any combination of these.
  • a hybridization reaction may constitute a step in a more extensive process, such as the initiation of a PC reaction, or the enzymatic cleavage of a polynucleotide by a ribozyme.
  • Examples of stringent hybridization conditions include: incubation temperatures of about 25° C. to about 37° C.; hybridization buffer concentrations of about 6 ⁇ SSC to about 10 ⁇ SSC; formamide concentrations of about 0% to about 25%; and wash solutions from about 4 ⁇ SSC to about 8 ⁇ SSC.
  • Examples of moderate hybridization conditions include: incubation temperatures of about 40° C. to about 50° C.; buffer concentrations of about 9 ⁇ SSC to about 2 ⁇ SSC; formamide concentrations of about 30% to about 50%; and wash solutions of about 5 ⁇ SSC to about 2 ⁇ SSC.
  • Examples of high stringency conditions include: incubation temperatures of about 55° C.
  • hybridization incubation times are from 5 minutes to 24 hours, with 1, 2, or more washing steps, and wash incubation times are about 1, 2, or 15 minutes.
  • SSC is 0.15 M NaCl and 15 mM citrate buffer. It is understood that equivalents of SSC using other buffer systems can be employed.
  • “Homology” or “identity” or “similarity” refers to sequence similarity between two peptides or between two nucleic acid molecules. Homology can be determined by comparing a position in each sequence which may be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same base or amino acid, then the molecules are homologous at that position. A degree of homology between sequences is a function of the number of matching or homologous positions shared by the sequences. An “unrelated” or “non-homologous”sequence shares less than 40% identity, or alternatively less than 25% identity, with one of the sequences of the present invention.
  • a cell of the disclosure is a prokaryotic cell.
  • a cell of the disclosure is a eukaryotic cell.
  • the cell is a mammalian cell.
  • the cell is a bovine, murine, feline, equine, porcine, canine, simian, or human cell.
  • the cell is a non-human mammalian cell such as a non-human primate cell.
  • a cell of the disclosure is a somatic cell. In some embodiments, a cell of the disclosure is a germline cell. In some embodiments, a germline cell of the disclosure is not a human cell.
  • a cell of the disclosure is a stem cell.
  • a cell of the disclosure is an embryonic stem cell.
  • an embryonic stem cell of the disclosure is not a human cell.
  • a cell of the disclosure is a multipotent stem cell or a pluripotent stem cell.
  • a cell of the disclosure is an adult stem cell.
  • a cell of the disclosure is an induced pluripotent stem cell (iPSC).
  • a cell of the disclosure is a hematopoietic stem cell (HSC).
  • a somatic cell of the disclosure is an immune cell.
  • an immune cell of the disclosure is a lymphocyte.
  • an immune cell of the disclosure is a T lymphocyte (also referred to herein as a T-cell).
  • Exemplary T-cells of the disclosure include, but are not limited to, na ⁇ ve T cells, effector T cells, helper T cells, memory T cells, regulatory T cells (Tregs) and Gamma delta T cells.
  • an immune cell of the disclosure is a B lymphocyte.
  • an immune cell of the disclosure is a natural killer cell.
  • an immune cell of the disclosure is an antigen-presenting cell.
  • a somatic cell of the disclosure is a muscle cell.
  • a muscle cell of the disclosure is a myoblast or a myocyte.
  • a muscle cell of the disclosure is a cardiac muscle cell, skeletal muscle cell or smooth muscle cell.
  • a muscle cell of the disclosure is a striated cell.
  • a somatic cell of the disclosure is an epithelial cell.
  • an epithelial cell of the disclosure forms a squamous cell epithelium, a cuboidal cell epithelium, a columnar cell epithelium, a stratified cell epithelium, a pseudostratified columnar cell epithelium or a transitional cell epithelium.
  • an epithelial cell of the disclosure forms a gland including, but not limited to, a pineal gland, a thymus gland, a pituitary gland, a thyroid gland, an adrenal gland, an apocrine gland, a holocrine gland, a merocrine gland, a serous gland, a mucous gland and a sebaceous gland.
  • an epithelial cell of the disclosure contacts an outer surface of an organ including, but not limited to, a lung, a spleen, a stomach, a pancreas, a bladder, an intestine, a kidney, a gallbladder, a liver, a larynx or a pharynx.
  • an epithelial cell of the disclosure contacts an outer surface of a blood vessel or a vein.
  • a somatic cell of the disclosure is a neuronal cell.
  • a neuron cell of the disclosure is a neuron of the central nervous system.
  • a neuron cell of the disclosure is a neuron of the brain or the spinal cord.
  • a neuron cell of the disclosure is a neuron of the retina.
  • a neuron cell of the disclosure is a neuron of a cranial nerve or an optic nerve.
  • a neuron cell of the disclosure is a neuron of the peripheral nervous system.
  • a neuron cell of the disclosure is a neuroglial or a glial cell.
  • a glial of the disclosure is a glial cell of the central nervous system including, but not limited to, oligodendrocytes, astrocytes, ependymal cells, and microglia.
  • a glial of the disclosure is a glial cell of the peripheral nervous system including, but not limited to, Schwann cells and satellite cells.
  • a somatic cell of the disclosure is a primary cell.
  • a somatic cell of the disclosure is a cultured cell.
  • a somatic cell of the disclosure is in vivo, in vitro, ex vivo or in situ.
  • a somatic cell of the disclosure is autologous or allogeneic.
  • the disclosure provides a method of modifying level of expression of an RNA molecule of the disclosure or a protein encoded by the RNA molecule comprising contacting the composition and the RNA molecule under conditions suitable for binding of one or more of the guide RNA or the fusion protein (or a portion thereof) to the RNA molecule.
  • the disclosure provides a method of modifying an activity of a protein encoded by an RNA molecule comprising contacting the composition and the RNA molecule under conditions suitable for binding of one or more of the guide RNA or the fusion protein (or a portion thereof) to the RNA molecule.
  • the disclosure provides a method of modifying level of expression of an RNA molecule of the disclosure or a protein encoded by the RNA molecule comprising contacting the composition and a cell comprising the RNA molecule under conditions suitable for binding of one or more of the guide RNA or the fusion protein (or a portion thereof) to the RNA molecule.
  • the cell is in vivo, in vitro, ex vivo or in situ.
  • the composition comprises a vector comprising composition comprising a guide RNA of the disclosure and a fusion protein of the disclosure.
  • the vector is an AAV.
  • the disclosure provides a method of modifying an activity of a protein encoded by an RNA molecule comprising contacting the composition and a cell comprising the RNA molecule under conditions suitable for binding of one or more of the guide RNA or the fusion protein (or a portion thereof) to the RNA molecule.
  • the cell is in vivo, in vitro, ex vivo or in situ.
  • the composition comprises a vector comprising composition comprising a guide RNA or a single guide RNA of the disclosure and a fusion protein of the disclosure.
  • the vector is an AAV.
  • the disclosure provides a method of modifying level of expression of an RNA molecule of the disclosure or a protein encoded by the RNA molecule comprising contacting the composition and the RNA molecule under conditions suitable for RNA nuclease activity wherein the fusion protein induces a break in the RNA molecule.
  • the disclosure provides a method of modifying an activity of a protein encoded by an RNA molecule comprising contacting the composition and the RNA molecule under conditions suitable for RNA nuclease activity wherein the fusion protein induces a break in the RNA molecule.
  • the disclosure provides a method of modifying a level of expression of an RNA molecule of the disclosure or a protein encoded by the RNA molecule comprising contacting the composition and a cell comprising the RNA molecule under conditions suitable for RNA nuclease activity wherein the fusion protein induces a break in the RNA molecule.
  • the cell is in vivo, in vitro, ex vivo or in situ.
  • the composition comprises a vector comprising composition comprising a guide RNA of the disclosure and a fusion protein of the disclosure.
  • the vector is an AAV.
  • the disclosure provides a method of modifying an activity of a protein encoded by an RNA molecule comprising contacting the composition and a cell comprising the RNA molecule under conditions suitable for RNA nuclease activity wherein the fusion protein induces a break in the RNA molecule.
  • the cell is in vivo, in vitro, ex vivo or in situ.
  • the composition comprises a vector comprising composition comprising a guide RNA or a single guide RNA of the disclosure and a fusion protein of the disclosure.
  • the vector is an AAV.
  • the disclosure provides a method of treating a disease or disorder comprising administering to a subject a therapeutically effective amount of a composition of the disclosure.
  • the disclosure provides a method of treating a disease or disorder comprising administering to a subject a therapeutically effective amount of a composition of the disclosure, wherein the composition comprises a vector comprising composition comprising a guide RNA of the disclosure and a fusion protein of the disclosure and wherein the composition modifies a level of expression of an RNA molecule of the disclosure or a protein encoded by the RNA molecule.
  • the disclosure provides a method of treating a disease or disorder comprising administering to a subject a therapeutically effective amount of a composition of the disclosure, wherein the composition comprises a vector comprising composition comprising a guide RNA of the disclosure and a fusion protein of the disclosure and wherein the composition modifies an activity of a protein encoded by an RNA molecule.
  • a disease or disorder of the disclosure includes, but is not limited to, a genetic disease or disorder.
  • the genetic disease or disorder is a single-gene disease or disorder.
  • the single-gene disease or disorder is an autosomal dominant disease or disorder, an autosomal recessive disease or disorder, an X-chromosome linked (X-linked) disease or disorder, an X-linked dominant disease or disorder, an X-linked recessive disease or disorder, a Y-linked disease or disorder or a mitochondrial disease or disorder.
  • the genetic disease or disorder is a multiple-gene disease or disorder.
  • the genetic disease or disorder is a multiple-gene disease or disorder.
  • the single-gene disease or disorder is an autosomal dominant disease or disorder including, but not limited to, Huntington's disease, neurofibromatosis type 1, neurofibromatosis type 2, Marfan syndrome, hereditary nonpolyposis colorectal cancer, hereditary multiple exostoses, Von Willebrand disease, and acute intermittent porphyria.
  • the single-gene disease or disorder is an autosomal recessive disease or disorder including, but not limited to, Albinism, Medium-chain acyl-CoA dehydrogenase deficiency, cystic fibrosis, sickle-cell disease, Tay-Sachs disease, Niemann-Pick disease, spinal muscular atrophy, and Roberts syndrome.
  • the single-gene disease or disorder is X-linked disease or disorder including, but not limited to, muscular dystrophy, Duchenne muscular dystrophy, Hemophilia, Adrenoleukodystrophy (ALD), Rett syndrome, and Hemophilia A.
  • the single-gene disease or disorder is a mitochondrial disorder including, but not limited to, Leber's hereditary optic neuropathy.
  • a disease or disorder of the disclosure includes, but is not limited to, an immune disease or disorder.
  • the immune disease or disorder is an immunodeficiency disease or disorder including, but not limited to, B-cell deficiency, T-cell deficiency, neutropenia, asplenia, complement deficiency, acquired immunodeficiency syndrome (AIDS) and immunodeficiency due to medical intervention (immunosuppression as an intended or adverse effect of a medical therapy).
  • the immune disease or disorder is an autoimmune disease or disorder including, but not limited to, Achalasia, Addison's disease, Adult Still's disease, Agammaglobulinemia, Alopecia areata, Amyloidosis, Anti-GBM/Anti-TBM nephritis, Antiphospholipid syndrome, Autoimmune angioedema, Autoimmune dysautonomia, Autoimmune encephalomyelitis, Autoimmune hepatitis, Autoimmune inner ear disease (AIED), Autoimmune myocarditis, Autoimmune oophoritis, Autoimmune orchitis, Autoimmune pancreatitis, Autoimmune retinopathy, Autoimmune urticaria, Axonal & neuronal neuropathy (AMAN), Baló disease, Behcet's disease, Benign mucosal pemphigoid, Bullous pemphigoid, Castleman disease (CD), Celiac disease, Cha
  • a disease or disorder of the disclosure includes, but is not limited to, an inflammatory disease or disorder.
  • a disease or disorder of the disclosure includes, but is not limited to, a metabolic disease or disorder.
  • a disease or disorder of the disclosure includes, but is not limited to, a degenerative or a progressive disease or disorder.
  • the degenerative or a progressive disease or disorder includes, but is not limited to, amyotrophic lateral sclerosis (ALS), Huntington's disease, Alzheimer's disease, and aging.
  • ALS amyotrophic lateral sclerosis
  • Huntington's disease Huntington's disease
  • Alzheimer's disease and aging.
  • a disease or disorder of the disclosure includes, but is not limited to, an infectious disease or disorder.
  • a disease or disorder of the disclosure includes, but is not limited to, a pediatric or a developmental disease or disorder.
  • a disease or disorder of the disclosure includes, but is not limited to, a cardiovascular disease or disorder.
  • a disease or disorder of the disclosure includes, but is not limited to, a proliferative disease or disorder.
  • the proliferative disease or disorder is a cancer.
  • the cancer includes, but is not limited to, Acute Lymphoblastic Leukemia (ALL), Acute Myeloid Leukemia (AML), Adrenocortical Carcinoma, AIDS-Related Cancers, Kaposi Sarcoma (Soft Tissue Sarcoma), AIDS-Related Lymphoma (Lymphoma), Primary CNS Lymphoma (Lymphoma), Anal Cancer, Appendix Cancer, Gastrointestinal Carcinoid Tumors, Astrocytomas, Atypical Teratoid/Rhabdoid Tumor, Central Nervous System (Brain Cancer), Basal Cell Carcinoma, Bile Duct Cancer, Bladder Cancer, Bone Cancer, Ewing Sarcoma, Osteosarcoma, Malignant Fibrous His
  • a subject of the disclosure has been diagnosed with the disease or disorder. In some embodiments, the subject of the disclosure presents at least one sign or symptom of the disease or disorder. In some embodiments, the subject has a biomarker predictive of a risk of developing the disease or disorder. In some embodiments, the biomarker is a genetic mutation.
  • a subject of the disclosure is female. In some embodiments of the methods of the disclosure, a subject of the disclosure is male. In some embodiments, a subject of the disclosure has two XX or XY chromosomes. In some embodiments, a subject of the disclosure has two XX or XY chromosomes and a third chromosome, either an X or a Y.
  • a subject of the disclosure is a neonate, an infant, a child, an adult, a senior adult, or an elderly adult. In some embodiments of the methods of the disclosure, a subject of the disclosure is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or 31 days old. In some embodiments of the methods of the disclosure, a subject of the disclosure is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12 months old.
  • a subject of the disclosure is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or any number of years or partial years in between of age.
  • a subject of the disclosure is a mammal. In some embodiments, a subject of the disclosure is a non-human mammal.
  • a subject of the disclosure is a human.
  • a therapeutically effective amount comprises a single dose of a composition of the disclosure. In some embodiments, a therapeutically effective amount comprises a therapeutically effective amount comprises at least one dose of a composition of the disclosure. In some embodiments, a therapeutically effective amount comprises a therapeutically effective amount comprises one or more dose(s) of a composition of the disclosure.
  • a therapeutically effective amount eliminates a sign or symptom of the disease or disorder. In some embodiments, a therapeutically effective amount reduces a severity of a sign or symptom of the disease or disorder.
  • a therapeutically effective amount eliminates the disease or disorder.
  • a therapeutically effective amount prevents an onset of a disease or disorder. In some embodiments, a therapeutically effective amount delays the onset of a disease or disorder. In some embodiments, a therapeutically effective amount reduces the severity of a sign or symptom of the disease or disorder. In some embodiments, a therapeutically effective amount improves a prognosis for the subject.
  • a composition of the disclosure is administered to the subject systemically. In some embodiments, the composition of the disclosure is administered to the subject by an intravenous route. In some embodiments, the composition of the disclosure is administered to the subject by an injection or an infusion.
  • a composition of the disclosure is administered to the subject locally.
  • the composition of the disclosure is administered to the subject by an intraosseous, intraocular, intracerebrospinal or intraspinal route.
  • the composition of the disclosure is administered directly to the cerebral spinal fluid of the central nervous system.
  • the composition of the disclosure is administered directly to a tissue or fluid of the eye and does not have bioavailability outside of ocular structures.
  • the composition of the disclosure is administered to the subject by an injection or an infusion.
  • compositions comprising the RNA-binding fusion proteins disclosed herein are formulated as pharmaceutical compositions.
  • pharmaceutical compositions for use as disclosed herein may comprise a fusion protein(s) or a polynucleotide encoding the fusion protein(s), optionally comprised in an AAV, which is optionally also immune orthogonal, in combination with one or more pharmaceutically or physiologically acceptable carriers, diluents or excipients.
  • compositions may comprise buffers such as neutral buffered saline, phosphate buffered saline and the like; carbohydrates such as glucose, mannose, sucrose or dextrans, mannitol; proteins; polypeptides or amino acids such as glycine; antioxidants; chelating agents such as EDTA or glutathione; adjuvants (e.g., aluminum hydroxide); and preservatives.
  • buffers such as neutral buffered saline, phosphate buffered saline and the like
  • carbohydrates such as glucose, mannose, sucrose or dextrans, mannitol
  • proteins polypeptides or amino acids
  • antioxidants e.g., antioxidants
  • chelating agents such as EDTA or glutathione
  • adjuvants e.g., aluminum hydroxide
  • preservatives e.g., aluminum hydroxide
  • Embodiment 1 A composition comprising:
  • RNA molecule (a) a sequence comprising a guide RNA (gRNA) that specifically binds a target sequence within an RNA molecule and
  • gRNA guide RNA
  • neither the first RNA-binding polypeptide nor the second RNA-binding polypeptide comprises a significant DNA-nuclease activity
  • first RNA-binding polypeptide and the second RNA-binding polypeptide are not identical, and
  • RNA-binding polypeptide comprises an RNA-nuclease activity
  • composition comprising nucleic acid sequence encoding a fusion protein, the fusion protein comprising a first RNA-binding polypeptide and a second RNA-binding polypeptide, wherein the first RNA-binding polypeptide is not a guided RNA-binding polypeptide, wherein the first RNA-binding polypeptide and the second RNA-binding polypeptide are not identical, and wherein the second RNA-binding polypeptide comprises an RNA-nuclease activity.
  • Embodiment 2 The composition of embodiment 1, wherein the target sequence comprises at least one repeated sequence.
  • Embodiment 3 The composition of embodiment 1 or 2, wherein the sequence comprising the gRNA comprises a promoter capable of expressing the gRNA in a eukaryotic cell.
  • Embodiment 4 The composition of embodiment 3, wherein the eukaryotic cell is an animal cell.
  • Embodiment 5 The composition of embodiment 4, wherein the animal cell is a mammalian cell.
  • Embodiment 6 The composition of embodiment 5, wherein the animal cell is a human cell.
  • Embodiment 7 The composition of any one of embodiments 1-6, wherein the promoter is a constitutively active promoter.
  • Embodiment 8 The composition of any one of embodiments 1-7, wherein the promoter is isolated or derived from a promoter capable of driving expression of an RNA polymerase.
  • Embodiment 9 The composition of embodiment 8, wherein the promoter is isolated or derived from a U6 promoter.
  • Embodiment 10 The composition of any one of embodiments 1-7, wherein the promoter is isolated or derived from a promoter capable of driving expression of a transfer RNA (tRNA).
  • tRNA transfer RNA
  • Embodiment 11 The composition of embodiment 10, wherein the promoter is isolated or derived from an alanine tRNA promoter, an arginine tRNA promoter, an asparagine tRNA promoter, an aspartic acid tRNA promoter, a cysteine tRNA promoter, a glutamine tRNA promoter, a glutamic acid tRNA promoter, a glycine tRNA promoter, a histidine tRNA promoter, an isoleucine tRNA promoter, a leucine tRNA promoter, a lysine tRNA promoter, a methionine tRNA promoter, a phenylalanine tRNA promoter, a proline tRNA promoter, a serine tRNA promoter, a threonine tRNA promoter, a tryptophan tRNA promoter, a tyrosine tRNA promoter, or a valine tRNA promoter.
  • Embodiment 12 The composition of embodiment 10, wherein the promoter is isolated or derived from a valine tRNA promoter.
  • Embodiment 13 The composition of any one of embodiments 1-12, wherein the sequence comprising the gRNA comprises a spacer sequence that specifically binds to the target RNA sequence.
  • Embodiment 14 The composition of embodiment 13, wherein the spacer sequence has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 87%, 90%, 95%, 97%, 99% or any percentage in between of complementarity to the target RNA sequence.
  • Embodiment 15 The composition of embodiment 13, wherein the spacer sequence has 100% complementarity to the target RNA sequence.
  • Embodiment 16 The composition of any one of embodiments 13-15, wherein the spacer sequence comprises or consists of 20 nucleotides.
  • Embodiment 17 The composition of any one of embodiments 13-15, wherein the spacer sequence comprises or consists of 21 nucleotides.
  • Embodiment 18 The composition of embodiment 17, wherein the spacer sequence comprises the sequence UGGAGCGAGCAUCCCCCAAA (SEQ ID NO: 1), GUUUGGGGGAUGCUCGCUCCA (SEQ ID NO: 2), CCCUCACUGCUGGGGAGUCC (SEQ ID NO: 3), GGACUCCCCAGCAGUGAGGG (SEQ ID NO: 4), GCAACUGGAUCAAUUUGCUG (SEQ ID NO: 5), GCAGCAAAUUGAUCCAGUUGC (SEQ ID NO: 6), GCAUUCUUAUCUGGUCAGUGC (SEQ ID NO: 7), GCACUGACCAGAUAAGAAUG (SEQ ID NO: 8), GAGCAGCAGCAGCAGCAGCAG (SEQ ID NO: 9), GCAGGCAGGCAGGCAGGCAGG (SEQ ID NO: 10), GCCCCGGCCCCGGCCCCGGC (SEQ ID NO: 11), or GCTGCTGCTGCTGCTGCTGC (SEQ ID NO: 12), GG
  • Embodiment 19 The composition of any one of embodiments 1-18, wherein the sequence comprising the gRNA comprises a scaffold sequence that specifically binds to the first RNA binding protein.
  • Embodiment 20 The composition of embodiment 19, wherein the scaffold sequence comprises a stem-loop structure.
  • Embodiment 21 The composition of embodiment 19 or 20, wherein the scaffold sequence comprises or consists of 90 nucleotides.
  • Embodiment 22 The composition of embodiment 19 or 20, wherein the scaffold sequence comprises or consists of 93 nucleotides.
  • Embodiment 23 The composition of embodiment 22, wherein the scaffold sequence comprises the sequence
  • Embodiment 24 The composition of embodiment 16, wherein the spacer sequence comprises the sequence GUGAUAAGUGGAAUGCCAUG (SEQ ID NO: 14), CUGGUGAACUUCCGAUAGUG (SEQ ID NO: 15), or GAGATATAGCCTGGTGGTTC (SEQ ID NO: 16).
  • Embodiment 25 The composition of embodiment 19 or 24, wherein the scaffold sequence comprises a step-loop structure.
  • Embodiment 26 The composition of embodiment 25, wherein the scaffold sequence comprises or consists of 85 nucleotides.
  • Embodiment 27 The composition of embodiment 26, wherein the scaffold sequence comprises the sequence
  • Embodiment 28 The composition of embodiment 16, wherein the spacer sequence comprises the sequence at least 1, 2, 3, 4, 5, 6, or 7 repeats of the sequence CUG (SEQ ID NO: 18), CCUG (SEQ ID NO: 19), CAG (SEQ ID NO: 80), GGGGCC (SEQ ID NO: 81) or any combination thereof.
  • Embodiment 29 The composition of embodiment 28, wherein the sequence comprising the gRNA comprises a scaffold sequence that specifically binds to the first RNA binding protein.
  • Embodiment 30 The composition of embodiment 29, wherein the scaffold sequence comprises a stem-loop structure.
  • Embodiment 31 The composition of embodiment 29 or 30, wherein the scaffold sequence comprises or consists of 90 nucleotides.
  • Embodiment 32 The composition of embodiment 30 or 31, wherein the scaffold sequence comprises or consists of 93 nucleotides.
  • Embodiment 33 The composition of embodiment 32, wherein the scaffold sequence comprises the sequence
  • Embodiment 34 The composition of any one of embodiments 1-33, wherein the gRNA does not bind or does not selectively bind to a second sequence within the RNA molecule.
  • Embodiment 35 The composition of embodiment 34, wherein an RNA genome or an RNA transcriptome comprises the RNA molecule.
  • Embodiment 36 The composition of any one of embodiments 1-35, wherein the first RNA binding protein comprises a CRISPR-Cas protein.
  • Embodiment 37 The composition of embodiment 36, wherein the CRISPR-Cas protein is a Type II CRISPR-Cas protein.
  • Embodiment 38 The composition of embodiment 37, wherein the first RNA binding protein comprises a Cas9 polypeptide or an RNA-binding portion thereof.
  • Embodiment 39 The composition of embodiment 36, wherein the CRISPR-Cas protein is a Type V CRISPR-Cas protein.
  • Embodiment 40 The composition of embodiment 39, wherein the first RNA binding protein comprises a Cpf1 polypeptide or an RNA-binding portion thereof.
  • Embodiment 41 The composition of embodiment 36, wherein the CRISPR-Cas protein is a Type VI CRISPR-Cas protein.
  • Embodiment 42 The composition of embodiment 41, wherein the first RNA binding protein comprises a Cas13 polypeptide or an RNA-binding portion thereof.
  • Embodiment 43 The composition of any one of embodiments 36-42, wherein the CRISPR-Cas protein comprises a native RNA nuclease activity.
  • Embodiment 44 The composition of embodiment 43, wherein the native RNA nuclease activity is reduced or inhibited.
  • Embodiment 45 The composition of embodiment 43, wherein the native RNA nuclease activity is increased or induced.
  • Embodiment 46 The composition of any one of embodiments 36-45, wherein the CRISPR-Cas protein comprises a native DNA nuclease activity and wherein the native DNA nuclease activity is inhibited.
  • Embodiment 47 The composition of embodiment 46, wherein the CRISPR-Cas protein comprises a mutation.
  • Embodiment 48 The composition of embodiment 47, wherein a nuclease domain of the CRISPR-Cas protein comprises the mutation.
  • Embodiment 49 The composition of embodiment 47, wherein the mutation occurs in a nucleic acid encoding the CRISPR-Cas protein.
  • Embodiment 50 The composition of embodiment 47, wherein the mutation occurs in an amino acid encoding the CRISPR-Cas protein.
  • Embodiment 51 The composition of any one of embodiments 47-50, wherein the mutation comprises a substitution, an insertion, a deletion, a frameshift, an inversion, or a transposition.
  • Embodiment 52 The composition of any one of embodiments 47-50, wherein the mutation comprises a deletion of a nuclease domain, a binding site within the nuclease domain, an active site within the nuclease domain, or at least one essential amino acid residue within the nuclease domain.
  • Embodiment 53 The composition of any one of embodiments 1-35, wherein the first RNA binding protein comprises a Pumilio and FBF (PUF) protein.
  • PEF Pumilio and FBF
  • Embodiment 54 The composition of embodiment 53, wherein the first RNA binding protein comprises a Pumilio-based assembly (PUMBY) protein.
  • PUMBY Pumilio-based assembly
  • Embodiment 55 The composition of any one of embodiments 1-54, wherein the first RNA binding protein does not require multimerization for RNA-binding activity.
  • Embodiment 56 The composition of embodiment 55, wherein the first RNA binding protein is not a monomer of a multimer complex
  • Embodiment 57 The composition of embodiment 55, wherein a multimer protein complex does not comprise the first RNA binding protein.
  • Embodiment 58 The composition of any one of embodiments 1-57, wherein the first RNA binding protein selectively binds to a target sequence within the RNA molecule.
  • Embodiment 59 The composition of embodiment 58, wherein the first RNA binding protein does not comprise an affinity for a second sequence within the RNA molecule.
  • Embodiment 60 The composition of embodiment 58 or 59, wherein the first RNA binding protein does not comprise a high affinity for or selectively bind a second sequence within the RNA molecule.
  • Embodiment 61 The composition of embodiment 60, wherein an RNA genome or an RNA transcriptome comprises the RNA molecule.
  • Embodiment 62 The composition of any one of embodiments 1-61, wherein the first RNA binding protein comprises between 2 and 1300 amino acids, inclusive of the endpoints.
  • Embodiment 63 The composition of any one of embodiments 1-62, wherein the sequence encoding the first RNA binding protein further comprises a sequence encoding a nuclear localization signal (NLS).
  • NLS nuclear localization signal
  • Embodiment 64 The composition of embodiment 63, wherein the sequence encoding a nuclear localization signal (NLS) is positioned 3′ to the sequence encoding the first RNA binding protein.
  • NLS nuclear localization signal
  • Embodiment 65 The composition of embodiment 64, wherein the first RNA binding protein comprises an NLS at a C-terminus of the protein.
  • Embodiment 66 The composition of any one of embodiments 1-62, wherein the sequence encoding the first RNA binding protein further comprises a first sequence encoding a first NLS and a second sequence encoding a second NLS.
  • Embodiment 67 The composition of embodiment 66, wherein the sequence encoding the first NLS or the second NLS is positioned 3′ to the sequence encoding the first RNA binding protein.
  • Embodiment 68 The composition of embodiment 67, wherein the first RNA binding protein comprises the first NLS or the second NLS at a C-terminus of the protein.
  • Embodiment 69 The composition of any one of embodiments 1-68, wherein the second RNA binding protein comprises or consists of a nuclease domain.
  • Embodiment 70 The composition of embodiment 69, wherein the sequence encoding the second RNA binding protein comprises or consists of an RNAse.
  • Embodiment 71 The composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAse1.
  • Embodiment 72 The composition of embodiment 71, wherein the RNAse1 protein comprises or consists of SEQ ID NO: 20.
  • Embodiment 73 The composition of embodiment 72, wherein the second RNA binding protein comprises or consists of an RNAse4.
  • Embodiment 74 The composition of embodiment 73, wherein the RNAse4 protein comprises or consists of: (SEQ ID NO: 21.
  • Embodiment 75 The composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAse6.
  • Embodiment 76 The composition of embodiment 75, wherein the RNAse6 protein comprises or consists of SEQ ID NO: 22.
  • Embodiment 77 The composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAse7.
  • Embodiment 78 The composition of embodiment 77, wherein the RNAse7 protein comprises or consists of SEQ ID NO: 23.
  • Embodiment 79 The composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAse8.
  • Embodiment 80 The composition of embodiment 79, wherein the RNAse8 protein comprises or consists of SEQ ID NO: 24.
  • Embodiment 81 The composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAse2.
  • Embodiment 82 The composition of embodiment 81, wherein the RNAse2 protein comprises or consists of SEQ ID NO: 25.
  • Embodiment 83 The composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAse6PL.
  • Embodiment 84 The composition of embodiment 83, wherein the RNAse6PL protein comprises or consists of SEQ ID NO: 26.
  • Embodiment 85 The composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAseL.
  • Embodiment 86 The composition of embodiment 85, wherein the RNAseL protein comprises or consists of SEQ ID NO: 27.
  • Embodiment 87 The composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAseT2.
  • Embodiment 88 The composition of embodiment 87, wherein the RNAseT2 protein comprises or consists of SEQ ID NO: 28.
  • Embodiment 89 The composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAse11.
  • Embodiment 90 The composition of embodiment 89, wherein the RNAse11 comprises or consists of SEQ ID NO: 29.
  • Embodiment 91 The composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAseT2-like.
  • Embodiment 92 The composition of embodiment 91, wherein the RNAseT2-like protein comprises or consists of SEQ ID NO: 30.
  • Embodiment 93 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a NOB1 polypeptide.
  • Embodiment 94 The composition of embodiment 93, wherein the NOB1 polypeptide comprises or consists of SEQ ID NO: 31.
  • Embodiment 95 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of an endonuclease.
  • Embodiment 96 The composition of embodiment 95, wherein the second RNA binding protein comprises or consists of an endonuclease V (ENDOV).
  • ENDOV endonuclease V
  • Embodiment 97 The composition of embodiment 96, wherein the ENDOV protein comprises or consists of SEQ ID NO: 32.
  • Embodiment 98 The composition of embodiment 95, wherein the second RNA binding protein comprises or consists of an endonuclease G (ENDOG).
  • ENDOG endonuclease G
  • Embodiment 99 The composition of embodiment 98, wherein the ENDOG protein comprises or consists of SEQ ID NO: 33.
  • Embodiment 100 The composition of embodiment 95, wherein the second RNA binding protein comprises or consists of an endonuclease D1 (ENDOD1).
  • ENDOD1 endonuclease D1
  • Embodiment 101 The composition of embodiment 100, wherein the ENDOD1 protein comprises or consists of SEQ ID NO: 34.
  • Embodiment 102 The composition of embodiment 95, wherein the second RNA binding protein comprises or consists of a Human flap endonuclease-1 (hFEN1).
  • hFEN1 Human flap endonuclease-1
  • Embodiment 103 The composition of embodiment 102, wherein the hFEN1 protein comprises or consists of SEQ ID NO: 35.
  • Embodiment 104 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a human Schlafen 14 (hSLFN14) polypeptide.
  • Embodiment 105 The composition of embodiment 104, wherein the hSLFN14 polypeptide comprises or consists of SEQ ID NO: 36.
  • Embodiment 106 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a human beta-lactamase-like protein 2 (hLACTB2) polypeptide.
  • hLACTB2 human beta-lactamase-like protein 2
  • Embodiment 107 The composition of embodiment 106, wherein the hLACTB2 polypeptide comprises or consists of SEQ ID NO: 37.
  • Embodiment 108 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of an apurinic/apyrimidinic (AP) endodeoxyribonuclease (APEX2) polypeptide.
  • AP apurinic/apyrimidinic endodeoxyribonuclease
  • Embodiment 109 The composition of embodiment 108, wherein the APEX2 polypeptide comprises or consists of SEQ ID NO: 38.
  • Embodiment 110 The composition of embodiment 108, wherein the APEX2 polypeptide comprises or consists of: SEQ ID NO: 39.
  • Embodiment 111 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of an angiogenin (ANG) polypeptide.
  • ANG angiogenin
  • Embodiment 112. The composition of embodiment 111, wherein the ANG polypeptide comprises or consists of SEQ ID NO: 40.
  • Embodiment 113 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a heat responsive protein 12 (HRSP12) polypeptide.
  • HRSP12 heat responsive protein 12
  • Embodiment 114 The composition of embodiment 113, wherein the HRSP12 polypeptide comprises or consists of SEQ ID NO: 41.
  • Embodiment 115 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a Zinc Finger CCCH-Type Containing 12A (ZC3H12A) polypeptide.
  • Embodiment 116 The composition of embodiment 115, wherein the ZC3H12A polypeptide comprises or consists of SEQ ID NO: 42.
  • Embodiment 117 The composition of embodiment 115, wherein the ZC3H12A polypeptide comprises or consists of SEQ ID NO: 43.
  • Embodiment 118 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a Reactive Intermediate Imine Deaminase A (RIDA) polypeptide.
  • RIDA Reactive Intermediate Imine Deaminase A
  • Embodiment 119 The composition of embodiment 118, wherein the RIDA polypeptide comprises or consists of SEQ ID NO: 44.
  • Embodiment 120 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a Phospholipase D Family Member 6 (PDL6) polypeptide.
  • PDL6 Phospholipase D Family Member 6
  • Embodiment 121 The composition of embodiment 120, wherein the PDL6 polypeptide comprises or consists of: (SEQ ID NO: 126.
  • Embodiment 122 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a Endonuclease III-like protein 1 (NTHL) polypeptide.
  • NTHL Endonuclease III-like protein 1
  • Embodiment 123 The composition of embodiment 122, wherein the NTHL polypeptide comprises or consists of SEQ ID NO: 123.
  • Embodiment 124 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a Mitochondrial ribonuclease P catalytic subunit (KIAA0391) polypeptide.
  • Embodiment 125 The composition of embodiment 124, wherein the KIAA0391 polypeptide comprises or consists of SEQ ID NO: 127.
  • Embodiment 126 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of an apurinic or apyrimidinic site lyase (APEX1) polypeptide.
  • APEX1 apurinic or apyrimidinic site lyase
  • Embodiment 127 The composition of embodiment 126, wherein the APEX1 polypeptide comprises or consists of SEQ ID NO: 125.
  • Embodiment 128 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of an argonaute 2 (AGO2) polypeptide.
  • AGO2 argonaute 2
  • Embodiment 129 The composition of embodiment 128, wherein the AGO2 polypeptide comprises or consists of SEQ ID NO: 128.
  • Embodiment 130 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a mitochondrial nuclease EXOG (EXOG) polypeptide.
  • EXOG mitochondrial nuclease EXOG
  • Embodiment 131 The composition of embodiment 130, wherein the EXOG polypeptide comprises or consists of SEQ ID NO: 129.
  • Embodiment 132 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a Zinc Finger CCCH-Type Containing 12D (ZC3H12D) polypeptide.
  • ZC3H12D Zinc Finger CCCH-Type Containing 12D
  • Embodiment 133 The composition of embodiment 132, wherein the ZC3H12D polypeptide comprises or consists of SEQ ID NO: 130.
  • Embodiment 134 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of an endoplasmic reticulum to nucleus signaling 2 (ERN2) polypeptide.
  • ERN2 nucleus signaling 2
  • Embodiment 135. The composition of embodiment 134, wherein the ERN2 polypeptide comprises or consists of SEQ ID NO: 131.
  • Embodiment 136 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a pelota mRNA surveillance and ribosome rescue factor (PELO) polypeptide.
  • PELO ribosome rescue factor
  • Embodiment 137 The composition of embodiment 136, wherein the PELO polypeptide comprises or consists of SEQ ID NO: 132.
  • Embodiment 138 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a YBEY metallopeptidase (YBEY) polypeptide.
  • YBEY YBEY metallopeptidase
  • Embodiment 139 The composition of embodiment 138, wherein the YBEY polypeptide comprises or consists of SEQ ID NO: 133.
  • Embodiment 140 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a cleavage and polyadenylation specific factor 4 like (CPSF4L) polypeptide.
  • CPSF4L polyadenylation specific factor 4 like
  • Embodiment 141 The composition of embodiment 140, wherein the CPSF4L comprises or consists of SEQ ID NO: 134.
  • Embodiment 142 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of an hCG_2002731 polypeptide.
  • Embodiment 143 The composition of embodiment 142, wherein the hCG_2002731 polypeptide comprises or consists of SEQ ID NO: 135.
  • Embodiment 144 The composition of embodiment 142, wherein the hCG_2002731 polypeptide comprises or consists of SEQ ID NO: 136.
  • Embodiment 145 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of an Excision Repair Cross-Complementation Group 1 (ERCC1) polypeptide.
  • ERCC1 Excision Repair Cross-Complementation Group 1
  • Embodiment 146 The composition of embodiment 145, wherein the ERCC1 polypeptide comprises or consists of SEQ ID NO: 137.
  • Embodiment 147 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a ras-related C3 botulinum toxin substrate 1 isoform (RAC1) polypeptide.
  • RAC1 ras-related C3 botulinum toxin substrate 1 isoform
  • Embodiment 148 The composition of embodiment 147, wherein the RAC1 polypeptide comprises or consists of SEQ ID NO: 138.
  • Embodiment 149 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a Ribonuclease A A1 (RAA1) polypeptide.
  • RAA1 Ribonuclease A A1
  • Embodiment 150 The composition of embodiment 149, wherein the RAA1 polypeptide comprises or consists of SEQ ID NO: 139.
  • Embodiment 151 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a Ras Related Protein (RAB1) polypeptide.
  • RAB1 Ras Related Protein
  • Embodiment 152 The composition of embodiment 151, wherein the RAB1 polypeptide comprises or consists of SEQ ID NO: 140.
  • Embodiment 153 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a DNA Replication Helicase/Nuclease 2 (DNA2) polypeptide.
  • DNA2 DNA Replication Helicase/Nuclease 2
  • Embodiment 154 The composition of embodiment 153, wherein the DNA2 polypeptide comprises or consists of SEQ ID NO: 141.
  • Embodiment 155 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a FLJ35220 polypeptide.
  • Embodiment 156 The composition of embodiment 155, wherein the FLJ35220 polypeptide comprises or consists of SEQ ID NO: 142.
  • Embodiment 157 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a FLJ13173 polypeptide.
  • Embodiment 158 The composition of embodiment 157, wherein the FLJ13173 polypeptide comprises or consists of: (SEQ ID NO: 143.
  • Embodiment 159 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a DNA repair endonuclease XPF (ERCC4) polypeptide.
  • ERCC4 DNA repair endonuclease XPF
  • Embodiment 160 The composition of embodiment 159, wherein the ERCC4 polypeptide comprises or consists of SEQ ID NO: 64.
  • Embodiment 161 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(K41R)) polypeptide.
  • Embodiment 162 The composition of embodiment 161, wherein the Rnase1(K41R) polypeptide comprises or consists of SEQ ID NO: 116.
  • Embodiment 163 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(K41R, D121E)) polypeptide.
  • Embodiment 164 The composition of embodiment 163, wherein the Rnase1 (Rnase1(K41R, D121E)) polypeptide comprises or consists of SEQ ID NO: 117.
  • Embodiment 165 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(K41R, D121E, H119N)) polypeptide.
  • Embodiment 166 The composition of embodiment 165, wherein the Rnase1 (Rnase1(K41R, D121E, H119N)) polypeptide comprises or consists of SEQ ID NO: 118.
  • Embodiment 167 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(H119N)) polypeptide.
  • Embodiment 168 The composition of embodiment 167, wherein the Rnase1 (Rnase1(H119N)) polypeptide comprises or consists of SEQ ID NO: 119.
  • Embodiment 169 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide.
  • Embodiment 170 The composition of embodiment 169, wherein the Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide comprises or consists of SEQ ID NO: 120.
  • Embodiment 171 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide.
  • Embodiment 172 The composition of embodiment 171, wherein the Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N, K41R, D121E)) polypeptide comprises or consists of SEQ ID NO: 121.
  • Embodiment 173 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide.
  • Embodiment 174 The composition of embodiment 173, wherein the Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D)) polypeptide comprises or consists of SEQ ID NO: 122.
  • Embodiment 175. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of Teneurin Transmembrane Protein 1 (TENM1) polypeptide.
  • TEM1 Teneurin Transmembrane Protein 1
  • Embodiment 176 The composition of embodiment 175, wherein the TENM1 polypeptide comprises or consists of SEQ ID NO: 144.
  • Embodiment 177 The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of Teneurin Transmembrane Protein 2 (TENM2) polypeptide.
  • TEM2 Teneurin Transmembrane Protein 2
  • Embodiment 178 The composition of embodiment 177, wherein the TENM2 polypeptide comprises or consists of SEQ ID NO: 145.
  • Embodiment 179 A composition comprising a sequence encoding a target RNA-binding fusion protein comprising (a) a sequence encoding a first RNA-binding polypeptide or portion thereof; and (b) a sequence encoding a second RNA-binding polypeptide, wherein the first RNA-biding polypeptide binds a target RNA not guided by a gRNA sequence, and wherein the second RNA-binding polypeptide comprises RNA-nuclease activity.
  • Embodiment 180 The composition of embodiment 179, wherein the first RNA-binding polypeptide or portion thereof is a PUF, PUMBY, or PPR polypeptide or portion thereof.
  • Embodiment 181 A method for modifying the level of expression of an RNA molecule or a protein encoded by the RNA molecule, the method comprising contacting the composition of embodiments 1 or 179 and the RNA molecule under conditions suitable for binding of the fusion protein or a portion thereof to the RNA molecule.
  • HEK-293 cells were cultured in DMEM with 10% FBS and 1% penicillin/streptomycin (GIBCO) and passaged at 90%-100% confluency.
  • Cells were seeded at 1 ⁇ 10 ⁇ circumflex over ( ) ⁇ 5 cells per well of a 24-well plate for RNA isolation or 0.5 ⁇ 10 ⁇ circumflex over ( ) ⁇ 5 cells per well of a 96-well plate for luciferase assays.
  • RNA isolations were carried out with RNAeasy columns (Qiagen) according to the manufacturer's protocol. RNA quality and concentrations were estimated using the Nanodrop spectrophotometer.
  • cDNA preparation was done using Superscript III (Thermo) with random primers according to the manufacturer's protocol.
  • qPCR was carried out with primers in a sequence adjacent to the CTG repeat in the reporter plasmid using the following primers:
  • Relative abundance of the CTG repeat reporter was determined by normalization to GAPDH. Next, levels of the CTG-targeting sgRNA were normalized to a non-targeting sgRNA to generate a final value reported in the associated data package.
  • Luciferase assays were conducted with the Promega Dual Luciferase kit according to manufacturer's directions. Reported values are a ratio of firefly and renilla luciferase luminescence readings.
  • RNA endonuclease activity Various fusions of human proteins with annotated RNA endonuclease activity and Cas9 ( Streptococcus pyogenes or Campylobacter jejuni ) were constructed. Plasmids encoding the above fusions were co-transfected with either a repeat-containing plasmid or a luciferase assay plasmid (comprising an mRNA sequence encoding a luciferase protein). A level of CTG repeat-containing RNA was measured with qPCR in the condition in which an RNA endonuclease/Cas9 fusion was co-transfected with a repetitive RNA.
  • a level of luciferase protein was measured using a luminescence assay in the condition in which an RNA endonuclease/Cas9 fusion was co-transfected with a luciferase assay plasmid. All measurements were normalized to a non-targeting sgRNA control construct ( FIGS. 3A-5 and FIG. 9 ).
  • A549 cells were cultured in DMEM with 10% FBS and 1% penicillin/streptomycin (GIBCO) and passaged at 90%-100% confluency. Cells were seeded at 1 ⁇ 10 ⁇ circumflex over ( ) ⁇ 5 cells per well of a 24-well plate for RNA isolation or 0.5 ⁇ 10 ⁇ circumflex over ( ) ⁇ 5 cells per well. Cells were transfected with plasmids encoding Campylobacter jejuni Cas9 (CjeCas9) fused to the gene NTHL1 (residues 31-312, E43) or CPSF4L (full length, E67) with plasmids encoding one of four sites in Zika NS5 RNA. CjeCas9 was driven by an EFS promoter while the guide RNAs were driven by U6 promoter. The sequences of the sgRNAs are presented in Table 1. The sequences of the constructs used in this study are presented below.
  • RNA isolations were carried out with RNAeasy columns (Qiagen) according to the manufacturer's protocol. RNA quality and concentrations were estimated using the Nanodrop spectrophotometer. cDNA preparation was done using Superscript III (Thermo) with random primers according to the manufacturer's protocol. qPCR was carried out with the following primers as listed in Table 2.
  • FIG. 7 shows expression levels of Zika NS5 assessed in the presence of both E43 and E67 endonucleases with sgRNAs containing the various NS5-targeting spacer sequences as indicated in Table 2.
  • Zika NS5 expression is displayed as fold change relative to the endonuclease loaded with an sgRNA containing a control (Lambda) spacer sequence.
  • FIG. 8A shows a fluorescence microscopy image of cells transfected with CjeCas9-endonuclease fusions loaded with an sgRNA containing a Zika NS5-targeting spacer sequence. Expression of Zika NS5 is markedly decreased in the presence of CjeCas9-endonuclease fusions loaded with the appropriate Zika NS5-targeting sgRNA as compared to CjeCas9-endonuclease fusions loaded with a non-Zika NS5 targeting sgRNA ( FIGS. 8A and 8B ).
  • FIG. 6 is a list of exemplary endonucleases for use in the compositions of the disclosure.

Abstract

Disclosed are compositions comprising: (a) a sequence comprising a guide RNA (gRNA) that specifically binds a target sequence within an RNA molecule and (b) a sequence encoding a fusion protein, the sequence comprising a sequence encoding a first RNA-binding polypeptide and a sequence encoding a second RNA-binding polypeptide, wherein neither the first RNA-binding polypeptide nor the second RNA-binding polypeptide comprises a significant DNA-nuclease activity, wherein the first RNA-binding polypeptide and the second RNA-binding polypeptide are not identical, and wherein the second RNA-binding polypeptide comprises an RNA-nuclease activity. Methods of making and methods of using compositions of the disclosure are also provided. For example, compositions of the disclosure may be used in the treatment of a disease or disorder in a subject. Exemplary disease or disorders of the disclosure include genetic and epigenetic diseases or disorders.

Description

    RELATED APPLICATIONS
  • This is a continuation of U.S. Ser. No. 16/723,079, filed Dec. 20, 2019, which is a continuation of U.S. Ser. No. 16/434,689, filed Jun. 7, 2019, which claims priority to U.S. Patent Application No. 62/682,271, filed Jun. 8, 2018, the contents of each are herein incorporated by reference in their entirety. The contents of U.S. Patent Application No. 62/682,276, filed Jun. 8, 2018, are herein incorporated by reference in their entirety.
    • FIELD OF THE DISCLOSURE
  • The disclosure is directed to molecular biology, and more, specifically, to compositions and methods for modifying expression and activity of RNA molecules.
    • INCORPORATION OF SEQUENCE LISTING
  • The contents of the text file named “LOCN-002_C02US SeqList.txt”, which was created on Aug. 24, 2020 and is 774 KB in size, are hereby incorporated by reference in their entirety.
    • BACKGROUND
  • There has been a long-felt but unmet need in the art for a method of specifically binding target RNA molecules for modification of expression or activity of the RNA molecule or a protein encoded by the RNA molecule. The disclosure provides compositions and methods for specifically targeting RNA molecules in sequence-specific manner that further precludes modification of DNA sequences.
    • SUMMARY
  • The disclosure provides a composition comprising (a) a sequence comprising a guide RNA (gRNA) that specifically binds a target sequence within an RNA molecule and (b) a sequence encoding a fusion protein, the sequence comprising a sequence encoding a first RNA-binding polypeptide and a sequence encoding a second RNA-binding polypeptide, wherein neither the first RNA-binding polypeptide nor the second RNA-binding polypeptide comprises a significant DNA-nuclease activity, wherein the first RNA-binding polypeptide and the second RNA-binding polypeptide are not identical, and wherein the second RNA-binding polypeptide comprises an RNA-nuclease activity wherein the first RNA-binding polypeptide and the second RNA-binding polypeptide are not identical, and wherein the second RNA-binding polypeptide comprises an RNA-nuclease activity.
  • The disclosure also provides a composition comprising a sequence encoding an RNA-guided target RNA-binding fusion protein comprising (a) a sequence encoding a first RNA-binding polypeptide or portion thereof; and (b) a sequence encoding a second RNA-binding polypeptide, wherein the first RNA-binding polypeptide binds a target RNA guided by a gRNA sequence, and wherein the second RNA-binding polypeptide comprises RNA-nuclease activity.
  • The disclosure additionally provides a composition comprising a sequence encoding a target RNA-binding fusion protein comprising (a) a sequence encoding a first RNA-binding polypeptide or portion thereof; and (b) a sequence encoding a second RNA-binding polypeptide, wherein the first RNA-binding polypeptide binds a target RNA without a gRNA sequence, and wherein the second RNA-binding polypeptide comprises RNA-nuclease activity.
  • In some embodiments of the compositions of the disclosure, the target sequence comprises at least one repeated sequence.
  • In some embodiments of the compositions of the disclosure, the sequence comprising the gRNA further comprises a sequence encoding a promoter capable of expressing the gRNA in a eukaryotic cell.
  • In some embodiments of the compositions of the disclosure, the eukaryotic cell is an animal cell. In some embodiments, the animal cell is a mammalian cell. In some embodiments, the animal cell is a human cell.
  • In some embodiments of the compositions of the disclosure, the promoter is a constitutively active promoter. In some embodiments, the promoter sequence is isolated or derived from a promoter capable of driving expression of an RNA polymerase. In some embodiments, the promoter sequence is isolated or derived from a U6 promoter. In some embodiments, the promoter is a sequence isolated or derived from a promoter capable of driving expression of a transfer RNA (tRNA). In some embodiments, the promoter is isolated or derived from an alanine tRNA promoter, an arginine tRNA promoter, an asparagine tRNA promoter, an aspartic acid tRNA promoter, a cysteine tRNA promoter, a glutamine tRNA promoter, a glutamic acid tRNA promoter, a glycine tRNA promoter, a histidine tRNA promoter, an isoleucine tRNA promoter, a leucine tRNA promoter, a lysine tRNA promoter, a methionine tRNA promoter, a phenylalanine tRNA promoter, a proline tRNA promoter, a serine tRNA promoter, a threonine tRNA promoter, a tryptophan tRNA promoter, a tyrosine tRNA promoter, or a valine tRNA promoter. In some embodiments, the promoter is isolated or derived from a valine tRNA promoter.
  • In some embodiments of the compositions of the disclosure, the sequence comprising the gRNA further comprises a spacer sequence that specifically binds to the target RNA sequence. In some embodiments, the spacer sequence has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 87%, 90%, 95%, 97%, 99% or any percentage in between of complementarity to the target RNA sequence. In some embodiments, the spacer sequence has 100% complementarity to the target RNA sequence. In some embodiments, the spacer sequence comprises or consists of 20 nucleotides. In some embodiments, the spacer sequence comprises or consists of 21 nucleotides. In some embodiments, the spacer sequence comprises or consists of the sequence
  • (SEQ ID NO: 1)
    UGGAGCGAGCAUCCCCCAAA,
    (SEQ ID NO: 2)
    GUUUGGGGGAUGCUCGCUCCA,
    (SEQ ID NO: 3)
    CCCUCACUGCUGGGGAGUCC,
    (SEQ ID NO: 4)
    GGACUCCCCAGCAGUGAGGG,
    (SEQ ID NO: 5)
    GCAACUGGAUCAAUUUGCUG,
    (SEQ ID NO: 6)
    GCAGCAAAUUGAUCCAGUUGC,
    (SEQ ID NO: 7)
    GCAUUCUUAUCUGGUCAGUGC,
    (SEQ ID NO: 8)
    GCACUGACCAGAUAAGAAUG,
    (SEQ ID NO: 9)
    GAGCAGCAGCAGCAGCAGCAG,
    (SEQ ID NO: 10)
    GCAGGCAGGCAGGCAGGCAGG,
    (SEQ ID NO: 11)
    GCCCCGGCCCCGGCCCCGGC,
    or
    (SEQ ID NO: 12)
    GCTGCTGCTGCTGCTGCTGC,
    (SEQ ID NO: 74)
    GGGGCCGGGGCCGGGGCCGG,
    (SEQ ID NO: 75)
    GGGCCGGGGCCGGGGCCGGG,
    (SEQ ID NO: 76)
    GGCCGGGGCCGGGGCCGGGG,
    (SEQ ID NO: 77)
    GCCGGGGCCGGGGCCGGGGC,
    (SEQ ID NO: 78)
    CCGGGGCCGGGGCCGGGGCC,
    or
    (SEQ ID NO: 79)
    CGGGGCCGGGGCCGGGGCCG.
  • In some embodiments of the compositions of the disclosure, the sequence comprising the gRNA further comprises a spacer sequence that specifically binds to the target RNA sequence. In some embodiments, the spacer sequence has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 87%, 90%, 95%, 97%, 99% or any percentage in between of complementarity to the target RNA sequence.
  • In some embodiments, the spacer sequence has 100% complementarity to the target RNA sequence. In some embodiments, the spacer sequence comprises or consists of 20 nucleotides. In some embodiments, the spacer sequence comprises or consists of 21 nucleotides. In some embodiments, the spacer sequence comprises or consists of the sequence
  • (SEQ ID NO: 14)
    GUGAUAAGUGGAAUGCCAUG,
    (SEQ ID NO: 15)
    CUGGUGAACUUCCGAUAGUG,
    or
    (SEQ ID NO: 16)
    GAGATATAGCCTGGTGGTTC.
  • In some embodiments of the compositions of the disclosure, the sequence comprising the gRNA further comprises a spacer sequence that specifically binds to the target RNA sequence. In some embodiments, the spacer sequence has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 87%, 90%, 95%, 97%, 99% or any percentage in between of complementarity to the target RNA sequence. In some embodiments, the spacer sequence has 100% complementarity to the target RNA sequence. In some embodiments, the spacer sequence comprises or consists of 20 nucleotides. In some embodiments, the spacer sequence comprises or consists of 21 nucleotides. In some embodiments, the spacer sequence comprises or consists of a sequence comprising at least 1, 2, 3, 4, 5, 6, or 7 repeats of the sequence CUG (SEQ ID NO: 18), CCUG (SEQ ID NO: 19), CAG (SEQ ID NO: 80), GGGGCC (SEQ ID NO: 81) or any combination thereof.
  • In some embodiments of the compositions of the disclosure, the sequence comprising the gRNA further comprises a scaffold sequence that specifically binds to the first RNA binding protein. In some embodiments, the scaffold sequence comprises a stem-loop structure. In some embodiments, the scaffold sequence comprises or consists of 90 nucleotides. In some embodiments, the scaffold sequence comprises or consists of 93 nucleotides. In some embodiments, the scaffold sequence comprises or consists of the sequence GUUUAAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUCCGUU AUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUUUU (SEQ ID NO: 13). In some embodiments, the scaffold sequence comprises or consists of the sequence GGACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGG CACCGAGUCGGUGCUUUUU (SEQ ID NO: 17). In some embodiments, the scaffold sequence comprises or consists of the sequence
  • (SEQ ID NO: 82)
    GUUUAAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUC
    CGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUUUU
    or
    (SEQ ID NO: 83)
    GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAAC
    UUGAAAAAGUGGCACCGAGUCGGUGCU.
  • In some embodiments of the compositions of the disclosure, the gRNA does not bind or does not selectively bind to a second sequence within the RNA molecule.
  • In some embodiments of the compositions of the disclosure, an RNA genome or an RNA transcriptome comprises the RNA molecule.
  • In some embodiments of the compositions of the disclosure, the first RNA binding protein comprises a CRISPR-Cas protein. In some embodiments, the CRISPR-Cas protein is a Type II CRISPR-Cas protein. In some embodiments, the first RNA binding protein comprises a Cas9 polypeptide or an RNA-binding portion thereof. In some embodiments, the CRISPR-Cas protein comprises a native RNA nuclease activity. In some embodiments, the native RNA nuclease activity is reduced or inhibited. In some embodiments, the native RNA nuclease activity is increased or induced. In some embodiments, the CRISPR-Cas protein comprises a native DNA nuclease activity and the native DNA nuclease activity is inhibited. In some embodiments, the CRISPR-Cas protein comprises a mutation. In some embodiments, a nuclease domain of the CRISPR-Cas protein comprises the mutation. In some embodiments, the mutation occurs in a nucleic acid encoding the CRISPR-Cas protein. In some embodiments, the mutation occurs in an amino acid encoding the CRISPR-Cas protein. In some embodiments, the mutation comprises a substitution, an insertion, a deletion, a frameshift, an inversion, or a transposition. In some embodiments, the mutation comprises a deletion of a nuclease domain, a binding site within the nuclease domain, an active site within the nuclease domain, or at least one essential amino acid residue within the nuclease domain.
  • In some embodiments of the compositions of the disclosure, the first RNA binding protein comprises a CRISPR-Cas protein. In some embodiments, the CRISPR-Cas protein is a Type V CRISPR-Cas protein. In some embodiments, the first RNA binding protein comprises a Cpf1 polypeptide or an RNA-binding portion thereof. In some embodiments, the CRISPR-Cas protein comprises a native RNA nuclease activity. In some embodiments, the native RNA nuclease activity is reduced or inhibited. In some embodiments, the native RNA nuclease activity is increased or induced. In some embodiments, the CRISPR-Cas protein comprises a native DNA nuclease activity and the native DNA nuclease activity is inhibited. In some embodiments, the CRISPR-Cas protein comprises a mutation. In some embodiments, a nuclease domain of the CRISPR-Cas protein comprises the mutation. In some embodiments, the mutation occurs in a nucleic acid encoding the CRISPR-Cas protein. In some embodiments, the mutation occurs in an amino acid encoding the CRISPR-Cas protein. In some embodiments, the mutation comprises a substitution, an insertion, a deletion, a frameshift, an inversion, or a transposition. In some embodiments, the mutation comprises a deletion of a nuclease domain, a binding site within the nuclease domain, an active site within the nuclease domain, or at least one essential amino acid residue within the nuclease domain.
  • In some embodiments of the compositions of the disclosure, the first RNA binding protein comprises a CRISPR-Cas protein. In some embodiments, the CRISPR-Cas protein is a Type VI CRISPR-Cas protein. In some embodiments, the first RNA binding protein comprises a Cas13 polypeptide or an RNA-binding portion thereof. In some embodiments, the first RNA binding protein comprises a CasRx/Cas13d polypeptide or an RNA-binding portion thereof. In some embodiments, the CRISPR-Cas protein comprises a native RNA nuclease activity. In some embodiments, the native RNA nuclease activity is reduced or inhibited. In some embodiments, the native RNA nuclease activity is increased or induced. In some embodiments, the CRISPR-Cas protein comprises a native DNA nuclease activity and the native DNA nuclease activity is inhibited. In some embodiments, the CRISPR-Cas protein comprises a mutation. In some embodiments, a nuclease domain of the CRISPR-Cas protein comprises the mutation. In some embodiments, the mutation occurs in a nucleic acid encoding the CRISPR-Cas protein. In some embodiments, the mutation occurs in an amino acid encoding the CRISPR-Cas protein. In some embodiments, the mutation comprises a substitution, an insertion, a deletion, a frameshift, an inversion, or a transposition. In some embodiments, the mutation comprises a deletion of a nuclease domain, a binding site within the nuclease domain, an active site within the nuclease domain, or at least one essential amino acid residue within the nuclease domain.
  • In some embodiments of the compositions of the disclosure, the first RNA binding protein comprises a Pumilio and FBF (PUF) protein or an RNA binding portion thereof. In some embodiments, the first RNA binding protein comprises a Pumilio-based assembly (PUMBY) protein or an RNA binding portion thereof.
  • In some embodiments of the compositions of the disclosure, the first RNA binding protein does not require multimerization for RNA-binding activity. In some embodiments, the first RNA binding protein is not a monomer of a multimer complex. In some embodiments, a multimer protein complex does not comprise the first RNA binding protein.
  • In some embodiments of the compositions of the disclosure, the first RNA binding protein selectively binds to a target sequence within the RNA molecule. In some embodiments, the first RNA binding protein does not comprise an affinity for a second sequence within the RNA molecule. In some embodiments, the first RNA binding protein does not comprise a high affinity for or selectively bind a second sequence within the RNA molecule.
  • In some embodiments of the compositions of the disclosure, an RNA genome or an RNA transcriptome comprises the RNA molecule.
  • In some embodiments of the compositions of the disclosure, the first RNA binding protein comprises between 2 and 1300 amino acids, inclusive of the endpoints.
  • In some embodiments of the compositions of the disclosure, the sequence encoding the first RNA binding protein further comprises a sequence encoding a nuclear localization signal (NLS), a nuclear export signal (NES) or tag. In some embodiments, the sequence encoding a nuclear localization signal (NLS) is positioned 3′ to the sequence encoding the first RNA binding protein. In some embodiments, the first RNA binding protein comprises an NLS at a C-terminus of the protein.
  • In some embodiments of the compositions of the disclosure, the sequence encoding the first RNA binding protein further comprises a first sequence encoding a first NLS and a second sequence encoding a second NLS. In some embodiments, the sequence encoding the first NLS or the second NLS is positioned 3′ to the sequence encoding the first RNA binding protein. In some embodiments, the first RNA binding protein comprises the first NLS or the second NLS at a C-terminus of the protein.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a nuclease domain. In some embodiments, the second RNA binding protein binds RNA in a manner in which it associates with RNA. In some embodiments, the second RNA binding protein associates with RNA in a manner in which it cleaves RNA.
  • In some embodiments of the compositions of the disclosure, the sequence encoding the second RNA binding protein comprises or consists of an RNAse. In some embodiments, the second RNA binding protein comprises or consists of an RNAse1. In some embodiments, the RNAse1 comprises or consists of SEQ ID NO: 20. In some embodiments, the second RNA binding protein comprises or consists of an RNAse4. In some embodiments, the RNAse4 comprises or consists of SEQ ID NO: 21. In some embodiments, the second RNA binding protein comprises or consists of an RNAse6. In some embodiments, the RNAse6 comprises or consists of SEQ ID NO: 22. In some embodiments, the second RNA binding protein comprises or consists of an RNAse7. In some embodiments, the RNAse7 comprises or consists of SEQ ID NO: 23. In some embodiments, the second RNA binding protein comprises or consists of an RNAse8. In some embodiments, the RNAse8 protein comprises or consists of SEQ ID NO: 24. In some embodiments, the second RNA binding protein comprises or consists of an RNAse2. In some embodiments, the RNAse2 protein comprises or consists of SEQ ID NO: 25. In some embodiments, the second RNA binding protein comprises or consists of an RNAse6PL. In some embodiments, the RNAse6PL protein comprises or consists of SEQ ID NO: 26. In some embodiments, the second RNA binding protein comprises or consists of an RNAseL. In some embodiments the RNAseL protein comprises or consists of SEQ ID NO: 27. In some embodiments, the second RNA binding protein comprises or consists of an RNAseT2. In some embodiments, the RNAseT2 protein comprises or consists of SEQ ID NO: 28. In some embodiments, the second RNA binding protein comprises or consists of an RNAse11. In some embodiments, the RNAse11 protein comprises or consists of SEQ ID NO: 29. In some embodiments, the second RNA binding protein comprises or consists of an RNAseT2-like. In some embodiments, the RNAseT2-like protein comprises or consists of SEQ ID NO: 30.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a mutated RNAse. In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(K41R)) polypeptide. In some embodiments, the Rnase1 (K41R) polypeptide comprises or consists of SEQ ID NO: 116. In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(K41R, D121E)) polypeptide. In some embodiments, the Rnase1 (Rnase1(K41R, D121E)) polypeptide comprises or consists of SEQ ID NO: 66. In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1(Rnase1(K41R, D121E, H119N)) polypeptide. In some embodiments, the Rnase1(Rnase1(K41R, D121E, H119N)) polypeptide comprises or consists of SEQ ID NO: 118. In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1. In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1(Rnase1(H119N)) polypeptide. In some embodiments, the Rnase1(Rnase1(H119N)) polypeptide comprises or consists SEQ ID NO: 119. In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1(Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide. In some embodiments, the Rnase1(Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide comprises or consists of SEQ ID NO: 120. In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1(Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide. In some embodiments, the Rnase1(Rnase1(R39D, N67D, N88A, G89D, R91D, H119N, K41R, D121E)) polypeptide comprises or consists of SEQ ID NO: 121. In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1(Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide. In some embodiments, the Rnase1(Rnase1(R39D, N67D, N88A, G89D, R91D)) polypeptide comprises or consists of SEQ ID NO: 122.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a NOB1 polypeptide. In some embodiments, the NOB1 polypeptide comprises or consists of SEQ ID NO: 31.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of an endonuclease. In some embodiments, the second RNA binding protein comprises or consists of an endonuclease V (ENDOV). In some embodiments, the ENDOV protein comprises or consists of SEQ ID NO: 32. In some embodiments, the second RNA binding protein comprises or consists of an endonuclease G (ENDOG). In some embodiments, the ENDOG protein comprises or consists of SEQ ID NO: 33. In some embodiments, the second RNA binding protein comprises or consists of an endonuclease D1 (ENDOD1). In some embodiments, the ENDOD1 protein comprises or consists of SEQ ID NO: 34. In some embodiments, the second RNA binding protein comprises or consists of a Human flap endonuclease-1 (hFEN1). In some embodiments, the hFEN1 protein comprises or consists of SEQ ID NO: 35. In some embodiments, the second RNA binding protein comprises or consists of a DNA repair endonuclease XPF (ERCC4) polypeptide. In some embodiments, the ERCC4 protein comprises or consists of SEQ ID NO: 64.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of an Endonuclease III-like protein 1 (NTHL) polypeptide. In some embodiments, the NTHL polypeptide comprises or consists of SEQ ID NO: 123.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a human Schlafen 14 (hSLFN14) polypeptide. In some embodiments, the hSLFN14 polypeptide comprises or consists of SEQ ID NO: 36.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a human beta-lactamase-like protein 2 (hLACTB2) polypeptide. In some embodiments, the hLACTB2 polypeptide comprises or consists of SEQ ID NO: 37.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of an apurinic/apyrimidinic (AP) endodeoxyribonuclease (APEX) polypeptide. In some embodiments, the second RNA binding protein comprises or consists of an apurinic/apyrimidinic (AP) endodeoxyribonuclease (APEX2) polypeptide. In some embodiments, the APEX2 polypeptide comprises or consists of SEQ ID NO: 38. In some embodiments, the APEX2 polypeptide comprises or consists of SEQ ID NO: 39. In some embodiments, the second RNA binding protein comprises or consists of an apurinic or apyrimidinic site lyase (APEX1) polypeptide. In some embodiments, the APEX1 polypeptide comprises or consists of SEQ ID NO: 125.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of an angiogenin (ANG) polypeptide. In some embodiments, the ANG polypeptide comprises or consists SEQ ID NO: 40.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a heat responsive protein 12 (HRSP12) polypeptide. In some embodiments, the HRSP12 polypeptide comprises or consists of SEQ ID NO: 41.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a Zinc Finger CCCH-Type Containing 12A (ZC3H12A) polypeptide. In some embodiments, the ZC3H12A polypeptide comprises or consists of SEQ ID NO: 42. In some embodiments, the ZC3H12A polypeptide comprises or consists of SEQ ID NO: 43.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a Reactive Intermediate Imine Deaminase A (RIDA) polypeptide. In some embodiments, the RIDA polypeptide comprises or consists of SEQ ID NO: 44.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a Phospholipase D Family Member 6 (PDL6) polypeptide. In some embodiments, the PDL6 polypeptide comprises or consists of SEQ ID NO: 126.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a mitochondrial ribonuclease P catalytic subunit (KIAA0391) polypeptide. In some embodiments, the KIAA0391 polypeptide comprises or consists of SEQ ID NO: 127.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of an argonaute 2 (AGO2) polypeptide.
  • In some embodiments of the compositions of the disclosure, the AGO2 polypeptide comprises or consists of SEQ ID NO: 128.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a mitochondrial nuclease EXOG (EXOG) polypeptide. In some embodiments, the EXOG polypeptide comprises or consists of SEQ ID NO: 129.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a Zinc Finger CCCH-Type Containing 12D (ZC3H12D) polypeptide. In some embodiments, the ZC3H12D polypeptide comprises or consists of SEQ ID NO: 130.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of an endoplasmic reticulum to nucleus signaling 2 (ERN2) polypeptide. In some embodiments, the ERN2 polypeptide comprises or consists of SEQ ID NO: 131.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a pelota mRNA surveillance and ribosome rescue factor (PELO) polypeptide. In some embodiments, the PELO polypeptide comprises or consists of SEQ ID NO: 132.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a YBEY metallopeptidase (YBEY) polypeptide. In some embodiments, the YBEY polypeptide comprises or consists of SEQ ID NO: 133.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a cleavage and polyadenylation specific factor 4 like (CPSF4L) polypeptide. In some embodiments, the CPSF4L polypeptide comprises or consists of SEQ ID NO: 134.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of an hCG_2002731 polypeptide. In some embodiments, the hCG_2002731 comprises or consists of SEQ ID NO: 135. In some embodiments, the hCG_2002731 polypeptide comprises or consists of SEQ ID NO: 136.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of an Excision Repair Cross-Complementation Group 1 (ERCC1) polypeptide. In some embodiments, the ERCC1 polypeptide comprises or consists of SEQ ID NO: 137.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a ras-related C3 botulinum toxin substrate 1 isoform (RAC1) polypeptide. In some embodiments, the RAC1 polypeptide comprises or consists of SEQ ID NO: 138.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a Ribonuclease A A1 (RAA1) polypeptide. In some embodiments, the RAA1 polypeptide comprises or consists of SEQ ID NO: 139.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a Ras Related Protein (RAB1) polypeptide. In some embodiments, the RAB1 polypeptide comprises or consists of SEQ ID NO: 140.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a DNA Replication Helicase/Nuclease 2 (DNA2) polypeptide. In some embodiments, the DNA2 polypeptide comprises or consists of SEQ ID NO: 141.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a FLJ35220 polypeptide. In some embodiments, the FLJ35220 polypeptide comprises or consists of SEQ ID NO: 142.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a FLJ13173 polypeptide. In some embodiments, the FLJ13173 polypeptide comprises or consists of SEQ ID NO: 143.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of Teneurin Transmembrane Protein (TENM) polypeptide. In some embodiments, the second RNA binding protein comprises or consists of Teneurin Transmembrane Protein 1 (TENM1) polypeptide. In some embodiments, the TENM1 polypeptide comprises or consists of SEQ ID NO: 144. In some embodiments, the second RNA binding protein comprises or consists of Teneurin Transmembrane Protein 2 (TENM2) polypeptide. In some embodiments, the TENM2 polypeptide comprises or consists of SEQ ID NO: 145.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a Ribonuclease Kappa (RNAseK) polypeptide. In some embodiments, the RNAseK polypeptide comprises or consists of SEQ ID NO: 204.
  • In some embodiments, the fusion proteins of the disclosure are used in methods for treating a subject in need thereof, the methods comprising contacting a target RNA with a fusion protein or the sequence encoding the fusion protein.
    • BRIEF DESCRIPTION OF THE DRAWINGS
  • The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
  • FIGS. 1A-B is a schematic diagram of an exemplary embodiment of a composition of the disclosure. (FIG. 1A) An RNA-targeting Cas9 system fused to an endonuclease targets and cleaves a disease-causing RNA. (FIG. 1B) Depicts an application of (A) in the context of myotonic dystrophy type 1, wherein an RNA-targeting Cas9 system fused to an endonuclease targets and cleaves a repetitive RNA composed of repeating CUG units. In the absence of the RNA-targeting Cas9 system, the repetitive RNA composed of repeating CUG units binds to a splicing factor MBNL and causes pathology via dysfunctional RNA splicing. Cleavage of this repetitive RNA ameliorates disease.
  • FIG. 2 is a schematic diagram depicting an exemplary modular therapeutic platform for treating genetic disease by targeting RNA molecules.
  • FIGS. 3A-B is a pair of schematic diagrams depicting (FIG. 3A) a “high expression” control system (also referred to as “pos control”) comprising a two plasmid system comprising a cytomegalovirus promoter driving expression of the RNA endonuclease/Cas9 fusion and (FIG. 3B) a “low expression” control system (also referred to as “P13”) comprising a single plasmid system comprising a lower-expression promoter (pEFS) driving expression of the RNA endonuclease/Cas9 fusion.
  • FIG. 4A is a pair of schematic diagrams depicting an exemplary RNA Endonuclease-C. jejuni Cas9 fusion protein (left) and a vector comprising an exemplary RNA Endonuclease-S. pyogenes Cas9 fusion protein (right)
  • FIG. 4B is a graph depicting the ability of a variety of fusion proteins comprising either C. jejuni Cas9 or S. pyogenes Cas9, as shown in FIG. 4A, to cleave repetitive RNA molecules.
  • FIG. 5A is a pair of schematic diagrams depicting an exemplary RNA Endonuclease-C. jejuni Cas9 fusion protein (left) and a vector comprising an exemplary RNA Endonuclease-S. pyogenes Cas9 fusion protein (right)
  • FIG. 5B is a graph depicting the ability of a variety of fusion proteins comprising either C. jejuni Cas9 or S. pyogenes Cas9, as shown in FIG. 5A, to cleave mRNA molecules encoding a luciferase protein.
  • FIG. 6 is a table providing a key to the endonucleases shown in FIGS. 4B, 5B, and 9.
  • FIG. 7A is a schematic diagram depicting an exemplary RNA Endonuclease-C. jejuni Cas9 fusion protein.
  • FIG. 7B is a graph depicting changes in expression levels of Zika NS5 in the presence of both E43 and E67 CjeCas9-endonuclease fusions with sgRNAs containing the various NS5-targeting spacer sequences as indicated in Table 2. Zika NS5 expression is displayed as fold change relative to the endonuclease loaded with an sgRNA containing a control (Lambda) spacer sequence.
  • FIG. 8A is a fluorescence microscopy image of cells transfected with CjeCas9-endonuclease fusions loaded with an sgRNA containing a Zika NS5-targeting spacer sequence.
  • FIG. 8B is a graph depicting changes of expression of Zika NS5 in the presence of CjeCas9-endonuclease fusions loaded with the appropriate Zika NS5-targeting sgRNA as compared to a CjeCas9-endonuclease fusions loaded with a non-Zika NS5 targeting sgRNA.
  • FIG. 9 is a graph depicting the cleavage efficiencies of a variety of exemplary fusion proteins (SpyCas9 fused to the annotated endonuclease).
    •  DETAILED DESCRIPTION
  • The disclosure provides an RNA-guided fusion protein that selectively binds and, optionally, cleaves RNA molecules. The disclosure provides vectors, compositions and cells comprising the RNA-guided fusion protein. The disclosure provides methods of using the RNA-guided fusion protein, vectors, compositions and cells of the disclosure to treat a disease or disorder.
    • Guide RNA
  • The terms guide RNA (gRNA) and single guide RNA (sgRNA) are used interchangeably throughout the disclosure.
  • Guide RNAs (gRNAs) of the disclosure may comprise of a spacer sequence and a scaffolding sequence. In some embodiments, a guide RNA is a single guide RNA (sgRNA) comprising a contiguous spacer sequence and scaffolding sequence. In some embodiments, the spacer sequence and the scaffolding sequence are not contiguous. In some embodiments, a scaffold sequence comprises a “direct repeat” (DR) sequence. DR sequences refer to the repetitive sequences in the CRISPR locus (naturally-occurring in a bacterial genome or plasmid) that are interspersed with the spacer sequences. It is well known that one would be able to infer the DR sequence of a corresponding Cas protein if the sequence of the associated CRISPR locus is known. In some embodiments, a sequence encoding a guide RNA or single guide RNA of the disclosure comprises or consists of a spacer sequence and a scaffolding sequence, that are separated by a linker sequence. In some embodiments, the linker sequence may comprise or consist of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or any number of nucleotides in between. In some embodiments, the linker sequence may comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or any number of nucleotides in between.
  • Guide RNAs (gRNAs) of the disclosure may comprise non-naturally occurring nucleotides. In some embodiments, a guide RNA of the disclosure or a sequence encoding the guide RNA comprises or consists of modified or synthetic RNA nucleotides. Exemplary modified RNA nucleotides include, but are not limited to, pseudouridine (Ψ), dihydrouridine (D), inosine (I), and 7-methylguanosine (m7G), hypoxanthine, xanthine, xanthosine, 7-methylguanine, 5, 6-Dihydrouracil, 5-methylcytosine, 5-methylcytidine, 5-hydropxymethylcytosine, isoguanine, and isocytosine.
  • Guide RNAs (gRNAs) of the disclosure may bind modified RNA within a target sequence. Within a target sequence, guide RNAs (gRNAs) of the disclosure may bind modified RNA. Exemplary epigenetically or post-transcriptionally modified RNA include, but are not limited to, 2′-O-Methylation (2′-OMe) (2′-O-methylation occurs on the oxygen of the free 2′-OH of the ribose moiety), N6-methyladenosine (m6A), and 5-methylcytosine (m5C).
  • In some embodiments of the compositions of the disclosure, a guide RNA of the disclosure comprises at least one sequence encoding a non-coding C/D box small nucleolar RNA (snoRNA) sequence. In some embodiments, the snoRNA sequence comprises at least one sequence that is complementary to the target RNA, wherein the target sequence of the RNA molecule comprises at least one 2′-OMe. In some embodiments, the snoRNA sequence comprises at least one sequence that is complementary to the target RNA, wherein the at least one sequence that is complementary to the target RNA comprises a box C motif (RUGAUGA) and a box D motif (CUGA).
  • Spacer sequences of the disclosure bind to the target sequence of an RNA molecule. Spacer sequences of the disclosure may comprise a CRISPR RNA (crRNA). Spacer sequences of the disclosure comprise or consist of a sequence having sufficient complementarity to a target sequence of an RNA molecule to bind selectively to the target sequence. Upon binding to a target sequence of an RNA molecule, the spacer sequence may guide one or more of a scaffolding sequence and a fusion protein to the RNA molecule. In some embodiments, a sequence having sufficient complementarity to a target sequence of an RNA molecule to bind selectively to the target sequence has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96, 97%, 98%, 99%, or any percentage identity in between to the target sequence. In some embodiments, a sequence having sufficient complementarity to a target sequence of an RNA molecule to bind selectively to the target sequence has 100% identity the target sequence.
  • Scaffolding sequences of the disclosure bind the first RNA-binding polypeptide of the disclosure. Scaffolding sequences of the disclosure may comprise a trans acting RNA (tracrRNA). Scaffolding sequences of the disclosure comprise or consist of a sequence having sufficient complementarity to a target sequence of an RNA molecule to bind selectively to the target sequence. Upon binding to a target sequence of an RNA molecule, the scaffolding sequence may guide a fusion protein to the RNA molecule. In some embodiments, a sequence having sufficient complementarity to a target sequence of an RNA molecule to bind selectively to the target sequence has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96, 97%, 98%, 99%, or any percentage identity in between to the target sequence. In some embodiments, a sequence having sufficient complementarity to a target sequence of an RNA molecule to bind selectively to the target sequence has 100% identity the target sequence. Alternatively, or in addition, in some embodiments, scaffolding sequences of the disclosure comprise or consist of a sequence that binds to a first RNA binding protein or a second RNA binding protein of a fusion protein of the disclosure. In some embodiments, scaffolding sequences of the disclosure comprise a secondary structure or a tertiary structure. Exemplary secondary structures include, but are not limited to, a helix, a stem loop, a bulge, a tetraloop and a pseudoknot. Exemplary tertiary structures include, but are not limited to, an A-form of a helix, a B-form of a helix, and a Z-form of a helix. Exemplary tertiary structures include, but are not limited to, a twisted or helicized stem loop. Exemplary tertiary structures include, but are not limited to, a twisted or helicized pseudoknot. In some embodiments, scaffolding sequences of the disclosure comprise at least one secondary structure or at least one tertiary structure. In some embodiments, scaffolding sequences of the disclosure comprise one or more secondary structure(s) or one or more tertiary structure(s).
  • In some embodiments of the compositions of the disclosure, a guide RNA or a portion thereof selectively binds to a tetraloop motif in an RNA molecule of the disclosure. In some embodiments, a target sequence of an RNA molecule comprises a tetraloop motif. In some embodiments, the tetraloop motif is a “GRNA” motif comprising or consisting of one or more of the sequences of GAAA, GUGA, GCAA or GAGA.
  • In some embodiments of the compositions of the disclosure, a guide RNA or a portion thereof that binds to a target sequence of an RNA molecule hybridizes to the target sequence of the RNA molecule. In some embodiments, a guide RNA or a portion thereof that binds to a first RNA binding protein or to a second RNA binding protein covalently binds to the first RNA binding protein or to the second RNA binding protein. In some embodiments, a guide RNA or a portion thereof that binds to a first RNA binding protein or to a second RNA binding protein non-covalently binds to the first RNA binding protein or to the second RNA binding protein.
  • In some embodiments of the compositions of the disclosure, a guide RNA or a portion thereof comprises or consists of between 10 and 100 nucleotides, inclusive of the endpoints. In some embodiments, a spacer sequence of the disclosure comprises or consists of between 10 and 30 nucleotides, inclusive of the endpoints. In some embodiments, a spacer sequence of the disclosure comprises or consists of 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 nucleotides. In some embodiments, the spacer sequence of the disclosure comprises or consists of 20 nucleotides. In some embodiments, the spacer sequence of the disclosure comprises or consists of 21 nucleotides. In some embodiments, a scaffold sequence of the disclosure comprises or consists of between 10 and 100 nucleotides, inclusive of the endpoints. In some embodiments, a scaffold sequence of the disclosure comprises or consists of 30, 35, 40, 45, 50, 55, 60, 65, 70, 76, 80, 87, 90, 95, 100 or any number of nucleotides in between. In some embodiments, the scaffold sequence of the disclosure comprises or consists of between 85 and 95 nucleotides, inclusive of the endpoints. In some embodiments, the scaffold sequence of the disclosure comprises or consists of 85 nucleotides. In some embodiments, the scaffold sequence of the disclosure comprises or consists of 90 nucleotides. In some embodiments, the scaffold sequence of the disclosure comprises or consists of 93 nucleotides.
  • In some embodiments of the compositions of the disclosure, a guide RNA or a portion thereof does not comprise a nuclear localization sequence (NLS).
  • In some embodiments of the compositions of the disclosure, a guide RNA or a portion thereof does not comprise a sequence complementary to a protospacer adjacent motif (PAM).
  • Therapeutic or pharmaceutical compositions of the disclosure do not comprise a PAMmer oligonucleotide. In other embodiments, optionally, non-therapeutic or non-pharmaceutical compositions may comprise a PAMmer oligonucleotide. The term “PAMmer” refers to an oligonucleotide comprising a PAM sequence that is capable of interacting with a guide nucleotide sequence-programmable RNA binding protein. Non-limiting examples of PAMmers are described in O'Connell et al. Nature 516, pages 263-266 (2014), incorporated herein by reference. A PAM sequence refers to a protospacer adjacent motif comprising about 2 to about 10 nucleotides. PAM sequences are specific to the guide nucleotide sequence-programmable RNA binding protein with which they interact and are known in the art. For example, Streptococcus pyogenes PAM has the sequence 5′-NGG-3′, where “N” is any nucleobase followed by two guanine (“G”) nucleobases. Cas9 of Francisella novicida recognizes the canonical PAM sequence 5′-NGG-3′, but has been engineered to recognize the PAM 5′-YG-3′ (where “Y” is a pyrimidine), thus adding to the range of possible Cas9 targets. The Cpf1 nuclease of Francisella novicida recognizes the PAM 5′-TTTN-3′ or 5′-YTN-3′.
  • In some embodiments of the compositions of the disclosure, a guide RNA or a portion thereof comprises a sequence complementary to a protospacer flanking sequence (PFS). In some embodiments, including those wherein a guide RNA or a portion thereof comprises a sequence complementary to a PFS, the first RNA binding protein may comprise a sequence isolated or derived from a Cas13 protein. In some embodiments, including those wherein a guide RNA or a portion thereof comprises a sequence complementary to a PFS, the first RNA binding protein may comprise a sequence encoding a Cas13 protein or an RNA-binding portion thereof. In some embodiments, the guide RNA or a portion thereof does not comprise a sequence complementary to a PFS.
  • In some embodiments of the compositions of the disclosure, guide RNA sequence of the disclosure comprises a promoter sequence to drive expression of the guide RNA. In some embodiments, a vector comprising a guide RNA sequence of the disclosure comprises a promoter sequence to drive expression of the guide RNA. In some embodiments, the promoter to drive expression of the guide RNA is a constitutive promoter. In some embodiments, the promoter sequence is an inducible promoter. In some embodiments, the promoter is a sequence is a tissue-specific and/or cell-type specific promoter. In some embodiments, the promoter is a hybrid or a recombinant promoter. In some embodiments, the promoter is a promoter capable of expressing the guide RNA in a mammalian cell. In some embodiments, the promoter is a promoter capable of expressing the guide RNA in a human cell. In some embodiments, the promoter is a promoter capable of expressing the guide RNA and restricting the guide RNA to the nucleus of the cell. In some embodiments, the promoter is a human RNA polymerase promoter or a sequence isolated or derived from a sequence encoding a human RNA polymerase promoter. In some embodiments, the promoter is a U6 promoter or a sequence isolated or derived from a sequence encoding a U6 promoter. In some embodiments, the promoter is a human tRNA promoter or a sequence isolated or derived from a sequence encoding a human tRNA promoter. In some embodiments, the promoter is a human valine tRNA promoter or a sequence isolated or derived from a sequence encoding a human valine tRNA promoter.
  • In some embodiments of the compositions of the disclosure, a promoter to drive expression of the guide RNA further comprises a regulatory element. In some embodiments, a vector comprising a promoter sequence to drive expression of the guide RNA further comprises a regulatory element. In some embodiments, a regulatory element enhances expression of the guide RNA. Exemplary regulatory elements include, but are not limited to, an enhancer element, an intron, an exon, or a combination thereof.
  • In some embodiments of the compositions of the disclosure, a vector of the disclosure comprises one or more of a sequence encoding a guide RNA, a promoter sequence to drive expression of the guide RNA and a sequence encoding a regulatory element. In some embodiments of the compositions of the disclosure, the vector further comprises a sequence encoding a fusion protein of the disclosure.
    • Fusion Proteins
  • Fusion proteins of the disclosure comprise a first RNA binding protein and a second RNA binding protein. In some embodiments, along a sequence encoding the fusion protein, the sequence encoding the first RNA binding protein is positioned 5′ of the sequence encoding the second RNA binding protein. In some embodiments, along a sequence encoding the fusion protein, the sequence encoding the first RNA binding protein is positioned 3′ of the sequence encoding the second RNA binding protein.
  • In some embodiments of the compositions of the disclosure, the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein capable of binding an RNA molecule. In some embodiments, the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein capable of selectively binding an RNA molecule and not binding a DNA molecule, a mammalian DNA molecule or any DNA molecule. In some embodiments, the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein capable of binding an RNA molecule and inducing a break in the RNA molecule. In some embodiments, the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein capable of binding an RNA molecule, inducing a break in the RNA molecule, and not binding a DNA molecule, a mammalian DNA molecule or any DNA molecule. In some embodiments, the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein capable of binding an RNA molecule, inducing a break in the RNA molecule, and neither binding nor inducing a break in a DNA molecule, a mammalian DNA molecule or any DNA molecule.
  • In some embodiments of the compositions of the disclosure, the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein with no DNA nuclease activity.
  • In some embodiments of the compositions of the disclosure, the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein having DNA nuclease activity, wherein the DNA nuclease activity does not induce a break in a DNA molecule, a mammalian DNA molecule or any DNA molecule when a composition of the disclosure is contacted to an RNA molecule or introduced into a cell or into a subject of the disclosure.
  • In some embodiments of the compositions of the disclosure, the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein having DNA nuclease activity, wherein the DNA nuclease activity is inactivated and wherein the DNA nuclease activity does not induce a break in a DNA molecule, a mammalian DNA molecule or any DNA molecule when a composition of the disclosure is contacted to an RNA molecule or introduced into a cell or into a subject of the disclosure. In some embodiments, the sequence encoding the first RNA binding protein comprises a mutation that inactivates or decreases the DNA nuclease activity to a level at which the DNA nuclease activity does not induce a break in a DNA molecule, a mammalian DNA molecule or any DNA molecule when a composition of the disclosure is contacted to an RNA molecule or introduced into a cell or into a subject of the disclosure. In some embodiments, the sequence encoding the first RNA binding protein comprises a mutation that inactivates or decreases the DNA nuclease activity and the mutation comprises one or more of a substitution, inversion, transposition, insertion, deletion, or any combination thereof to a nucleic acid sequence or amino acid sequence encoding the first RNA binding protein or a nuclease domain thereof.
  • In some embodiments of the compositions of the disclosure, the sequence encoding the first RNA binding protein of an RNA-guided fusion protein disclosed herein comprises a sequence isolated or derived from a CRISPR Cas protein. In some embodiments, the CRISPR Cas protein comprises a Type II CRISPR Cas protein. In some embodiments, the Type II CRISPR Cas protein comprises a Cas9 protein. Exemplary Cas9 proteins of the disclosure may be isolated or derived from any species, including, but not limited to, a bacteria or an archaea. Exemplary Cas9 proteins of the disclosure may be isolated or derived from any species, including, but not limited to, Streptococcus pyogenes, Haloferax mediteranii, Mycobacterium tuberculosis, Francisella tularensis subsp. novicida, Pasteurella multocida, Neisseria meningitidis, Campylobacter jejune, Streptococcus thermophilus, Campylobacter lari CF89-12, Mycoplasma gallisepticum str. F, Nitratifractor salsuginis str. DSM 16511, Parvibaculum lavamentivorans, Roseburia intestinalis, Neisseria cinerea, a Gluconacetobacter diazotrophicus, an Azospirillum B510, a Sphaerochaeta globus str. Buddy, Flavobacterium columnare, Fluviicola taffensis, Bacteroides coprophilus, Mycoplasma mobile, Lactobacillus farciminis, Streptococcus pasteurianus, Lactobacillus johnsonii, Staphylococcus pseudintermedius, Filifactor alocis, Treponema denticola, Legionella pneumophila str. Paris, Sutterella wadsworthensis, Corynebacter diphtherias, Streptococcus aureus, and Francisella novicida.
  • Exemplary wild type S. pyogenes Cas9 proteins of the disclosure may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 147)
       1 MDKKYSIGLD IGTNSVGWAV ITDEYKVPSK KFKVLGNTDR HSIKKNLIGA LLFDSGETAE
      61 ATRLKRTARR RYTRRKNRIC YLQEIFSNEM AKVDDSFFHR LEESFLVEED KKHERHPIFG
     121 NIVDEVAYHE KYPTIYHLRK KLVDSTDKAD LRLIYLALAH MIKFRGHFLI EGDLNPDNSD
     181 VDKLFIQLVQ TYNQLFEENP INASGVDAKA ILSARLSKSR RLENLIAQLP GEKKNGLFGN
     241 LIALSLGLTP NFKSNFDLAE DAKLQLSKDT YDDDLDNLLA QIGDQYADLF LAAKNLSDAI
     301 LLSDILRVNT EITKAPLSAS MIKRYDEHHQ DLTLLKALVR QQLPEKYKEI FFDQSKNGYA
     361 GYIDGGASQE EFYKFIKPIL EKMDGTEELL VKLNREDLLR KQRTFDNGSI PHQIHLGELH
     421 AILRRQEDFY PFLKDNREKI EKILTFRIPY YVGPLARGNS RFAWMTRKSE ETITPWNFEE
     481 VVDKGASAQS FIERMTNFDK NLPNEKVLPK HSLLYEYFTV YNELTKVKYV TEGMRKPAFL
     541 SGEQKKAIVD LLFKTNRKVT VKQLKEDYFK KIECFDSVEI SGVEDRFNAS LGTYHDLLKI
     601 IKDKDFLDNE ENEDILEDIV LTLTLFEDRE MIEERLKTYA HLFDDKVMKQ LKRRRYTGWG
     661 RLSRKLINGI RDKQSGKTIL DFLKSDGFAN RNFMQLIHDD SLTFKEDIQK AQVSGQGDSL
     721 HEHIANLAGS PAIKKGILQT VKVVDELVKV MGRHKPENIV IEMARENQTT QKGQKNSRER
     781 MKRIEEGIKE LGSQILKEHP VENTQLQNEK LYLYYLQNGR DMYVDQELDI NRLSDYDVDH
     841 IVPQSFLKDD SIDNKVLTRS DKNRGKSDNV PSEEVVKKMK NYWRQLLNAK LITQRKFDNL
     901 TKAERGGLSE LDKAGFIKRQ LVETRQITKH VAQILDSRMN TKYDENDKLI REVKVITLKS
     961 KLVSDFRKDF QFYKVREINN YHHAHDAYLN AVVGTALIKK YPKLESEFVY GDYKVYDVRK
    1021 MIAKSEQEIG KATAKYFFYS NIMNFFKTEI TLANGEIRKR PLIETNGETG EIVWDKGRDF
    1081 ATVRKVLSMP QVNIVKKTEV QTGGFSKESI LPKRNSDKLI ARKKDWDPKK YGGFDSPTVA
    1141 YSVLVVAKVE KGKSKKLKSV KELLGITIME RSSFEKNPID FLEAKGYKEV KKDLIIKLPK
    1201 YSLFELENGR KRMLASAGEL QKGNELALPS KYVNFLYLAS HYEKLKGSPE DNEQKQLFVE
    1261 QHKHYLDEII EQISEFSKRV ILADANLDKV LSAYNKHRDK PIREQAENII HLFTLTNLGA
    1321 PAAFKYFDTT IDRKRYTSTK EVLDATLIHQ SITGLYETRI DLSQLGGD.
  • Nuclease inactivated S. pyogenes Cas9 proteins may comprise a substitution of an Alanine (A) for an Aspartic Acid (D) at position 10 and an alanine (A) for a Histidine (H) at position 840. Exemplary nuclease inactivated S. pyogenes Cas9 proteins of the disclosure may comprise or consist of the amino acid sequence (D10A and H840A bolded and underlined):
  • (SEQ ID NO: 148)
       1 MDKKYSIGL A  IGTNSVGWAV ITDEYKVPSK KFKVLGNTDR HSIKKNLIGA LLFDSGETAE
      61 ATRLKRTARR RYTRRKNRIC YLQEIFSNEM AKVDDSFFHR LEESFLVEED KKHERHPIFG
     121 NIVDEVAYHE KYPTIYHLRK KLVDSTDKAD LRLIYLALAH MIKFRGHFLI EGDLNPDNSD
     181 VDKLFIQLVQ TYNQLFEENP INASGVDAKA ILSARLSKSR RLENLIAQLP GEKKNGLFGN
     241 LIALSLGLTP NFKSNFDLAE DAKLQLSKDT YDDDLDNLLA QIGDQYADLF LAAKNLSDAI
     301 LLSDILRVNT EITKAPLSAS MIKRYDEHHQ DLTLLKALVR QQLPEKYKEI FFDQSKNGYA
     361 GYIDGGASQE EFYKFIKPIL EKMDGTEELL VKLNREDLLR KQRTFDNGSI PHQIHLGELH
     421 AILRRQEDFY PFLKDNREKI EKILTFRIPY YVGPLARGNS RFAWMTRKSE ETITPWNFEE
     481 VVDKGASAQS FIERMTNFDK NLPNEKVLPK HSLLYEYFTV YNELTKVKYV TEGMRKPAFL
     541 SGEQKKAIVD LLFKTNRKVT VKQLKEDYFK KIECFDSVEI SGVEDRFNAS LGTYHDLLKI
     601 IKDKDFLDNE ENEDILEDIV LTLTLFEDRE MIEERLKTYA HLFDDKVMKQ LKRRRYTGWG
     661 RLSRKLINGI RDKQSGKTIL DFLKSDGFAN RNFMQLIHDD SLTFKEDIQK AQVSGQGDSL
     721 HEHIANLAGS PAIKKGILQT VKVVDELVKV MGRHKPENIV IEMARENQTT QKGQKNSRER
     781 MKRIEEGIKE LGSQILKEHP VENTQLQNEK LYLYYLQNGR DMYVDQELDI NRLSDYDVD A
     841 IVPQSFLKDD SIDNKVLTRS DKNRGKSDNV PSEEVVKKMK NYWRQLLNAK LITQRKFDNL
     901 TKAERGGLSE LDKAGFIKRQ LVETRQITKH VAQILDSRMN TKYDENDKLI REVKVITLKS
     961 KLVSDFRKDF QFYKVREINN YHHAHDAYLN AVVGTALIKK YPKLESEFVY GDYKVYDVRK
    1021 MIAKSEQEIG KATAKYFFYS NIMNFFKTEI TLANGEIRKR PLIETNGETG EIVWDKGRDF
    1081 ATVRKVLSMP QVNIVKKTEV QTGGFSKESI LPKRNSDKLI ARKKDWDPKK YGGFDSPTVA
    1141 YSVLVVAKVE KGKSKKLKSV KELLGITIME RSSFEKNPID FLEAKGYKEV KKDLIIKLPK
    1201 YSLFELENGR KRMLASAGEL QKGNELALPS KYVNFLYLAS HYEKLKGSPE DNEQKQLFVE
    1261 QHKHYLDEII EQISEFSKRV ILADANLDKV LSAYNKHRDK PIREQAENII HLFTLTNLGA
    1321 PAAFKYFDTT IDRKRYTSTK EVLDATLIHQ SITGLYETRI DLSQLGGD.
  • Nuclease inactivated S. pyogenes Cas9 proteins may comprise deletion of a RuvC nuclease domain or a portion thereof, an HNH domain, a DNAse active site, a ββα-metal fold or a portion thereof comprising a DNAse active site or any combination thereof.
  • Other exemplary Cas9 proteins or portions thereof may comprise or consist of the following amino acid sequences.
  • In some embodiments the Cas9 protein can be S. pyogenes Cas9 and may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 149)
    MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGA
    LLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHR
    LEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKAD
    LRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENP
    INASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTP
    NFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAI
    LLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEI
    FFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLR
    KQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPY
    YVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDK
    NLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVD
    LLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKI
    IKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQ
    LKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDD
    SLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVVDELVKV
    MGRHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHP
    VENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSFLKDD
    SIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNL
    TKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLI
    REVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKK
    YPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEI
    TLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEV
    QTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLWAKVEK
    GKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKY
    SLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPED
    NEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKP
    IREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQS
    ITGLYETRIDLSQLGGD
  • In some embodiments the Cas9 protein can be S. aureus Cas9 and may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 150)
    MKRNYILGLDIGITSVGYGIIDYETRDVIDAGVRLFKEANVENNEGRRSK
    RGARRLKRRRRHRIQRVKKLLFDYNLLTDHSELSGINPYEARVKGLSQKL
    SEEEFSAALLHLAKRRGVHNVNEVEEDTGNELSTKEQISRNSKALEEKYV
    AELQLERLKKDGEVRGSINRFKTSDYVKEAKQLLKVQKAYHQLDQSFIDT
    YIDLLETRRTYYEGPGEGSPFGWKDIKEWYEMLMGHCTYFPEELRSVKYA
    YNADLYNALNDLNNLVITRDENEKLEYYEKFQIIENVFKQKKKPTLKQIA
    KEILVNEEDIKGYRVTSTGKPEFTNLKVYHDIKDITARKEIIENAELLDQ
    IAKILTIYQSSEDIQEELTNLNSELTQEEIEQISNLKGYTGTHNLSLKAI
    NLILDELWHTNDNQIAIFNRLKLVPKKVDLSQQKEIPTTLVDDFILSPVV
    KRSFIQSIKVINAIIKKYGLPNDIIIELAREKNSKDAQKMINEMQKRNRQ
    TNERIEEIIRTTGKENAKYLIEKIKLHDMQEGKCLYSLEAIPLEDLLNNP
    FNYEVDHIIPRSVSFDNSFNNKVLVKQEENSKKGNRTPFQYLSSSDSKIS
    YETFKKHILNLAKGKGRISKTKKEYLLEERDINRFSVQKDFINRNLVDTR
    YATRGLMNLLRSYFRVNNLDVKVKSINGGFTSFLRRKWKFKKERNKGYKH
    HAEDALIIANADFIFKEWKKLDKAKKVMENQMFEEKQAESMPEIETEQEY
    KEIFITPHQIKHIKDFKDYKYSHRVDKKPNRELINDTLYSTRKDDKGNTL
    IVNNLNGLYDKDNDKLKKLINKSPEKLLMYHHDPQTYQKLKLIMEQYGDE
    KNPLYKYYEETGNYLTKYSKKDNGPVIKKIKYYGNKLNAHLDITDDYPNS
    RNKVVKLSLKPYRFDVYLDNGVYKFVTVKNLDVIKKENYYEVNSKCYEEA
    KKLKKISNQAEFIASFYNNDLIKINGELYRVIGVNNDLLNRIEVNMIDIT
    YREYLENMNDKRPPRIIKTIASKTQSIKKYSTDILGNLYEVKSKKHPQII
    KKG
  • In some embodiments the Cas9 protein can be S. thermophiles CRISPR1 Cas9 and may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 151)
    MSDLVLGLDIGIGSVGVGILNKVTGEIIHKNSRIFPAAQAENNLVRRTNR
    QGRRLARRKKHRRVRLNRLFEESGLITDFTKISINLNPYQLRVKGLTDEL
    SNEELFIALKNMVKHRGISYLDDASDDGNSSVGDYAQIVKENSKQLETKT
    PGQIQLERYQTYGQLRGDFTVEKDGKKHRLINVFPTSAYRSEALRILQTQ
    QEFNPQITDEFINRYLEILTGKRKYYHGPGNEKSRTDYGRYRTSGETLDN
    IFGILIGKCTFYPDEFRAAKASYTAQEFNLLNDLNNLTVPTETKKLSKEQ
    KNQIINYVKNEKAMGPAKLFKYIAKLLSCDVADIKGYRIDKSGKAEIHTF
    EAYRKMKTLETLDIEQMDRETLDKLAYVLTLNTEREGIQEALEHEFADGS
    FSQKQVDELVQFRKANSSIFGKGWHNFSVKLMMELIPELYETSEEQMTIL
    TRLGKQKTTSSSNKTKYIDEKLLTEEIYNPVVAKSVRQAIKIVNAAIKEY
    GDFDNIVIEMARETNEDDEKKAIQKIQKANKDEKDAAMLKAANQYNGKAE
    LPHSVFHGHKQLATKIRLWHQQGERCLYTGKTISIHDLINNSNQFEVDHI
    LPLSITFDDSLANKVLVYATANQEKGQRTPYQALDSMDDAWSFRELKAFV
    RESKTLSNKKKEYLLTEEDISKFDVRKKFIERNLVDTRYASRVVLNALQE
    HFRAHKIDTKVSVVRGQFTSQLRRHWGIEKTRDTYHHHAVDALIIAASSQ
    LNLWKKQKNTLVSYSEDQLLDIETGELISDDEYKESVFKAPYQHFVDTLK
    SKEFEDSILFSYQVDSKFNRKISDATIYATRQAKVGKDKADETYVLGKIK
    DIYTQDGYDAFMKIYKKDKSKFLMYRHDPQTFEKVIEPILENYPNKQIND
    KGKEVPCNPFLKYKEEHGYIRKYSKKGNGPEIKSLKYYDSKLGNHIDITP
    KDSNNKVVLQSVSPWRADVYFNKTTGKYEILGLKYADLQFDKGTGTYKIS
    QEKYNDIKKKEGVDSDSEFKFTLYKNDLLLVKDTETKEQQLFRFLSRTMP
    KQKHYVELKPYDKQKFEGGEALIKVLGNVANSGQCKKGLGKSNISIYKVR
    TDVLGNQHIIKNEGDKPKLDF
  • In some embodiments the Cas9 protein can be N. meningitidis Cas9 and may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 152)
    MAAFKPNPINYILGLDIGIASVGWAMVEIDEDENPICLIDLGVRVFERAE
    VPKTGDSLAMARRLARSVRRLTRRRAHRLLRARRLLKREGVLQAADFDEN
    GLIKSLPNTPWQLRAAALDRKLTPLEWSAVLLHLIKHRGYLSQRKNEGET
    ADKELGALLKGVADNAHALQTGDFRTPAELALNKFEKESGHIRNQRGDYS
    HTFSRKDLQAELILLFEKQKEFGNPHVSGGLKEGIETLLMTQRPALSGDA
    VQKMLGHCTFEPAEPKAAKNTYTAERFIWLTKLNNLRILEQGSERPLTDT
    ERATLMDEPYRKSKLTYAQARKLLGLEDTAFFKGLRYGKDNAEASTLMEM
    KAYHAISRALEKEGLKDKKSPLNLSPELQDEIGTAFSLFKTDEDITGRLK
    DRIQPEILEALLKHISFDKFVQISLKALRRIVPLMEQGKRYDEACAEIYG
    DHYGKKNTEEKIYLPPIPADEIRNPVVLRALSQARKVINGVVRRYGSPAR
    IHIETAREVGKSFKDRKEIEKRQEENRKDREKAAAKFREYFPNFVGEPKS
    KDILKLRLYEQQHGKCLYSGKEINLGRLNEKGYVEIDHALPFSRTWDDSF
    NNKVLVLGSENQNKGNQTPYEYFNGKDNSREWQEFKARVETSRFPRSKKQ
    RILLQKFDEDGFKERNLNDTRYVNRFLCQFVADRMRLTGKGKKRVFASNG
    QITNLLRGFWGLRKVRAENDRHHALDAVVVACSTVAMQQKITRFVRYKEM
    NAFDGKTIDKETGEVLHQKTHFPQPWEFFAQEVMIRVFGKPDGKPEFEEA
    DTPEKLRTLLAEKLSSRPEAVHEYVTPLFVSRAPNRKMSGQGHMETVKSA
    KRLDEGVSVLRVPLTQLKLKDLEKMVNREREPKLYEALKARLEAHKDDPA
    KAFAEPFYKYDKAGNRTQQVKAVRVEQVQKTGVWVRNHNGIADNATMVRV
    DVFEKGDKYYLVPIYSWQVAKGILPDRAVVQGKDEEDWQLIDDSFNFKFS
    LHPNDLVEVITKKARMFGYFASCHRGTGNINIRIHDLDHKIGKNGILEGI
    GVKTALSFQKYQIDELGKEIRPCRLKKRPPVR
  • In some embodiments the Cas9 protein can be Parvibaculum. lavamentivorans Cas9 and may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 153)
    MERIFGFDIGTTSIGFSVIDYSSTQSAGNIQRLGVRIFPEARDPDGTPLN
    QQRRQKRMMRRQLRRRRIRRKALNETLHEAGFLPAYGSADWPVVMADEPY
    ELRRRGLEEGLSAYEFGRAIYHLAQHRHFKGRELEESDTPDPDVDDEKEA
    ANERAATLKALKNEQTTLGAWLARRPPSDRKRGIHAHRNVVAEEFERLWE
    VQSKFHPALKSEEMRARISDTIFAQRPVFWRKNTLGECRFMPGEPLCPKG
    SWLSQQRRMLEKLNNLAIAGGNARPLDAEERDAILSKLQQQASMSWPGVR
    SALKALYKQRGEPGAEKSLKFNLELGGESKLLGNALEAKLADMFGPDWPA
    HPRKQEIRHAVHERLWAADYGETPDKKRVIILSEKDRKAHREAAANSFVA
    DFGITGEQAAQLQALKLPTGWEPYSIPALNLFLAELEKGERFGALVNGPD
    WEGWRRTNFPHRNQPTGEILDKLPSPASKEERERISQLRNPTVVRTQNEL
    RKVVNNLIGLYGKPDRIRIEVGRDVGKSKREREEIQSGIRRNEKQRKKAT
    EDLIKNGIANPSRDDVEKWILWKEGQERCPYTGDQIGFNALFREGRYEVE
    HIWPRSRSFDNSPRNKTLCRKDVNIEKGNRMPFEAFGHDEDRWSAIQIRL
    QGMVSAKGGTGMSPGKVKRFLAKTMPEDFAARQLNDTRYAAKQILAQLKR
    LWPDMGPEAPVKVEAVTGQVTAQLRKLWTLNNILADDGEKTRADHRHHAI
    DALTVACTHPGMTNKLSRYWQLRDDPRAEKPALTPPWDTIRADAEKAVSE
    IVVSHRVRKKVSGPLHKETTYGDTGTDIKTKSGTYRQFVTRKKIESLSKG
    ELDEIRDPRIKEIVAAHVAGRGGDPKKAFPPYPCVSPGGPEIRKVRLTSK
    QQLNLMAQTGNGYADLGSNHHIAIYRLPDGKADFEIVSLFDASRRLAQRN
    PIVQRTRADGASFVMSLAAGEAIMIPEGSKKGIWIVQGVWASGQVVLERD
    TDADHSTTTRPMPNPILKDDAKKVSIDPIGRVRPSND
  • In some embodiments the Cas9 protein can be Corynebacter diphtheria Cas9 and may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 154)
    MKYHVGIDVGTFSVGLAAIEVDDAGMPIKTLSLVSHIHDSGLDPDEIKSA
    VTRLASSGIARRTRRLYRRKRRRLQQLDKFIQRQGWPVIELEDYSDPLYP
    WKVRAELAASYIADEKERGEKLSVALRHIARHRGWRNPYAKVSSLYLPDG
    PSDAFKAIREEIKRASGQPVPETATVGQMVTLCELGTLKLRGEGGVLSAR
    LQQSDYAREIQEICRMQEIGQELYRKIIDVVFAAESPKGSASSRVGKDPL
    QPGKNRALKASDAFQRYRIAALIGNLRVRVDGEKRILSVEEKNLVFDHLV
    NLTPKKEPEWVTIAEILGIDRGQLIGTATMTDDGERAGARPPTHDTNRSI
    VNSRIAPLVDWWKTASALEQHAMVKALSNAEVDDFDSPEGAKVQAFFADL
    DDDVHAKLDSLHLPVGRAAYSEDTLVRLTRRMLSDGVDLYTARLQEFGIE
    PSWTPPTPRIGEPVGNPAVDRVLKTVSRWLESATKTWGAPERVIIEHVRE
    GFVTEKRAREMDGDMRRRAARNAKLFQEMQEKLNVQGKPSRADLWRYQSV
    QRQNCQCAYCGSPITFSNSEMDHIVPRAGQGSTNTRENLVAVCHRCNQSK
    GNTPFAIWAKNTSIEGVSVKEAVERTRHWVTDTGMRSTDFKKFTKAVVER
    FQRATMDEEIDARSMESVAWMANELRSRVAQHFASHGTTVRVYRGSLTAE
    ARRASGISGKLKFFDGVGKSRLDRRHHAIDAAVIAFTSDYVAETLAVRSN
    LKQSQAHRQEAPQWREFTGKDAEHRAAWRVWCQKMEKLSALLTEDLRDDR
    VVVMSNVRLRLGNGSAHKETIGKLSKVKLSSQLSVSDIDKASSEALWCAL
    TREPGFDPKEGLPANPERHIRVNGTHVYAGDNIGLFPVSAGSIALRGGYA
    ELGSSFHHARVYKITSGKKPAFAMLRVYTIDLLPYRNQDLFSVELKPQTM
    SMRQAEKKLRDALATGNAEYLGWLVVDDELVVDTSKIATDQVKAVEAELG
    TIRRWRVDGFFSPSKLRLRPLQMSKEGIKKESAPELSKIIDRPGWLPAVN
    KLFSDGNVTVVRRDSLGRVRLESTAHLPVTWKVQ
  • In some embodiments the Cas9 protein can be Streptococcus pasteurianus Cas9 and may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 155)
    MTNGKILGLDIGIASVGVGIIEAKTGKVVHANSRLFSAANAENNAERRGF
    RGSRRLNRRKKHRVKRVRDLFEKYGIVTDFRNLNLNPYELRVKGLTEQLK
    NEELFAALRTISKRRGISYLDDAEDDSTGSTDYAKSIDENRRLLKNKTPG
    QIQLERLEKYGQLRGNFTVYDENGEAHRLINVFSTSDYEKEARKILETQA
    DYNKKITAEFIDDYVEILTQKRKYYHGPGNEKSRTDYGRFRTDGTTLENI
    FGILIGKCNFYPDEYRASKASYTAQEYNFLNDLNNLKVSTETGKLSTEQK
    ESLVEFAKNTATLGPAKLLKEIAKILDCKVDEIKGYREDDKGKPDLHTFE
    PYRKLKFNLESINIDDLSREVIDKLADILTLNIIREGIEDAIKRNLPNQF
    TEEQISEIIKVRKSQSTAFNKGWHSFSAKLMNELIPELYATSDEQMTILT
    RLEKFKVNKKSSKNTKTIDEKEVTDEIYNPVVAKSVRQTIKIINAAVKKY
    GDFDKIVIEMPRDKNADDEKKFIDKRNKENKKEKDDALKRAAYLYNSSDK
    LPDEVFHGNKQLETKIRLWYQQGERCLYSGKPISIQELVHNSNNFEIDHI
    LPLSLSFDDSLANKVLVYAWTNQEKGQKTPYQVIDSMDAAWSFREMKDYV
    LKQKGLGKKKRDYLLTTENIDKIEVKKKFIERNLVDTRYASRVVLNSLQS
    ALRELGKDTKVSVVRGQFTSQLRRKWKIDKSRETYHHHAVDALIIAASSQ
    LKLWEKQDNPMFVDYGKNQVVDKQTGEILSVSDDEYKELVFQPPYQGFVN
    TISSKGFEDEILFSYQVDSKYNRKVSDATIYSTRKAKIGKDKKEETYVLG
    KIKDIYSQNGFDTFIKKYNKDKTQFLMYQKDSLTWENVIEVILRDYPTTK
    KSEDGKNDVKCNPFEEYRRENGLICKYSKKGKGTPIKSLKYYDKKLGNCI
    DITPEESRNKVILQSINPWRADVYFNPETLKYELMGLKYSDLSFEKGTGN
    YHISQEKYDAIKEKEGIGKKSEFKFTLYRNDLILIKDIASGEQEIYRFLS
    RTMPNVNHYVELKPYDKEKFDNVQELVEALGEADKVGRCIKGLNKPNISI
    YKVRTDVLGNKYFVKKKGDKPKLDFKNNKK
  • In some embodiments the Cas9 protein can be Neisseria cinerea Cas9 and may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 156)
    MAAFKPNPMNYILGLDIGIASVGWAIVEIDEEENPIRLIDLGVRVFERAE
    VPKTGDSLAAARRLARSVRRLTRRRAHRLLRARRLLKREGVLQAADFDEN
    GLIKSLPNTPWQLRAAALDRKLTPLEWSAVLLHLIKHRGYLSQRKNEGET
    ADKELGALLKGVADNTHALQTGDFRTPAELALNKFEKESGHIRNQRGDYS
    HTFNRKDLQAELNLLFEKQKEFGNPHVSDGLKEGIETLLMTQRPALSGDA
    VQKMLGHCTFEPTEPKAAKNTYTAERFVWLTKLNNLRILEQGSERPLTDT
    ERATLMDEPYRKSKLTYAQARKLLDLDDTAFFKGLRYGKDNAEASTLMEM
    KAYHAISRALEKEGLKDKKSPLNLSPELQDEIGTAFSLFKTDEDITGRLK
    DRVQPEILEALLKHISFDKFVQISLKALRRIVPLMEQGNRYDEACTEIYG
    DHYGKKNIEEKIYLPPIPADEIRNPVVLRALSQARKVINGVVRRYGSPAR
    IHIETAREVGKSFKDRKEIEKRQEENRKDREKSAAKFREYFPNFVGEPKS
    KDILKLRLYEQQHGKCLYSGKEINLGRLNEKGYVEIDHALPFSRTWDDSF
    NNKVLALGSENQNKGNQTPYEYFNGKDNSREWQEFKARVETSRFPRSKKQ
    RILLQKFDEDGFKERNLNDTRYINRFLCQFVADHMLLTGKGKRRVFASNG
    QITNLLRGFWGLRKVRAENDRHHALDAVVVACSTIAMQQKITRFVRYKEM
    NAFDGKTIDKETGEVLHQKAHFPQPWEFFAQEVMIRVFGKPDGKPEFEEA
    DTPEKLRTLLAEKLSSRPEAVHKYVTPLFISRAPNRKMSGQGHMETVKSA
    KRLDEGISVLRVPLTQLKLKDLEKMVNREREPKLYEALKARLEAHKDDPA
    KAFAEPFYKYDKAGNRTQQVKAVRVEQVQKTGVWVHNHNGIADNATIVRV
    DVFEKGGKYYLVPIYSWQVAKGILPDRAVVQGKDEEDWTVMDDSFEFKFV
    LYANDLIKLTAKKNEFLGYFVSLNRATGAIDIRTHDTDSTKGKNGIFQSV
    GVKTALSFQKYQIDELGKEIRPCRLKKRPPVR
  • In some embodiments the Cas9 protein can be Campylobacter lari Cas9 and may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 157)
    MRILGFDIGINSIGWAFVENDELKDCGVRIFTKAENPKNKESLALPRRNA
    RSSRRRLKRRKARLIAIKRILAKELKLNYKDYVAADGELPKAYEGSLASV
    YELRYKALTQNLETKDLARVILHIAKHRGYMNKNEKKSNDAKKGKILSAL
    KNNALKLENYQSVGEYFYKEFFQKYKKNTKNFIKIRNTKDNYNNCVLSSD
    LEKELKLILEKQKEFGYNYSEDFINEILKVAFFQRPLKDFSHLVGACTFF
    EEEKRACKNSYSAWEFVALTKIINEIKSLEKISGEIVPTQTINEVLNLIL
    DKGSITYKKFRSCINLHESISFKSLKYDKENAENAKLIDFRKLVEFKKAL
    GVHSLSRQELDQISTHITLIKDNVKLKTVLEKYNLSNEQINNLLEIEFND
    YINLSFKALGMILPLMREGKRYDEACEIANLKPKTVDEKKDFLPAFCDSI
    FAHELSNPVVNRAISEYRKVLNALLKKYGKVHKIHLELARDVGLSKKARE
    KIEKEQKENQAVNAWALKECENIGLKASAKNILKLKLWKEQKEICIYSGN
    KISIEHLKDEKALEVDHIYPYSRSFDDSFINKVLVFTKENQEKLNKTPFE
    AFGKNIEKWSKIQTLAQNLPYKKKNKILDENFKDKQQEDFISRNLNDTRY
    IATLIAKYTKEYLNFLLLSENENANLKSGEKGSKIHVQTISGMLTSVLRH
    TWGFDKKDRNNHLHHALDAIIVAYSTNSIIKAFSDFRKNQELLKARFYAK
    ELTSDNYKHQVKFFEPFKSFREKILSKIDEIFVSKPPRKRARRALHKDTF
    HSENKIIDKCSYNSKEGLQIALSCGRVRKIGTKYVENDTIVRVDIFKKQN
    KFYAIPIYAMDFALGILPNKIVITGKDKNNNPKQWQTIDESYEFCFSLYK
    NDLILLQKKNMQEPEFAYYNDFSISTSSICVEKHDNKFENLTSNQKLLFS
    NAKEGSVKVESLGIQNLKVFEKYIITPLGDKIKADFQPRENISLKTSKKY
    GLR
  • In some embodiments the Cas9 protein can be T. denticola Cas9 and may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 158)
    MKKEIKDYFLGLDVGTGSVGWAVTDTDYKLLKANRKDLWGMRCFETAETA
    EVRRLHRGARRRIERRKKRIKLLQELFSQEIAKTDEGFFQRMKESPFYAE
    DKTILQENTLFNDKDFADKTYHKAYPTINHLIKAWIENKVKPDPRLLYLA
    CHNIIKKRGHFLFEGDFDSENQFDTSIQALFEYLREDMEVDIDADSQKVK
    EILKDSSLKNSEKQSRLNKILGLKPSDKQKKAITNLISGNKINFADLYDN
    PDLKDAEKNSISFSKDDFDALSDDLASILGDSFELLLKAKAVYNCSVLSK
    VIGDEQYLSFAKVKIYEKHKTDLTKLKNVIKKHFPKDYKKVFGYNKNEKN
    NNNYSGYVGVCKTKSKKLIINNSVNQEDFYKFLKTILSAKSEIKEVNDIL
    TEIETGTFLPKQISKSNAEIPYQLRKMELEKILSNAEKHFSFLKQKDEKG
    LSHSEKIIMLLTFKIPYYIGPINDNHKKFFPDRCWVVKKEKSPSGKTTPW
    NFFDHIDKEKTAEAFITSRTNFCTYLVGESVLPKSSLLYSEYTVLNEINN
    LQIIIDGKNICDIKLKQKIYEDLFKKYKKITQKQISTFIKHEGICNKTDE
    VIILGIDKECTSSLKSYIELKNIFGKQVDEISTKNMLEEIIRWATIYDEG
    EGKTILKTKIKAEYGKYCSDEQIKKILNLKFSGWGRLSRKFLETVTSEMP
    GFSEPVNIITAMRETQNNLMELLSSEFTFTENIKKINSGFEDAEKQFSYD
    GLVKPLFLSPSVKKMLWQTLKLVKEISHITQAPPKKIFIEMAKGAELEPA
    RTKTRLKILQDLYNNCKNDADAFSSEIKDLSGKIENEDNLRLRSDKLYLY
    YTQLGKCMYCGKPIEIGHVFDTSNYDIDHIYPQSKIKDDSISNRVLVCSS
    CNKNKEDKYPLKSEIQSKQRGFWNFLQRNNFISLEKLNRLTRATPISDDE
    TAKFIARQLVETRQATKVAAKVLEKMFPETKIVYSKAETVSMFRNKFDIV
    KCREINDFHHAHDAYLNIVVGNVYNTKFTNNPWNFIKEKRDNPKIADTYN
    YYKVFDYDVKRNNITAWEKGKTIITVKDMLKRNTPIYTRQAACKKGELFN
    QTIMKKGLGQHPLKKEGPFSNISKYGGYNKVSAAYYTLIEYEEKGNKIRS
    LETIPLYLVKDIQKDQDVLKSYLTDLLGKKEFKILVPKIKINSLLKINGF
    PCHITGKTNDSFLLRPAVQFCCSNNEVLYFKKIIRFSEIRSQREKIGKTI
    SPYEDLSFRSYIKENLWKKTKNDEIGEKEFYDLLQKKNLEIYDMLLTKHK
    DTIYKKRPNSATIDILVKGKEKFKSLIIENQFEVILEILKLFSATRNVSD
    LQHIGGSKYSGVAKIGNKISSLDNCILIYQSITGIFEKRIDLLKV
  • In some embodiments the Cas9 protein can be S. mutans Cas9 and may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 159)
    MKKPYSIGLDIGTNSVGWAVVTDDYKVPAKKMKVLGNTDKSHIEKNLLGA
    LLFDSGNTAEDRRLKRTARRRYTRRRNRILYLQEIFSEEMGKVDDSFFHR
    LEDSFLVTEDKRGERHPIFGNLEEEVKYHENFPTIYHLRQYLADNPEKVD
    LRLVYLALAHIIKFRGHFLIEGKFDTRNNDVQRLFQEFLAVYDNTFENSS
    LQEQNVQVEEILTDKISKSAKKDRVLKLFPNEKSNGRFAEFLKLIVGNQA
    DFKKHFELEEKAPLQFSKDTYEEELEVLLAQIGDNYAELFLSAKKLYDSI
    LLSGILTVTDVGTKAPLSASMIQRYNEHQMDLAQLKQFIRQKLSDKYNEV
    FSDVSKDGYAGYIDGKTNQEAFYKYLKGLLNKIEGSGYFLDKIEREDFLR
    KQRTFDNGSIPHQIHLQEMRAIIRRQAEFYPFLADNQDRIEKLLTFRIPY
    YVGPLARGKSDFAWLSRKSADKITPWNFDEIVDKESSAEAFINRMTNYDL
    YLPNQKVLPKHSLLYEKFTVYNELTKVKYKTEQGKTAFFDANMKQEIFDG
    VFKVYRKVTKDKLMDFLEKEFDEFRIVDLTGLDKENKVFNASYGTYHDLC
    KILDKDFLDNSKNEKILEDIVLTLTLFEDREMIRKRLENYSDLLTKEQVK
    KLERRHYTGWGRLSAELIHGIRNKESRKTILDYLIDDGNSNRNFMQLIND
    DALSFKEEIAKAQVIGETDNLNQVVSDIAGSPAIKKGILQSLKIVDELVK
    IMGHQPENIVVEMARENQFTNQGRRNSQQRLKGLTDSIKEFGSQILKEHP
    VENSQLQNDRLFLYYLQNGRDMYTGEELDIDYLSQYDIDHIIPQAFIKDN
    SIDNRVLTSSKENRGKSDDVPSKDVVRKMKSYWSKLLSAKLITQRKFDNL
    TKAERGGLTDDDKAGFIKRQLVETRQITKHVARILDERFNTETDENNKKI
    RQVKIVTLKSNLVSNFRKEFELYKVREINDYHHAHDAYLNAVIGKALLGV
    YPQLEPEFVYGDYPHFHGHKENKATAKKFFYSNIMNFFKKDDVRTDKNGE
    IIWKKDEHISNIKKVLSYPQVNIVKKVEEQTGGFSKESILPKGNSDKLIP
    RKTKKFYWDTKKYGGFDSPIVAYSILVIADIEKGKSKKLKTVKALVGVTI
    MEKMTFERDPVAFLERKGYRNVQEENIIKLPKYSLFKLENGRKRLLASAR
    ELQKGNEIVLPNHLGTLLYHAKNIHKVDEPKHLDYVDKHKDEFKELLDVV
    SNFSKKYTLAEGNLEKIKELYAQNNGEDLKELASSFINLLTFTAIGAPAT
    FKFFDKNIDRKRYTSTTEILNATLIHQSITGLYETRIDLNKLGGD
  • In some embodiments the Cas9 protein can be S. thermophilus CRISPR 3 Cas9 and may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 160)
    MTKPYSIGLDIGTNSVGWAVTTDNYKVPSKKMKVLGNTSKKYIKKNLLGV
    LLFDSGITAEGRRLKRTARRRYTRRRNRILYLQEIFSTEMATLDDAFFQR
    LDDSFLVPDDKRDSKYPIFGNLVEEKAYHDEFPTIYHLRKYLADSTKKAD
    LRLVYLALAHMIKYRGHFLIEGEFNSKNNDIQKNFQDFLDTYNAIFESDL
    SLENSKQLEEIVKDKISKLEKKDRILKLFPGEKNSGIFSEFLKLIVGNQA
    DFRKCFNLDEKASLHFSKESYDEDLETLLGYIGDDYSDVFLKAKKLYDAI
    LLSGFLTVTDNETEAPLSSAMIKRYNEHKEDLALLKEYIRNISLKTYNEV
    FKDDTKNGYAGYIDGKTNQEDFYVYLKKLLAEFEGADYFLEKIDREDFLR
    KQRTFDNGSIPYQIHLQEMRAILDKQAKFYPFLAKNKERIEKILTFRIPY
    YVGPLARGNSDFAWSIRKRNEKITPWNFEDVIDKESSAEAFINRMTSFDL
    YLPEEKVLPKHSLLYETFNVYNELTKVRFIAESMRDYQFLDSKQKKDIVR
    LYFKDKRKVTDKDIIEYLHAIYGYDGIELKGIEKQFNSSLSTYHDLLNII
    NDKEFLDDSSNEAIIEEIIHTLTIFEDREMIKQRLSKFENIFDKSVLKKL
    SRRHYTGWGKLSAKLINGIRDEKSGNTILDYLIDDGISNRNFMQLIHDDA
    LSFKKKIQKAQIIGDEDKGNIKEVVKSLPGSPAIKKGILQSIKIVDELVK
    VMGGRKPESIVVEMARENQYTNQGKSNSQQRLKRLEKSLKELGSKILKEN
    IPAKLSKIDNNALQNDRLYLYYLQNGKDMYTGDDLDIDRLSNYDIDHIIP
    QAFLKDNSIDNKVLVSSASNRGKSDDVPSLEVVKKRKTFWYQLLKSKLIS
    QRKFDNLTKAERGGLSPEDKAGFIQRQLVETRQITKHVARLLDEKFNNKK
    DENNRAVRTVKIITLKSTLVSQFRKDFELYKVREINDFHHAHDAYLNAVV
    ASALLKKYPKLEPEFVYGDYPKYNSFRERKSATEKVYFYSNIMNIFKKSI
    SLADGRVIERPLIEVNEETGESVWNKESDLATVRRVLSYPQVNVVKKVEE
    QNHGLDRGKPKGLFNANLSSKPKPNSNENLVGAKEYLDPKKYGGYAGISN
    SFTVLVKGTIEKGAKKKITNVLEFQGISILDRINYRKDKLNFLLEKGYKD
    IELIIELPKYSLFELSDGSRRMLASILSTNNKRGEIHKGNQIFLSQKFVK
    LLYHAKRISNTINENHRKYVENHKKEFEELFYYILEFNENYVGAKKNGKL
    LNSAFQSWQNHSIDELCSSFIGPTGSERKGLFELTSRGSAADFEFLGVKI
    PRYRDYTPSSLLKDATLIHQSVTGLYETRIDLAKLGEG
  • In some embodiments the Cas9 protein can be C. jejuni Cas9 and may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 161)
    MARILAFDIGISSIGWAFSENDELKDCGVRIFTKVENPKTGESLALPRRL
    ARSARKRLARRKARLNHLKHLIANEFKLNYEDYQSFDESLAKAYKGSLIS
    PYELRFRALNELLSKQDFARVILHIAKRRGYDDIKNSDDKEKGAILKAIK
    QNEEKLANYQSVGEYLYKEYFQKFKENSKEFTNVRNKKESYERCIAQSFL
    KDELKLIFKKQREFGFSFSKKFEEEVLSVAFYKRALKDFSHLVGNCSFFT
    DEKRAPKNSPLAFWVALTRIINLLNNLKNTEGILYTKDDLNALLNEVLKN
    GTLTYKQTKKLLGLSDDYEFKGEKGTYFIEFKKYKEFIKALGEHNLSQDD
    LNEIAKDITLIKDEIKLKKALAKYDLNQNQIDSLSKLEFKDHLNISFKAL
    KLVTPLMLEGKKYDEACNELNLKVAINEDKKDFLPAFNETYYKDEVTNPV
    VLRAIKEYRKVLNALLKKYGKVHKINIELAREVGKNHSQRAKIEKEQNEN
    YKAKKDAELECEKLGLKINSKNILKLRLFKEQKEFCAYSGEKIKISDLQD
    EKMLEIDHIYPYSRSFDDSYMNKVLVFTKQNQEKLNQTPFEAFGNDSAKW
    QKIEVLAKNLPTKKQKRILDKNYKDKEQKNFKDRNLNDTRYIARLVLNYT
    KDYLDFLPLSDDENTKLNDTQKGSKVHVEAKSGMLTSALRHTWGFSAKDR
    NNHLHHAIDAVIIAYANNSIVKAFSDFKKEQESNSAELYAKKISELDYKN
    KRKFFEPFSGFRQKVLDKIDEIFVSKPERKKPSGALHEETFRKEEEFYQS
    YGGKEGVLKALELGKIRKVNGKIVKNGDMFRVDIFKHKKTNKFYAVPIYT
    MDFALKVLPNKAVARSKKGEIKDWILMDENYEFCFSLYKDSLILIQTKDM
    QEPEFVYYNAFTSSTVSLIVSKHDNKFETLSKNQKILFKNANEKEVIAKS
    IGIQNLKVFEKYIVSALGEVTKAEFRQREDFKK
  • In some embodiments the Cas9 protein can be P. multocida Cas9 and may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 162)
    MQTTNLSYILGLDLGIASVGWAVVEINENEDPIGLIDVGVRIFERAEVPK
    TGESLALSRRLARSTRRLIRRRAHRLLLAKRFLKREGILSTIDLEKGLPN
    QAWELRVAGLERRLSAIEWGAVLLHLIKHRGYLSKRKNESQTNNKELGAL
    LSGVAQNHQLLQSDDYRTPAELALKKFAKEEGHIRNQRGAYTHTFNRLDL
    LAELNLLFAQQHQFGNPHCKEHIQQYMTELLMWQKPALSGEAILKMLGKC
    THEKNEFKAAKHTYSAERFVWLTKLNNLRILEDGAERALNEEERQLLINH
    PYEKSKLTYAQVRKLLGLSEQAIFKHLRYSKENAESATFMELKAWHAIRK
    ALENQGLKDTWQDLAKKPDLLDEIGTAFSLYKTDEDIQQYLTNKVPNSVI
    NALLVSLNFDKFIELSLKSLRKILPLMEQGKRYDQACREIYGHHYGEANQ
    KTSQLLPAIPAQEIRNPVVLRTLSQARKVINAIIRQYGSPARVHIETGRE
    LGKSFKERREIQKQQEDNRTKRESAVQKFKELFSDFSSEPKSKDILKFRL
    YEQQHGKCLYSGKEINIHRLNEKGYVEIDHALPFSRTWDDSFNNKVLVLA
    SENQNKGNQTPYEWLQGKINSERWKNFVALVLGSQCSAAKKQRLLTQVID
    DNKFIDRNLNDTRYIARFLSNYIQENLLLVGKNKKNVFTPNGQITALLRS
    RWGLIKARENNNRHHALDAIVVACATPSMQQKITRFIRFKEVHPYKIENR
    YEMVDQESGEIISPHFPEPWAYFRQEVNIRVFDNHPDTVLKEMLPDRPQA
    NHQFVQPLFVSRAPTRKMSGQGHMETIKSAKRLAEGISVLRIPLTQLKPN
    LLENMVNKEREPALYAGLKARLAEFNQDPAKAFATPFYKQGGQQVKAIRV
    EQVQKSGVLVRENNGVADNASIVRTDVFIKNNKFFLVPIYTWQVAKGILP
    NKAIVAHKNEDEWEEMDEGAKFKFSLFPNDLVELKTKKEYFFGYYIGLDR
    ATGNISLKEHDGEISKGKDGVYRVGVKLALSFEKYQVDELGKNRQICRPQ
    QRQPVR
  • In some embodiments the Cas9 protein can be F. novicida Cas9 and may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 163)
    MNFKILPIAIDLGVKNTGVFSAFYQKGTSLERLDNKNGKVYELSKDSYTL
    LMNNRTARRHQRRGIDRKQLVKRLFKLIWTEQLNLEWDKDTQQAISFLFN
    RRGFSFITDGYSPEYLNIVPEQVKAILMDIFDDYNGEDDLDSYLKLATEQ
    ESKISEIYNKLMQKILEFKLMKLCTDIKDDKVSTKTLKEITSYEFELLAD
    YLANYSESLKTQKFSYTDKQGNLKELSYYHHDKYNIQEFLKRHATINDRI
    LDTLLTDDLDIWNFNFEKFDFDKNEEKLQNQEDKDHIQAHLHHFVFAVNK
    IKSEMASGGRHRSQYFQEITNVLDENNHQEGYLKNFCENLHNKKYSNLSV
    KNLVNLIGNLSNLELKPLRKYFNDKIHAKADHWDEQKFIETYCHWILGEW
    RVGVKDQDKKDGAKYSYKDLCNELKQKVTKAGLVDFLLELDPCRTIPPYL
    DNNNRKPPKCQSLILNPKFLDNQYPNWQQYLQELKKLQSIQNYLDSFETD
    LKVLKSSKDQPYFVEYKSSNQQIASGQRDYKDLDARILQFIFDRVKASDE
    LLLNEIYFQAKKLKQKASSELEKLESSKKLDEVIANSQLSQILKSQHTNG
    IFEQGTFLHLVCKYYKQRQRARDSRLYIMPEYRYDKKLHKYNNTGRFDDD
    NQLLTYCNHKPRQKRYQLLNDLAGVLQVSPNFLKDKIGSDDDLFISKWLV
    EHIRGFKKACEDSLKIQKDNRGLLNHKINIARNTKGKCEKEIFNLICKIE
    GSEDKKGNYKHGLAYELGVLLFGEPNEASKPEFDRKIKKFNSIYSFAQIQ
    QIAFAERKGNANTCAVCSADNAHRMQQIKITEPVEDNKDKIILSAKAQRL
    PAIPTRIVDGAVKKMATILAKNIVDDNWQNIKQVLSAKHQLHIPIITESN
    AFEFEPALADVKGKSLKDRRKKALERISPENIFKDKNNRIKEFAKGISAY
    SGANLTDGDFDGAKEELDHIIPRSHKKYGTLNDEANLICVTRGDNKNKGN
    RIFCLRDLADNYKLKQFETTDDLEIEKKIADTIWDANKKDFKFGNYRSFI
    NLTPQEQKAFRHALFLADENPIKQAVIRAINNRNRTFVNGTQRYFAEVLA
    NNIYLRAKKENLNTDKISFDYFGIPTIGNGRGIAEIRQLYEKVDSDIQAY
    AKGDKPQASYSHLIDAMLAFCIAADEHRNDGSIGLEIDKNYSLYPLDKNT
    GEVFTKDIFSQIKITDNEFSDKKLVRKKAIEGFNTHRQMTRDGIYAENYL
    PILIHKELNEVRKGYTWKNSEEIKIFKGKKYDIQQLNNLVYCLKFVDKPI
    SIDIQISTLEELRNILTTNNIAATAEYYYINLKTQKLHEYYIENYNTALG
    YKKYSKEMEFLRSLAYRSERVKIKSIDDVKQVLDKDSNFIIGKITLPFKK
    EWQRLYREWQNTTIKDDYEFLKSFFNVKSITKLHKKVRKDFSLPISTNEG
    KFLVKRKTWDNNFIYQILNDSDSRADGTKPFIPAFDISKNEIVEAIIDSF
    TSKNIFWLPKNIELQKVDNKNIFAIDTSKWFEVETPSDLRDIGIATIQYK
    IDNNSRPKVRVKLDYVIDDDSKINYFMNHSLLKSRYPDKVLEILKQSTII
    EFESSGFNKTIKEMLGMKLAGIYNETSNN
  • In some embodiments the Cas9 protein can be Lactobacillus buchneri Cas9 and may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 164)
    MKVNNYHIGLDIGTSSIGWVAIGKDGKPLRVKGKTAIGARLFQEGNPAAD
    RRMFRTTRRRLSRRKWRLKLLEEIFDPYITPVDSTFFARLKQSNLSPKDS
    RKEFKGSMLFPDLTDMQYHKNYPTIYHLRHALMTQDKKFDIRMVYLAIHH
    IVKYRGNFLNSTPVDSFKASKVDFVDQFKKLNELYAAINPEESFKINLAN
    SEDIGHQFLDPSIRKFDKKKQIPKIVPVMMNDKVTDRLNGKIASEIIHAI
    LGYKAKLDVVLQCTPVDSKPWALKFDDEDIDAKLEKILPEMDENQQSIVA
    ILQNLYSQVTLNQIVPNGMSLSESMIEKYNDHHDHLKLYKKLIDQLADPK
    KKAVLKKAYSQYVGDDGKVIEQAEFWSSVKKNLDDSELSKQIMDLIDAEK
    FMPKQRTSQNGVIPHQLHQRELDEIIEHQSKYYPWLVEINPNKHDLHLAK
    YKIEQLVAFRVPYYVGPMITPKDQAESAETVFSWMERKGTETGQITPWNF
    DEKVDRKASANRFIKRMTTKDTYLIGEDVLPDESLLYEKFKVLNELNMVR
    VNGKLLKVADKQAIFQDLFENYKHVSVKKLQNYIKAKTGLPSDPEISGLS
    DPEHFNNSLGTYNDFKKLFGSKVDEPDLQDDFEKIVEWSTVFEDKKILRE
    KLNEITWLSDQQKDVLESSRYQGWGRLSKKLLTGIVNDQGERIIDKLWNT
    NKNFMQIQSDDDFAKRIHEANADQMQAVDVEDVLADAYTSPQNKKAIRQV
    VKVVDDIQKAMGGVAPKYISIEFTRSEDRNPRRTISRQRQLENTLKDTAK
    SLAKSINPELLSELDNAAKSKKGLTDRLYLYFTQLGKDIYTGEPINIDEL
    NKYDIDHILPQAFIKDNSLDNRVLVLTAVNNGKSDNVPLRMFGAKMGHFW
    KQLAEAGLISKRKLKNLQTDPDTISKYAMHGFIRRQLVETSQVIKLVANI
    LGDKYRNDDTKIIEITARMNHQMRDEFGFIKNREINDYHHAFDAYLTAFL
    GRYLYHRYIKLRPYFVYGDFKKFREDKVTMRNFNFLHDLTDDTQEKIADA
    ETGEVIWDRENSIQQLKDVYHYKFMLISHEVYTLRGAMFNQTVYPASDAG
    KRKLIPVKADRPVNVYGGYSGSADAYMAIVRIHNKKGDKYRVVGVPMRAL
    DRLDAAKNVSDADFDRALKDVLAPQLTKTKKSRKTGEITQVIEDFEIVLG
    KVMYRQLMIDGDKKFMLGSSTYQYNAKQLVLSDQSVKTLASKGRLDPLQE
    SMDYNNVYTEILDKVNQYFSLYDMNKFRHKLNLGFSKFISFPNHNVLDGN
    TKVSSGKREILQEILNGLHANPTFGNLKDVGITTPFGQLQQPNGILLSDE
    TKIRYQSPTGLFERTVSLKDL
  • In some embodiments the Cas9 protein can be Listeria innocua Cas9 and may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 165)
    MKKPYTIGLDIGTNSVGWAVLTDQYDLVKRKMKIAGDSEKKQIKKNFWGV
    RLFDEGQTAADRRMARTARRRIERRRNRISYLQGIFAEEMSKTDANFFCR
    LSDSFYVDNEKRNSRHPFFATIEEEVEYHKNYPTIYHLREELVNSSEKAD
    LRLVYLALAHIIKYRGNFLIEGALDTQNTSVDGIYKQFIQTYNQVFASGI
    EDGSLKKLEDNKDVAKILVEKVTRKEKLERILKLYPGEKSAGMFAQFISL
    IVGSKGNFQKPFDLIEKSDIECAKDSYEEDLESLLALIGDEYAELFVAAK
    NAYSAVVLSSIITVAETETNAKLSASMIERFDTHEEDLGELKAFIKLHLP
    KHYEEIFSNTEKHGYAGYIDGKTKQADFYKYMKMTLENIEGADYFIAKIE
    KENFLRKQRTFDNGAIPHQLHLEELEAILHQQAKYYPFLKENYDKIKSLV
    TFRIPYFVGPLANGQSEFAWLTRKADGEIRPWNIEEKVDFGKSAVDFIEK
    MTNKDTYLPKENVLPKHSLCYQKYLVYNELTKVRYINDQGKTSYFSGQEK
    EQIFNDLFKQKRKVKKKDLELFLRNMSHVESPTIEGLEDSFNSSYSTYHD
    LLKVGIKQEILDNPVNIEMLENIVKILTVFEDKRMIKEQLQQFSDVLDGV
    VLKKLERRHYTGWGRLSAKLLMGIRDKQSHLTILDYLMNDDGLNRNLMQL
    INDSNLSFKSIIEKEQVTTADKDIQSIVADLAGSPAIKKGILQSLKIVDE
    LVSVMGYPPQTIVVEMARENQTTGKGKNNSRPRYKSLEKAIKEFGSQILK
    EHPTDNQELRNNRLYLYYLQNGKDMYTGQDLDIHNLSNYDIDHIVPQSFI
    TDNSIDNLVLTSSAGNREKGDDVPPLEIVRKRKVFWEKLYQGNLMSKRKF
    DYLTKAERGGLTEADKARFIHRQLVETRQITKNVANILHQRFNYEKDDHG
    NTMKQVRIVTLKSALVSQFRKQFQLYKVRDVNDYHHAHDAYLNGVVANTL
    LKVYPQLEPEFVYGDYHQFDWFKANKATAKKQFYTNIMLFFAQKDRIIDE
    NGEILWDKKYLDTVKKVMSYRQMNIVKKTEIQKGEFSKATIKPKGNSSKL
    IPRKTNWDPMKYGGLDSPNMAYAVVIEYAKGKNKLVFEKKIIRVTIMERK
    AFEKDEKAFLEEQGYRQPKVLAKLPKYTLYECEEGRRRMLASANEAQKGN
    QQVLPNHLVTLLHHAANCEVSDGKSLDYIESNREMFAELLAHVSEFAKRY
    TLAEANLNKINQLFEQNKEGDIKAIAQSFVDLMAFNAMGAPASFKFFETT
    IERKRYNNLKELLNSTIIYQSITGLYESRKRLDD
  • In some embodiments the Cas9 protein can be L. pneumophilia Cas9 and may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 166)
    MESSQILSPIGIDLGGKFTGVCLSHLEAFAELPNHANTKYSVILIDHNNF
    QLSQAQRRATRHRVRNKKRNQFVKRVALQLFQHILSRDLNAKEETALCHY
    LNNRGYTYVDTDLDEYIKDETTINLLKELLPSESEHNFIDWFLQKMQSSE
    FRKILVSKVEEKKDDKELKNAVKNIKNFITGFEKNSVEGHRHRKVYFENI
    KSDITKDNQLDSIKKKIPSVCLSNLLGHLSNLQWKNLHRYLAKNPKQFDE
    QTFGNEFLRMLKNFRHLKGSQESLAVRNLIQQLEQSQDYISILEKTPPEI
    TIPPYEARTNTGMEKDQSLLLNPEKLNNLYPNWRNLIPGIIDAHPFLEKD
    LEHTKLRDRKRIISPSKQDEKRDSYILQRYLDLNKKIDKFKIKKQLSFLG
    QGKQLPANLIETQKEMETHFNSSLVSVLIQIASAYNKEREDAAQGIWFDN
    AFSLCELSNINPPRKQKILPLLVGAILSEDFINNKDKWAKFKIFWNTHKI
    GRTSLKSKCKEIEEARKNSGNAFKIDYEEALNHPEHSNNKALIKIIQTIP
    DIIQAIQSHLGHNDSQALIYHNPFSLSQLYTILETKRDGFHKNCVAVTCE
    NYWRSQKTEIDPEISYASRLPADSVRPFDGVLARMMQRLAYEIAMAKWEQ
    IKHIPDNSSLLIPIYLEQNRFEFEESFKKIKGSSSDKTLEQAIEKQNIQW
    EEKFQRIINASMNICPYKGASIGGQGEIDHIYPRSLSKKHFGVIFNSEVN
    LIYCSSQGNREKKEEHYLLEHLSPLYLKHQFGTDNVSDIKNFISQNVANI
    KKYISFHLLTPEQQKAARHALFLDYDDEAFKTITKFLMSQQKARVNGTQK
    FLGKQIMEFLSTLADSKQLQLEFSIKQITAEEVHDHRELLSKQEPKLVKS
    RQQSFPSHAIDATLTMSIGLKEFPQFSQELDNSWFINHLMPDEVHLNPVR
    SKEKYNKPNISSTPLFKDSLYAERFIPVWVKGETFAIGFSEKDLFEIKPS
    NKEKLFTLLKTYSTKNPGESLQELQAKSKAKWLYFPINKTLALEFLHHYF
    HKEIVTPDDTTVCHFINSLRYYTKKESITVKILKEPMPVLSVKFESSKKN
    VLGSFKHTIALPATKDWERLFNHPNFLALKANPAPNPKEFNEFIRKYFLS
    DNNPNSDIPNNGHNIKPQKHKAVRKVFSLPVIPGNAGTMMRIRRKDNKGQ
    PLYQLQTIDDTPSMGIQINEDRLVKQEVLMDAYKTRNLSTIDGINNSEGQ
    AYATFDNWLTLPVSTFKPEIIKLEMKPHSKTRRYIRITQSLADFIKTIDE
    ALMIKPSDSIDDPLNMPNEIVCKNKLFGNELKPRDGKMKIVSTGKIVTYE
    FESDSTPQWIQTLYVTQLKKQP
  • In some embodiments the Cas9 protein can be N. lactamica Cas9 and may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 167)
    MAAFKPNPMNYILGLDIGIASVGWAMVEVDEEENPIRLIDLGVRVFERAE
    VPKTGDSLAMARRLARSVRRLTRRRAHRLLRARRLLKREGVLQDADFDEN
    GLVKSLPNTPWQLRAAALDRKLTCLEWSAVLLHLVKHRGYLSQRKNEGET
    ADKELGALLKGVADNAHALQTGDFRTPAELALNKFEKESGHIRNQRGDYS
    HTFSRKDLQAELNLLFEKQKEFGNPHVSDGLKEDIETLLMAQRPALSGDA
    VQKMLGHCTFEPAEPKAAKNTYTAERFIWLTKLNNLRILEQGSERPLTDT
    ERATLMDEPYRKSKLTYAQARKLLGLEDTAFFKGLRYGKDNAEASTLMEM
    KAYHAISRALEKEGLKDKKSPLNLSTELQDEIGTAFSLFKTDKDITGRLK
    DRVQPEILEALLKHISFDKFVQISLKALRRIVPLMEQGKRYDEACAEIYG
    DHYCKKNAEEKIYLPPIPADEIRNPVVLRALSQARKVINCVVRRYGSPAR
    IHIETAREVGKSFKDRKEIEKRQEENRKDREKAAAKFREYFPNFVGEPKS
    KDILKLRLYEQQHGKCLYSGKEINLVRLNEKGYVEIDHALPFSRTWDDSF
    NNKVLVLGSENQNKGNQTPYEYFNGKDNSREWQEFKARVETSRFPRSKKQ
    RILLQKFDEEGFKERNLNDTRYVNRFLCQFVADHILLTGKGKRRVFASNG
    QITNLLRGFWGLRKVTENDRHHALDAVVVACSTVAMQQKITRFVRYKEMN
    AFDGKTIDKETGEVLHQKAHFPQPWEFFAQEVMIRVFGKPDGKPEFEEAD
    TPEKLRTLLAEKLSSRPEAVHEYVTPLFVSRAPNRKMSGQGHMETVKSAK
    RLDEGISVLRVPLTQLKLKGLEKMVNREREPKLYDALKAQLETHKDDPAK
    AFAEPFYKYDKAGSRTQQVKAVRIEQVQKTGVWVRNHNGIADNATMVRVD
    VFEKGGKYYLVPIYSWQVAKGILPDRAVVAFKDEEDWTVMDDSFEFRFVL
    YANDLIKLTAKKNEFLGYFVSLNRATGAIDIRTHDTDSTKGKNGIFQSVG
    VKTALSFQKNQIDELGKEIRPCRLKKRPPVR
  • In some embodiments the Cas9 protein can be N. meningitides Cas9 and may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 168)
    MAAFKPNPINYILGLDIGIASVGWAMVEIDEDENPICLIDLGVRVFERAE
    VPKTGDSLAMARRLARSVRRLTRRRAHRLLRARRLLKREGVLQAADFDEN
    GLIKSLPNTPWQLRAAALDRKLTPLEWSAVLLHLIKHRGYLSQRKNEGET
    ADKELGALLKGVADNAHALQTGDFRTPAELALNKFEKESGHIRNQRGDYS
    HTFSRKDLQAELILLFEKQKEFGNPHVSGGLKEGIETLLMTQRPALSGDA
    VQKMLGHCTFEPAEPKAAKNTYTAERFIWLTKLNNLRILEQGSERPLTDT
    ERATLMDEPYRKSKLTYAQARKLLGLEDTAFFKGLRYGKDNAEASTLMEM
    KAYHAISRALEKEGLKDKKSPLNLSPELQDEIGTAFSLFKTDEDITGRLK
    DRIQPEILEALLKHISFDKFVQISLKALRRIVPLMEQGKRYDEACAEIYG
    DHYGKKNTEEKIYLPPIPADEIRNPVVLRALSQARKVINGVVRRYGSPAR
    IHIETAREVGKSFKDRKEIEKRQEENRKDREKAAAKFREYFPNFVGEPKS
    KDILKLRLYEQQHGKCLYSGKEINLGRLNEKGYVEIDHALPFSRTWDDSF
    NNKVLVLGSENQNKGNQTPYEYFNGKDNSREWQEFKARVETSRFPRSKKQ
    RILLQKFDEDGFKERNLNDTRYVNRFLCQFVADRMRLTGKGKKRVFASNG
    QITNLLRGFWGLRKVRAENDRHHALDAVVVACSTVAMQQKITRFVRYKEM
    NAFDGKTIDKETGEVLHQKTHFPQPWEFFAQEVMIRVFGKPDGKPEFEEA
    DTPEKLRTLLAEKLSSRPEAVHEYVTPLFVSRAPNRKMSGQGHMETVKSA
    KRLDEGVSVLRVPLTQLKLKDLEKMVNREREPKLYEALKARLEAHKDDPA
    KAFAEPFYKYDKAGNRTQQVKAVRVEQVQKTGVWVRNHNGIADNATMVRV
    DVFEKGDKYYLVPIYSWQVAKGILPDRAVVQGKDEEDWQLIDDSFNFKFS
    LHPNDLVEVITKKARMFGYFASCHRGTGNINIRIHDLDHKIGKNGILEGI
    GVKTALSFQKYQIDELGKEIRPCRLKKRPPVR
  • In some embodiments the Cas9 protein can be B. longum Cas9 and may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 169)
    MLSRQLLGASHLARPVSYSYNVQDNDVHCSYGERCFMRGKRYRIGIDVGL
    NSVGLAAVEVSDENSPVRLLNAQSVIHDGGVDPQKNKEAITRKNMSGVAR
    RTRRMRRRKRERLHKLDMLLGKFGYPVIEPESLDKPFEEWHVRAELATRY
    IEDDELRRESISIALRHMARHRGWRNPYRQVDSLISDNPYSKQYGELKEK
    AKAYNDDATAAEEESTPAQLVVAMLDAGYAEAPRLRWRTGSKKPDAEGYL
    PVRLMQEDNANELKQIFRVQRVPADEWKPLFRSVFYAVSPKGSAEQRVGQ
    DPLAPEQARALKASLAFQEYRIANVITNLRIKDASAELRKLTVDEKQSIY
    DQLVSPSSEDITWSDLCDFLGFKRSQLKGVGSLTEDGEERISSRPPRLTS
    VQRIYESDNKIRKPLVAWWKSASDNEHEAMIRLLSNTVDIDKVREDVAYA
    SAIEFIDGLDDDALTKLDSVDLPSGRAAYSVETLQKLTRQMLTTDDDLHE
    ARKTLFNVTDSWRPPADPIGEPLGNPSVDRVLKNVNRYLMNCQQRWGNPV
    SVNIEHVRSSFSSVAFARKDKREYEKNNEKRSIFRSSLSEQLRADEQMEK
    VRESDLRRLEAIQRQNGQCLYCGRTITFRTCEMDHIVPRKGVGSTNTRTN
    FAAVCAECNRMKSNTPFAIWARSEDAQTRGVSLAEAKKRVTMFTFNPKSY
    APREVKAFKQAVIARLQQTEDDAAIDNRSIESVAWMADELHRRIDWYFNA
    KQYVNSASIDDAEAETMKTTVSVFQGRVTASARRAAGIEGKIHFIGQQSK
    TRLDRRHHAVDASVIAMMNTAAAQTLMERESLRESQRLIGLMPGERSWKE
    YPYEGTSRYESFHLWLDNMDVLLELLNDALDNDRIAVMQSQRYVLGNSIA
    HDATIHPLEKVPLGSAMSADLIRRASTPALWCALTRLPDYDEKEGLPEDS
    HREIRVHDTRYSADDEMGFFASQAAQIAVQEGSADIGSAIHHARVYRCWK
    TNAKGVRKYFYGMIRVFQTDLLRACHDDLFTVPLPPQSISMRYGEPRVVQ
    ALQSGNAQYLGSLVVGDEIEMDFSSLDVDGQIGEYLQFFSQFSGGNLAWK
    HWVVDGFFNQTQLRIRPRYLAAEGLAKAFSDDVVPDGVQKIVTKQGWLPP
    VNTASKTAVRIVRRNAFGEPRLSSAHHMPCSWQWRHE
  • In some embodiments the Cas9 protein can be A. muciniphila Cas9 and may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 170)
    MSRSLTFSFDIGYASIGWAVIASASHDDADPSVCGCGTVLFPKDDCQAFK
    RREYRRLRRNIRSRRVRIERIGRLLVQAQIITPEMKETSGHPAPFYLASE
    ALKGHRTLAPIELWHVLRWYAHNRGYDNNASWSNSLSEDGGNGEDIERVK
    HAQDLMDKHGTATMAETICRELKLEEGKADAPMEVSTPAYKNLNTAFPRL
    IVEKEVRRILELSAPLIPGLTAEIIELIAQHHPLTTEQRGVLLQHGIKLA
    RRYRGSLLFGQLIPRFDNRIISRCPVTWAQVYEAELKKGNSEQSARERAE
    KLSKVPTANCPEFYEYRMARILCNIRADGEPLSAEIRRELMNQARQEGKL
    TKASLEKAISSRLGKEIETNVSNYFTLHPDSEEALYLNPAVEVLQRSGIG
    QILSPSVYRIAANRLRRGKSVTPNYLLNLLKSRGESGEALEKKIEKESKK
    KEADYADTPLKPKYATGRAPYARTVLKKVVEEILDGEDPTRPARGEAHPD
    GELKAHDGCLYCLLDTDSSVNQHQKERRLDTMTNNHLVRHRMLILDRLLK
    DLIQDFADGQKDRISRVCVEVGKELTTFSAMDSKKIQRELTLRQKSHTDA
    VNRLKRKLPGKALSANLIRKCRIAMDMNWTCPFTGATYGDHELENLELEH
    IVPHSFRQSNALSSLVLTWPGVNRMKGQRTGYDFVEQEQENPVPDKPNLH
    ICSLNNYRELVEKLDDKKGHEDDRRRKKKRKALLMVRGLSHKHQSQNHEA
    MKEIGMIEGMMTQSSHLMKLACKSIKTSLPDAHIDMIPGAVTAEVRKAWD
    VFGVFKELCPEAADPDSGKILKENLRSLTHLHHALDACVLGLIPYIIPAH
    HNGLLRRVLAMRRIPEKLIPQVRPVANQRHYVLNDDGRMMLRDLSASLKE
    NIREQLMEQRVIQHVPADMGGALLKETMQRVLSVDGSGEDAMVSLSKKKD
    GKKEKNQVKASKLVGVFPEGPSKLKALKAAIEIDGNYGVALDPKPVVIRH
    IKVFKRIMALKEQNGGKPVRILKKGMLIHLTSSKDPKHAGVVVRIESIQD
    SKGGVKLDLQRAHCAVPKNKTHECNWREVDLISLLKKYQMKRYPTSYTGT
    PR
  • In some embodiments the Cas9 protein can be O. laneus Cas9 and may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 171)
    METTLGIDLGTNSIGLALVDQEEHQILYSGVRIFPEGINKDTIGLGEKEE
    SRNATRRAKRQMRRQYFRKKLRKAKLLELLIAYDMCPLKPEDVRRWKNWD
    KQQKSTVRQFPDTPAFREWLKQNPYELRKQAVTEDVTRPELGRILYQMIQ
    RRGFLSSRKGKEEGKIFTGKDRMVGIDETRKNLQKQTLGAYLYDIAPKNG
    EKYRFRTERVRARYTLRDMYIREFEIIWQRQAGHLGLAHEQATRKKNIFL
    EGSATNVRNSKLITHLQAKYGRGHVLIEDTRITVTFQLPLKEVLGGKIEI
    EEEQLKFKSNESVLFWQRPLRSQKSLLSKCVFEGRNFYDPVHQKWIIAGP
    TPAPLSHPEFEEFRAYQFINNIIYGKNEHLTAIQREAVFELMCTESKDFN
    FEKIPKHLKLFEKFNFDDTTKVPACTTISQLRKLFPHPVWEEKREEIWHC
    FYFYDDNTLLFEKLQKDYALQTNDLEKIKKIRLSESYGNVSLKAIRRINP
    YLKKGYAYSTAVLLGGIRNSFGKRFEYFKEYEPEIEKAVCRILKEKNAEG
    EVIRKIKDYLVHNRFGFAKNDRAFQKLYHHSQAITTQAQKERLPETGNLR
    NPIVQQGLNELRRTVNKLLATCREKYGPSFKFDHIHVEMGRELRSSKTER
    EKQSRQIRENEKKNEAAKVKLAEYGLKAYRDNIQKYLLYKEIEEKGGTVC
    CPYTGKTLNISHTLGSDNSVQIEHIIPYSISLDDSLANKTLCDATFNREK
    GELTPYDFYQKDPSPEKWGASSWEEIEDRAFRLLPYAKAQRFIRRKPQES
    NEFISRQLNDTRYISKKAVEYLSAICSDVKAFPGQLTAELRHLWGLNNIL
    QSAPDITFPLPVSATENHREYYVITNEQNEVIRLFPKQGETPRIEKGELL
    LTGEVERKVFRCKGMQEFQTDVSDGKYWRRIKLSSSVTWSPLFAPKPISA
    DGQIVLKGRIEKGVFVCNQLKQKLKTGLPDGSYWISLPVISQTFKEGESV
    NNSKLTSQQVQLFGRVREGIFRCHNYQCPASGADGNFWCTLDTDTAQPAF
    TPIKNAPPGVGGGQIILTGDVDDKGIFHADDDLHYELPASLPKGKYYGIF
    TVESCDPTLIPIELSAPKTSKGENLIEGNIWVDEHTGEVRFDPKKNREDQ
    RHHAIDAIVIALSSQSLFQRLSTYNARRENKKRGLDS1EHFPSPWPGFAQ
    DVRQSVVPLLVSYKQNPKTLCKISKTLYKDGKKIHSCGNAVRGQLHKETV
    YGQRTAPGA1EKSYHIRKDIRELKTSKHIGKVVDITIRQMLLKHLQENYH
    IDITQEFNIPSNAFFKEGVYRIFLPNKHGEPVPIKKIRMKEELGNAERLK
    DNINQYVNPRNNHHVMIYQDADGNLKEEIVSFWSVIERQNQGQPIYQLPR
    EGRNIVSILQINDTFLIGLKEEEPEVYRNDLSTLSKHLYRVQKLSGMYYT
    FRHHLASTLNNEREEFRIQSLEAWKRANPVKVQIDEIGRITFLNGPLC.
  • In some embodiments of the compositions of the disclosure, the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a CRISPR Cas protein or portion thereof. In some embodiments, the CRISPR Cas protein comprises a Type V CRISPR Cas protein. In some embodiments, the Type V CRISPR Cas protein comprises a Cpf1 protein. Exemplary Cpf1 proteins of the disclosure may be isolated or derived from any species, including, but not limited to, a bacteria or an archaea. Exemplary Cpf1 proteins of the disclosure may be isolated or derived from any species, including, but not limited to, Francisella tularensis subsp. novicida, Acidaminococcus sp. BV3L6 and Lachnospiraceae bacterium sp. ND2006. Exemplary Cpf1 proteins of the disclosure may be nuclease inactivated.
  • Exemplary wild type Francisella tularensis subsp. Novicida Cpf1 (FnCpf1) proteins of the disclosure may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 172)
       1 MSIYQEFVNK YSLSKTLRFE LIPQGKTLEN IKARGLILDD EKRAKDYKKA KQIIDKYHQF
      61 FIEEILSSVC ISEDLLQNYS DVYFKLKKSD DDNLQKDFKS AKDTIKKQIS EYIKDSEKFK
     121 NLFNQNLIDA KKGQESDLIL WLKQSKDNGI ELFKANSDIT DIDEALEIIK SFKGWTTYFK
     181 GFHENRKNVY SSNDIPTSII YRIVDDNLPK FLENKAKYES LKDKAPEAIN YEQIKKDLAE
     241 ELTFDIDYKT SEVNQRVFSL DEVFEIANFN NYLNQSGITK FNTIIGGKFV NGENTKRKGI
     301 NEYINLYSQQ INDKTLKKYK MSVLFKQILS DTESKSFVID KLEDDSDVVT TMQSFYEQIA
     361 AFKTVEEKSI KETLSLLFDD LKAQKLDLSK IYFKNDKSLT DLSQQVFDDY SVIGTAVLEY
     421 ITQQIAPKNL DNPSKKEQEL IAKKTEKAKY LSLETIKLAL EEFNKHRDID KQCRFEEILA
     481 NFAAIPMIFD EIAQNKDNLA QISIKYQNQG KKDLLQASAE DDVKAIKDLL DQTNNLLHKL
     541 KIFHISQSED KANILDKDEH FYLVFEECYF ELANIVPLYN KIRNYITQKP YSDEKFKLNF
     601 ENSTLANGWD KNKEPDNTAI LFIKDDKYYL GVMNKKNNKI FDDKAIKENK GEGYKKIVYK
     661 LLPGANKMLP KVFFSAKSIK FYNPSEDILR IRNHSTHTKN GSPQKGYEKF EFNIEDCRKF
     721 IDFYKQSISK HPEWKDFGFR FSDTQRYNSI DEFYREVENQ GYKLTFENIS ESYIDSVVNQ
     781 GKLYLFQIYN KDFSAYSKGR PNLHTLYWKA LFDERNLQDV VYKLNGEAEL FYRKQSIPKK
     841 ITHPAKEAIA NKNKDNPKKE SVFEYDLIKD KRFTEDKFFF HCPITINFKS SGANKFNDEI
     901 NLLLKEKAND VHILSIDRGE RHLAYYTLVD GKGNIIKQDT FNIIGNDRMK TNYHDKLAAI
     961 EKDRDSARKD WKKINNIKEM KEGYLSQVVH EIAKLVIEYN AIVVFEDLNF GFKRGRFKVE
    1021 KQVYQKLEKM LIEKLNYLVF KDNEFDKTGG VLRAYQLTAP FETFKKMGKQ TGIIYYVPAG
    1081 FTSKICPVTG FVNQLYPKYE SVSKSQEFFS KFDKICYNLD KGYFEFSFDY KNFGDKAAKG
    1141 KWTIASFGSR LINFRNSDKN HNWDTREVYP TKELEKLLKD YSIEYGHGEC IKAAICGESD
    1201 KKFFAKLTSV LNTILQMRNS KTGTELDYLI SPVADVNGNF FDSRQAPKNM PQDADANGAY
    1261 HIGLKGLMLL GRIKNNQEGK KLNLVIKNEE YFEFVQNRNN.
  • Exemplary wild type Lachnospiraceae bacterium sp. ND2006 Cpf1 (LbCpf1) proteins of the disclosure may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 173)
       1 AASKLEKFTN CYSLSKTLRF KAIPVGKTQE NIDNKRLLVE DEKRAEDYKG VKKLLDRYYL
      61 SFINDVLHSI KLKNLNNYIS LFRKKTRTEK ENKELENLEI NLRKEIAKAF KGAAGYKSLF
     121 KKDIIETILP EAADDKDEIA LVNSENGETT AFTGFFDNRE NMFSEEAKST SIAFRCINEN
     181 LTRYISNMDI FEKVDAIFDK HEVQEIKEKI LNSDYDVEDF FEGEFFNFVL TQEGIDVYNA
     241 IIGGFVTESG EKIKGLNEYI NLYNAKTKQA LPKFKPLYKQ VLSDRESLSF YGEGYTSDEE
     301 VLEVFRNTLN KNSEIFSSIK KLEKLFKNFD EYSSAGIFVK NGPAISTISK DIFGEWNLIR
     361 DKWNAEYDDI HLKKKAVVTE KYEDDRRKSF KKIGSFSLEQ LQEYADADLS VVEKLKEIII
     421 QKVDEIYKVY GSSEKLFDAD FVLEKSLKKN DAVVAIMKDL LDSVKSFENY IKAFFGEGKE
     481 TNRDESFYGD FVLAYDILLK VDHIYDAIRN YVTQKPYSKD KFKLYFQNPQ FMGGWDKDKE
     541 TDYRATILRY GSKYYLAIMD KKYAKCLQKI DKDDVNGNYE KINYKLLPGP NKMLPKVFFS
     601 KKWMAYYNPS EDIQKIYKNG TFKKGDMFNL NDCHKLIDFF KDSISRYPKW SNAYDFNFSE
     661 TEKYKDIAGF YREVEEQGYK VSFESASKKE VDKLVEEGKL YMFQIYNKDF SDKSHGTPNL
     721 HTMYFKLLFD ENNHGQIRLS GGAELFMRRA SLKKEELVVH PANSPIANKN PDNPKKTTTL
     781 SYDVYKDKRF SEDQYELHIP IAINKCPKNI FKINTEVRVL LKHDDNPYVI GIDRGERNLL
     841 YIVVVDGKGN IVEQYSLNEI INNFNGIRIK TDYHSLLDKK EKERFEARQN WTSIENIKEL
     901 KAGYISQVVH KICELVEKYD AVIALEDLNS GFKNSRVKVE KQVYQKFEKM LIDKLNYMVD
     961 KKSNPCATGG ALKGYQITNK FESFKSMSTQ NGFIFYIPAW LTSKIDPSTG FVNLLKTKYT
    1021 SIADSKKFIS SFDRIMYVPE EDLFEFALDY KNFSRTDADY IKKWKLYSYG NRIRIFAAAK
    1081 KNNVFAWEEV CLTSAYKELF NKYGINYQQG DIRALLCEQS DKAFYSSFMA LMSLMLQMRN
    1141 SITGRTDVDF LISPVKNSDG IFYDSRNYEA QENAILPKNA DANGAYNIAR KVLWAIGQFK
    1201 KAEDEKLDKV KIAISNKEWL EYAQTSVK.
  • Exemplary wild type Acidaminococcus sp. BV3L6 Cpf1 (AsCpf1) proteins of the disclosure may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 174)
       1 MTQFEGFTNL YQVSKTLRFE LIPQGKTLKH IQEQGFIEED KARNDHYKEL KPIIDRIYKT
      61 YADQCLQLVQ LDWENLSAAI DSYRKEKTEE TRNALIEEQA TYRNAIHDYF IGRIDNLIDA
     121 INKRHAEIYK GLFKAELENG KVLKQLGTVT TTEHENALLR SFDKFTTYFS GFYENRKNVF
     181 SAEDISTAIP HRIVQDNFPK FKENCHIFTR LITAVPSLRE HFENVKKAIG IFVSTSIEEV
     241 FSFPFYNQLL TQTQIDLYNQ LLGGISREAG TEKIKGLNEV LNLAIQKNDE TAHIIASLPH
     301 RFIPLFKQIL SDRNTLSFIL EEFKSDEEVI QSFCKYKTLL RNENVLETAE ALFNELNSID
     361 LTHIFISHKK LETISSALCD HWDTLRNALY ERRISELTGK ITKSAKEKVQ RSLKHEDINL
     421 QEIISAAGKE LSEAFKQKTS EILSHAHAAL DQPLPTTLKK QEEKEILKSQ LDSLLGLYHL
     481 LDWFAVDESN EVDPEFSARL TGIKLEMEPS LSFYNKARNY ATKKPYSVEK FKLNFQMPTL
     541 ASGWDVNKEK NNGAILFVKN GLYYLGIMPK QKGRYKALSF EPTEKTSEGF DKMYYDYFPD
     601 AAKMIPKCST QLKAVTAHFQ THTTPILLSN NFIEPLEITK EIYDLNNPEK EPKKFQTAYA
     661 KKTGDQKGYR EALCKWIDFT RDFLSKYTKT TSIDLSSLRP SSQYKDLGEY YAELNPLLYH
     721 ISFQRIAEKE IMDAVETGKL YLFQIYNKDF AKGHHGKPNL HTLYWTGLFS PENLAKTSIK
     781 LNGQAELFYR PKSRMKRMAH RLGEKMLNKK LKDQKTPIPD TLYQELYDYV NHRLSHDLSD
     841 EARALLPNVI TKEVSHEIIK DRRFTSDKFF FHVPITLNYQ AANSPSKFNQ RVNAYLKEHP
     901 ETPIIGIDRG ERNLIYITVI DSTGKILEQR SLNTIQQFDY QKKLDNREKE RVAARQAWSV
     961 VGTIKDLKQG YLSQVIHEIV DLMIHYQAVV VLENLNFGFK SKRTGIAEKA VYQQFEKMLI
    1021 DKLNCLVLKD YPAEKVGGVL NPYQLTDQFT SFAKMGTQSG FLFYVPAPYT SKIDPLTGFV
    1081 DPFVWKTIKN HESRKHFLEG FDFLHYDVKT GDFILHFKMN RNLSFQRGLP GFMPAWDIVF
    1141 EKNETQFDAK GTPFIAGKRI VPVIENHRFT GRYRDLYPAN ELIALLEEKG IVFRDGSNIL
    1201 PKLLENDDSH AIDTMVALIR SVLQMRNSNA ATGEDYINSP VRDLNGVCFD SRFQNPEWPM
    1261 DADANGAYHI ALKGQLLLNH LKESKDLKLQ NGISNQDWLA YIQELRN.
  • In some embodiments of the compositions of the disclosure, the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a CRISPR Cas protein. In some embodiments, the CRISPR Cas protein comprises a Type VI CRISPR Cas protein or portion thereof. In some embodiments, the Type VI CRISPR Cas protein comprises a Cas13 protein or portion thereof. Exemplary Cas13 proteins of the disclosure may be isolated or derived from any species, including, but not limited to, a bacteria or an archaea. Exemplary Cas13 proteins of the disclosure may be isolated or derived from any species, including, but not limited to, Leptotrichia wadei, Listeria seeligeri serovar 1/2b (strain ATCC 35967/DSM 20751/CIP 100100/SLCC 3954), Lachnospiraceae bacterium, Clostridium aminophilum DSM 10710, Carnobacterium gallinarum DSM 4847, Paludibacter propionicigenes WB4, Listeria weihenstephanensis FSL R9-0317, Listeria weihenstephanensis FSL R9-0317, bacterium FSL M6-0635 (Listeria newyorkensis), Leptotrichia wadei F0279, Rhodobacter capsulatus SB 1003, Rhodobacter capsulatus R121, Rhodobacter capsulatus DE442 and Corynebacterium ulcerans. Exemplary Cas13 proteins of the disclosure may be DNA nuclease inactivated. Exemplary Cas13 proteins of the disclosure include, but are not limited to, Cas13a, Cas13b, Cas13c, Cas13d and orthologs thereof. Exemplary Cas13b proteins of the disclosure include, but are not limited to, subtypes 1 and 2 referred to herein as Csx27 and Csx28, respectively.
  • Exemplary Cas13a proteins include, but are not limited to:
  • Cas13a
    Cas13a abbre-
    number viation Organism name Accession number Direct Repeat sequence
    Cas13a1 LshCas13a Leptotrichia WP_018451595.1 CCACCCCAATATCGAAGGGGACTAA
    shahii AAC (SEQ ID NO: 175)
    Cas13a2 LwaCas13a Leptotrichia WP_021746774.1 GATTTAGACTACCCCAAAAACGAAG
    wadei GGGACTAAAAC (SEQ ID NO: 176)
    Cas13a3 LseCas13a Listeria WP_012985477.1 GTAAGAGACTACCTCTATATGAAAG
    seeligeri AGGACTAAAAC (SEQ ID NO: 177)
    Cas13a4 LbmCas13a Lachnospiraceae WP_044921188.1 GTATTGAGAAAAGCCAGATATAGTT
    bacterium GGCAATAGAC (SEQ ID NO: 178)
    MA2020
    Cas13a5 LbnCas13a Lachnospiraceae WP_022785443.1 GTTGATGAGAAGAGCCCAAGATAG
    bacterium AGGGCAATAAC (SEQ ID NO: 179)
    NK4A179
    Cas13a6 CamCas13a [Clostridium] WP_031473346.1 GTCTATTGCCCTCTATATCGGGCTGT
    aminophilum TCTCCAAAC (SEQ ID NO: 180)
    DSM 10710
    Cas13a7 CgaCas13a Carnobacterium WP_034560163.1 ATTAAAGACTACCTCTAAATGTAAG
    gallinarum DSM AGGACTATAAC (SEQ ID NO:
    4847 181)
    Cas13a8 Cga2Cas13a Carnobacterium WP_034563842.1 AATATAAACTACCTCTAAATGTAAG
    gallinarum DSM AGGACTATAAC (SEQ ID NO:
    4847 182)
    Cas13a9 Pprcas13a Paludibacter WP_013443710.1 CTTGTGGATTATCCCAAAATTGAAG
    propionicigenes  GGAACTACAAC (SEQ ID NO:
    WB4 183)
    Cas13a10 LweCas13a Listeria WP_036059185.1 GATTTAGAGTACCTCAAAATAGAAG
    weihen- AGGTCTAAAAC (SEQ ID NO:
    stephanensis 184)
    FSL R9-0317
    Cas13a11 LbfCas13a Listeriaceae WP_036091002.1 GATTTAGAGTACCTCAAAACAAAAG
    bacterium FSL AGGACTAAAAC (SEQ ID NO:
    M6-0635 185)
    (Listeria
    newyorkensis)
    Cas13a12 Lwa2cas13a Leptotrichia WP_021746774.1 GATATAGATAACCCCAAAAACGAA
    wadei F0279 GGGATCTAAAAC (SEQ ID NO:
    186)
    Cas13a13 RcsCas13a Rhodobacter WP_013067728.1 GCCTCACATCACCGCCAAGACGACG
    capsulatus SB GCGGACTGAAC (SEQ ID NO: 187)
    1003
    Cas13a14 RcrCas13a Rhodobacter WP_023911507.1 GCCTCACATCACCGCCAAGACGACG
    capsulatus R121 GCGGACTGAAC (SEQ ID NO:
    188)
    Cas13a15 RcdCas13a Rhodobacter WP_023911507.1 GCCTCACATCACCGCCAAGACGACG
    capsulatus GCGGACTGAAC (SEQ ID NO:
    DE442 189)
  • Exemplary wild type Cas13a proteins of the disclosure may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 190)
       1 MGNLFGHKRW YEVRDKKDFK IKRKVKVKRN YDGNKYILNI NENNNKEKID NNKFIRKYIN
      61 YKKNDNILKE FTRKFHAGNI LFKLKGKEGI IRIENNDDFL ETEEVVLYIE AYGKSEKLKA
     121 LGITKKKIID EAIRQGITKD DKKIEIKRQE NEEEIEIDIR DEYTNKTLND CSIILRIIEN
     181 DELETKKSIY EIFKNINMSL YKIIEKIIEN ETEKVFENRY YEEHLREKLL KDDKIDVILT
     241 NFMEIREKIK SNLEILGFVK FYLNVGGDKK KSKNKKMLVE KILNINVDLT VEDIADFVIK
     301 ELEFWNITKR IEKVKKVNNE FLEKRRNRTY IKSYVLLDKH EKFKIERENK KDKIVKFFVE
     361 NIKNNSIKEK IEKILAEFKI DELIKKLEKE LKKGNCDTEI FGIFKKHYKV NFDSKKFSKK
     421 SDEEKELYKI IYRYLKGRIE KILVNEQKVR LKKMEKIEIE KILNESILSE KILKRVKQYT
     481 LEHIMYLGKL RHNDIDMITV NTDDFSRLHA KEELDLELIT FFASTNMELN KIFSRENINN
     541 DENIDFFGGD REKNYVLDKK ILNSKIKIIR DLDFIDNKNN ITNNFIRKFT KIGTNERNRI
     601 LHAISKERDL QGTQDDYNKV INIIQNLKIS DEEVSKALNL DVVFKDKKNI ITKINDIKIS
     661 EENNNDIKYL PSFSKVLPEI LNLYRNNPKN EPFDTIETEK IVLNALIYVN KELYKKLILE
     721 DDLEENESKN IFLQELKKTL GNIDEIDENI IENYYKNAQI SASKGNNKAI KKYQKKVIEC
     781 YIGYLRKNYE ELFDFSDFKM NIQEIKKQIK DINDNKTYER ITVKISDKTI VINDDFEYII
     841 SIFALLNSNA VINKIRNRFF ATSVWLNTSE YQNIIDILDE IMQLNTLRNE CITENWNLNL
     901 EEFIQKMKEI EKDFDDFKIQ TKKEIFNNYY EDIKNNILTE FKDDINGCDV LEKKLEKIVI
     961 FDDETKFEID KKSNILQDEQ RKLSNINKKD LKKKVDQYIK DKDQEIKSKI LCRIIFNSDF
    1021 LKKYKKEIDN LIEDMESENE NKFQEIYYPK ERKNELYIYK KNLFLNIGNP NFDKIYGLIS
    1081 NDIKMADAKF LFNIDGKNIR KNKISEIDAI LKNLNDKLNG YSKEYKEKYI KKLKENDDFF
    1141 AKNIQNKNYK SFEKDYNRVS EYKKIRDLVE FNYLNKIESY LIDINWKLAI QMARFERDMH
    1201 YIVNGLRELG IIKLSGYNTG ISRAYPKRNG SDGFYTTTAY YKFFDEESYK KFEKICYGFG
    1261 IDLSENSEIN KPENESIRNY ISHFYIVRNP FADYSIAEQI DRVSNLLSYS TRYNNSTYAS
    1321 VFEVFKKDVN LDYDELKKKF KLIGNNDILE RLMKPKKVSV LELESYNSDY IKNLIIELLT
    1381 KIENINDIL.
  • Exemplary Cas13b proteins include, but are not limited to:
  • Species Cas13b Accession Cas13b Size (aa)
    Paludibacter propionicigenes WB4 WP_013446107.1 1155
    Prevotella sp. P5-60 WP_044074780.1 1091
    Prevotella sp. P4-76 WP_044072147.1 1091
    Prevotella sp. P5-125 WP_044065294.1 1091
    Prevotella sp. P5-119 WP_042518169.1 1091
    Capnocytophaga canimorsus Cc5 WP_013997271.1 1200
    Phaeodactylibacter xiamenensis WP_044218239.1 1132
    Porphyromonas gingivalis W83 WP_005873511.1 1136
    Porphyromonas gingivalis F0570 WP_021665475.1 1136
    Porphyromonas gingivalis ATCC 33277 WP_012458151.1 1136
    Porphyromonas gingivalis F0185 ERJ81987.1 1136
    Porphyromonas gingivalis F0185 WP_021677657.1 1136
    Porphyromonas gingivalis SJD2 WP_023846767.1 1136
    Porphyromonas gingivalis F0568 ERJ65637.1 1136
    Porphyromonas gingivalis W4087 ERJ87335.1 1136
    Porphyromonas gingivalis W4087 WP_021680012.1 1136
    Porphyromonas gingivalis F0568 WP_021663197.1 1136
    Porphyromonas gingivalis WP_061156637.1 1136
    Porphyromonas gulae WP_039445055.1 1136
    Bacteroides pyogenes F0041 ERI81700.1 1116
    Bacteroides pyogenes JCM 10003 WP_034542281.1 1116
    Alistipes sp. ZOR0009 WP_047447901.1 954
    Flavobacterium branchiophilum FL-15 WP_014084666.1 1151
    Prevotella sp. MA2016 WP_036929175.1 1323
    Myroides odoratimimus CCUG 10230 EHO06562.1 1160
    Myroides odoratimimus CCUG 3837 EKB06014.1 1158
    Myroides odoratimimus CCUG 3837 WP_006265509.1 1158
    Myroides odoratimimus CCUG 12901 WP_006261414.1 1158
    Myroides odoratimimus CCUG 12901 EHO08761.1 1158
    Myroides odoratimimus (NZ CP013690.1) WP_058700060.1 1160
    Bergeyella zoohelcum ATCC 43767 EKB54193.1 1225
    Capnocytophaga cynodegmi WP_041989581.1 1219
    Bergeyella zoohelcum ATCC 43767 WP_002664492.1 1225
    Flavobacterium sp. 316 WP_045968377.1 1156
    Psychroflexus torquis ATCC 700755 WP_015024765.1 1146
    Flavobacterium columnare ATCC 49512 WP_014165541.1 1180
    Flavobacterium columnare WP_060381855.1 1214
    Flavobacterium columnare WP_063744070.1 1214
    Flavobacterium columnare WP_065213424.1 1215
    Chryseobacterium sp. YR477 WP_047431796.1 1146
    Riemerella anatipestifer ATCC 11845 = DSM 15868 WP_004919755.1 1096
    Riemerella anatipestifer RA-CH-2 WP_015345620.1 949
    Riemerella anatipestifer WP_049354263.1 949
    Riemerella anatipestifer WP_061710138.1 951
    Riemerella anatipestifer WP_064970887.1 1096
    Prevotella saccharolytica F0055 EKY00089.1 1151
    Prevotella saccharolytica JCM 17484 WP_051522484.1 1152
    Prevotella buccae ATCC 33574 EFU31981.1 1128
    Prevotella buccae ATCC 33574 WP_004343973.1 1128
    Prevotella buccae D17 WP_004343581.1 1128
    Prevotella sp. MSX73 WP_007412163.1 1128
    Prevotella pallens ATCC 700821 EGQ18444.1 1126
    Prevotella Miens ATCC 700821 WP_006044833.1 1126
    Prevotella intermedia ATCC 25611 = DSM 20706 WP_036860899.1 1127
    Prevotella intermedia WP_061868553.1 1121
    Prevotella intermedia 17 AFJ07523.1 1135
    Prevotella intermedia WP_050955369.1 1133
    Prevotella intermedia BAU18623.1 1134
    Prevotella intermedia ZT KJJ86756.1 1126
    Prevotella aurantiaca JCM 15754 WP_025000926.1 1125
    Prevotella pleuritidis F0068 WP_021584635.1 1140
    Prevotella pleuritidis JCM 14110 WP_036931485.1 1117
    Prevotella falsenii DSM 22864 = JCM 15124 WP_036884929.1 1134
    Porphyromonas gulae WP_039418912.1 1176
    Porphyromonas sp. COT-052 OH4946 WP_039428968.1 1176
    Porphyromonas gulae WP_039442171.1 1175
    Porphyromonas gulae WP_039431778.1 1176
    Porphyromonas gulae WP_046201018.1 1176
    Porphyromonas gulae WP_039434803.1 1176
    Porphyromonas gulae WP_039419792.1 1120
    Porphyromonas gulae WP_039426176.1 1120
    Porphyromonas gulae WP_039437199.1 1120
    Porphyromonas gingivalis TDC60 WP_013816155.1 1120
    Porphyromonas gingivalis ATCC 33277 WP_012458414.1 1120
    Porphyromonas gingivalis A7A1-28 WP_058019250.1 1176
    Porphyromonas gingivalis JCVI SC001 EOA10535.1 1176
    Porphyromonas gingivalis W50 WP_005874195.1 1176
    Porphyromonas gingivalis WP_052912312.1 1176
    Porphyromonas gingivalis AJW4 WP_053444417.1 1120
    Porphyromonas gingivalis WP_039417390.1 1120
    Porphyromonas gingivalis WP_061156470.1 1120
  • Exemplary wild type Bergeyella zoohelcum ATCC 43767 Cas13b (BzCas13b) proteins of the disclosure may comprise or consist of the amino acid sequence:
  • (SEQ ID NO: 191)
       1 menktslgnn iyynpfkpqd ksyfagyfna amentdsvfr elgkrlkgke ytsenffdai
      61 fkenislvey eryvkllsdy fpmarlldkk evpikerken fkknfkgiik avrdlrnfyt
     121 hkehgeveit deifgvldem lkstvltvkk kkvktdktke ilkksiekql dilcqkkley
     181 lrdtarkiee krrnqrerge kelvapfkys dkrddliaai yndafdvyid kkkdslkess
     241 kakyntksdp qqeegdlkip iskngvvfll slfltkqeih afkskiagfk atvideatvs
     301 eatvshgkns icfmatheif shlaykklkr kvrtaeinyg eaenaeqlsv yaketlmmqm
     361 ldelskvpdv vyqn1sedvg ktfiedwney lkenngdvgt meeeqvihpv irkryedkfn
     421 yfairfldef aqfptlrfqv hlgnylhdsr pkenlisdrr ikekitvfgr lselehkkal
     481 fikntetned rehyweifpn pnydfpkeni svndkdfpia gsildrekqp vagkigikvk
     541 llnqqyvsev dkavkahqlk grkaskpsig niieeivpin esnpkeaivf ggutaylsm
     601 ndihsilyef fdkwekkkek lekkgekelr keigkelekk ivgkigagiq qiidkdtnak
     661 ilkpyqdgns taidkeklik dlkqegnilq klkdeqtvre keyndfiayq dknreinkvr
     721 drnhkqylkd nlkrkypeap arkevlyyre kgkvavwlan dikrfmptdf knewkgeqhs
     781 llqkslayye qckeelknll pekvfqhlpf klggyfqqky lyqfytcyld krleyisglv
     841 qqaenfksen kvfkkvenec fkflkkqnyt hkeldarvqs ilgypifler gfmdekptii
     901 kgktfkgnea lfadwfryyk eyqnfqtfyd tenyplvele kkqadrkrkt kiyqqkkndv
     961 ftllmakhif ksvfkqdsid qfsledlyqs reerlgnger arqtgerntn yiwnktvdlk
    1021 lcdgkitven vklknvgdfi kyeydgrvqa flkyeeniew qaflikeske eenypyvver
    1081 eiegyekvrr eellkevhli eeyilekvkd keilkkgdnq nfkyyilngl lkqlknedve
    1141 sykvfnlnte pedvninqlk geatdlegka fvltyirnkf ahnqlpkkef wdycqekygk
    1201 ektyaey faevfkkeke alik.
  • In some embodiments of the compositions of the disclosure, the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a CasRX/Cas13d protein. CasRX/Cas13d is an effector of the type VI-D CRISPR-Cas systems. In some embodiments, the CasRX/Cas13d protein is an RNA-guided RNA endonuclease enzyme that can cut or bind RNA. In some embodiments, the CasRX/Cas13d protein can include one or more higher eukaryotes and prokaryotes nucleotide-binding (HEPN) domains. In some embodiments, the CasRX/Cas13d protein can include either a wild-type or mutated HEPN domain. In some embodiments, the CasRX/Cas13d protein includes a mutated HEPN domain that cannot cut RNA but can process guide RNA. In some embodiments, the CasRX/Cas13d protein does not require a protospacer flanking sequence. Also see WO Publication No. WO2019/040664 & US2019/0062724, which is incorporated herein by reference in its entirety, for further examples and sequences of CasRX/Cas13d protein, without limitation, specific reference is made to Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig6049000251:
  • (SEQ ID NO: 54)
    LYLTSFGKGN AAVIEQKIEP ENGYRVTGMQ ITPSITVNKA TDESVRFRVK RKIAQKDEFI  60
    ADNPMHEGRH RIEPSAGSDM LGLKTKLEKY YFGKEFDDNL HIQIIYNILD IEKILAVYST 120
    NITA. 124
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig546000275:
  • (SEQ ID NO: 57)
    MDSYRPKLYK LIDFCIFKHY HEYTEISEKN VDTLRLAVSE EQKESFYADE AKRLWGIFDK  60
    QFLGFCKKIN VWVNGSHEKE ILGYIDKDAY RKKSDVSYFS KFLYAMSFFL DGKEINDLLT 120
    TLINKFDNIA SFISTAKELD AEIDRILEKK LDPVTGKPLK GKNSFRNFIA NNVIENKRFI 180
    YVIKFCNPKN VLKLVKNTKV TEFVLKRMPE SQIDRYYSSC IDTEKNPSVD KKISDLAEMI 240
    KKIAFDDFRN VRQKTRTREE SLEKERFKAV IGLYLTVVYL LIKNLVNVNS RYVMAFHCLE 300
    RDAKLYGINI GKNYIELTED LCRENENSRS AYLARNKRLR DCVKQNIDNA KNMKSKEK. 358
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig4114000374:
  • (SEQ ID NO: 61)
    DTKINPQTWL YQLENTPDLD NEYRDTLDHF FDERFNEINE HFVTQNATNL CIMKEVFPDE  60
    DFKSIADLYY DFIVVKSYKN IGFSIKKLRE KMLELPEAKR VTSTEMDSVR SKLYKLIDFC 120
    IFKHYHEKPE TVEMIVSMLR AYTSEDMKE. 149
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig721000619:
  • (SEQ ID NO: 67)
    KEGSTMAKNE KKKSTAKALG LKSSFVVNND IYMTSFGKGN KAVLEKKITE NTIENKSDTT  60
    YFDVINRDPK GFTLEGRRIA DMTAFSNDPK YHVNVVNGKF LEDQLGARSE LEKKVFGRTF 120
    DDNVHIQLIH NILDIEKIMA QYVSDIVYLL HNTIKRDMND DIMGYISIRN SFDDFCHPER 180
    IPDRKAKDNL QKQHDIFFDE ILKCGRLAYF GNAFFEDGSD NKEIAKLKRY KEIYHIIALM 240
    GSLRQSYFHG ENSDKNFQGP TWAYTLESNL TGKYKEFKDT LDKTFDERYE MISKDFGSTN 300
    MVNLQILEEL LKMLYGNVSP. 320
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig2002000411:
  • (SEQ ID NO: 69)
    EKQNKAKYQA IISLYLMVMY QIVKNMIYVN SRYVIAFHCL ERDSNQLLGR FNSRDASMYN  60
    KLTQKFITDK YLNDGAQGCS KKVGNYLSHN ITCCSDELRK EYRNQVDHFA VVRMIGKYAA 120
    DIGKFSTWFE LYHYVMQRII FDKRNPLSET ERTYKQLIAK HHTYCKDLVK ALNTPFGYNL 180
    ARYKNLSIGE LFDRNNYNAK TKET. 204
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig13552000311:
  • (SEQ ID NO: 71)
    LIDFLIYDLY YNRKPARIEE IVDKLRESVN DEEKESIYSA ETKYVYEALG KVLVRSLKKY  60
    LNGATIRDLK NRYDAKTANR IWDISEHSKS GHVNCFCKLI YMMTLMLDGK EINDLLTTLV 120
    NKFDNIASFI DVMDELGLEH SFTDNYKMFA DSKAICLDLQ FINSFARMSK IDDEKSKRQL 180
    FRDALVVLDI GDKNEDWIEK YLTSDIFKRD ENGNKIDGEK RDFRNFIANN VIKSARFKYL 240
    VKYSSADGMI KLKKNEKLIS FVLEQLPETQ IDRYYESCGL DCAVADRKVR IEKLTGLIRD 300
    MRFDNFRGVN YSNDACKKDK QAKAKYQAII SLYLMVLYQI VKNMIYVNSR YVIAFHCLER 360
    DLLFFNIELD NSYQYSNCNE LTEKFIKDKY MKEGALGFNM KAGRYLTKNI GNCSNELRKI 420
    YRNQVDHFAV VRKIGNYAAD IASVGSWFE. 449
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig10037000527:
  • (SEQ ID NO: 72)
    YMDQNFANSD AWAIHVYRNK IQHLDAVRHA DMYIGDIREF HSWFELYHYI IQRRIIDQYA 60
    YESTPGSSRD GSAIIDEERL NPATRRYFRL ITTYKT. 96
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig238000329:
  • (SEQ ID NO: 73)
    RYDKDRSKIY TMMDFVIYRY YIDNNNDSID FINKLRSSID EKSKEKLYNE EANRLWNKLK  60
    EYMLYIKEFN GKLASRTPDR DGNISEFVES LPKIHRLLPR GQKISNFSKL MYLLTMFLDG 120
    KEINDLLTTL INKFENIQGF LDIMPEINVN AKFEPEYVFF NKSHEIAGEL KLIKGFAQMG 180
    EPAATLKLEM TADAIKILGT EKEDAELIKL AESLFKDENG KLLGNKQHGM RNFIGNNVIK 240
    SKRFHYLIRY GDPAHLHKIA TNKNVVRFVL GRIADMQKKQ GQKGKNQIDR YYEVCVGNKD 300
    IKKTIEEKID ALTDIIVNMN YDQFEKKKAV IENQNRGKTF EEKNKYKRDN AEREKFKKII 360
    SLYLTVIYHI LKNIVNVNSR YILGFHCLER DKQLYIEKYN KDKLDGFVAL TKFCLGDEER 420
    YEDLKAKAQA SIQALETANP KLYAKYMNYS DEEKKEEFKK QLNRERVKNA RNAYLKNIKN 480
    YIMIRLQLRD QTDSSGYLCG EFRDKVAHLE VARHAHEYI. 519
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig2643000492:
  • (SEQ ID NO: 84)
    NGEIVSLAEK EAFSAKIADK NIGCKIENKQ FRHPKGYDVI ADNPIYKGSP RQDMLGLKET  60
    LEKRYFSPSD SIDNVRVQVA HNILDIEKIL AEYITNAVYS FDNIAGFGKD IIGDDFSPVY 120
    TYDKFEKSDR YEYFKNLLNN SRLGYYGQAF FECDDSKENK KKKDAIKCYN IIALLSGLRH 180
    W. 181
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig874000057:
  • (SEQ ID NO: 85)
    MSKNKESYAK GMGLKSALVS GSKVYMTSFE GGNDAKLEKV VENSEIVSLA EKESFSAEIF  60
    KKNIGCKIEN KKFKHPKRYD VIADNPLYKG SVRQDMLGLK ETLEKRYFNS ADGTDNVCIQ 120
    VIHNILDIEK ILAEYITNAV YSFDNIAGFG EDIIGMGGFK PIYTYKQFKE PDKYNKKFDD 180
    ILNNSRLGYY GKAFFEKNDL KHNPNKKKRD KNPYILKYDN ECYYIIALLS GLRHWNIHSH 240
    AKDDLVSYRW LYNLDSILNR EYISTLNYLY DDIADELTES FSKNSSANVN YIAETLNIDP 300
    SEFAQQYFRF SIMKEQKNMG FNVSKLREIM LDRKELSDIR DNHRVFDSIR SKLYTMMDFV 360
    IYRYYIEEAA KTEAENRNLP ENEKKISEKD FFVINLRGSF DENQKEKLYI EEAKRLWEKL 420
    KDIMLKIKEF RGEKVKEYKK. 440
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig4781000489:
  • (SEQ ID NO: 86)
    LDKQLDYEYI RTLNYMFNDI ADELTRTFSK NSAANVNYIA ETLNIDPNKF AEQYFRFSIM  60
    KEQKNLGFNL TKLRESMLDR RELSDIRDNH NVFDSIRPKL YTMMDFVIYK HYIDEAKKTE 120
    AENKSLPDDR KNLSEKD. 137
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig12144000352:
  • (SEQ ID NO: 87)
    RMGEPVANTK RVMMIDAVKI LGTDLSDDEL KEMADSFFKD SDGNLLKKGK HGMRNFITNN 60
    VIKNKRFHYL IRYGDPAHLH EIAKNEA. 87
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig5590000448:
  • (SEQ ID NO: 88)
    VHNNEEKDLI KYTWLYNLDK YLDAEYITTL NYMYNDIGDE LTDSFSKNSA ANINYIAETL  60
    GIDPKTFAEQ YFRFSIMKEQ KNLGFNLTKL REVMLDRKDM SEIRENHNDF DSIRAKVYTM 120
    MDFVIYRYYI EEAAKVNAAN KSLPDNEKSL SEKDIFVISL RGSFNEDQKD RLYYDEAQRL 180
    WSKVGKLMLK IKKFRGKDTR KYKNMGTPRI RRLIPEGRDI STFSKLMYAL TMFLDGKEIN 240
    DLLTTLINKF DNIQSFLKVM PLIGVNAKFA EEYSFFNNSE KIADELRLIK SFARMGEPVA 300
    DARRAMYIDA IRILGTDLSD DELKALADSF SLDENGNKLG KGKHGMRNFI INNVITNKRF 360
    HYLIRYGNPV HLHEIAKNEA VVKFVLGRIA DIQKKQGQNG KNQIDRYYET CIGK. 414
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig525000349:
  • (SEQ ID NO: 89)
    MSKKENRKSY VKGLGLKSTL VSDSKVYLTT FADGSNAKLE KCVENNKIIC ISNDKEAFAA  60
    SIANKNVGYK IKNDEKFRHP KGYDIISNNP LLHNNSVQQD MLGLKNVLEK RYFGKSSGGD 120
    NNLCIQIIHN IIDIEKILSE YIPNVVYAFN NIAGFKDEHN NIIDIIGTQT YNSSYTYADF 180
    SKDKSDKKYI EFQKLLKNKR LGYWGKAFFT GQGNNAKVRQ ENQCFHIIAL LISLRNWATH 240
    SNELDKHTKR TWLYKLDDTN ILNAEYVKTL NYLYDTIADE LTKSFSKNGA VNVNYLAKKY 300
    NIKDDLPGFS EQYFRFSIMK EQKNLGFNIS KLRENMLDFK DMSVI. 345
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig7229000302:
  • (SEQ ID NO: 90)
    KKISSLTKFC LGESDEKKLK ALAKKSLEEL KTTNSKLYEN YIKYSDERKA EEAKRQINRE  60
    RAKTAMNAHL RNTKWNDIMY GQLKDLADSK SRICSEFRNK AAHLEVARYA HMYINDISEV 120
    KSYFRLYHYI MQRRIIDVIE NNPKAKYEGK VKVYFEDVKK NKKYNKNLLK LMCVPFGYCI 180
    PRFKNLSIEQ MFDMNETDNS DKKKEK. 206
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig3227000343:
  • (SEQ ID NO: 91)
    IGDISEVNSY FQLYHYIMQR ILIDKIGSKT TGKAKEYFDS VIVNKKYDDR LLKLLCSPLG 60
    YCLTRYKDLS IEALFDMNEA AKYDKLNKER KNKKK. 95
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig7030000469:
  • (SEQ ID NO: 92)
    SIRSKLYTMM DFVIYRYYIE ESAKAAAENK PSESDSFVIR LRGSFNENQK EELYIEEAER  60
    LWKKFGEIML KIKEFRGEKV KEYKKEVPRI ERILPHGKDI SAFSKLMYML SMFLD. 115
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d gut_metagenome_P17E0k2120140920, c87000043:
  • (SEQ ID NO: 93)
    MYFSKMIYML TYFLDGKEIN DLLTTLISKF DNIKEFLKIM KSSAVDVECE LTAGYKLFND  60
    SQRITNELFI VKNIASMRKP AASAKLTMFR DALTILGIDD KITDDRISEI LKLKEKGKGI 120
    HGLRNFITNN VIESSRFVYL IKYANAQKIR EVAKNEKVVM FVLGGIPDTQ IERYYKSCVE 180
    FPDMNSSLEA KRSELARMIK NISFDDFKNV KQQAKGRENV AKERAKAVIG LYLT. 234
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb|OBVH01003037.1, human gut metagenome sequence (also found in WGS contigs emb|OBXZ01000094.1| and emb|OBJF01000033.1|):
  • (SEQ ID NO: 94)
    MAKKKRITAK ERKQNHRELL MKKADSNAEK EKAKKPVVEN KPDTAISKDN TPKPNKEIKK  60
    SKAKLAGVKW VIKANDDVAY ISSFGKGNNS VLEKRIMGDV SSNVNKDSHM YVNPKYTKKN 120
    YEIKNGFSSG SSLVTYPNKP DKNSGMDALC LKPYFEKDFF GHIFTDNMHI QAIYNIFDIE 180
    KILAKHITNI IYTVNSFDRN YNQSGNDTIG FGLNYRVPYS EYGGGKDSNG EPKNQSKWEK 240
    RDNFIKFYNE SKPHLGYYEN IFYDHGEPIS EEKFYNYLNI LNFIRNNTFH YKDDDIELYS 300
    ENYSEEFVFI NCLNKFVKNK FKNVNKNFIS NEKNNLYIIL NAYGKDTENV EVVKKYSKEL 360
    YKLSVLKTNK NLGVNVKKLR ESAIEYGYCP LPYDKEKEVA KLSSVKHKLY KTYDFVITHY 420
    LNSNDKLLLE IVETLRLSKN DDEKENVYKK YAEKLFKADD VINPIKAISK LFARKGNKLF 480
    KEKIIIKKEY IEDVSIDKNI YDFTKVIFFM TCFLDGKEIN DLLTNIISKL QVIEDHNNVI 540
    KFISNNKDAV YKDYSDKYAI FRNAGKIATE LEAIKSIARM ENKIENAPQE PLLKDALLSL 600
    GVSDDTKVLE NTYNKYFDSK EKTDKQSQKV STFLMNNVIN NNRFKYVIKY INPADINGLA 660
    KNRYLVKFVL SKIPEEQIDS YYKLFSNEEE PGCEEKIKLL TKKISKLNFQ TLFENNKIPN 720
    VEKEKKKAII TLYFTIVYIL VKNLVNINGL YTLALYFVER DGYFYKDICG KKDKKKSYND 780
    VDYLLLPEIF SGSKYREETK NLKLPKEKDR DIMKKYLPND KDREKYNKFF TAYRNNIVHL 840
    NIIAKLSELT KNIDKDINSY FDIYHYCTQR VMFNYCKEKN DVVLAKMKDL AHIKSDCNEF 900
    SSKHTYPFSS AVLRFMNLPF AYNVPRFKNL SYKKFFDKQ. 939
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig tpg|DJXD01000002.1| (uncultivated Ruminococcus assembly, UBA7013, from sheep gut metagenome):
  • (SEQ ID NO: 95)
    MKKQKSKKTV SKTSGLKEAL SVQGTVIMTS FGKGNMANLS YKIPSSQKPQ NLNSSAGLKN  60
    VEVSGKKIKF QGRHPKIATT DNPLFKPQPG MDLLCLKDKL EMHYFGKTFD DNIHIQLIYQ 120
    ILDIEKILAV HVNNIVFTLD NVLHPQKEEL TEDFIGAGGW RINLDYQTLR GQTNKYDRFK 180
    NYIKRKELLY FGEAFYHENE RRYEEDIFAI LTLLSALRQF CFHSDLSSDE SDHVNSFWLY 240
    QLEDQLSDEF KETLSILWEE VTERIDSEFL KTNTVNLHIL CHVFPKESKE TIVRAYYEFL 300
    IKKSFKNMGF SIKKLREIML EQSDLKSFKE DKYNSVRAKL YKLFDFIITY YYDHHAFEKE 360
    ALVSSLRSSL TEENKEEIYI KTARTLASAL GADFKKAAAD VNAKNIRDYQ KKANDYRISF 420
    EDIKIGNTGI GYFSELIYML TLLLDGKEIN DLLTTLINKF DNIISFIDIL KKLNLEFKFK 480
    PEYADFFNMT NCRYTLEELR VINSIARMQK PSADARKIMY RDALRILGMD NRPDEEIDRE 540
    LERTMPVGAD GKFIKGKQGF RNFIASNVIE SSRFHYLVRY NNPHKTRTLV KNPNVVKFVL 600
    EGIPETQIKR YFDVCKGQEI PPTSDKSAQI DVLARIISSV DYKIFEDVPQ SAKINKDDPS 660
    RNFSDALKKQ RYQAIVSLYL TVMYLITKNL VYVNSRYVIA FHCLERDAFL HGVTLPKMNK 720
    KIVYSQLTTH LLTDKNYTTY GHLKNQKGHR KWYVLVKNNL QNSDITAVSS FRNIVAHISV 780
    VRNSNEYISG IGELHSYFEL YHYLVQSMIA KNNWYDTSHQ PKTAEYLNNL KKHHTYCKDF 840
    VKAYCIPFGY VVPRYKNLTI NELFDRNNPN PEPKEEV. 877
  • An exemplary direct repeat sequence of CasRX/Cas13d Metagenomic hit (no protein accession): contig tpg|DJXD01000002.1| (uncultivated Ruminococcus assembly, UBA7013, from sheep gut metagenome) (SEQ ID NO: 95) comprises or consists of the nucleic acid sequence:
  • CasRX/Cas13dDR:
    (SEQ ID NO: 96)
    caactacaac cccgtaaaaa tacggggttc tgaaac. 36
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig OGZC01000639.1 (human gut metagenome assembly):
  • (SEQ ID NO: 97)
    MKKKNIRATR EALKAQKIKK SQENEALKKQ KLAEEAAQKR REELEKKNLA QWEETSAEGR  60
    RSRVKAVGVK SVFVVGDDLY LATFGNGNET VLEKKITPDG KITTFPEEET FTAKLKFAQT 120
    EPTVATSIGI SNGRIVLPEI SVDNPLHTTM QKNTIKRSAG EDILQLKDVL ENRYFDRSFN 180
    DDLHIRLIYN ILDIEKILAE YTTNAVFAID NVSGCSDDFL SNFSTRNQWD EFQNPEQHRE 240
    HFGNKDNVIC SVKKQQDLFF NFFKNNRIGY FGKAFFHAES ERKIVKKTEK EVYHILTLIG 300
    SLRQWITHST EGGISRLWLY QLEDALSREY QETMNNCYNS TIYGLQKDFE KTNAPNLNFL 360
    AEILGKNASE LAEPYFRFII TKEYKNLGFS IKTLREMLLD QPDLQEIREN HNVYDSIRSK 420
    LYKMIDFVLV YAYSNERKSK ADALASNLRS AITEDAKKRI YQNEADQLWT SYQELFKRIR 480
    GFKGAQVKEY SSKNMPIPIQ KQIQNILKPA EQVTYFTKLM YLLTMFLDGK EINDLLTTLI 540
    NKFDNISSLL KTMEQLELQT TFKEDYTFFQ QSSRLCKEIT QLKSFARMGN PISNLKEVAM 600
    VDAIQILGTE KSEQELQSMA CFFFRDKNGK KLNTGEHGMR NFIGNNVISN TRFQYLIRYG 660
    NPQKLHTLSQ NETVVRFVLS RIAKNQRVQG MNGKNQIDRY YETCGGTNSW SVSEEEKINF 720
    LCKILTNMSY DQFQDVKQSG AEITAEEKRK KERYKAIISL YLTVLYQLIK NLVNINARYI 780
    IAFHCLERDA ILYSSKFNTS INLKKRYTAL TEMILGYETD EKARRKDTRT VYEKAEAAKN 840
    RHLKNVKWNC KTRENLENAD KNAIVAFRNI VAHLWIIRDA DRFITGMGAM KRYFDCYHYL 900
    LQRELGYILE KSNQGSEYTK KSLEKVQQYH SYCKDFLHML CLPFAYCIPR YKNLSIAELF 960
    DRHEPEAEPK EEASSVNNSQ FITT. 984
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb|OHBM01000764.1 (human gut metagenome assembly):
  • (SEQ ID NO: 98)
    XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX  60
    XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX 120
    XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX 180
    XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXHPLQKRYR YLTSTNLKSF 240
    ETYKNNLVNK KKFDLDRVKK IPQLAYFGSA FYNTPEDTSA KITKTKIKSN EEIYYTFMLL 300
    STARNFSAHY LDRNRAKSSD AEDFDGTSVI MYNLDNEELY KKLYNKKVHM ALTGMKKVLD 360
    ANFNKKVEHL NNSFIKNSAK DFVILCEVLG IKSRDEKTKF VKDYYDFVVR KNYKHLGFSV 420
    KELRELLFAN HDSNKYIKEF DKISNKKFDS VRSRLNRLAD YIIYDYYNKN NAKVSDLVKY 480
    LRAAADDEQK KKIYLNESIN LVKSGILERI KKILPKLNGK IIGNMQPDST ITASMLHNTG 540
    KDWHPISENA HYFTKWIYTL TLFMDGKEIN DLVTTLINKF DNIASFIEVL KSQSVCTHFS 600
    EERKMFIDSA EICSELSAMN SFARMEAPGA SSKRAMFVEA ARILGDNRSK EELEEYFDTL 660
    FDKSASKKEK GFRNFIRNNV VDSNRFKYLT RYTDTSSVKA FSNNKALVKF AIKDIPQEQI 720
    LRYYNSCFGA SERYYNDGMS DKLVEAIGKI NLMQFNGVIQ QADRNMLPEE KKKANAQKEK 780
    YKSIIRLYLT VCYLFFKNLV YVNSRYYSAF YNLEKDRSLF EINGELKPTG KFDEGHYTGL 840
    VKLFIDNGWI NPRASAYLTV NLANSDETAI RTFRNTAEHL EALRNADKYL NDLKQFDSYF 900
    EIYHYITQRN IKEKCEMLKE QTVKYNNDLL KYHGYSKDFV KALCVPFGYN LPRFKNLSID 960
    ALFDKNDKRE KLKKGFED. 978
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb|OHCP01000044.1 (human gut metagenome assembly):
  • (SEQ ID NO: 99)
    MAKKITAKQK REEKERLNKQ KWAKNDSVII VPETKEEIKT GEIQDNNRKR SRQKSQAKAM   60
    GLKAVLSFDN KIAIASFVSS KNAKSSHIER ITDKEGTTIS VNSKMFESSV NKRDINIEKR  120
    ITIEEPQQDG TIKKEEKGVK STTCNPYFKV GGKDYIGIKE IAEEHFFGRA FPNENLRVQI  180
    AYNIFDVQKI LGTFVNNIIY SFYNLSRDEV QSDNDVIGML YSISDYDRQK ETETFLQAKS  240
    LLKQTEAYYA YFDDVFKKNK KPDKNKEGDN SKQYQENLRH NFNILRVLSF LRQICMHAEV  300
    HVSDDEGCTR TQNYTDSLEA LFNISKAFGK KMPELKTLID NIYSKGINAI NDEFVKNGKN  360
    NLYILSKVYP NEKREVLLRE YYNFVVCKEG SNIGISTRKL KETMIAQNMP SLKEENTYRN  420
    KLYTVMNFIL VRELKNCATI REQMIKELRA NMDEEEGRDR IYSKYAKEIY LYVKDKLKLM  480
    LNVFKEEAEG IIIPGKEDPV KFSHGKLDKK EIESFCLTTK NTEDITKVIY FLCKFLDGKE  540
    INELCCAMMN KLDGISDLIE TAKQCGEDVE FVDQFKCLSK CATMSNQIRI VKNISRMKKE  600
    MTIDNDTIFL DALELLGRKI EKYQKDKNGD YVKDEKGKKV YTKDYNNFQD MFFEGKNHRV  660
    RNFVSNNVIK SKWFSYVVRY NKPAECQALM RNSKLVKFAL DELPDSQIEK YYISVFGEKS  720
    SSSNEEMRRE LLKKLCDFSV RGFLDEIVLL SEDEMKQKDK FSEKEKKKSL IRLYLTIVYL  780
    ITKSMVKINT RFSIACATYE RDYILLCQSE KAERAWEKGA TAFALTRKFL NHDKPTFEQY  840
    YTREREISAM PQEKRKELRK ENDQLLKKTH YSKHAYCYIV DNVNNLTGAV ANDNGRGLPC  900
    LSEKNDNANL FLEMRNKIVH LNVVHDMVKY INEIKNITSY YAFFCYVLQR MIIGNNSNEQ  960
    NKFKAKYSKT LQEFGTYSKD LMWVLNLPFA YNLPRYKNLS NEQLFYDEEE RMEKIVGRKN 1020
    DSR. 1023
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb|OGDF01008514.1| (human gut metagenome assembly):
  • (SEQ ID NO: 100)
    MTETKPKRED IAKTPAAKSR SKAAGLKSTF AVNGSVLLTS FGRGNDAVPE KLITEKAVSE  60
    INTVKPRFSV EKPATSYSSS FGIKSHISAT ADNPLAGRAP VGEDAIHAKE VLEQRVFGKT 120
    FSDDNIHIQL IYNILDIRKI LSTYANNVVF TINSMRRLDE YDREQDYLGY LYTGNSYERL 180
    LDIADKYAVD GEDWRNTAAG ISNDFEKKQF QTINGFWDLL DMIEPYMCYF SEAFFCETTV 240
    KDPDSGRIVP CLEQRSDGDI YNILRILSIV RQTCMHDNAS MRTVMFTLGQ NSVRDRKNGF 300
    DELAELLDYL YDEKIDIVNR DFLRNQKNNI ELLSRIYGSS ADSPERDRLV QNFYDFRVLS 360
    QDKNLGFSIK KLREKLLDSP ALSVVRSKKY DTMRSKIYSL IDFMIYRKFS ENHVAVDDFV 420
    EELRSLLTED EKESAYSRWA ETLINDGFAQ EILVKLLPQT DPAVIGKIKG KKLLNDSIAG 480
    IKLKKDASFF TKIINVLCMF QDGKEINELV SSLVNKFANI QSFVDVMRSQ GIDSGFTADY 540
    AMFAESGRIS RELHILKGIA RMQHSIAGLG DVKIYGSDDK FHGVSRRVYT DAAYILGFGE 600
    RSEDNDGYVD DYVSSKLLGG ADKNLRNFIT NNVIKNRRFL YTVRYMNPKR AKKLVQNDAL 660
    VVLALSGIPE TQIDRYYKSC IEKRSFNPDL NEKIAALSEM ITTLKIDDFE DVKQNPEKNA 720
    NYEAKKNQRI SKERYKACIG LYLTVLYLIC KNLVKINARY SIAIGCLERD TQLHGVDFKG 780
    AAYMTRDVFI AKGWINPKKP TVKSIKEQYA FLTPYIFTTY RNMIAHLAAV TNAYKYIPQM 840
    DRFKSWFHLY HTVIQHSLIQ QYEYDRDYGR KGAPVVSERV LQLLEQCREH SNYSRDLLHI 900
    LNLPFGYNLP RYLNLSSEKY FDANAI. 926
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb|OGPN01002610.1 (human gut metagenome assembly):
  • (SEQ ID NO: 101)
    MAKKITAKQK REEKERLNKQ KWAKQDTPVV PKSKTEEKPV AASDDKLLKT TQVKKVQTKS   60
    KAKAMGLKTV LSFDDKIAIA SFVNDKKTKL PHIERITDKS GTTIHENARM FDSSVDEQNV  120
    NIEKRMTIEE KQNDGTFKKD EKDVKATICN PYFKTCGKDY IGIKDVAEKY FFGKTFPNEN  180
    LRVQIAYNVF DIQKILGTYV NNIIYSFYNL RRDGKSDVDI IGSLYAFADF DNQLKDKPAF  240
    REAKDLLKNT EAYFSYFGDV FKKSKKGKKD ENNEDYEKNL RHNFNVLRVL SFLRQICTHA  300
    YVKCTGGAKN NGDSTKVEAE SLDALFNITE YFAKTAPELS KTINEIYKEG IDRINNDFVT  360
    NGKNNLYILS KVYPDMQRNE LVKKYYQFVV CKEGNNVGIN TRKLKESIIS QHPWITTPQD  420
    NNKANDYESC RHKLYTIMCF ILVAELDAHE SIRDNMVAEL RANMDGDDGR DAIYEKYAKD  480
    IYHIVKDKLL AMQKVFDEEL VPVKVEGKND PQQFTHGKLG KKEIESFCLS DKNTSDIAKV  540
    VYFLCNFLDG KEINELCCAM MNKFDGIGDL IDTAKQCGEE VKFIEEFACL SNCRKITNDI  600
    RVAKSISKMK NKVNIDNDII YLDAIELLGR KIEKYQKDEN GKILLGTDGK RLYTQEYKYF  660
    NDMFFNAGNH KVRNFIANNV MQSKWFFYVV RYNKPAECQI IMRNKTLVKF TLDDLPDMQI  720
    QRYYSSVFGD NNMPAVDEMR KRLLDKINQF SVRGFLDELD EIVLMSDEES KRNKSSEKEQ  780
    KKSLIRLYLT IAYLITKSMV KINTRFSIAC AMYERDYALL CQSEMKGGPW DGGAQALAVT  840
    RKFLNHDREV FDRYCAREAE IARLPSEERK PLRKANDKLL KQTHYTNHSY TYIVNNLNSF  900
    TDIDYCAKDV GLPAPNDKND NASILGEMRN DIAHLNIVHD MVKYIEELKD ISSYYAFYCY  960
    VLQRRLVGKD PNCQNKFKAK YAKELNDYGT YNKNLMWMLN LPFAYNLPRY KNLSSEFLFY 1020
    DMEYNKKDDE. 1030
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): from contig emb|OBLI01020244 and emb|OBLI01038679 (from pig gut metagenome):
  • (SEQ ID NO: 102)
    MAKKITAKQR REERERQNKQ KWAKKQADAT AVFECEADIK PADSKDEDCT NIYIKREKKK   60
    TQAKAMGLKT VLGFDNKIAI ASFMSSKDSK SSHIERITDP NGKTIREDVR MFDSNVDECS  120
    INLEKRMTVE ERQKDGTIKK DEKDVKSTIC NPYSNECGKD YIGIKSVAEE LFFGRTFPND  180
    NLRVQIAYNI FDIQKILGTY INNIIYSFYN LSRDESQSDN DVIGTLYMLK DFDGQKETDT  240
    FRQARALLER TEAYYSYFDN VFKKIDKNKK KSDDCKRERN EILRYNFNVL RVLSFLRQIC  300
    AHAQVKISNE HDREKGGGLV DSLDALFNIS RFFDAVAPEL NEVINSVYSK GIDDINDNFV  360
    KNGKNNFYIL SKIYPEVARE DLLREYYYFV VSKEGNNIGI STKKLKEAII VQDMSYIKSE  420
    DYDTYRNKLY TVLCFILVKE LNERTTIREQ MVADLRANMN GDIGREDIYS KYAKIIYAQV  480
    KPRFDTMKSA FEEEAKDVIV PDKKKPVKFS HGKLDKNEIE RFCITSANTD SVAKIIYFLC  540
    KFLDGKEINE LCCAAMNKLD GINDLIETAE QCGAKVEFVD KFSVLSNCET ISDQIRIVKS  600
    ISKMKKEIAI DNDTIFLDAL ELLGRKIDKY KKDATGKYLK DENGKYLYSK EYDDFQYMFF  660
    KDSHRVRNFI SNSVIKSKWF SYIVRYNQPS ECRAIMKNKT LVKFALDELP DLQIQRYFVA  720
    LYGDEDLPSY GEMRKILLKK LHDFSIKGFL DEIVLLSDLD MESQDKYCEK EQKKSLFRLY  780
    LTIAYLITKS MVKINTRFSI ACATYERDYA LLCASNKQER AWSSGATALA LTRRFLNQDK  840
    LIFEKHYARE GEISKLPKEE RKAMRKVNDQ LLKRTHFSKH SYCYIVDNVN RLTGGECRTD  900
    KRVLPVLNEK NDNAGILLDF RKTIAHLNVV HKMVDYVDEI KGITSYYAFF CYVLQRMLVG  960
    NNLNEKNAIK EKYSATVKSF GTYSKDFMWL INLPFAYNLP RYKNLSNEQL FYDEEERNET 1020
    EEQIDRL. 1027
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig OIZX01000427.1:
  • (SEQ ID NO: 103)
    MAKKKKTARQ LREEMQQQRK QAIQKQQEQR QEKAAAARET AAPEQPAAAP VPKRQRKSLA  60
    KAAGLKSNFI LDPQRRTTVM TAFGQGSTAI LEKQIVDRAI SDLQPVQQFQ VEPASAAKYR 120
    LKNSRVRFPN VTADDPLYRR KDGGFVPGMD ALRRKNVLEQ RFFGKSFADN IHIQMIYSIL 180
    DIHKILAAAS GHIVHLLNIV NGSKDRDFIG MLAAHVLYNE LNEEAKRSIA DFCKSPRLIY 240
    YSAAFYETLD NGKSERRSNE DIFNILALMT CLRNFSSHHS IAIKVKDYSA AGLYNLRRLG 300
    PDMKKMLDTF YTEAFIQLNQ SFQDHNTTNL TCLFDILNIS DSARQKQLAE EFYRYVVFKE 360
    QKNLGFSVRK LREEMLLLPD AAVIADKRYD TCRSKLYNLM DFLILRVYRT GRADRCDKLP 420
    EALRAALTDE EKAVVYHKEA LSLWNEMRTL ILDGLLPQMT PENLSRLSGQ KRKGELSLDD 480
    AMLKECLYEP GPVPEDAAPE EANAEYFCRM IYLATLFMDG KEINTLLTTL ISKFENIAAF 540
    LQTMEQLNIE AELGPEYAMF TRSRAVAEQL RVINSFALMK KPQVNAKQQL YRAAVTLLGT 600
    EDPDGVTDEM LCIDPVTGKM LPPNQRHHGD TGLRNFIANN VVESRRFQYL IRYSDPAQLH 660
    QLASNKKLVR FVLSSIPDTQ INRYYETCGQ TRLAGRAAKV EFLTDMIAAI RFDQFRDVNQ 720
    KERGANTQKE RYKAMLGLYQ TVLYLAVKNL VNINARYVMA FHCVERDMFL YDGELTDPKG 780
    ESVSAFLAMN GKKGVQPQYL LLTQLFIRRD YLKRSACEQI QHNMENISDR LLREYRNAVA 840
    HLNVIAHLAD YSADMREITS YYGLYHYLMQ RHLFKRHAWQ IRQPERPTEE EQKLIEQEQK 900
    QLAWEKALFD KTLQYHSYNK DLVKALNAPF GYNLARYKNL SIEPLFSKEA APAAEIKATH 960
    A. 961
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig OCTWO11587266.1:
  • (SEQ ID NO: 104)
    MKQNDRENNN KIKKSAAKAV GVKSLARLSD GSTVVSSFGK GAAAELESLI TGGEIRKLSD  60
    KAILEITDDT QNKNAYNVKS SRIPNLTART DKLSDKSGMD DLGFKRELEL EVFGQCFDDS 120
    IHIQIAHAVF DIQKSLAAVI PNVLYTLNNL DRSYSTDNTS DKKDIIGNTL NYQHSYESFN 180
    VEKRGEFTEY YNAAKDRFSY FPDILCVLEK VNGKDRYQPK SEKDAFNVLS SVNMLRNSLF 240
    HFAPKSNDGK ARIAVFKNQF DSDFSHITST VNKIYSAKIA GVNENFLNNE GNNLYIILKA 300
    TNWDIKKIVP QLYRFSVLKS DKNMGFNMRK LREFAVESKN IDLSRLNDKF LTNNRKKLYK 360
    VIDFIIYYHL NKVLKDSFVD DFVAALRASQ SEEEKEKLYA QYSERLFADE GLKSAIKKAV 420
    DMISDTKSNI FKMKTPLDKA LIENIKVNSD ASDFCKLIYV FTRFLDGKEI NILLNSLIKK 480
    FQDIHSFNTT VKKLSENNLI INADYVDDYS LFEQSGTVAR ELMLIKSISK MDFGLDNINL 540
    SFMYDDALRT LGVSDENLPE VKREYFGKTK NLSAYIRNNV LENRRFKYVI KYIHPSDVQK 600
    IACNKAIAGF VLNRMPDTQI KRYYDSLINK GATDIQAQAK ALLDCITGIS FDAIKDDKHL 660
    HKSKEKSPQR SADRERKKAM LTLYYTIVYI FVKQMLHINS LYTIGFFYLE RDQRFIYSRA 720
    KKENKNPSKN SYLNDFRSVT AYFIPSEIMK RIEKNENKGF LEDFEALWNS CGKTSRLRKE 780
    DVLLYARYIS PDHALKNYKM ILNSYRNKIA HINVIMSAGK YTGGIKRMDS YFSVFQHLVQ 840
    CDILSNPNNK GKCFESESLK PLLLDMKFDG TDEKLYSKRL TRALNIPFGY NVPRYKNLTF 900
    EKIYLKSSIN E. 911
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb|OGNF01009141.1:
  • (SEQ ID NO: 105)
    MADIDKKKSS AKAAGLKSTF VLENNKLLMT SFGNGNKAVI EKIIDEKVDS INEPEVFSVT  60
    PCDKKFELQP AKRGLAADSL VDNPLKSKKT AGDDAIHSRK FLERQFFDGN TFNDNIHIQL 120
    IYNILDIEKI LSVHVNDIVY SVNNILSRGE GMEYNDYIGT LNLKSFETYK NNLVNKKKFD 180
    LDRVKKIPQL AYFGSAFYNT PEDTSAKITK TKIKSNEEIY YTFMLLSTAR NFSAHYLDRN 240
    RAKSSDAEDF DGTSVIMYNL DNEELYKKLY NKKVHMALTG MKKVLDANFN KKVEHLNNSF 300
    IKNSAKDFVI LCEVLGIKSR DEKTKFVKDY YDFVVRKNYK HLGFSVKELR ELLFANHDSN 360
    KYIKEFDKIS NKKFDSVRSR LNRLADYIIY DYYNKNNAKV SDLVKYLRAA ADDEQKKKIY 420
    LNESINLVKS GILERIKKIL PKLNGKIIGN MQPDSTITAS MLHNTGKDWH PISENAHYFT 480
    KWIYTLTLFM DGKEINDLVT TLINKFDNIA SFIEVLKSQS VCTHFSEERK MFIDSAEICS 540
    ELSAMNSFAR MEAPGASSKR AMFVEAARIL GDNRSKEELE EYFDTLFDKS ASKKEKGFRN 600
    FIRNNVVDSN RFKYLTRYTD TSSVKAFSNN KALVKFAIKD IPQEQILRYY NSCFGASERY 660
    YNDGMSDKLV EAIGKINLMQ FNGVIQQADR NMLPEEKKKA NAQKEKYKSI IRLYLTVCYL 720
    FFKNLVYVNS RYYSAFYNLE KDRSLFEING ELKPTGKFDE GHYTGLVKLF IDNGWINPRA 780
    SAYLTVNLAN SDETAIRTFR NTAEHLEALR NADKYLNDLK QFDSYFEIYH YITQRNIKEK 840
    CEMLKEQTVK YNNDLLKYHG YSKDFVKALC VPFGYNLPRF KNLSIDALFD KNDKREKLKK 900
    GFED. 904
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb|OIEN01002196.1:
  • (SEQ ID NO: 106)
    MERQKRKMKS KSKMAGVKSV FVIGDELLMT SFGDGDDAVL EKDIDENGVV NDCRNPAAYD  60
    AVYGTDSIRV KKTNNNIRAK VNNPLAKSNI RSEESALFRT RVNEYKREQK DKYETLFFGK 120
    TFDDNIHIQL ISKILDIEKT FSVVIGNIVY AINNLSLEQS IDRPIDIFGD KNTQGISLRE 180
    DNDYLKTMLP RCEYLFHNIL NSDSDNNSKM NYNKVNKGKE EKDNRNNENI EKLKKALEVI 240
    KIIRVDSFHG VDGIKGDQKF PRSKYNLAVN YNEEIQKTIS EPFNRKVEEV QQDFYRNSCV 300
    NIDFLKEIMY GSNYTDRGSD SLECSYFNFA ILKQNKNMGF SITSIRECLL DLYELNFESM 360
    QNLRPRANSF CDFLIYDYYC KNESERANLV DCLRSAASEE EKKNIYFQTA ERVKEKFRNA 420
    FNRISRFDAS YIKNSREKNL SGGSSLPKYS FIEGFTKRSK KINDNDEKNA DLFCNMLYYL 480
    AQFLDGKEIN IFLTSIHNIF QNIDSFLKVM KEKGMECKFQ KDFKMFSHAG HVAKKIEIVI 540
    SLAKMKKTLD FYNAQALKDA VTILGVSKKH QYLDMNSYLD FYMFDNRSGA TGKNAGKDHN 600
    LRNFLVSNVI RSRKFNYLSR YSNLAEVKKL AQNPSLVQFV LSRIEPSLIC RYYESSQGIS 660
    SEGITIDEQI KKLTGIIVDM NIDSFENINN GEIGMRYSKA TPQSIERRNQ MRVCVGLYLN 720
    VLYQIEKNLM NVNARYVLAF AFAERDALML NFTLEECKKN KKRSSGGFSF IEMTQFFIDK 780
    KLFKVATEAI KKNVLKYNGN PESLNHIPGE YICKNMEGYH ENTVRNFRNM VAHLTAVARV 840
    PLYISEVTQI DSYYALYHYC MQMNILQGIE QSGKILDNIK LKNALENARV HRTYSKDAVK 900
    YLCLPFAYNI SRYKALTIKD LFDWTEYSCK KDE. 933
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig e-k87_11092736:
  • (SEQ ID NO: 107)
    MKRQKTFAKR IGIKSTVAYG QGKYAITTFG KGSKAEIAVR SADPPEETLP TESDATLSIH   60
    AKFAKAGRDG REFKCGDVDE TRIHTSRSEY ESLISNPAES PREDYLGLKG TLERKFFGDE  120
    YPKDNLRIQI IYSILDIQKI LGLYVEDILH FVDGLQDEPE DLVGLGLGDE KMQKLLSKAL  180
    PYMGFFGSTD VFKVTKKREE RAAADEHNAK VFRALGAIRQ KLAHFKWKES LAIFGANANM  240
    PIRFFQGATG GRQLWNDVIA PLWKKRIERV RKSFLSNSAK NLWVLYQVFK DDTDEKKKAR  300
    ARQYYHFSVL KEGKNLGFNL TKTREYFLDK FFPIFHSSAP DVKRKVDTFR SKFYAILDFI  360
    IYEASVSVAN SGQMGKVAPW KGAIDNALVK LREAPDEEAK EKIYNVLAAS IRNDSLFLRL  420
    KSACDKFGAE QNRPVFPNEL RNNRDIRNVR SEWLEATQDV DAAAFVQLIA FLCNFLEGKE  480
    INELVTALIK KFEGIQALID LLRNLEGVDS IRFENEFALF NDDKGNMAGR IARQLRLLAS  540
    VGKMKPDMTD AKRVLYKSAL EILGAPPDEV SDEWLAENIL LDKSNNDYQK AKKTVNPFRN  600
    YIAKNVITSR SFYYLVRYAK PTAVRKLMSN PKIVRYVLKR LPEKQVASYY SAIWTQSESN  660
    SNEMVKLIEM IDRLTTEIAG FSFAVLKDKK DSIVSASRES RAVNLEVERL KKLTTLYMSI  720
    AYIAVKSLVK VNARYFIAYS ALERDLYFFN EKYGEEFRLH FIPYELNGKT CQFEYLAILK  780
    YYLARDEETL KRKCEICEEI KVGCEKHKKN ANPPYEYDQE WIDKKKALNS ERKACERRLH  840
    FSTHWAQYAT KRDENMAKHP QKWYDILASH YDELLALQAT GWLATQARND AEHLNPVNEF  900
    DVYIEDLRRY PEGTPKNKDY HIGSYFEIYH YIRQRAYLEE VLAKRKEYRD SGSFTDEQLD  960
    KLQKILDDIR ARGSYDKNLL KLEYLPFAYN LPRYKNLTTE ALFDDDSVSG KKRVAEWRER 1020
    EKTREAEREQ RRQR. 1034
  • An exemplary direct repeat sequence of CasRX/Cas13d Metagenomic hit (no protein accession): contig e-k87_11092736 (SEQ ID NO: 107) comprises or consists of the nucleic acid sequence:
  • CasRX/Cas13d Direct repeat 1:
    (SEQ ID NO: 108)
    gtgagaagtc tccttatggg gagatgctac.
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Ga0129306_1000735:
  • (SEQ ID NO: 109)
    MQKQREQQTV TDESERKKKP LKSGAKAAGL KSVFVLSEGK ELLTSFGRGN EAVPEKRVTG  60
    GTIANARTDN KEAFSAALQN KRFEVFGRTA GSSDDPLAVS RAPGQDLIGA KTALEERYFG 120
    RAFADNIHMQ VIYAIQDINK ILAVHANNIV YTLNNLDREA DPETDDFIGS GYLTLKNTFE 180
    TYCDPAALNE REREKVTVSK QHFDAFMQNP RLAYYGNAFF RKLSKAERLA RGREIFDKES 240
    PERRQEILGS RGKNKSVDDE IRALAPEWVK REERDVYSEL VLMSELRQSC FHGQQKNSAR 300
    IFRLDNDLGP GVDGARELLD RLYAEKINDL RSFDKTSASS NFRLLFNAYH ADNEKKKELA 360
    QEFYRFSVLK VSKNTGFSIR TLREKIIEDH AAQYRDKIYD SMRKKLFSTF DFFLWRFYEE 420
    REDEAEELRA CLRAARSDEE KEQIYAEAAA SCWPSVKPFV ESVAATLCDV VKGRTKLNKL 480
    KLSADESTLV RNAIDGVRIS PRASYFTKLI YLMTLFLDGK EINDLLTTLI HAFENIDSFL 540
    SVLGSERLER TFDANYRIFA DSGVIAQELR AVNSFARMTT EPFNSKLVMF EDAAQLFGMS 600
    GGLVEHAEEL REYLDNKMLD KTKLRLLPDG KVDTGFRNFI ISNVTESRRF RYLVRYCEPR 660
    AVRDYMSCRP LIRLTLRDMP DTILRRYYEQ SVGAATVDRE RILDTLADKL LSLRFTDFEN 720
    VNQRANAERN REKQKMMGII SLYLNVAYQI VKNLVYVNAR YTMAYHCAER DTELLLNAAG 780
    EGNLLRRDRS WPARLHLPRR ALARRRDRVE VMERDVARGP EAYNRDEWLG LVRTLRREKR 840
    VCDNLHNNYA YLCGADAEPG DASLSLLFVY RNKAAHLSVL NKGGRLSGDL KEAKSWFYVY 900
    HFLMQRVLEE EFRNTQALPE RLRELLMMAE RYRGCSKDLI KVLNLTFAYN LPRYKNLSID 960
    GRFDKNHPDP SDE. 973
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Ga0129317_1008067:
  • (SEQ ID NO: 110)
    MKKQKKSLVK AAGLKSAFVV GDSVYLTSFG KGNAARLDTK INPDNSTERY VSDSEKHTLK  60
    INSITDTELR LSGPFPKQAE AKNPTHKKDN EQKNTRQDML GLKSTLEKFY FGSTFDDNIH 120
    IQIIHNIQDI AKILAAHSNN AGYALDNMLA YQGVEFSDMI GYMGTSRTFD NYDPNHKNNK 180
    DFFRFLKLPR LGYFGSAFYS QKGKDFEKRS DEEVYNICAL MGQIRQCCFH GKQEKYQLKW 240
    LYNFHNFKSN KPFLDTLDKH FDEMIDRINK NFIKNNTPDL IILSGLYPDM AKKELVRLFY 300
    DFTTVKEYKN MGFSVKKLRE KMLESEEASD FRDKDYDSVR RKLYKLMDFC IYYLYYSDSE 360
    RNENLVSRLR ESLTDENKDI IYSKEAKIVW NELRKKFSTI LDNVKGSNIK KLENVKEKFI 420
    SEDEFDDIKL DIDISYFSKL MYVMCYFLDG KEINDLLTTL VSKFDNIGSI IEAATQIGIN 480
    IEFIDDFKFF DRSKDISVEL NIIRNFARMQ APVPNAKRAM QEDAIRILGG SEEDIFSILD 540
    DMTGYDKSGK KLAQSKKGFR NFIINNVVES SRFKYIVRYS NPQKIRKLAN NSVVVGFVLG 600
    KLPDAQIESY FNSCLPNRVY STPDKARESL RDMLHNISFN DFADVKQDDR RATPEEKVEK 660
    ERYKAIIGLY LTVMYHLVKN LVYVNSRYVM AFHCLERDAM HYDVSLDNYR DLIRHLISEG 720
    DSSCNHFISH NRRMRDCIEE NVKNSEQLIF GKEDAVIRFR NNVAHLSAIR NANEYIGDIR 780
    EITSYFALYH YLMQRKLIDD CKVNDTAHKY FEQLTKYKTY VMDMVKALCS PFGYNLPRFK 840
    NLSIEGKFDM HESK. 854
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Ga0224415_10048792:
  • (SEQ ID NO: 111)
    MSKKENRKSY VKGLGLKSTL VSDSKVYLTT FADGSNAKLE KCVENNKIIC ISNDKEAFAA  60
    SIANKNVGYK IKNDEKFRHP KGYDIISNNP LLHNNSVQQD MLGLKNVLEK RYFGKSSGGD 120
    NNLCIQIIHN IIDIEKILSE YIPNVVYAFN NIAGFKDEHN NIIDIIGTQT YNSSYTYADF 180
    SKDKSDKKYI EFQKLLKNKR LGYWGKAFFT GQGNNAKVRQ ENQCFHIIAL LISLRNWATH 240
    SNELDKHTKR TWLYKLDDTN ILNAEYVKTL NYLYDTIADE LTKSFSKNGA VNVNYLAKKY 300
    NIKDDLPGFS EQYFRFSIMK EQKNLGFNIS KLRENMLDFK DMSVIRDDHN RYDKDRSKIY 360
    TMMDFVIYRY YIDNNNDSID FINKLRSSID EKSKEKLYNE EANRLWNKLK EYMLYIKEFN 420
    GKLASRTPDR DGNISEFVES LPKIHRLLPR GQKISNFSKL MYLLTMFLDG KEINDLLTTL 480
    INKFENIQGF LDIMPEINVN AKFEPEYVFF NKSHEIAGEL KLIKGFAQMG EPAATLKLEM 540
    TADAIKILGT EKEDAELIKL AESLFKDENG KLLGNKQHGM RNFIGNNVIK SKRFHYLIRY 600
    GDPAHLHKIA TNKNVVRFVL GRIADMQKKQ GQKGKNQIDR YYEVCVGNKD IKKTIEEKID 660
    ALTDIIVNMN YDQFEKKKAV IENQNRGKTF EEKNKYKRDN AEREKFKKII SLYLTVIYHI 720
    LKNIVNVNSR YILGFHCLER DKQLYIEKYN KDKLDGFVAL TKFCLGDEER FEDLKAKAQA 780
    SIQALETANP KLYAKYMNYS DEEKKEEFKK QLNRERVKNA RNAYLKNIKN YIMIRLQLRD 840
    QTDSSGYLCG EFRDKVAHLE VARHAHEYIG NIKEVNSYFQ LYHYIMQCRL YDVLKNNTKA 900
    EAMVKGKAKE YFEALEKEGT YNDKLLKIAC VPFGYCIPRY KNLSMEELFD MNEEKKFKKK 960
    APENT. 965
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence CasRX/Cas13d 160582958_gene49834:
  • (SEQ ID NO: 112)
    MKNSVTFKLI QAQENKEAAR KKAKDIAEQA RIAKRNGVVK KEENRINRIQ IEIQTQKKSN   60
    TQNAYHLKSL AKAAGVKSVF AIGNDLLMTG FGPGNDATIE KRVFQNRAIE TLSSPEQYSA  120
    EFQNKQFKIK GNIKVLNHST QKMEEIQTEL QDNYNRPHFD LLGCKNVLEQ KYFGRTFSDN  180
    IHVQIAYNIM DIEKLLTPYI NNIIYTLNEL MRDNSKDDFF GCDSHFSVAY LYDELKAGYS  240
    DRLKTKPNLS KNIDRIWNNF CNYMNSDSGN TEARLAYFGE LFYKPKETGD AKSDYKTHLS  300
    NNQKEEWELK SDKEVYNIFA ILCDLRHFCT HGESITPSGK PFPYNLEKNL FPEAKQVLNS  360
    LFEEKAESLG AEAFGKTAGK TDVSILLKVF EKEQASQKEQ QALLKEYYDF KVQKTYKNMG  420
    FSIKKLREAI MEIPDAAKFK DDLYSSLRHK LYGLFDFILV KHFLDTSDSE NLQNNDIFRQ  480
    LRACRCEEEK DQVYRSIAVK VWEKVKKKEL NMFKQVVVIP SLSKDELKQM EMTKNTELLS  540
    SIETISTQAS LFSEMIFMMT YLLDGKEINL LCTSLIEKFE NIASFNEVLK SPQIGYETKY  600
    TEGYAFFKNA DKTAKELRQV NNMARMTKPL GGVNTKCVMY NEAAKILGAK PMSKAELESV  660
    FNLDNHDYTY SPSGKKIPNK NFRNFIINNV ITSRRFLYLI RYGNPEKIRK IAINPSIISF  720
    VLKQIPDEQI KRYYPPCIGK RTDDVTLMRD ELGKMLQSVN FEQFSRVNNK QNAKQNPNGE  780
    KARLQACVRL YLTVPYLFIK NMVNINARYV LAFHCLERDH ALCFNSRKLN DDSYNEMANK  840
    FQMVRKAKKE QYEKEYKCKK QETGTAHTKK IEKLNQQIAY IDKDIKNMHS YTCRNYRNLV  900
    AHLNVVSKLQ NYVSELPNDY QITSYFSFYH YCMQLGLMEK VSSKNIPLVE SLKNEANDAQ  960
    SYSAKKTLEY FDLIEKNRTY CKDFLKALNA PFSYNLPRFK NLSIEALFDK NIVYEQADLK 1020
    KE. 1022
  • An exemplary direct repeat sequence of CasRX/Cas13d proteins may comprise or consist of the sequence CasRX/Cas13d 160582958_gene49834 (SEQ ID NO: 112) comprises or consists of the nucleic acid sequence: CasRX/Cas13d DR:
  • (SEQ ID NO: 113)
    gaactacacc cctctgttct tgtaggggtc taacac. 36
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d 250twins_35838_GL0110300:
  • (SEQ ID NO: 114)
    MGNKQRVSAQ KRRENAKLCN QQKARQAESQ RDKIKNMNVE KMKNINTNDI KHTKTTAKKL  60
    GLKSTIIADK KIILTSFINE QSSKTANIEK VAGFKGDTID TISYTPRMFR SEINPGEIVI 120
    SKGDDLSEFA NPANFPIGRD YVKIRSALEK QYFGKEFPED NLHVQIAYNV ADIKKILSVY 180
    INNIIYMFYN LARSEEYDIF YNSQSENSGR DCDVIGSLYY QASYRNQDAN RFEKDGKKKA 240
    IDSLLDDTRA YYTYFDGLFS VPKREDDGKI KESEKEKAKD QNFDVLRLLS VGRQLTFHSD 300
    KSNNEAYLFD LSKLTRAAQD ENRRQDIQSL LNILNSTCRS NLEGVNGDFV KHAKNNLYVL 360
    NQLYPSLKAN DLIGEYYNFI VKKENRNIGI RLITVRELII EHNYTNLKDS KYDTYRNKIY 420
    TVLNFILFRE IQENSIAIKN FREKLRSTEK AEQPALYQAF ANKIYPMVQA KFAKAIDLFE 480
    EQYKTKFKSE FKGGISIENM QQQNILLQTE NIDYFSKYVL FLTKFLDGKE INELLCALIN 540
    KFDNIADLLD ISKQIGTPVV FCADYESLND AAKIAENIRL IKNIAHLRPA IQEAQSSKDN 600
    ADAAGTPATL LIDAYNMLNT DIQLVYGEAA YEELRKDLFE RKNGTKYNKK GKKVDVYDHK 660
    FRNFLINNVI KSKWFFYIAK YVKPADCAKM MSNKKMIEFA LRDLPETQIK RYYYTITGNE 720
    ALGDAESLKG VIIEQLHAFS IKNTLLSIKN MGEGEYKIQQ IGSSKEKLKA IVNLYLTVAY 780
    LLTKSLVKVN IRFSIAFGCL ERDLVLQKKS EKKFDAIINE ILLEDDKIRK ECDKERAQAK 840
    TLPRELAQER FAQIKRRESG CYFKSYHVYD YLSKNSNEFK QNHIDFAVTS YRNNVEHLNV 900
    VHCMTKYFSE VKDVKSYYGV YCYIMQRMLC DELIIKNQDK PDVRQTFEEY NRLLKDHGTY 960
    SKNLMWLLNF PFAYNLARYK NLSNEDLFNA KNNDQKSK. 998
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d 250twins_36050_GL0158985:
  • (SEQ ID NO: 115)
    MKKKHQSAAE KRQVKKLKNQ EKAQKYASEP SPLQSDTAGV ECSQKKTVVS HIASSKTLAK   60
    AMGLKSTLVM GDKLVITSFA ASKAVGGAGY KSANIEKITD LQGRVIEEHE RMFSADVGEK  120
    NIELSKNDCH TNVNNPVVTN IGKDYIGLKS RLEQEFFGKT FENDNLHVQL AYNILDIKKI  180
    LGTYVNNIIY IFYNLNRAGT GRDERMYDDL IGTLYAYKPM EAQQTYLLKG DKDMRRFEEV  240
    KQLLQNTSAY YVYYGTLFEK VKAKSKKEQR AKEAEIDACT AHNYDVLRLL SLMRQLCMHS  300
    VAGTAFKLAE SALFNIEDVL SADLKEILDE AFSGAVNKLN DGFVQHSGNN LYVLQQLYPN  360
    ETIERIAEKY YRLTVRKEDL NMGVNIKKLR ELIVGQYFPE VLDKEYDLSK NGDSVVTYRS  420
    KIYTVMNYIL LYYLEDHDSS RESMVEALRQ NREGDEGKEE IYRQFAKKVW NGVSGLFGVC  480
    LNLFKTEKRN KFRSKVALPD VSGAAYMLSS ENIDYFVKML FFVCKFLDGK EINELLCALI  540
    NKFDNIADIL DAAAQCGSSV WFVDSYRFFE RSRRISAQIR IVKNIASKDF KKSKKDSDES  600
    YPEQLYLDAL ALLGDVISKY KQNRDGSVVI DDQGNAVLTE QYKRFRYEFF EEIKRDESGG  660
    IKYKKSGKPE YNHQRRNFIL NNVLKSKWFF YVVKYNRPSS CRELMKNKEI LRFVLRDIPD  720
    SQVRRYFKAV QGEEAYASAE AMRTRLVDAL SQFSVTACLD EVGGMTDKEF ASQRAVDSKE  780
    KLRAIIRLYL TVAYLITKSM VKVNTRFSIA FSVLERDYYL LIDGKKKSSD YTGEDMLALT  840
    RKFVGEDAGL YREWKEKNAE AKDKYFDKAE RKKVLRQNDK MIRKMHFTPH SLNYVQKNLE  900
    SVQSNGLAAV IKEYRNAVAH LNIINRLDEY IGSARADSYY SLYCYCLQMY LSKNFSVGYL  960
    INVQKQLEEH HTYMKDLMWL LNIPFAYNLA RYKNLSNEKL FYDEEAAAEK ADKAENERGE. 1020
  • Yan et al. (2018) Mol Cell. 70(2):327-339 (doi: 10.1016/j.molcel.2018.02.2018) and Konermann et al. (2018) Cell 173(3):665-676 (doi: 10.1016/j.cell/2018.02.033) have described CasRX/Cas13d proteins and both of which are incorporated by reference herein in their entireties. Also see WO Publication Nos. WO2018/183703 (CasM) and WO2019/006471 (Cas13d), which are incorporated herein by reference in their entirety.
  • Exemplary wild type Cas13d proteins of the disclosure may comprise or consist of the amino acid sequence:
  • Cas13d (Ruminococcus Flavefaciens XPD3002) Sequence:
  • (SEQ ID NO: 45)
      1 IEKKKSFAKG MGVKSTLVSG SKVYMTTFAE GSDARLEKIV EGDSIRSVNE GEAFSAEMAD
     61 KNAGYKIGNA KFSHPKGYAV VANNPLYTGP VQQDMLGLKE TLEKRYFGES ADGNDNICIQ
    121 VIHNILDIEK ILAEYITNAA YAVNNISGLD KDIIGFGKFS TVYTYDEFKD PEHHRAAFNN
    181 NDKLINAIKA QYDEFDNFLD NPRLGYFGQA FFSKEGRNYI INYGNECYDI LALLSGLAHW
    241 VVANNEEESR ISRTWLYNLD KNLDNEYIST LNYLYDRITN ELTNSFSKNS AANVNYIAET
    301 LGINPAEFAE QYFRFSIMKE QKNLGFNITK LREVMLDRKD MSEIRKNHKV FDSIRTKVYT
    361 MMDFVIYRYY IEEDAKVAAA NKSLPDNEKS LSEKDIFVIN LRGSFNDDQK DALYYDEANR
    421 IWRKLENIMH NIKEFRGNKT REYKKKDAPR LPRILPAGRD VSAFSKLMYA LTMFLDGKEI
    481 NDLLTTLINK FDNIQSFLKV MPLIGVNAKF VEEYAFFKDS AKIADELRLI KSFARMGEPI
    541 ADARRAMYID AIRILGTNLS YDELKALADT FSLDENGNKL KKGKHGMRNF IINNVISNKR
    601 FHYLIRYGDP AHLHEIAKNE AVVKFVLGRI ADIQKKQGQN GKNQIDRYYE TCIGKDKGKS
    661 VSEKVDALTK IITGMNYDQF DKKRSVIEDT GRENAEREKF KKIISLYLTV IYHILKNIVN
    721 INARYVIGFH CVERDAQLYK EKGYDINLKK LEEKGFSSVT KLCAGIDETA PDKRKDVEKE
    781 MAERAKESID SLESANPKLY ANYIKYSDEK KAEEFTRQIN REKAKTALNA YLRNTKWNVI
    841 IREDLLRIDN KTCTLFANKA VALEVARYVH AYINDIAEVN SYFQLYHYIM QRIIMNERYE
    901 KSSGKVSEYF DAVNDEKKYN DRLLKLLCVP FGYCIPRFKN LSIEALFDRN EAAKFDKEKK
    961 KVSGNS.
  • Exemplary wild type Cas13d proteins of the disclosure may comprise or consist of the amino acid sequence:
  • Cas13d (contig e-k87_11092736):
  • (SEQ ID NO: 46)
    MKRQKTFAKRIGIKSTVAYGQGKYAITTFGKGSKAEIAVRSADPPEETLP
    TESDATLSIHAKFAKAGRDGREFKCGDVDETRIHTSRSEYESLISNPAES
    PREDYLGLKGTLERKFFGDEYPKDNLRIQIIYSILDIQKILGLYVEDILH
    FVDGLQDEPEDLVGLGLGDEKMQKLLSKALPYMGFFGSTDVFKVTKKREE
    RAAADEHNAKVFRALGAIRQKLAHFKWKESLAIFGANANMPIRFFQGATG
    GRQLWNDVIAPLWKKRIERVRKSFLSNSAKNLWVLYQVFKDDTDEKKKAR
    ARQYYHFSVLKEGKNLGFNLTKTREYFLDKFFPIFHSSAPDVKRKVDTFR
    SKFYAILDFIIYEASVSVANSGQMGKVAPWKGAIDNALVKLREAPDEEAK
    EKIYNVLAASIRNDSLFLRLKSACDKFGAEQNRPVFPNELRNNRDIRNVR
    SEWLEATQDVDAAAFVQLIAFLCNFLEGKEINELVTALIKKFEGIQALID
    LLRNLEGVDSIRFENEFALFNDDKGNMAGRIARQLRLLASVGKMKPDMTD
    AKRVLYKSALEILGAPPDEVSDEWLAENILLDKSNNDYQKAKKTVNPFRN
    YIAKNVITSRSFYYLVRYAKPTAVRKLMSNPKIVRYVLKRLPEKQVASYY
    SAIWTQSESNSNEMVKLIEMIDRLTTEIAGFSFAVLKDKKDSIVSASRES
    RAVNLEVERLKKLTTLYMSIAYIAVKSLVKVNARYFIAYSALERDLYFFN
    EKYGEEFRLHFIPYELNGKTCQFEYLAILKYYLARDEETLKRKCEICEEI
    KVGCEKHKKNANPPYEYDQEWIDKKKALNSERKACERRLHFSTHWAQYAT
    KRDENMAKHPQKWYDILASHYDELLALQATGWLATQARNDAEHLNPVNEF
    DVYIEDLRRYPEGTPKNKDYHIGSYFEIYHYIRQRAYLEEVLAKRKEYRD
    SGSFTDEQLDKLQKILDDIRARGSYDKNLLKLEYLPFAYNLPRYKNLTTE
    ALFDDDSVSGKKRVAEWREREKTREAEREQRRQR.
  • An exemplary direct repeat sequence of Cas13d (contig e-k87_11092736) (SEQ ID NO: 46) comprises or consists of the nucleic acid sequence:Cas13d (contig e-k87_11092736) Direct Repeat Sequence): GTGAGAAGTCTCCTTATGGGGAGATGCTAC (SEQ ID NO: 47).
  • Exemplary wild type Cas13d proteins of the disclosure may comprise or consist of the amino acid sequence:
  • Cas13d (160582958_gene49834):
  • (SEQ ID NO: 48) 
    MKNSVTFKLIQAQENKEAARKKAKDIAEQARIAKRNGVVKKEENRINRIQ
    IEIQTQKKSNTQNAYHLKSLAKAAGVKSVFAIGNDLLMTGFGPGNDATIE
    KRVFQNRAIETLSSPEQYSAEFQNKQFKIKGNIKVLNHSTQKMEEIQTEL
    QDNYNRPHFDLLGCKNVLEQKYFGRTFSDNIHVQIAYNIMDIEKLLTPYI
    NNIIYTLNELMRDNSKDDFFGCDSHFSVAYLYDELKAGYSDRLKTKPNLS
    KNIDRIWNNFCNYMNSDSGNTEARLAYFGELFYKPKETGDAKSDYKTHLS
    NNQKEEWELKSDKEVYNIFAILCDLRHFCTHGESITPSGKPFPYNLEKNL
    FPEAKQVLNSLFEEKAESLGAEAFGKTAGKTDVSILLKVFEKEQASQKEQ
    QALLKEYYDFKVQKTYKNMGFSIKKLREAIMEIPDAAKFKDDLYSSLRHK
    LYGLFDFILVKHFLDTSDSENLQNNDIFRQLRACRCEEEKDQVYRSIAVK
    VWEKVKKKELNMFKQVVVIPSLSKDELKQMEMTKNTELLSSIETISTQAS
    LFSEMIFMMTYLLDGKEINLLCTSLIEKFENIASFNEVLKSPQIGYETKY
    TEGYAFFKNADKTAKELRQVNNMARMTKPLGGVNTKCVMYNEAAKILGAK
    PMSKAELESVFNLDNHDYTYSPSGKKIPNKNFRNFIINNVITSRRFLYLI
    RYGNPEKIRKIAINPSIISFVLKQIPDEQIKRYYPPCIGKRTDDVTLMRD
    ELGKMLQSVNFEQFSRVNNKQNAKQNPNGEKARLQACVRLYLTVPYLFIK
    NMVNINARYVLAFHCLERDHALCFNSRKLNDDSYNEMANKFQMVRKAKKE
    QYEKEYKCKKQETGTAHTKKIEKLNQQIAYIDKDIKNMHSYTCRNYRNLV
    AHLNVVSKLQNYVSELPNDYQITSYFSFYHYCMQLGLMEKVSSKNIPLVE
    SLKNEANDAQSYSAKKTLEYFDLIEKNRTYCKDFLKALNAPFSYNLPRFK
    NLSIEALFDKNIVYEQADLKKE.
  • An exemplary direct repeat sequence of Cas13d (160582958_gene49834) (SEQ ID NO: 48) comprises or consists of the nucleic acid sequence:
  • Cas13d (160582958_gene49834) Direct Repeat Sequence:
  • (SEQ ID NO: 49)
    GAACTACACCCCTCTGTTCTTGTAGGGGTCTAACAC.
  • Exemplary wild type Cas13d proteins of the disclosure may comprise or consist of the amino acid sequence:
  • Cas13d (contig tpg|DJXD01000002.1|; uncultivated Ruminococcus assembly, UBA7013, from sheep gut metagenome):
  • (SEQ ID NO: 50)
    MKKQKSKKTVSKTSGLKEALSVQGTVIMTSFGKGNMANLSYKIPSSQKPQ
    NLNSSAGLKNVEVSGKKIKFQGRHPKIATTDNPLFKPQPGMDLLCLKDKL
    EMHYFGKTFDDNIHIQLIYQILDIEKILAVHVNNIVFTLDNVLHPQKEEL
    TEDFIGAGGWRINLDYQTLRGQTNKYDRFKNYIKRKELLYFGEAFYHENE
    RRYEEDIFAILTLLSALRQFCFHSDLSSDESDHVNSFWLYQLEDQLSDEF
    KETLSILWEEVTERIDSEFLKTNTVNLHILCHVFPKESKETIVRAYYEFL
    IKKSFKNMGFSIKKLREIMLEQSDLKSFKEDKYNSVRAKLYKLFDFIITY
    YYDHHAFEKEALVSSLRSSLTEENKEEIYIKTARTLASALGADFKKAAAD
    VNAKNIRDYQKKANDYRISFEDIKIGNTGIGYFSELIYMLILLLDGKEIN
    DLLTTLINKFDNIISFIDILKKLNLEFKFKPEYADFFNMTNCRYTLEELR
    VINSIARMQKPSADARKIMYRDALRILGMDNRPDEEIDRELERTMPVGAD
    GKFIKGKQGFRNFIASNVIESSRFHYLVRYNNPHKTRTLVKNPNVVKFVL
    EGIPETQIKRYFDVCKGQEIPPTSDKSAQIDVLARIISSVDYKIFEDVPQ
    SAKINKDDPSRNFSDALKKQRYQAIVSLYLTVMYLITKNLVYVNSRYVIA
    FHCLERDAFLHGVTLPKMNKKIVYSQLTTHLLTDKNYTTYGHLKNQKGHR
    KWYVLVKNNLQNSDITAVSSFRNIVAHISVVRNSNEYISGIGELHSYFEL
    YHYLVQSMIAKNNWYDTSHQPKTAEYLNNLKKHHTYCKDFVKAYCIPFGY
    VVPRYKNLTINELFDRNNPNPEPKEEV.
  • An exemplary direct repeat sequence of Cas13d (contig tpg|DJXD01000002.1|; uncultivated Ruminococcus assembly, UBA7013, from sheep gut metagenome) (SEQ ID NO: 50) comprises or consists of the nucleic acid sequence:Cas13d (contig tpg|DXJD01000002.1|; uncultivated Ruminococcus assembly, UBA7013, from sheep gut metagenome) Direct Repeat Sequence: CAACTACAACCCCGTAAAAATACGGGGTTCTGAAAC (SEQ ID NO: 51).
  • gRNA Target Sequences
  • In some embodiments of the compositions of the disclosure, a target sequence of an RNA molecule comprises a sequence motif corresponding to the first RNA binding protein and/or the second RNA binding protein.
  • In some embodiments of the compositions and methods of the disclosure, the sequence motif is a signature of a disease or disorder.
  • A sequence motif of the disclosure may be isolated or derived from a sequence of foreign or exogenous sequence found in a genomic sequence, and therefore translated into an mRNA molecule of the disclosure or a sequence of foreign or exogenous sequence found in an RNA sequence of the disclosure.
  • A sequence motif of the disclosure may comprise or consist of a mutation in an endogenous sequence that causes a disease or disorder. The mutation may comprise or consist of a sequence substitution, inversion, deletion, insertion, transposition, or any combination thereof.
  • A sequence motif of the disclosure may comprise or consist of a repeated sequence. In some embodiments, the repeated sequence may be associated with a microsatellite instability (MSI). MSI at one or more loci results from impaired DNA mismatch repair mechanisms of a cell of the disclosure. A hypervariable sequence of DNA may be transcribed into an mRNA of the disclosure comprising a target sequence comprising or consisting of the hypervariable sequence.
  • A sequence motif of the disclosure may comprise or consist of a biomarker. The biomarker may indicate a risk of developing a disease or disorder. The biomarker may indicate a healthy gene (low or no determinable risk of developing a disease or disorder. The biomarker may indicate an edited gene. Exemplary biomarkers include, but are not limited to, single nucleotide polymorphisms (SNPs), sequence variations or mutations, epigenetic marks, splice acceptor sites, exogenous sequences, heterologous sequences, and any combination thereof.
  • A sequence motif of the disclosure may comprise or consist of a secondary, tertiary or quaternary structure. The secondary, tertiary or quaternary structure may be endogenous or naturally occurring. The secondary, tertiary or quaternary structure may be induced or non-naturally occurring. The secondary, tertiary or quaternary structure may be encoded by an endogenous, exogenous, or heterologous sequence.
  • In some embodiments of the compositions and methods of the disclosure, a target sequence of an RNA molecule comprises or consists of between 2 and 100 nucleotides or nucleic acid bases, inclusive of the endpoints. In some embodiments, the target sequence of an RNA molecule comprises or consists of between 2 and 50 nucleotides or nucleic acid bases, inclusive of the endpoints. In some embodiments, the target sequence of an RNA molecule comprises or consists of between 2 and 20 nucleotides or nucleic acid bases, inclusive of the endpoints.
  • In some embodiments of the compositions and methods of the disclosure, a target sequence of an RNA molecule is continuous. In some embodiments, the target sequence of an RNA molecule is discontinuous. For example, the target sequence of an RNA molecule may comprise or consist of one or more nucleotides or nucleic acid bases that are not contiguous because one or more intermittent nucleotides are positioned in between the nucleotides of the target sequence.
  • In some embodiments of the compositions and methods of the disclosure, a target sequence of an RNA molecule is naturally occurring. In some embodiments, the target sequence of an RNA molecule is non-naturally occurring. Exemplary non-naturally occurring target sequences may comprise or consist of sequence variations or mutations, chimeric sequences, exogenous sequences, heterologous sequences, chimeric sequences, recombinant sequences, sequences comprising a modified or synthetic nucleotide or any combination thereof.
  • In some embodiments of the compositions and methods of the disclosure, a target sequence of an RNA molecule binds to a guide RNA of the disclosure.
  • In some embodiments of the compositions and methods of the disclosure, a target sequence of an RNA molecule binds to a first RNA binding protein of the disclosure.
  • In some embodiments of the compositions and methods of the disclosure, a target sequence of an RNA molecule binds to a second RNA binding protein of the disclosure.
    • RNA Molecules
  • In some embodiments of the compositions and methods of the disclosure, an RNA molecule of the disclosure comprises a target sequence. In some embodiments, the RNA molecule of the disclosure comprises at least one target sequence. In some embodiments, the RNA molecule of the disclosure comprises one or more target sequence(s). In some embodiments, the RNA molecule of the disclosure comprises two or more target sequences.
  • In some embodiments of the compositions and methods of the disclosure, an RNA molecule of the disclosure is a naturally occurring RNA molecule. In some embodiments, the RNA molecule of the disclosure is a non-naturally occurring molecule. Exemplary non-naturally occurring RNA molecules may comprise or consist of sequence variations or mutations, chimeric sequences, exogenous sequences, heterologous sequences, chimeric sequences, recombinant sequences, sequences comprising a modified or synthetic nucleotide or any combination thereof.
  • In some embodiments of the compositions and methods of the disclosure, an RNA molecule of the disclosure comprises or consists of a sequence isolated or derived from a virus.
  • In some embodiments of the compositions and methods of the disclosure, an RNA molecule of the disclosure comprises or consists of a sequence isolated or derived from a prokaryotic organism. In some embodiments, an RNA molecule of the disclosure comprises or consists of a sequence isolated or derived from a species or strain of archaea or a species or strain of bacteria.
  • In some embodiments of the compositions and methods of the disclosure, the RNA molecule of the disclosure comprises or consists of a sequence isolated or derived from a eukaryotic organism. In some embodiments, an RNA molecule of the disclosure comprises or consists of a sequence isolated or derived from a species of protozoa, parasite, protist, algae, fungi, yeast, amoeba, worm, microorganism, invertebrate, vertebrate, insect, rodent, mouse, rat, mammal, or a primate. In some embodiments, an RNA molecule of the disclosure comprises or consists of a sequence isolated or derived from a human.
  • In some embodiments of the compositions and methods of the disclosure, the RNA molecule of the disclosure comprises or consists of a sequence derived from a coding sequence from a genome of an organism or a virus. In some embodiments, the RNA molecule of the disclosure comprises or consists of a primary RNA transcript, a precursor messenger RNA (pre-mRNA) or messenger RNA (mRNA). In some embodiments, the RNA molecule of the disclosure comprises or consists of a gene product that has not been processed (e.g. a transcript). In some embodiments, the RNA molecule of the disclosure comprises or consists of a gene product that has been subject to post-transcriptional processing (e.g. a transcript comprising a 5′ cap and a 3′ polyadenylation signal). In some embodiments, the RNA molecule of the disclosure comprises or consists of a gene product that has been subject to alternative splicing (e.g. a splice variant). In some embodiments, the RNA molecule of the disclosure comprises or consists of a gene product that has been subject to removal of non-coding and/or intronic sequences (e.g. a messenger RNA (mRNA)).
  • In some embodiments of the compositions and methods of the disclosure, the RNA molecule of the disclosure comprises or consists of a sequence derived from a non-coding sequence (e.g. a non-coding RNA (ncRNA)). In some embodiments, the RNA molecule of the disclosure comprises or consists of a ribosomal RNA. In some embodiments, the RNA molecule of the disclosure comprises or consists of a small ncRNA molecule. Exemplary small RNA molecules of the disclosure include, but are not limited to, microRNAs (miRNAs), small interfering (siRNAs), piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs), extracellular or exosomal RNAs (exRNAs), and small Cajal body-specific RNAs (scaRNAs). In some embodiments, the RNA molecule of the disclosure comprises or consists of a long ncRNA molecule. Exemplary long RNA molecules of the disclosure include, but are not limited to, X-inactive specific transcript (Xist) and HOX transcript antisense RNA (HOTAIR).
  • In some embodiments of the compositions and methods of the disclosure, the RNA molecule of the disclosure contacted by a composition of the disclosure in an intracellular space. In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in a cytosolic space. In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in a nucleus. In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in a vesicle, membrane-bound compartment of a cell, or an organelle.
  • In some embodiments of the compositions and methods of the disclosure, the RNA molecule of the disclosure contacted by a composition of the disclosure in an extracellular space. In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in an exosome. In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in a liposome, a polymersome, a micelle or a nanoparticle. In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in an extracellular matrix. In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in a droplet. In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in a microfluidic droplet.
  • In some embodiments of the compositions and methods of the disclosure, a RNA molecule of the disclosure comprises or consists of a single-stranded sequence. In some embodiments, the RNA molecule of the disclosure comprises or consists of a double-stranded sequence. In some embodiments, the double-stranded sequence comprises two RNA molecules. In some embodiments, the double-stranded sequence comprises one RNA molecule and one DNA molecule. In some embodiments, including those wherein the double-stranded sequence comprises one RNA molecule and one DNA molecule, compositions of the disclosure selectively bind and, optionally, selectively cut the RNA molecule.
    • RNA-Binding Endonucleases
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a nuclease domain. In some embodiments, the second RNA binding protein binds RNA in a manner in which it associates with RNA. In some embodiments, the second RNA binding protein associates with RNA in a manner in which it cleaves RNA.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of an RNAse.
  • In some embodiments, the second RNA binding protein comprises or consists of an RNAse1. In some embodiments, the RNAse1 protein comprises or consists of:
  • (SEQ ID NO: 20)
    KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGLCKPVNTFVHEP
    LVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTS
    PKERHIIVACEGSPYVPVHFDASVEDST.
  • In some embodiments, the second RNA binding protein comprises or consists of an RNAse4. In some embodiments, the RNAse4 protein comprises or consists of:
  • (SEQ ID NO: 21)
    QDGMYQRFLRQHVHPEETGGSDRYCDLMMQRRKMTLYHCKRFNTFIHEDI
    WNIRSICSTTNIQCKNGKMNCHEGVVKVTDCRDTGSSRAPNCRYRAIAST
    RRVVIACEGNPQVPVHFDG.
  • In some embodiments, the second RNA binding protein comprises or consists of an RNAse6. In some embodiments, the RNAse6 protein comprises or consists of:
  • (SEQ ID NO: 22)
    WPKRLTKAHWFEIQHIQPSPLQCNRAMSGINNYTQHCKHQNTFLHDSFQN
    VAAVCDLLSIVCKNRRHNCHQSSKPVNMTDCRLTSGKYPQCRYSAAAQYK
    FFIVACDPPQKSDPPYKLVPVHLDSIL.
  • In some embodiments, the second RNA binding protein comprises or consists of an RNAse7. In some embodiments, the RNAse7 protein comprises or consists of:
  • (SEQ ID NO: 23)
    APARAGFCPLLLLLLLGLWVAEIPVSAKPKGMTSSQWFKIQHMQPSPQAC
    NSAMKNINKHTKRCKDLNTFLHEPFSSVAATCQTPKIACKNGDKNCHQSH
    GPVSLTMCKLTSGKYPNCRYKEKRQNKSYVVACKPPQKKDSQQFHLVPVH
    LDRVL.
  • In some embodiments, the second RNA binding protein comprises or consists of an RNAse8. In some embodiments, the RNAse8 protein comprises or consists of:
  • (SEQ ID NO: 24)
    TSSQWFKTQHVQPSPQACNSAMSIINKYTERCKDLNTFLHEPFSSVAITC
    QTPNIACKNSCKNCHQSHGPMSLTMGELTSGKYPNCRYKEKHLNTPYIVA
    CDPPQQGDPGYPLVPVHLDKVV.
  • In some embodiments, the second RNA binding protein comprises or consists of an RNAse2. In some embodiments, the RNAse2 protein comprises or consists of:
  • (SEQ ID NO: 25)
    KPPQFTWAQWFETQHINMTSQQCTNAMQVINNYQRRCKNQNTFLLTTFAN
    VVNVCGNPNWITCPSNKTRKNCHHSGSQVPLIFICNLTTPSPQNISNCRY
    AQTPANMFYIVACDNRDQRRDPPQYPVVPVHLDRII.
  • In some embodiments, the second RNA binding protein comprises or consists of an RNAse6PL. In some embodiments, the RNAse6PL protein comprises or consists of:
  • (SEQ ID NO: 26)
    DKRLRDNHEWKKLIMVQHWPETVCEKIQNDCRDPPDYWTIHGLWPDKSEG
    CNRSWPFNLEEIKKNWMEITDSSLPSPSMGPAPPRWMRSTPRRSTLAEAW
    NSTGSWTSTGGCALPPAALPSGDLCCRPSLTAGSRGVGVDLTALHQLLHV
    HYSATGIIPEECSEPTKPFQIILHHDHTEWVQSIGMPIWGTISSSESAIG
    KNEESQPACAVLSHDS.
  • In some embodiments, the second RNA binding protein comprises or consists of an RNAseL. In some embodiments, the RNAseL protein comprises or consists of:
  • (SEQ ID NO: 27)
    AAVEDNHLLIKAVQNEDVDLVQQLLEGGANVNFQEEEGGWTPLHNAVQMS
    REDIVELLLRHGADPVLRKKNGATPFILAAIAGSVKdLLKLFLSKGADVN
    ECDFYGFTAFMEAAVYGKVKALKFLYKRGANVNLRRKTKEDQERLRKGGA
    TALMDAAEKGHVEVLKILLDEMGADVNACDNMGRNALIHALLSSDDSDVE
    AITHLLLDHGADVNVRGERGKTPLILAVEKKHLGLVQRLLEQEHIEINDT
    DSDGKTALLLAVELKLKKIAELLCKRGASTDCGDLVMTARRNYDHSLVKV
    LLSHGAKEDFHPPAEDWKPQSSHWGAALKDLHRIYRPMIGKLKFFIDEKY
    KIADTSEGGIYLGFYEKQEVAVKTFCEGSPRAQREVSCLQSSRENSHLVT
    FYGSESHRGHLFVCVTLCEQTLEACLDVHRGEDVENEEDEFARNVLSSIF
    KAVQELHLSCGYTHQDLQPQNILIDSKKAAHLADFDKSIKWAGDPQEVKR
    DLEDLGRLVLYVVKKGSISFEDLKAQSNEEVVQLSPDEETKDLIHRLFHP
    GEHVRDCLSDLLGHPFFWTWESRYRTLRNVGNESDIKTRKSESEILRLLQ
    PGPSEHSKSFDKWTTKINECVMKKMNKFYEKRGNFYQNTVGDLLKFIRNL
    GEHIDEEKHKKMKLKIGDPSLYFQKTFPDLVIYVYTKLQNTEYRKHFPQT
    HSPNKPQCDGAGGASGLASPGC.
  • In some embodiments, the second RNA binding protein comprises or consists of an RNAseT2. In some embodiments, the RNAseT2 protein comprises or consists of:
  • (SEQ ID NO: 28)
    VQHWPETVCEKIQNDCRDPPDYWTIHGLWPDKSEGCNRSWPFNLEEIKDL
    LPEMRAYWPDVIHSFPNRSRFWKHEWEKHGTCAAQVDALNSQKKYFGRSL
    ELYRELDLNSVLLKLGIKPSINYYQVADFKDALARVYGVIPKIQCLPPSQ
    DEEVQTIGQIELCLTKQDQQLQNCTEPGEQPSPKQEVWLANGAAESRGLR
    VCEDGPVFYPPPKKTKH.
  • In some embodiments, the second RNA binding protein comprises or consists of an RNAse11. In some embodiments, the RNAse11 protein comprises or consists of:
  • (SEQ ID NO: 29)
    EASESTMKIIKEEFTDEEMQYDMAKSGQEKQTIEILMNPILLVKNTSLSM
    SKDDMSSTLLTFRSLHYNDPKGNSSGNDKECCNDMTVWRKVSEANGSCKW
    SNNFIRSSTEVMRRVHRAPSCKFVQNPGISCCESLELENTVCQFTTGKQF
    PRCQYHSVTSLEKILTVLTGHSLMSWLVCGSKL.
  • In some embodiments, the second RNA binding protein comprises or consists of an RNAseT2-like. In some embodiments, the RNAseT2-like protein comprises or consists of:
  • (SEQ ID NO: 30)
    XLGGADKRLRDNHEWKKLIMVQHWPETVCEKIQNDCRDPPDYWTIHGLWP
    DKSEGCNRSWPFNLEEIKDLLPEMRAYWPDVIHSFPNRSRFWKHEWEKHG
    TCAAQVDALNSQKKYFGRSLELYRELDLNSVLLKLGIKPSINYYQTTEED
    LNLDVEPTTEDTAEEVTIHVLLHSALFGEIGPRRW.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a mutated RNAse.
  • In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(K41R)) polypeptide. In some embodiments, the Rnase1(K41R) polypeptide comprises or consists of:
  • (SEQ ID NO: 116)
    KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCRPVNTFVHEP
    LVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTS
    PKERHIIVACEGSPYVPVHFDASVEDST.
  • In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(K41R, D121E)) polypeptide. In some embodiments, the Rnase1 (Rnase1(K41R, D121E)) polypeptide comprises or consists of:
  • (SEQ ID NO: 117)
    KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCRPVNTFVHE
    PLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYR
    TSPKERHIIVACEGSPYVPVHFEASVEDST.
  • In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(K41R, D121E, H119N)) polypeptide. In some embodiments, the Rnase1 (Rnase1(K41R, D121E, H119N)) polypeptide comprises or consists of:
  • (SEQ ID NO: 118)
    KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCRPVNTFVHE
    PLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYR
    TSPKERHIIVACEGSPYVPVNFEASVEDST.
  • In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1. In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(H119N)) polypeptide. In some embodiments, the Rnase1 (Rnase1(H119N)) polypeptide comprises or consists of:
  • (SEQ ID NO: 119)
    KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCKPVNTFVHE
    PLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYR
    TSPKERHIIVACEGSPYVPVNFDASVEDST.
  • In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide. In some embodiments, the Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide comprises or consists of: KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGDCKPVNTFVHEPLVDVQNV CFQEKVTCKDGQGNCYKSNSSMHITDCRLTADSDYPNCAYRTSPKERHIIVACEGSPYV PVNFDASVEDST (SEQ ID NO: 120). In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide. In some embodiments, the Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N, K41R, D121E)) polypeptide comprises or consists of:
  • (SEQ ID NO: 121)
    KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGDCRPVNTFVHE
    PLVDVQNVCFQEKVTCKDGQGNCYKSNSSMHITDCRLTADSDYPNCAYR
    TSPKERHIIVACEGSPYVPVNFEASVEDST.

    In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1 (R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide. In some embodiments, the Rnase1 (Rnase1 (R39D, N67D, N88A, G89D, R91D)) polypeptide comprises or consists of:
  • (SEQ ID NO: 122)
    KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGDCKPVNTFVHEP
    LVDVQNVCFQEKVTCKDGQGNCYKSNSSMHITDCRLTADSDYPNCAYRTS
    PKERHIIVACEGSPYVPVHFDASVEDST.

    In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1 (R39D, N67D, N88A, G89D, R91D, H119N, K41R, D121E)) polypeptide that comprises or consists of:
  • (SEQ ID NO: 208)
    KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGDCRPVNTFVHEP
    LVDVQNVCFQEKVTCKDGQGNCYKSNSSMHITDCRLTADSDYPNCAYRTS
    PKERHIIVACEGSPYVPVNFEASVEDST.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a NOB1 polypeptide. In some embodiments, the NOB1 polypeptide comprises or consists of:
  • (SEQ ID NO: 31)
    APVEHVVADAGAFLRHAALQDIGKNIYTIREVVTEIRDKATRRRLAVLPY
    ELRFKEPLPEYVRLVTEFSKKTGDYPSLSATDIQVLALTYQLEAEFVGVS
    HLKQEPQKVKVSSSIQHPETPLHISGFHLPYKPKPPQETEKGHSACEPEN
    LEFSSFMFWRNPLPNIDHELQELLIDRGEDVPSEEEEEEENGFEDRKDDS
    DDDGGGWITPSNIKQIQQELEQCDVPEDVRVGCLTTDFAMQNVLLQMGLH
    VLAVNGMLIREARSYILRCHGCFKTTSDMSRVFCSHCGNKTLKKVSVTV.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of an endonuclease. In some embodiments, the second RNA binding protein comprises or consists of an endonuclease V (ENDOV). In some embodiments, the ENDOV protein comprises or consists of:
  • (SEQ ID NO: 32)
    AFSGLQRVGGVDVSFVKGDSVRACASLVVLSFPELEVVYEESRMVSLTAP
    YVSGFLAFREVPFLLELVQQLREKEPGLMPQVLLVDGNGVLHHRGFGVAC
    HLGVLTDLPCVGVAKKLLQVDGLENNALHKEKIRLLQTRGDSFPLLGDSG
    TVLGMALRSHDRSTRPLYISVGHRMSLEAAVRLTCCCCRFRIPEPVRQAD
    ICSREHIRKS.
  • In some embodiments, the second RNA binding protein comprises or consists of an endonuclease G (ENDOG). In some embodiments, the ENDOG protein comprises or consists of:
  • (SEQ ID NO: 33)
    AELPPVPGGPRGPGELAKYGLPGLAQLKSRESYVLCYDPRTRGALWVVEQ
    LRPERLRGDGDRRECDFREDDSVHAYHRATNADYRGSGFDRGHLAAAANH
    RWSQKAMDDTFYLSNVAPQVPHLNQNAWNNLEKYSRSLTRSYQNVYVCTG
    PLFLPRTEADGKSYVKYQVIGKNHVAVPTHFFKVLILEAAGGQIELRTYV
    MPNAPVDEAIPLERFLVPIESIERASGLLFVPNILARAGSLKAITAGSK.
  • In some embodiments, the second RNA binding protein comprises or consists of an endonuclease D1 (ENDOD1). In some embodiments, the ENDOD1 protein comprises or consists of:
  • (SEQ ID NO: 34)
    RLVGEEEAGFGECDKFFYAGTPPAGLAADSHVKICQRAEGAERFATLYST
    RDRIPVYSAFRAPRPAPGGAEQRWLVEPQIDDPNSNLEEAINEAEAITSV
    NSLGSKQALNTDYLDSDYQRGQLYPFSLSSDVQVATFTLTNSAPMTQSFQ
    ERWYVNLHSLMDRALTPQCGSGEDLYILTGTVPSDYRVKDKVAVPEFVWL
    AACCAVPGGGWAMGFVKHTRDSDIIEDVMVKDLQKLLPFNPQLFQNNCGE
    TEQDTEKMKKILEVVNQIQDEERMVQSQKSSSPLSSTRSKRSTLLPPEAS
    EGSSSFLGKLMGFIATPFIKLFQLIYYLVVAILKNIVYFLWCVTKQVING
    IESCLYRLGSATISYFMAIGEELVSIPWKVLKVVAKVIRALLRILCCLLK
    AICRVLSIPVRVLVDVATFPVYTMGAIPIVCKDIALGLGGTVSLLFDTAF
    GTLGGLFQVVFSVCKRIGYKVTFDNSGEL.
  • In some embodiments, the second RNA binding protein comprises or consists of a Human flap endonuclease-1 (hFEN1). In some embodiments, the hFEN1 polypeptide comprises or consists of:
  • (SEQ ID NO: 35)
    MGIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGG
    DVLQNEEGETTSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKR
    SERRAEAEKQLQQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGI
    PYLDAPSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAK
    KLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLI
    QKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVLDPESVELKWSE
    PNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGSTQGRLDDFFKVTGSL
    SSAKRKEPEPKGSTKKKAKTGAAGKFKRGK.
  • In some embodiments, the second RNA binding protein comprises or consists of a DNA repair endonuclease XPF (ERCC4) polypeptide. In some embodiments, the ERCC4 polypeptide comprises or consists of:
  • (SEQ ID NO: 124)
    MESGQPARRIAMAPLLEYERQLVLELLDTDGLVVCARGLGADRLLYHFLQ
    LHCHPACLVLVLNTQPAEEEYFINQLKIEGVEHLPRRVTNEITSNSRYEV
    YTQGGVIFATSRILVVDFLTDRIPSDLITGILVYRAHRIIESCQEAFILR
    LFRQKNKRGFIKAFTDNAVAFDTGFCHVERVMRNLFVRKLYLWPRFHVAV
    NSFLEQHKPEVVEIHVSMTPTMLAIQTAILDILNACLKELKCHNPSLEVE
    DLSLENAIGKPFDKTIRHYLDPLWHQLGAKTKSLVQDLKILRTLLQYLSQ
    YDCVTFLNLLESLRATEKAFGQNSGWLFLDSSTSMFINARARVYHLPDAK
    MSKKEKISEKMEIKEGEGILWG.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of an Endonuclease III-like protein 1 (NTHL) polypeptide. In some embodiments, the NTHL polypeptide comprises or consists of:
  • (SEQ ID NO: 123)
    CSPQESGMTALSARMLTRSRSLGPGAGPRGCREEPGPLRRREAAAEARKS
    HSPVKRPRKAQRLRVAYEGSDSEKGEGAEPLKVPVWEPQDWQQQLVNIRA
    MRNKKDAPVDHLGTEHCYDSSAPPKVRRYQVLLSLMLSSQTKDQVTAGAM
    QRLRARGLTVDSILQTDDATLGKLIYPVGFWRSKVKYIKQTSAILQQHYG
    GDIPASVAELVALPGVGPKMAHLAMAVAWGTVSGIAVDTHVHRIANRLRW
    TKKATKSPEETRAALEEWLPRELWHEINGLLVGFGQQTCLPVHPRCHACL
    NQALCPAAQGL.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a human Schlafen 14 (hSLFN14) polypeptide. In some embodiments, the hSLFN14 polypeptide comprises or consists of:
  • (SEQ ID NO: 36)
    ESTHVEFKRFTTKKVIPRIKEMLPHYVSAFANTQGGYVLIGVDDKSKEVV
    GCKWEKVNPDLLKKEIENCIEKLPTFHFCCEKPKVNFTTKILNVYQKDVL
    DGYVCVIQVEPFCCVVFAEAPDSWIMKDNSVTRLTAEQWVVMMLDTQSAP
    PSLVTDYNSCLISSASSARKSPGYPIKVHKFKEALQ.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a human beta-lactamase-like protein 2 (hLACTB2) polypeptide.
  • In some embodiments, the hLACTB2 polypeptide comprises or consists of:
  • (SEQ ID NO: 37)
    TLQGTNTYLVGTGPRRILIDTGEPAIPEYISCLKQALTEFNTAIQEIVVT
    HWHRDHSGGIGDICKSINNDTTYCIKKLPRNPQREDIGNGEQQYVYLKDG
    DVIKTEGATLRVLYTPGHTDDHMALLLEEENAIFSGDCILGEGTTVFEDL
    YDYMNSLKELLKIKADITYPGHGPVIHNAEAKIQQYISHRNIREQQILTL
    FRENFEKSFTVMELVKIIYKNTPENLHEMAKHNLLLHLKKLEKEGKIFSN
    TDPDKKWKAHL.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of an apurinic/apyrimidinic (AP) endodeoxyribonuclease (APEX) polypeptide. In some embodiments, the second RNA binding protein comprises or consists of an apurinic/apyrimidinic (AP) endodeoxyribonuclease (APEX2) polypeptide. In some embodiments, the APEX2 polypeptide comprises or consists of:
  • (SEQ ID NO: 38)
    MLRVVSWNINGIRRPLQGVANQEPSNCAAVAVGRILDELDADIVCLQETK
    VTRDALTEPLAIVEGYNSYFSFSRNRSGYSGVATFCKDNATPVAAEEGLS
    GLFATQNGDVGCYGNMDEFTQEELRALDSEGRALLTQHKIRTWEGKEKTL
    TLINVYCPHADPGRPERLVFKMRFYRLLQIRAEALLAAGSHVIILGDLNT
    AHRPIDHWDAVNLECFEEDPGRKWMDSLLSNLGCQSASHVGPFIDSYRCF
    QPKQEGAFTCWSAVTGARHLNYGSRLDYVLGDRTLVIDTFQASFLLPEVM
    GSDHCPVGAVLSVSSVPAKQCPPLCTRFLPEFAGTQLKILRFLVPLEQSP
    VLEQSTLQHNNQTRVQTCQNKAQVRSTRPQPSQVGSSRGQKNLKSYFQPS
    PSCPQASPDIELPSLPLMSALMTPKTPEEKAVAKVVKGQAKTSEAKDEKE
    LRTSFWKSVLAGPLRTPLCGGHREPCVMRTVKKPGPNLGRRFYMCARPRG
    PPTDPSSRCNFFLWSRPS.
  • In some embodiments, the APEX2 polypeptide comprises or consists of:
  • (SEQ ID NO: 39)
    MLRVVSWNINGIRRPLQGVANQEPSNCAAVAVGRILDELDADIVCLQETK
    VTRDALTEPLAIVEGYNSYFSFSRNRSGYSGVATFCKDNATPVAAEEGLS
    GLFATQNGDVGCYGNMDEFTQEELRALDSEGRALLTQHKIRTWEGKEKTL
    TLINVYCPHADPGRPERLVFKMRFYRLLQIRAEALLAAGSHVIILGDLNT
    AHRPIDHWDAVNLECFEEDPGRKWMDSLLSNLGCQSASHVGPFIDSYRCF
    QPKQEGAFTCWSAVTGARHLNYGSRLDYVLGDRTLVIDTFQASFLLPEVM
    GSDHCPVGAVLSVSSVPAKQCPPLCTRFLPEFAGTQLKILRFLVPLEQS
    P.
  • In some embodiments, the second RNA binding protein comprises or consists of an apurinic or apyrimidinic site lyase (APEX1) polypeptide. In some embodiments, the APEX1 polypeptide comprises or consists of:
  • (SEQ ID NO: 125)
    PKRGKKGAVAEDGDELRTEPEAKKSKTAAKKNDKEAAGEGPALYEDPPDQ
    KTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSE
    NKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEH
    DQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLAS
    RKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLAD
    SFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLS.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of an angiogenin (ANG) polypeptide. In some embodiments, the ANG polypeptide comprises or consists of:
  • (SEQ ID NO: 40)
    QDNSRYTHFLTQHYDAKPQGRDDRYCESIMRRRGLTSPCKDINTFIEGNK
    RSIKAICENKNGNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGF
    RNVVVACENGLPVHLDQSIFRRP.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a heat responsive protein 12 (HRSP12) polypeptide. In some embodiments, the HRSP12 polypeptide comprises or consists of:
  • (SEQ ID NO: 41)
    SSLIRRVISTAKAPGAIGPYSQAVLVDRTIYISGQIGMDPSSGQLVSGGV
    AEEAKQALKNMGEILKAAGCDFTNVVKTTVLLADINDFNTVNEIYKQYFK
    SNFPARAAYQVAALPKGSRIEIEAVAIQGPLTTASL.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a Zinc Finger CCCH-Type Containing 12A (ZC3H12A) polypeptide. In some embodiments, the ZC3H12A polypeptide comprises or consists of:
  • (SEQ ID NO: 42)
    GGGTPKAPNLEPPLPEEEKEGSDLRPVVIDGSNVAMSHGNKEVFSCRGIL
    LAVNWFLERGHTDITVFVPSWRKEQPRPDVPITDQHILRELEKKKILVFT
    PSRRVGGKRVVCYDDRFIVKLAYESDGIVVSNDTYRDLQGERQEWKRFIE
    ERLLMYSFVNDKFMPPDDPLGRHGPSLDNFLRKKPLTLE.
  • In some embodiments, the ZC3H12A polypeptide comprises or consists of:
  • (SEQ ID NO: 43)
    SGPCGEKPVLEASPTMSLWEFEDSHSRQGTPRPGQELAAEEASALELQMK
    VDFFRKLGYSSTEIHSVLQKLGVQADTNTVLGELVKHGTATERERQTSPD
    PCPQLPLVPRGGGTPKAPNLEPPLPEEEKEGSDLRPVVIDGSNVAMSHGN
    KEVFSCRGILLAVNWFLERGHTDITVFVPSWRKEQPRPDVPITDQHILRE
    LEKKKILVFTPSRRVGGKRVVCYDDRFIVKLAYESDGIVVSNDTYRDLQG
    ERQEWKRFIEERLLMYSFVNDKFMPPDDPLGRHGPSLDNFLRKKPLTLEH
    RKQPCPYGRKCTYGIKCRFFHPERPSCPQRSVADELRANALLSPPRAPSK
    DKNGRRPSPSSQSSSLLTESEQCSLDGKKLGAQASPGSRQEGLTQTYAPS
    GRSLAPSGGSGSSFGPTDWLPQTLDSLPYVSQDCLDSGIGSLESQMSELW
    GVRGGGPGEPGPPRAPYTGYSPYGSELPATAAFSAFGRAMGAGHFSVPAD
    YPPAPPAFPPREYWSEPYPLPPPTSVLQEPPVQSPGAGRSPWGRAGSLAK
    EQASVYTKLCGVFPPHLVEAVMGRFPQLLDPQQLAAEILSYKSQHPSE.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a Reactive Intermediate Imine Deaminase A (RIDA) polypeptide. In some embodiments, the RIDA polypeptide comprises or consists of:
  • (SEQ ID NO: 44)
    SSLIRRVISTAKAPGAIGPYSQAVLVDRTIYISGQIGMDPSSGQLVSGGV
    AEEAKQALKNMGEILKAAGCDFTNVVKTTVLLADINDFNTVNEIYKQYFK
    SNFPARAAYQVAALPKGSRIEIEAVAIQGPLTTASL.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a Phospholipase D Family Member 6 (PDL6) polypeptide. In some embodiments, the PDL6 polypeptide comprises or consists of:
  • (SEQ ID NO: 126)
    EALFFPSQVTCTEALLRAPGAELAELPEGCPCGLPHGESALSRLLRALLA
    ARASLDLCLFAFSSPQLGRAVQLLHQRGVRVRVVTDCDYMALNGSQIGLL
    RKAGIQVRHDQDPGYMHHKFAIVDKRVLITGSLNWTTQAIQNNRENVLIT
    EDDEYVRLFLEEFERIWEQFNPTKYTFFPPKKSHGSCAPPVSRAGGRLLS
    WHRTCGTSSESQT.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a mitochondrial ribonuclease P catalytic subunit (KIAA0391) polypeptide. In some embodiments, the KIAA0391 polypeptide comprises or consists of:
  • (SEQ ID NO: 127)
    KARYKTLEPRGYSLLIRGLIHSDRWREALLLLEDIKKVITPSKKNYNDCI
    QGALLHQDVNTAWNLYQELLGHDIVPMLETLKAFFDFGKDIKDDNYSNKL
    LDILSYLRNNQLYPGESFAHSIKTWFESVPGKQWKGQFTTVRKSGQCSGC
    GKTIESIQLSPEEYECLKGKIMRDVIDGGDQYRKTTPQELKRFENFIKSR
    PPFDVVIDGLNVAKMFPKVRESQLLLNVVSQLAKRNLRLLVLGRKHMLRR
    SSQWSRDEMEEVQKQASCFFADDISEDDPFLLYATLHSGNHCRFITRDLM
    RDHKACLPDAKTQRLFFKWQQGHQLAIVNRFPGSKLTFQRILSYDTVVQT
    TGDSWHIPYDEDLVERCSCEVPTKWLCLHQKT.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of an argonaute 2 (AGO2) polypeptide.
  • In some embodiments of the compositions of the disclosure, the AGO2 polypeptide comprises or consists of:
  • (SEQ ID NO: 128)
    SVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQM
    KNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVIFLGADVT
    HPPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVREL
    LIQFYKSTRFKPTRIIFYRDGVSEGQFQQVLHHELLAIREACIKLEKDYQ
    PGITFIVVQKRHHTRLFCTDKNERVGKSGNIPAGTTVDTKITHPTEFDFY
    LCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQLCHTYVRCTRSVSI
    PAPAYYAHLVAFRARYHLVDKEHDSAEGSHTSGQSNGRDHQALAKAVQVH
    QDTLRTMYFA.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a mitochondrial nuclease EXOG (EXOG) polypeptide. In some embodiments, the EXOG polypeptide comprises or consists of:
  • (SEQ ID NO: 129)
    QGAEGALTGKQPDGSAEKAVLEQFGFPLTGTEARCYTNHALSYDQAKRVP
    RWVLEHISKSKIMGDADRKHCKFKPDPNIPPTFSAFNEDYVGSGWSRGHM
    APAGNNKFSSKAMAETFYLSNIVPQDFDNNSGWNRIEMYCRELTERFEDV
    WVVSGPLTLPQTRGDGKKIVSYQVIGEDNVAVPSHLYKVILARRSSVSTE
    PLALGAFVVPNEAIGFQPQLTEFQVSLQDLEKLSGLVFFPHLDRTSDIRN
    ICSVDTCKLLDFQEFTLYLSTRKIEGARSVLRLEKIMENLKNAEIEPDDY
    FMSRYEKKLEELKAKEQSGTQIRKPS.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a Zinc Finger CCCH-Type Containing 12D (ZC3H12D) polypeptide. In some embodiments, the ZC3H12D polypeptide comprises or consists of:
  • (SEQ ID NO: 130)
    EHPSKMEFFQKLGYDREDVLRVLGKLGEGALVNDVLQELIRTGSRPGALE
    HPAAPRLVPRGSCGVPDSAQRGPGTALEEDFRTLASSLRPIVIDGSNVAM
    SHGNKETFSCRGIKLAVDWERDRGHTYIKVFVPSWRKDPPRADTPIREQH
    VLAELERQAVLVYTPSRKVHGKRLVCYDDRYIVKVAYEQDGVIVSNDNYR
    DLQSENPEWKWFIEQRLLMFSEVNDREMPPDDPLGRHGPSLSNFLSRKPK
    PPEPSWQHCPYGKKCTYGIKCKFYHPERPHHAQLAVADELRAKTGARPGA
    GAEEQRPPRAPGGSAGARAAPREPFAHSLPPARGSPDLAALRGSFSRLAF
    SDDLGPLGPPLPVPACSLTPRLGGPDWVSAGGRVPGPLSLPSPESQFSPG
    DLPPPPGLQLQPRGEHRPRDLHGDLLSPRRPPDDPWARPPRSDRFPGRSV
    WAEPAWGDGATGGLSVYATEDDEGDARARARIALYSVFPRDQVDRVMAAF
    PELSDLARLILLVQRCQSAGAPLGKP.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of an endoplasmic reticulum to nucleus signaling 2 (ERN2) polypeptide. In some embodiments, the ERN2 polypeptide comprises or consists of:
  • (SEQ ID NO: 131)
    RQQQPQVVEKQQETPLAPADFAHISQDAQSLHSGASRRSQKRLQSPSKQA
    QPLDDPEAEQLTVVGKISFNPKDVLGRGAGGTFVFRGQFEGRAVAVKRLL
    RECFGLVRREVQLLQESDRHPNVLRYFCTERGPQFHYIALELCRASLQEY
    VENPDLDRGGLEPEVVLQQLMSGLAHLHSLHIVHRDLKPGNILITGPDSQ
    GLGRVVLSDFGLCKKLPAGRCSFSLHSGIPGTEGWMAPELLQLLPPDSPT
    SAVDIFSAGCVFYYVLSGGSHPFGDSLYRQANILTGAPCLAHLEEEVHDK
    VVARDLVGAMLSPLPQPRPSAPQVLAHPFFWSRAKQLQFFQDVSDWLEKE
    SEQEPLVRALEAGGCAVVRDNWHEHISMPLQTDLRKFRSYKGTSVRDLLR
    AVRNKKHHYRELPVEVRQALGQVPDGFVQYFTNRFPRLLLHTHRAMRSCA
    SESLFLPYYPPDSEARRPCPGATGR.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a pelota mRNA surveillance and ribosome rescue factor (PELO) polypeptide. In some embodiments, the PELO polypeptide comprises or consists of:
  • (SEQ ID NO: 132)
    KLVRKNIEKDNAGQVTLVPEEPEDMWHTYNLVQVGDSLRASTIRKVQTES
    STGSVGSNRVRTTLTLCVEAIDFDSQACQLRVKGTNIQENEYVKMGAYHT
    IELEPNRQFTLAKKQWDSVVLERIEQACDPAWSADVAAVVMQEGLAHICL
    VTPSMTLTRAKVEVNIPRKRKGNCSQHDRALERFYEQVVQAIQRHIHFDV
    VKCILVASPGFVREQFCDYLFQQAVKTDNKLLLENRSKFLQVHASSGHKY
    SLKEALCDPTVASRLSDTKAAGEVKALDDFYKMLQHEPDRAFYGLKQVEK
    ANEAMAIDTLLISDELFRHQDVATRSRYVRLVDSVKENAGTVRIFSSLHV
    SGEQLSQLTGVAAILRFPVPELSDQEGDSSSEED.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a YBEY metallopeptidase (YBEY) polypeptide. In some embodiments, the YBEY polypeptide comprises or consists of:
  • (SEQ ID NO: 133)
    SLVIRNLQRVIPIRRAPLRSKIEIVRRILGVQKFDLGIICVDNKNIQHIN
    RIYRDRNVPTDVLSFPFHEHLKAGEFPQPDFPDDYNLGDIFLGVEYIFHQ
    CKENEDYNDVLTVTATHGLCHLLGFTHGTEAEWQQMFQKEKAVLDELGRR
    TGTRLQPLTRGLFGGS.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a cleavage and polyadenylation specific factor 4 like (CPSF4L) polypeptide. In some embodiments, the CPSF4L polypeptide comprises or consists of:
  • (SEQ ID NO: 134)
    QEVIAGLERFTFAFEKDVEMQKGTGLLPFQGMDKSASAVCNFFTKGLCEK
    GKLCPFRHDRGEKMVVCKHWLRGLCKKGDHCKFLHQYDLTRMPECYFYSK
    FGDCSNKECSFLHVKPAFKSQDCPWYDQGFCKDGPLCKYRHVPRIMCLNY
    LVGFCPEGPKCQFAQKIREFKLLPGSKI.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of an hCG_2002731 polypeptide. In some embodiments, the hCG_2002731 polypeptide comprises or consists of:
  • (SEQ ID NO: 135)
    KLVRKNIEKDNAGQVTLVPEEPEDMWHTYNLVQVGDSLRASTIRKVQTES
    STGSVGSNRVRTTLTLCVEAIDFDSQACQLRVKGTNIQENEYVKMGAYHT
    IELEPNRQFTLAKKQWDSVVLERIEQACDPAWSADVAAVVMQEGLAHICL
    VTPSMTLTRAKVEVNIPRKRKGNCSQHDRALERFYEQVVQAIQRHIHFDV
    VKCILVASPGFVREQFCDYMFQQAVKTDNKLLLENRSKFLQVHASSGHKY
    SLKEALCDPTVASRLSDTKAAGEVKALDDFYKMLQHEPDRAFYGLKQVEK
    ANEAMAIDTLLISDELFRHQDVATRSRYVRLVDSVKENAGTVRIFSSLHV
    SGEQLSQLTGVAAILRFPVPELSDQEGDSSSEED.
  • In some embodiments, the hCG_2002731 polypeptide comprises or consists of:
  • (SEQ ID NO: 136)
    DPAWSADVAAVVMQEGLAHICLVTPSMTLTRAKVEVNIPRKRKGNCSQHD
    RALERFYEQVVQAIQRHIHFDVVKCILVASPGFVREQFCDYMFQQAVKTD
    NKLLLENRSKFLQVHASSGHKYSLKEALCDPTVASRLSDTKAAGEVKALD
    DFYKMLQHEPDRAFYGLKQVEKANEAMAIDTLLISDELFRHQDVATRSRY
    VRLVDSVKENAGTVRIFSSLHVSGEQLSQLTGVAAILRFPVPELSDQEGD
    SSSEED.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of an Excision Repair Cross-Complementation Group 1 (ERCC1) polypeptide. In some embodiments, the ERCC1 polypeptide comprises or consists of:
  • (SEQ ID NO: 137)
    MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVRGNPVLKFVRNVPWE
    FGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQ
    VDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADL
    LMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLA
    LCPGLGPQK.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a ras-related C3 botulinum toxin substrate 1 isoform (RAC1) polypeptide. In some embodiments, the RAC1 polypeptide comprises or consists of:
  • (SEQ ID NO: 138)
    KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCKPVNTFVHEP
    LVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTS
    PKERHIIVACEGSPYVPVHFDASVEDST.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a Ribonuclease A A1 (RAA1) polypeptide. In some embodiments, the RAA1 polypeptide comprises or consists of:
  • (SEQ ID NO: 139)
    QDNSRYTHFLTQHYDAKPQGRDDRYCESIMRRRGLTSPCKDINTFIHGNK
    RSIKAICENKNGNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGF
    RNVVVACENGLPVHLDQSIFRRP.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a Ras Related Protein (RAB1) polypeptide. In some embodiments, the RAB1 polypeptide comprises or consists of:
  • (SEQ ID NO: 140)
    GLGLVQPSYGQDGMYQRFLRQHVHPEETGGSDRYCNLMMQRRKMTLYHCK
    RFNTFIHEDIWNIRSICSTTNIQCKNGKMNCHEGVVKVTDCRDTGSSRAP
    NCRYRAIASTRRVVIACEGNPQVPVHFDG.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a DNA Replication Helicase/Nuclease 2 (DNA2) polypeptide. In some embodiments, the DNA2 polypeptide comprises or consists of:
  • (SEQ ID NO: 141)
    XSAVDNILLKLAKFKIGFLRLGQIQKVHPAIQQFTEQEICRSKSIKSLAL
    LEELYNSQLIVATTCMGINHPIFSRKIFDFCIVDEASQISQPICLGPLFF
    SRRFVLVGDHQQLPPLVLNREARALGMSESLFKRLEQNKSAVVQLTVQYR
    MNSKIMSLSNKLTYEGKLECGSDKVANAVINLRHFKDVKLELEFYADYSD
    NPWLMGVFEPNNPVCFLNTDKVPAPEQVEKGGVSNVTEAKLIVFLTSIFV
    KAGCSPSDIGIIAPYRQQLKIINDLLARSIGMVEVNTVDKYQGRDKSIVL
    VSFVRSNKDGTVGELLKDWRRLNVAITRAKHKLILLGCVPSLNCYPPLEK
    LLNHLNSEKLISFFFCIWSHLIALL.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a FLJ35220 polypeptide. In some embodiments, the FLJ35220 polypeptide comprises or consists of:
  • (SEQ ID NO: 142)
    MALRSHDRSTRPLYISVGHRNISLEAAVRLTCCCCRFRIPEPVRQADICS
    REHIRKSLGLPGPPTPRSPKAQRPVACPKGDSGESSALC.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a FLJ13173 polypeptide. In some embodiments, the FLJ13173 polypeptide comprises or consists of:
  • (SEQ ID NO: 143)
    CYTNHALSYDQAKRVPRWVLEHISKSKIMGDADRKHCKFKPDPNIPPTFS
    AFNEDYVGSGWSRGHMAPAGNNKFSSKAMAETFYLSNIVPQDFDNNSGYW
    NRIEMYCRELTERFEDVWVVSGPLTLPQTRGDGKKIVSYQVIGEDNVAVP
    SHLYKVILARRSSVSTEPLALGAFVVPNEAIGFQPQLTEFQVSLQDLEKL
    SGLVFFPHLDRT.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of Teneurin Transmembrane Protein (TENM) polypeptide. In some embodiments, the second RNA binding protein comprises or consists of Teneurin Transmembrane Protein 1 (TENM1) polypeptide. In some embodiments, the TENM1 polypeptide comprises or consists of:
  • (SEQ ID NO: 144)
    VTVSQMTSVLNGKTRRFADIQLQHGALCFNIRYGTTVEEEKNHVLEIARQ
    RAVAQAWTKEQRRLQEGEEGIRAWTEGEKQQLLSTGRVQGYDGYFVLSVE
    QYLELSDSANNIHFMRQSEIGRR.

    In some embodiments, the second RNA binding protein comprises or consists of Teneurin Transmembrane Protein 2 (TENM2) polypeptide. In some embodiments, the TENM2 polypeptide comprises or consists of:
  • (SEQ ID NO: 145)
    TVSQPTLLVNGKTRRFTNIEFQYSTLLLSIRYGLTPDTLDEEKARVLDQA
    RQRALGTAWAKEQQKARDGREGSRLWTEGEKQQLLSTGRVQGYEGYYVLP
    VEQYPELADSSSNIQFLRQNEMGKR.

    In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a Ribonuclease Kappa (RNAseK) polypeptide. In some embodiments, the RNAseK polypeptide comprises or consists of:
  • (SEQ ID NO: 204)
    MGWLRPGPRPLCPPARASWAFSHRFPSPLAPRRSPTPFFMASLLCCGPKL
    AACGIVLSAWGVIMLIMLGIFFNVHSAVLIEDVPFTEKDFENGPQNIYNL
    YEQVSYNCFIAAGLYLLLGGFSFCQVRLNKRKEYMVR.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a transcription activator-like effector nuclease (TALEN) polypeptide or a nuclease domain thereof. In some embodiments, the TALEN polypeptide comprises or consists of:
  • (SEQ ID NO: 205)
    1 MRIGKSSGWL NESVSLEYEH VSPPTRPRDT RRRPRAAGDG
    GLAHLHRRLA VGYAEDTPRT
    61 EARSPAPRRP LPVAPASAPP APSLVPEPPM PVSLPAVSSP
    RFSAGSSAAI TDPFPSLPPT
    121 PVLYAMAREL EALSDATWQP AVPLPAEPPT DARRGNTVFD
    EASASSPVIA SACPQAFASP
    181 PRAPRSARAR RARTGGDAWP APTFLSRPSS SRIGRDVFGK
    LVALGYSREQ IRKLKQESLS
    241 EIAKYHTTLT GQGFTHADIC RISRRRQSLR VVARNYPELA
    AALPELTRAH IVDIARQRSG
    301 DLALQALLPV ATALTAAPLR LSASQIATVA QYGERPAIQA
    LYRLRRKLTR APLHLTPQQV
    361 VAIASNTGGK RALEAVCVQL PVLRAAPYRL STEQVVAIAS
    NKGGKQALEA VKAHLLDLLG
    421 APYVLDTEQV VAIASHNGGK QALEAVKADL LDLRGAPYAL
    STEQVVAIAS HNGGKQALEA
    481 VKADLLELRG APYALSTEQV VAIASHNGGK QALEAVKAHL
    LDLRGVPYAL STEQVVAIAS
    541 HNGGKQALEA VKAQLLDLRG APYALSTAQV VAIASNGGGK
    QALEGIGEQL LKLRTAPYGL
    601 STEQVVAIAS HDGGKQALEA VGAQLVALRA APYALSTEQV
    VAIASNKGGK QALEAVKAQL
    661 LELRGAPYAL STAQVVAIAS HDGGNQALEA VGTQLVALRA
    APYALSTEQV VAIASHDGGK
    721 QALEAVGAQL VALRAAPYAL NTEQVVAIAS SHGGKQALEA
    VRALFPDLRA APYALSTAQL
    781 VAIASNPGGK QALEAVRALF RELRAAPYAL STEQVVAIAS
    NHGGKQALEA VRALFRGLRA
    841 APYGLSTAQV VAIASSNGGK QALEAVWALL PVLRATPYDL
    NTAQIVAIAS HDGGKPALEA
    901 VWAKLPVLRG APYALSTAQV VAIACISGQQ ALEAIEAHMP
    TLRQASHSLS PERVAAIACI
    961 GGRSAVEAVR QGLPVKAIRR IRREKAPVAG PPPASLGPTP
    QELVAVLHFF RAHQQPRQAF
    1021 VDALAAFQAT RPALLRLLSS VGVTEIEALG GTIPDATERW
    QRLLGRLGFR PATGAAAPSP
    1081 DSLQGFAQSL ERTLGSPGMA GQSACSPHRK RPAETAIAPR
    SIRRSPNNAG QPSEPWPDQL
    1141 AWLQRRKRTA RSHIRADSAA SVPANLHLGT RAQFTPDRLR
    AEPGPIMQAH TSPASVSFGS
    1201 HVAFEPGLPD PGTPTSADLA SFEAEPFGVG PLDFHLDWLL
    QILET.

    In some embodiments, the TALEN polypeptide comprises or consists of:
  • (SEQ ID NO: 206)
    1 mdpirsrtps parellpgpq pdrvqptadr ggappaggpl
    dglparrtms rtrlpsppap
    61 spafsagsfs dllrqfdpsl ldtslldsmp avgtphtaaa
    paecdevqsg lraaddpppt
    121 vrvavtaarp prakpaprrr aaqpsdaspa aqvdlrtlgy
    sqqqqekikp kvgstvaqhh
    181 ealvghgfth ahivalsrhp aalgtvavky qdmiaalpea
    thedivgvgk qwsgaralea
    241 lltvagelrg pplqldtgql vkiakrggvt aveavhasrn
    altgaplnlt paqvvaiasn
    301 nggkgaletv grllpvlcqa hgltpaqvva iashdggkqa
    letmqrllpv lcgahglppd
    361 qvvaiasnig gkqaletvqr llpvlcqahg ltpdqvvaia
    shgggkqale tvqrllpvlc
    421 qahgltpdqv vaiashdggk galetvqrll pvlcqahglt
    pdqvvaiasn gggkqaletv
    481 qrllpvlcqa hgltpdqvva iasnggkqal etvqrllpvl
    cqahgltpdq vvaiashdgg
    541 kqaletvqrl lpvlcgthgl tpaqvvaias hdggkqalet
    vqqllpvlcq ahgltpdqvv
    601 aiasniggkq alatvqrllp vlcqahgltp dqvvaiasng
    ggkqaletvq rllpvlcqah
    661 gltpdqvvai asngggkqal etvqrllpvl cqahgltqvq
    vvaiasnigg kqaletvqrl
    721 lpvlcqahgl tpaqvvaias hdggkqalet vqrllpvlcq
    ahgltpdqvv aiasngggkq
    781 aletvqrllp vlcqahgltq eqvvaiasnn ggkqaletvq
    rllpvlcqah gltpdqvvai
    841 asngggkqal etvqrllpvl cqahgltpaq vvaiasnigg
    kqaletvqrl lpvlcqdhgl
    901 tlaqvvaias niggkqalet vqrllpvlcq ahgltqdqvv
    aiasniggkq aletvqrllp
    961 vlcqdhgltp dqvvaiasni ggkqaletvq rllpvlcqdh
    gltldqvvai asnggkqale
    1021 tvqrllpvlc qdhgltpdqv vaiasnsggk qaletvqrll
    pvlcqdhglt pnqvvaiasn
    1081 ggkqalesiv aqlsrpdpal aaltndhlva laclggrpam
    davkkglpha pelirrvnrr
    1141 igertshrva dyaqvvrvle ffqchshpay afdeamtqfg
    msrnglvqlf rrvgvtelea
    1201 rggtlppasq rwdrilqasg mkrakpspts aqtpdqaslh
    afadslerdl dapspmhegd
    1261 qtgassrkrs rsdravtgps aqhsfevrvp eqrdalhlpl
    swrvkrprtr iggglpdpgt
    1321 piaadlaass tvmweqdaap fagaaddfpa fneeelawlm
    ellpqsgsvg gti.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists a zinc finger nuclease polypeptide or a nuclease domain thereof. In some embodiments, the second RNA binding protein comprises or consists of a ZNF638 polypeptide or a nuclease domain thereof. In some embodiments, the ZNF638 polypeptide polypeptide comprises or consists of:
  • (SEQ ID NO: 207)
    1 MSRPRFNPRG DFPLQRPRAP NPSGMRPPGP FMRPGSMGLP
    RFYPAGRARG IPHRFAGHES
    61 YQNMGPQRMN VQVTQHRTDP RLTKEKLDFH EAQQKKGKPH
    GSRWDDEPHI SASVAVKQSS
    121 VTQVTEQSPK VQSRYTKESA SSILASFGLS NEDLEELSRY
    PDEQLTPENM PLILRDIRMR
    181 KMGRRLPNLP SQSRNKETLG SEAVSSNVID YGHASKYGYT
    EDPLEVRIYD PEIPTDEVEN
    241 EFQSQQNISA SVPNPNVICN SMFPVEDVFR QMDFPGESSN
    NRSFFSVESG TKMSGLHISG
    301 GQSVLEPIKS VNQSINQTVS QTMSQSLIPP SMNQQPFSSE
    LISSVSQQER IPHEPVINSS
    361 NVHVGSRGSK KNYQSQADIP IRSPFGIVKA SWLPKFSHAD
    AQKMKRLPTP SMMNDYYAAS
    421 PRIFPHLCSL CNVECSHLKD WIQHQNTSTH IESCRQLRQQ
    YPDWNPEILP SRRNEGNRKE
    481 NETPRRRSHS PSPRRSRRSS SSHRFRRSRS PMHYMYRPRS
    RSPRICHRFI SRYRSRSRSR
    541 SPYRIRNPFR GSPKCFRSVS PERMSRRSVR SSDRKKALED
    VVQRSGHGTE FNKQKHLEAA
    601 DKGHSPAQKP KTSSGTKPSV KPTSATKSDS NLGGHSIRCK
    SKNLEDDTLS ECKQVSDKAV
    661 SLQRKLRKEQ SLHYGSVLLI TELPEDGCTE EDVRKLFQPF
    GKVNDVLIVP YRKEAYLEME
    721 FKEAITAIMK YIETTPLTIK GKSVKICVPG KKKAQNKEVK
    KKTLESKKVS ASTLKRDADA
    781 SKAVEIVTST SAAKTGQAKA SVAKVNKSTG KSASSVKSVV
    TVAVKGNKAS IKTAKSGGKK
    841 SLEAKKTGNV KNKDSNKPVT IPENSEIKTS IEVKATENCA
    KEAISDAALE ATENEPLNKE
    901 TEEMCVMLVS NLPNKGYSVE EVYDLAKPFG GLKDILILSS
    HKKAYIEINR KAAESMVKFY
    961 TCFPVLMDGN QLSISMAPEN MNIKDEEAIF ITLVKENDPE
    ANIDTIYDRF VHLDNLPEDG
    1021 LQCVLCVGLQ FGKVDHHVFI SNRNKAILQL DSPESAQSMY
    SFLKQNPQNI GDHMLTCSLS
    1081 PKIDLPEVQI EHDPELEKES PGLKNSPIDE SEVQTATDSP
    SVKPNELEEE STPSIQTETL
    1141 VQQEEPCEEE AEKATCDSDF AVETLELETQ GEEVKEEIPL
    VASASVSIEQ FTENAEECAL
    1201 NQQMFNSDLE KKGAEIINPK TALLPSDSVF AEERNLKGIL
    EESPSEAEDF ISGITQTMVE
    1261 AVAEVEKNET VSEILPSTCI VTLVPGIPTG DEKTVDKKNI
    SEKKGNMDEK EEKEFNTKET
    1321 RMDLQIGTEK AEKNEGRMDA EKVEKMAAMK EKPAENTLFK
    AYPNKGVGQA NKPDETSKTS
    1381 ILAVSDVSSS KPSIKAVIVS SPKAKATVSK TENQKSFPKS
    VPRDQINAEK KLSAKEFGLL
    1441 KPTSARSGLA ESSSKFKPTQ SSLTRGGSGR ISALQGKLSK
    LDYRDITKQS QETEARPSIM
    1501 KRDDSNNKTL AEQNTKNPKS TTGRSSKSKE EPLFPFNLDE
    FVTVDEVIEE VNPSQAKQNP
    1561 LKGKRKETLK NVPFSELNLK KKKGKTSTPR GVEGELSFVT
    LDEIGEEEDA AAHLAQALVT
    1621 VDEVIDEEEL NMEEMVKNSN SLFTLDELID QDDCISHSEP
    KDVTVLSVAE EQDLLKQERL
    1681 VTVDEIGEVE ELPLNESADI TFATLNTKGN EGDTVRDSIG
    FISSQVPEDP STLVTVDEIQ
    1741 DDSSDLHLVT LDEVTEEDED SLADFNNLKE ELNFVTVDEV
    GEEEDGDNDL KVELAQSKND
    1801 HPTDKKGNRK KRAVDTKKTK LESLSQVGPV NENVMEEDLK
    TMIERHLTAK TPTKRVRIGK
    1861 TLPSEKAVVT EPAKGEEAFQ MSEVDEESGL KDSEPERKRK
    KTEDSSSGKS VASDVPEELD
    1921 FLVPKAGFFC PICSLFYSGE KAMTNHCKST RHKQNTEKFM
    AKQRKEKEQN EAEERSSR.
  • In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a PIN domain derived from the human SMG6 protein, also commonly known as telomerase-binding protein EST1A isoform 3, NCBI Reference Sequence: NP_001243756.1. In some embodiments, the PIN from hSMG6 is used herein in the form of a Cas fusion protein and as an internal control, for example, and without limitation, see FIG. 9, which shows PIN-dSauCas9, PIN-dSauCas9dHNH, PIN-dSPCas9, and dcjeCas9-PIN.
  • In some embodiments of the compositions of the disclosure, the composition further comprises (a) a sequence comprising a gRNA that specifically binds within an RNA molecule and (b) a sequence encoding a nuclease. In some embodiments, a nuclease comprises a sequence isolated or derived from a CRISPR/Cas protein. In some embodiments, the CRISPR/Cas protein is isolated or derived from any one of a type I, a type IA, a type IB, a type IC, a type ID, a type IE, a type IF, a type IU, a type III, a type IIIA, a type IIIB, a type IIIC, a type IIID, a type IV, a type IVA, a type IVB, a type II, a type IIA, a type IIB, a type ITC, a type V, or a type VI CRISPR/Cas protein. In some embodiments, a nuclease comprises a sequence isolated or derived from a TALEN or a nuclease domain thereof. In some embodiments, a nuclease comprises a sequence isolated or derived from a zinc finger nuclease or a nuclease domain thereof.
    • Fusion Proteins
  • In some embodiments of the compositions and methods of the disclosure, the composition comprises a sequence encoding a target RNA-binding fusion protein comprising (a) a sequence encoding a first RNA-binding polypeptide or portion thereof; and (b) a sequence encoding a second RNA-binding polypeptide, wherein the first RNA-biding polypeptide binds a target RNA, and wherein the second RNA-binding polypeptide comprises RNA-nuclease activity.
  • In some embodiments, a target RNA-binding fusion protein is an RNA-guided target RNA-binding fusion protein. RNA-guided target RNA-binding fusion proteins comprise at least one RNA-binding polypeptide which corresponds to a gRNA which guides the RNA-binding polypeptide to target RNA. RNA-guided target RNA-binding fusion proteins include without limitation, RNA-binding polypeptides which are CRISPR/Cas-based RNA-binding polypeptides or portions thereof.
  • In some embodiments, a target RNA-binding fusion protein is not an RNA-guided target RNA-binding fusion protein and as such comprises at least one RNA-binding polypeptide which is capable of binding a target RNA without a corresponding gRNA sequence. Such non-guided RNA-binding polypeptides include, without limitation, at least one RNA-binding protein or RNA-binding portion thereof which is a PUF (Pumilio and FBF homology family). This type RNA-binding polypeptide can be used in place of a gRNA-guided RNA binding protein such as CRISPR/Cas. The unique RNA recognition mode of PUF proteins (named for Drosophila Pumilio and C. elegans fem-3 binding factor) that are involved in mediating mRNA stability and translation are well known in the art. The PUF domain of human Pumiliol, also known in the art, binds tightly to cognate RNA sequences and its specificity can be modified. It contains eight PUF repeats that recognize eight consecutive RNA bases with each repeat recognizing a single base. Since two amino acid side chains in each repeat recognize the Watson-Crick edge of the corresponding base and determine the specificity of that repeat, a PUF domain can be designed to specifically bind most 8-nt RNA. Wang et al., Nat Methods. 2009; 6(11): 825-830. See also WO2012/068627 which is incorporated by reference herein in its entirety.
  • In some embodiments of the non-guided RNA-binding fusion proteins of the disclosure, the fusion protein comprises at least one RNA-binding protein or RNA-binding portion thereof which is a PUMBY (Pumilio-based assembly) protein. RNA-binding protein PumHD (Pumilio homology domain, a member of the PUF family), which has been widely used in native and modified form for targeting RNA, has been engineered to yield a set of four canonical protein modules, each of which targets one RNA base. These modules (i.e., Pumby, for Pumilio-based assembly) can be concatenated in chains of varying composition and length, to bind desired target RNAs. The specificity of such Pumby-RNA interactions is high, with undetectable binding of a Pumby chain to RNA sequences that bear three or more mismatches from the target sequence. Katarzyna et al., PNAS, 2016; 113(19): E2579-E2588. See also US 2016/0238593 which is incorporated by reference herein in its entirety.
  • In some embodiments of the compositions of the disclosure, the first RNA binding protein comprises a Pumilio and FBF (PUF) protein. In some embodiments, the first RNA binding protein comprises a Pumilio-based assembly (PUMBY) protein. In some embodiments, a PUF1 protein of the disclosure comprises or consists of the amino acid sequence of
  • (SEQ ID NO: 209)
    MDKSKQMNIN NLSNIPEVID PGITIPIYEE EYENNGESNS QLQQQPQKLG SYRSRAGKES 60
    NTLSNLLPSI SAKLHHSKKN SHGKNGAEFS SSNNSSQSTV ASKTPRASPS RSKMMESSID 120
    GVTMDRPGSL TPPQDMEKLV HFPDSSNNFL IPAPRGSSDS FNLPHQISRT RNNTMSSQIT 180
    SISSIAPKPR TSSGIWSSNA SANDPMQQHL LQQLQPTTSN NTTNSNTLND YSTKTAYFDN 240
    MVSTSGSQMA DNKMNTNNLA IPNSVWSNTR QRSQSNASSI YTDAPLYEQP ARASISSHYT 300
    IPTQESPLIA DEIDPQSINW VTMDPTVPSI NQISNLLPTN TISISNVFPL QHQQPQLNNA 360
    INLTSTSLAT LCSKYGEVIS ARTLRNLNMA LVEFSSVESA VKALDSLQGK EVSMIGAPSK 420
    ISFAKILPMH QQPPQFLLNS QGLPLGLENN NLQPQPLLQE QLFNGAVTFQ QQGNVSIPVF 480
    NQQSQQSQHQ NHSSGSAGFS NVLHGYNNNN SMHGNNNNSA NEKEQCPFPL PPPNVNEKED 540
    LLREIIELFE ANSDEYQINS LIKKSLNHKG TSDTQNFGPL PEPLSGREFD PPKLRELRKS 600
    IDSNAFSDLE IEQLAIAMLD ELPELSSDYL GNTIVQKLFE HSSDIIKDIM LRKTSKYLTS 660
    MGVHKNGTWA CQKMITMAHT PRQIMQVTQG VKDYCTPLIN DQFGNYVIQC VLKFGFPWNQ 720
    FIFESIIANF WVIVQNRYGA RAVRACLEAH DIVTPEQSIV LSAMIVTYAE YLSTNSNGAL 780
    LVTWFLDTSV LPNRHSILAP RLTKRIVELC GHRLASLTIL KVLNYRGDDN ARKIILDSLF 840
    GNVNAHDSSP PKELTKLLCE TNYGPTFVHK VLAMPLLEDD LRAHIIKQVR KVLTDSTQIQ 900
    PSRRLLEEVG LASPSSTHNK TKQQQQQHHN SSISHMFATP DTSGQHMRGL SVSSVKSGGS 960
    KHTTMNTTTT NGSSASTLSP GQPLNANSNS SMGYFSYPGV FPVSGFSGNA SNGYAMNNDD 1020
    LSSQFDMLNF NNGTRLSLPQ LSLTNHNNTT MELVNNVGSS QPHTNNNNNN NNTNYNDDNT 1080
    VEETLTLHSA N. 1091

    In some embodiments, a PUF3 protein of the disclosure comprises or consists of the amino acid sequence of
  • (SEQ ID NO: 210)
    1 MEMNMDMDMD MELASIVSSL SALSHSENNG GQAAAAGIVN
    GGAAGSQQIG GERRSSETTA 
    61 NEVDSEILLL HGSSESSPIF KKTALSVGTA PPFSTNSKEF
    FGNGGNYYQY RSTDTASLSS 
    121 ASYNNYHTHE TAANLGKNNK VNHLLGQYSA SIAGPVYYNG
    NDNNNSGGEG FFEKFGKSLI 
    181 DGTRELESQD RPDAVNTQSQ FISKSVSNAS LDTQNTFEQN
    VESDKNENKL NRNTTNSGSL 
    241 YESSSNSGSS ASLESERAHY PKRNIWNVAN TPVFRPSNNT
    AAVGATNVAL PNQCDGPANN 
    301 NFPPYMNGFP PNQFHQGPHY QNFPNYLIGS PSNFISQMIS
    VQIPANEDTE DSNGKKKKKA 
    361 NRPSSVSSPS SPPNNSPFPF AYPNPMMFMP PPPLSAPQQQ
    QQQQQQQQQE DQQQQQQQEN 
    421 PYIYYPTPNP IPVKMPKDEK TFKKRNNKNH PANNSNNANK
    QANPYLENSI PTKNTSKKNA 
    481 SSKSNESTAN NHKSHSHSHP HSQSLQQQQQ TYHRSPLLEQ
    LRNSSSDKNS NSNMSLKDIF 
    541 GHSLEFCKDQ HGSRFIQREL ATSPASEKEV IFNEIRDDAI
    ELSNDVFGNY VIQKFFEFGS 
    601 KIQKNTLVDQ FKGNMKQLSL QMYACRVIQK ALEYIDSNQR
    IELVLELSDS VLQMIKDQNG 
    661 NEVIQKAIET IPIEKLPFIL SSLTGHIYHL STHSYGCRVI
    QRLLEFGSSE DQESILNELK 
    721 DFIPYLIQDQ YGNYVIQYVL QQDQFTNKEM VDIKQEIIET
    VANNVVEYSK HKFASNVVEK 
    781 SILYGSKNQK DLIISKILPR DKNRALNLED DSPMILMaKD
    QFANYVIQKL VNVSEGEGKK 
    841 LIVIAIRAYL DKINKSNSLO NRHLASVEKL AALVENAEV.

    In some embodiments, a PUF4 protein of the disclosure comprises or consists of the amino acid sequence of
  • (SEQ ID NO: 211)
    1 MSTKGLKEEI DDVPSVDPVV SETVNSALEQ LQLDDPEENA
    TSNAFANKVS QDSQFANGPP
    61 SQMFPHTQMM GGMGFMPYSQ MMQVPHNPCP FFPPPDFNDP
    TAPLSSSPLN AGGPPMLFKN
    121 DSLPFQMLSS GAAVATQGGQ NLNPLINDNS MKVLPIASAD
    PLWTHSNVPG SASVAIEETT
    181 ATLQESLPSK GRESNNKASS FRRQTFHALS PTDLINAANN
    VTLSKDFQSD MQNFSKAKKP
    241 SVGANNTAKT RTQSISFDNT PSSTSFIPPT NSVSEKLSDF
    KIETSKEDLI NKTAPAKKES
    301 PTTYGAAYPY GGPLLQPNPI MPGHPHNISS PIYGIRSPFP
    NSYEMGAQFQ PFSPILNPTS
    361 HSLNANSPIP LTQSPIHLAP VLNPSSNSVA FSDMKNDGGK
    PTTDNDKAGP NVRMDLINPN
    421 LGPSMQPFHI LPPQQNTPPP PWLYSTPPPF NAMVPPHLLA
    QNHMPLMNSA NNKHHGRNNN
    481 SMSSHNDNDN IGNSNYNNKD TGRSNVGKMK NMKNSYHGYY
    NNNNNNNNNN NNNNNSNATN
    541 SNSAEKQRKI EESSRFADAV LDQYIGSIHS LCKDQHGCRF
    LQKQLDILGS KAADAIFEET
    601 KDYTVELMTD SFGNYLIQKL LEEVTTEQRI VLTKISSPHF
    VEISLNPHGT RALQKLIECI
    661 KTDEEAQIVV DSLRPYTVQL SKDLNGNHVI QKCLQRLKPE
    NFQFIFDAIS DSCIDIATHR
    721 HGCCVLQRCL DHGTTEQCDN LCDKLLALVD KLTLDPFGNY
    VVQYIITKEA EKNKYDYTHK
    781 IVHLLKPRAI ELSIHKFGSN VIEKILKTAI VSEPMILEIL
    NNGGETGIQS LLNDSYGNYV
    841 LQTALDISHK QNDYLYKRLS EIVAPLLVGP IRNTPHGKRI
    IGMLHLDS.

    In some embodiments, a PUF5 protein of the disclosure comprises or consists of the amino acid sequence of
  • (SEQ ID NO: 212)
    1 MSDSTGRINS KASDSSSISD HQTADLSIFN GSFDGGAFSS
    SNIPLFNFMG TGNQPFQYSP 
    61 HPFAKSSDPC PLAALTPSTP KGPLNLTPAD FGLADFSVGN
    ESEADFTANN TSFVGNVQSN 
    121 VRSTRLLPAW AVDNSGNIRD DLTLQDVVSN GSLIDFAMDR
    TGVKFLERHF PEDHDNEMHF 
    181 VLFDKLTEOG AVFTSLCRSA AGNFIIQKFV EHATLDEOER
    LVRKMCDNGL IEMCLDKFAC 
    241 RVVQMSIOKF DVSIAMKLVE KISSLDFLPL CTDQCAIHVI
    QKVVKLLPIS AWSFFVKFLC 
    301 RDDNLMTVCQ DKYGCRIVQQ TIDKLSDNPK LHCFNTRLQL
    LHGLMTSVAR NCFRLSSNEF 
    361 ANYVVQYVIK SSGVMEMYRD TIIEKCLLRN ILSMSQDKYA
    SHVVEGAFLF APPLLLSEMM 
    421 DEIFDGYVKD QETNRDALDI LLFHQYGNYV VQQMISICIS
    ALLGKEERKM VASEMRLYAK 
    481 WFDRIKNRVN RHSGRLERFS SGKEIIESLQ KLEVPMTMTN
    EPMPYWAMPT PLMDISAHFM 
    541 NKINFONNSV FDE. 

    In some embodiments, a PUF6 protein of the disclosure comprises or consists of the amino acid sequence of
  • (SEQ ID NO: 213)
    1 MTPNRRSTDS YNMLGASFDF DPDFSLLSNK THKNKNPKPP
    VKLLPYRHGS NTTSSDLDNY 
    61 IFNSGSGSSD DETPPPAAPI FISLEEVLLN GLLIDFAIDP
    SGVKFLEANY PLDSEDQIRK 
    121 AVFEKLTEST TLFVGLCHSR NGNFIVQKLV ELATPAEORE
    LLROMIDGGL LVMCKDKFAC 
    181 RVVQLALOKF DHSNVFQLIQ ELSTFDLAAM CTDQISIHVI
    QRVVKQLPVD MWTEFVHFLS 
    241 SGDSLMAVCQ DKYGCRIVQQ VIDRLAENPK LPCFKFPIQL
    LHSLMTCIVR NCYRLSSNEF 
    301 ANYVIQYVIK SSGIMEMYRD TIIDKCLLRN LLSMSQDKYA
    SHVIEGAFLF APPALLHEMM 
    361 EEIFSGYVKD VELNRDALDI LLFHOYGNYV VQOMISICTA
    ALIGKEEROL PPAILLLYSG 
    421 WYEKMKQRVL OHASRLERFS SGKEIIDSVM RHGVPTAAAI
    NAQAAPSLME LTAQFDAMFP 
    481 SFLAR. 

    In some embodiments, a PUF7 protein of the disclosure comprises or consists of the amino acid sequence of
  • (SEQ ID NO: 214)
    1 MTPNRRSTDS YNMLGASFDF DPDFSLLSNK THKNKNPKTP
    VKLLPYRHGS NTTSSDSDSY 
    61 IFNSGSGSSD AETPAPVAPI FISLEDVLLN GQLIDFAIDP
    SGVKFLEANY PLDSEDQIRK 
    121 AVFEKFTEST TLFVGLCHSR NGNFTVQKLV ELATPAEQRE
    LLRQMIDGGI LAMCKDKFAC 
    181 RVVQLALQKF DHSNVFQLIQ ELSTFDLAAM CTDQISIHVI
    QRVVKQLPVD MWTFFVHFLS 
    241 SGDSLMAVCQ DKYGCRLVQQ VIDRLAENTK LPCFKFRIQL
    LHSLMTCIVR NCYRLSSNEF 
    301 ANYVIQYVIK SSGIMEMYRD TIIDKCLLRN LLSMSQDKYA
    SHVIEGAFLF APPALLHEMM 
    361 EEIFSGYVKD VESNRDALDI LLFHQYGNYV VQQMISICTA
    ALIGKEEREL PPAILLLYSG 
    421 WYEKMKQPVL QHASPIERFS SGYKTIDSVM RHGVPTAAAV
    NAQAAPSLME LTAQFDAMFP 
    481 SFLAR. 

    In some embodiments, a PUF8 protein of the disclosure comprises or consists of the amino acid sequence of
  • (SEQ ID NO: 215) 
    1 MSRPISIGNT CTFDPSASPI ESLGRSIGAQ KIVDSVCGSP
    IRSYGRHIST NPKNERLPDT 
    61 PEFQFATYMH QGGKVIGQNT LHMFGTPPSC YCAQENIPIS
    SNVGHVLSTI NNNYMNHQYN 
    121 GSMMFSNQMT QMLQAQAYND LQMBQAHSQS IRVPVQPSAT
    GIFSNPYREP TTTDDLLTRY 
    181 RkNPAMMKNL KLSDIRGALL KFAKDQVGSR FIQQELASSK
    DRFEKDSIFD EVVSNADELV 
    241 DDIFGNYVVQ KFFEYGEERH WARLVDAIID RVPEYAFQMY
    ACRVLQKkLE KINEPLQIKI 
    301 LSQIRHVIHR CMEDQNGNHV VQKAIEKVSP QYVQFIVDTL
    LESSNTIYEM SVDPYGCRVV 
    361 QPCLEHCSPS QTKPVIGQIH KRFDEIANNQ YGNYVVQHVI
    EHGSEEDRMV IVTRVSNNLF
    421 EFATHKYSSN VIEKCLEQGA VYHKSMIVGA ACHHQEGSVP
    IVVQMMKDQY ANYVVQKMFD 
    481 QVTSEQRREL ILTVRPHIPV LRQFPHGKHI LAKIEKYFQK
    PAVMSYPYQD MQGSH.

    In some embodiments, a PUF9 protein of the disclosure comprises or consists of the amino acid sequence of
  • (SEQ ID NO: 216)
    1 MADPNWAIAP PTNYYADHSI AKPIMISGGH PSQDQGHSPK
    SESFGQSVTT AFNGMVDNLV 
    61 GSPSSSVQQR NYFTTTPFPI SRSPNDRNDD KIMGNGSYGV
    PIPIPQDGVP QGIPDFQMTP 
    121 FLQQGGHLIG GSPNGPVQVS GNWYSGGAGI FSTMQQADPS
    NGMPGMAAEF VNNENGMPGP 
    181 NGMEQQAMIS GSPPFPYQNM MNLTTSFGAM GLGPQQIQQR
    DPQMFQQPIL HEPIQGMAQN 
    241 GEGQQVFFTQ MQNQQHPQGQ AQQQLQQLAQ QHQQQQNSQQ
    FFGQGPNGMG NGGVMNDWS0 
    301 RSFGMPQQQA QQNGLPPNFS QNPPRRRGPE DPNGQTPKTL
    QDIKNNVIEF AKDQHGSRFI 
    361 QQKLERASLR DKAAIFTPVL ENAEELMTDV EGNYVIQKFF
    EFGNNEQRNQ LVGTIRGNVM 
    421 KLALQMYGCR VIQKALEYVE EKYQHEILGE MEGQVLKCVK
    DQNGNHVIQK VIERVEPERL 
    481 QFIIDAFTKN NSDNVYTLSV HPYGCRVIQR VLEYCNEEQK
    QPVIDALQIH LKQLVLDQYG 
    541 NYVIQHVIEH GSPSDKEQIV QDVISDDLLK FAQHKFASNV
    IEKCLTFGGH AERNLIIDKV 
    601 CGDPNDPSPP LLQMMKDPFA NYVVQKMIDV ADPQHRKKIT
    LTIKPHIATL RKYNFGKHIL 
    661 LKLEKYFAKQ APANSSNSSS NDQIYEHSPF DIPLGADFSN
    HPF. 
  • In some embodiments of the compositions of the disclosure, at least one of the RNA-binding proteins or RNA-binding portions thereof is a PPR protein. PPR proteins (proteins with pentatricopeptide repeat (PPR) motifs derived from plants) are nuclear-encoded and exclusively controlled at the RNA level organelles (chloroplasts and mitochondria), cutting, translation, splicing, RNA editing, genes specifically acting on RNA stability. PPR proteins are typically a motif of 35 amino acids and have a structure in which a PPR motif is about 10 contiguous amino acids. The combination of PPR motifs can be used for sequence-selective binding to RNA. PPR proteins are often comprised of PPR motifs of about 10 repeat domains. PPR domains or RNA-binding domains may be configured to be catalytically inactive. WO 2013/058404 incorporated herein by reference in its entirety.
  • In some embodiments, the fusion protein disclosed herein comprises a linker between the at least two RNA-binding polypeptides. In some embodiments, the linker is a peptide linker. In some embodiments, the peptide linker comprises one or more repeats of the tri-peptide GGS. In other embodiments, the linker is a non-peptide linker. In some embodiments, the non-peptide linker comprises polyethylene glycol (PEG), polypropylene glycol (PPG), co-poly(ethylene/propylene) glycol, polyoxyethylene (POE), polyurethane, polyphosphazene, polysaccharides, dextran, polyvinyl alcohol, polyvinylpyrrolidones, polyvinyl ethyl ether, polyacryl amide, polyacrylate, polycyanoacrylates, lipid polymers, chitins, hyaluronic acid, heparin, or an alkyl linker.
  • In some embodiments, the at least one RNA-binding protein does not require multimerization for RNA-binding activity. In some embodiments, the at least one RNA-binding protein is not a monomer of a multimer complex. In some embodiments, a multimer protein complex does not comprise the RNA binding protein. In some embodiments, the at least one of RNA-binding protein selectively binds to a target sequence within the RNA molecule. In some embodiments, the at least one RNA-binding protein does not comprise an affinity for a second sequence within the RNA molecule. In some embodiments, the at least one RNA-binding protein does not comprise a high affinity for or selectively bind a second sequence within the RNA molecule. In some embodiments, the at least one RNA-binding protein comprises between 2 and 1300 amino acids, inclusive of the endpoints.
  • In some embodiments, the at least one RNA-binding protein of the fusion proteins disclosed herein further comprises a sequence encoding a nuclear localization signal (NLS). In some embodiments, a nuclear localization signal (NLS) is positioned 3′ to the RNA binding protein. In some embodiments, the at least one RNA-binding protein comprises an NLS at a C-terminus of the protein. In some embodiments, the at least one RNA-binding protein further comprises a first sequence encoding a first NLS and a second sequence encoding a second NLS. In some embodiments, the first NLS or the second NLS is positioned 3′ to the RNA-binding protein. In some embodiments, the at least one RNA-binding protein comprises the first NLS or the second NLS at a C-terminus of the protein. In some embodiments, the at least one RNA-binding protein further comprises an NES (nuclear export signal) or other peptide tag or secretory signal.
  • In some embodiments, a fusion protein disclosed herein comprises the at least one RNA-binding protein as a first RNA-binding protein together with a second RNA-binding protein comprising or consisting of a nuclease domain.
  • In some embodiments, the second RNA-binding polypeptide is operably configured to the first RNA-binding polypeptide at the C-terminus of the first RNA-binding polypeptide. In some embodiments, the second RNA-binding polypeptide is operably configured to the first RNA-binding polypeptide at the N-terminus of the first RNA-binding polypeptide. For example, one such exemplary fusion protein is E99 which is configured so that RNAse1(R39D, N67D, N88A, G89D, R19D, H119N, K41R) is located at the N-terminus of SpyCas9 whereas another exemplary fusion protein, E100, is configured so that RNAse1(R39D, N67D, N88A, G89D, R19D, H119N, K41R) is located at the C-terminus of SpyCas9. See FIG. 6.
    • Vectors
  • In some embodiments of the compositions and methods of the disclosure, a vector comprises a guide RNA of the disclosure. In some embodiments, the vector comprises at least one guide RNA of the disclosure. In some embodiments, the vector comprises one or more guide RNA(s) of the disclosure. In some embodiments, the vector comprises two or more guide RNAs of the disclosure. In some embodiments, the vector further comprises a fusion protein of the disclosure. In some embodiments, the fusion protein comprises a first RNA binding protein and a second RNA binding protein.
  • In some embodiments of the compositions and methods of the disclosure, a first vector comprises a guide RNA of the disclosure and a second vector comprises a fusion protein of the disclosure. In some embodiments, the first vector comprises at least one guide RNA of the disclosure. In some embodiments, the first vector comprises one or more guide RNA(s) of the disclosure. In some embodiments, the first vector comprises two or more guide RNA(s) of the disclosure. In some embodiments, the fusion protein comprises a first RNA binding protein and a second RNA binding protein. In some embodiments, the first vector and the second vector are identical. In some embodiments, the first vector and the second vector are not identical.
  • In some embodiments of the compositions and methods of the disclosure, the vector is or comprises a component of a “2-component RNA targeting system” comprising (a) nucleic acid sequence encoding a RNA-targeted fusion protein of the disclosure; and (b) a single guide RNA (sgRNA) sequence comprising: on its 5′ end, an RNA sequence (or spacer sequence) that hybridizes to or binds to a target RNA sequence; and on its 3′ end, an RNA sequence (or scaffold sequence) capable of binding to or associating with the CRISPR/Cas protein of the fusion protein; and wherein the 2-component RNA targeting system recognizes and alters the target RNA in a cell in the absence of a PAMmer. In some embodiments, the sequences of the 2-component system are in a single vector. In some embodiments, the spacer sequence of the 2-component system targets a repeat sequence selected from the group consisting of CUG, CCUG, CAG, and GGGGCC.
  • In some embodiments of the compositions and methods of the disclosure, a vector of the disclosure is a viral vector. In some embodiments, the viral vector comprises a sequence isolated or derived from a retrovirus. In some embodiments, the viral vector comprises a sequence isolated or derived from a lentivirus. In some embodiments, the viral vector comprises a sequence isolated or derived from an adenovirus. In some embodiments, the viral vector comprises a sequence isolated or derived from an adeno-associated virus (AAV). In some embodiments, the viral vector is replication incompetent. In some embodiments, the viral vector is isolated or recombinant. In some embodiments, the viral vector is self-complementary.
  • In some embodiments of the compositions and methods of the disclosure, the viral vector comprises a sequence isolated or derived from an adeno-associated virus (AAV). In some embodiments, the viral vector comprises an inverted terminal repeat sequence or a capsid sequence that is isolated or derived from an AAV of serotype AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11 or AAV12. In some embodiments, the viral vector is replication incompetent. In some embodiments, the viral vector is isolated or recombinant (rAAV). In some embodiments, the viral vector is self-complementary (scAAV).
  • In some embodiments of the compositions and methods of the disclosure, a vector of the disclosure is a non-viral vector. In some embodiments, the vector comprises or consists of a nanoparticle, a micelle, a liposome or lipoplex, a polymersome, a polyplex or a dendrimer. In some embodiments, the vector is an expression vector or recombinant expression system. As used herein, the term “recombinant expression system” refers to a genetic construct for the expression of certain genetic material formed by recombination.
  • In some embodiments of the compositions and methods of the disclosure, an expression vector, viral vector or non-viral vector provided herein, includes without limitation, an expression control element. An “expression control element” as used herein refers to any sequence that regulates the expression of a coding sequence, such as a gene. Exemplary expression control elements include but are not limited to promoters, enhancers, microRNAs, post-transcriptional regulatory elements, polyadenylation signal sequences, and introns. Expression control elements may be constitutive, inducible, repressible, or tissue-specific, for example. A “promoter” is a control sequence that is a region of a polynucleotide sequence at which initiation and rate of transcription are controlled. It may contain genetic elements at which regulatory proteins and molecules may bind such as RNA polymerase and other transcription factors. In some embodiments, expression control by a promoter is tissue-specific. Non-limiting exemplary promoters include CMV, CBA, CAG, Cbh, EF-1a, PGK, UBC, GUSB, UCOE, hAAT, TBG, Desmin, MCK, C5-12, NSE, Synapsin, PDGF, MecP2, CaMKII, mGluR2, NFL, NFH, nβ2, PPE, ENK, EAAT2, GFAP, MBP, and U6 promoters. An “enhancer” is a region of DNA that can be bound by activating proteins to increase the likelihood or frequency of transcription. Non-limiting exemplary enhancers and posttranscriptional regulatory elements include the CMV enhancer and WPRE.
  • In some embodiments of the compositions and methods of the disclosure, an expression vector, viral vector or non-viral vector provided herein, includes without limitation, vector elements such as an IRES or 2A peptide sites for configuration of “multicistronic” or “polycistronic” or “bicistronic” or tricistronic” constructs, i.e., having double or triple or multiple coding areas or exons, and as such will have the capability to express from mRNA two or more proteins from a single construct. Multicistronic vectors simultaneously express two or more separate proteins from the same mRNA. The two strategies most widely used for constructing multicistronic configurations are through the use of an IRES or a 2A self-cleaving site. An “IRES” refers to an internal ribosome entry site or portion thereof of viral, prokaryotic, or eukaryotic origin which are used within polycistronic vector constructs. In some embodiments, an IRES is an RNA element that allows for translation initiation in a cap-independent manner. The term “self-cleaving peptides” or “sequences encoding self-cleaving peptides” or “2A self-cleaving site” refer to linking sequences which are used within vector constructs to incorporate sites to promote ribosomal skipping and thus to generate two polypeptides from a single promoter, such self-cleaving peptides include without limitation, T2A, and P2A peptides or sequences encoding the self-cleaving peptides.
  • In some embodiments, the vector is a viral vector. In some embodiments, the vector is an adenoviral vector, an adeno-associated viral (AAV) vector, or a lentiviral vector. In some embodiments, the vector is a retroviral vector, an adenoviral/retroviral chimera vector, a herpes simplex viral I or II vector, a parvoviral vector, a reticuloendotheliosis viral vector, a polioviral vector, a papillomaviral vector, a vaccinia viral vector, or any hybrid or chimeric vector incorporating favorable aspects of two or more viral vectors. In some embodiments, the vector further comprises one or more expression control elements operably linked to the polynucleotide. In some embodiments, the vector further comprises one or more selectable markers. In some embodiments, the AAV vector has low toxicity. In some embodiments, the AAV vector does not incorporate into the host genome, thereby having a low probability of causing insertional mutagenesis. In some embodiments, the AAV vector can encode a range of total polynucleotides from 4.5 kb to 4.75 kb. In some embodiments, exemplary AAV vectors that may be used in any of the herein described compositions, systems, methods, and kits can include an AAV1 vector, a modified AAV1 vector, an AAV2 vector, a modified AAV2 vector, an AAV3 vector, a modified AAV3 vector, an AAV4 vector, a modified AAV4 vector, an AAV5 vector, a modified AAV5 vector, an AAV6 vector, a modified AAV6 vector, an AAV7 vector, a modified AAV7 vector, an AAV8 vector, an AAV9 vector, an AAV.rh10 vector, a modified AAV.rh10 vector, an AAV.rh32/33 vector, a modified AAV.rh32/33 vector, an AAV.rh43 vector, a modified AAV.rh43 vector, an AAV.rh64R1 vector, and a modified AAV.rh64R1 vector and any combinations or equivalents thereof. In some embodiments, the lentiviral vector is an integrase-competent lentiviral vector (ICLV). In some embodiments, the lentiviral vector can refer to the transgene plasmid vector as well as the transgene plasmid vector in conjunction with related plasmids (e.g., a packaging plasmid, a rev expressing plasmid, an envelope plasmid) as well as a lentiviral-based particle capable of introducing exogenous nucleic acid into a cell through a viral or viral-like entry mechanism. Lentiviral vectors are well-known in the art (see, e.g., Trono D. (2002) Lentiviral vectors, New York: Spring-Verlag Berlin Heidelberg and Durand et al. (2011) Viruses 3(2):132-159 doi: 10.3390/v3020132). In some embodiments, exemplary lentiviral vectors that may be used in any of the herein described compositions, systems, methods, and kits can include a human immunodeficiency virus (HIV) 1 vector, a modified human immunodeficiency virus (HIV) 1 vector, a human immunodeficiency virus (HIV) 2 vector, a modified human immunodeficiency virus (HIV) 2 vector, a sooty mangabey simian immunodeficiency virus (SIVsM) vector, a modified sooty mangabey simian immunodeficiency virus (SIVsM) vector, a African green monkey simian immunodeficiency virus (SIVAGm) vector, a modified African green monkey simian immunodeficiency virus (SIVAGm) vector, an equine infectious anemia virus (EIAV) vector, a modified equine infectious anemia virus (EIAV) vector, a feline immunodeficiency virus (FIV) vector, a modified feline immunodeficiency virus (FIV) vector, a Visna/maedi virus (VNV/VMV) vector, a modified Visna/maedi virus (VNV/VMV) vector, a caprine arthritis-encephalitis virus (CAEV) vector, a modified caprine arthritis-encephalitis virus (CAEV) vector, a bovine immunodeficiency virus (BIV), or a modified bovine immunodeficiency virus (BIV).
    • Nucleic Acids
  • Provided herein are the nucleic acid sequences encoding the fusion proteins disclosed herein for use in gene transfer and expression techniques described herein. It should be understood, although not always explicitly stated that the sequences provided herein can be used to provide the expression product as well as substantially identical sequences that produce a protein that has the same biological properties. These “biologically equivalent” or “biologically active” or “equivalent” polypeptides are encoded by equivalent polynucleotides as described herein. They may possess at least 60%, or alternatively, at least 65%, or alternatively, at least 70%, or alternatively, at least 75%, or alternatively, at least 80%, or alternatively at least 85%, or alternatively at least 90%, or alternatively at least 95% or alternatively at least 98%, identical primary amino acid sequence to the reference polypeptide when compared using sequence identity methods run under default conditions. Specific polypeptide sequences are provided as examples of particular embodiments. Modifications to the sequences to amino acids with alternate amino acids that have similar charge. Additionally, an equivalent polynucleotide is one that hybridizes under stringent conditions to the reference polynucleotide or its complement or in reference to a polypeptide, a polypeptide encoded by a polynucleotide that hybridizes to the reference encoding polynucleotide under stringent conditions or its complementary strand. Alternatively, an equivalent polypeptide or protein is one that is expressed from an equivalent polynucleotide.
  • The nucleic acid sequences (e.g., polynucleotide sequences) disclosed herein may be codon-optimized which is a technique well known in the art. In some embodiments disclosed herein, exemplary Cas sequences, such as e.g., SEQ ID NO: 46 (Cas13d), are codon optimized for expression in human cells. Codon optimization refers to the fact that different cells differ in their usage of particular codons. This codon bias corresponds to a bias in the relative abundance of particular tRNAs in the cell type. By altering the codons in the sequence to match with the relative abundance of corresponding tRNAs, it is possible to increase expression. It is also possible to decrease expression by deliberately choosing codons for which the corresponding tRNAs are known to be rare in a particular cell type. Codon usage tables are known in the art for mammalian cells, as well as for a variety of other organisms. Based on the genetic code, nucleic acid sequences coding for, e.g., a Cas protein, can be generated. In some embodiments, such a sequence is optimized for expression in a host or target cell, such as a host cell used to express the Cas protein or a cell in which the disclosed methods are practiced (such as in a mammalian cell, e.g., a human cell). Codon preferences and codon usage tables for a particular species can be used to engineer isolated nucleic acid molecules encoding a Cas protein (such as one encoding a protein having at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to its corresponding wild-type protein) that takes advantage of the codon usage preferences of that particular species. For example, the Cas proteins disclosed herein can be designed to have codons that are preferentially used by a particular organism of interest. In one example, an Cas nucleic acid sequence is optimized for expression in human cells, such as one having at least 70%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 98%, or at least 99% sequence identity to its corresponding wild-type or originating nucleic acid sequence. In some embodiments, an isolated nucleic acid molecule encoding at least one Cas protein (which can be part of a vector) includes at least one Cas protein coding sequence that is codon optimized for expression in a eukaryotic cell, or at least one Cas protein coding sequence codon optimized for expression in a human cell. In one embodiment, such a codon optimized Cas coding sequence has at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to its corresponding wild-type or originating sequence. In another embodiment, a eukaryotic cell codon optimized nucleic acid sequence encodes a Cas protein having at least 85%, at least 90%, at least 92%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to its corresponding wild-type or originating protein. In another embodiment, a variety of clones containing functionally equivalent nucleic acids may be routinely generated, such as nucleic acids which differ in sequence but which encode the same Cas protein sequence. Silent mutations in the coding sequence result from the degeneracy (i.e., redundancy) of the genetic code, whereby more than one codon can encode the same amino acid residue. Thus, for example, leucine can be encoded by CTT, CTC, CTA, CTG, TTA, or TTG; serine can be encoded by TCT, TCC, TCA, TCG, AGT, or AGC; asparagine can be encoded by AAT or AAC; aspartic acid can be encoded by GAT or GAC; cysteine can be encoded by TGT or TGC; alanine can be encoded by GCT, GCC, GCA, or GCG; glutamine can be encoded by CAA or CAG; tyrosine can be encoded by TAT or TAC; and isoleucine can be encoded by ATT, ATC, or ATA. Tables showing the standard genetic code can be found in various sources (see, for example, Stryer, 1988, Biochemistry, 3.sup.rd Edition, W.H. 5 Freeman and Co., NY).
  • “Hybridization” refers to a reaction in which one or more polynucleotides react to form a complex that is stabilized via hydrogen bonding between the bases of the nucleotide residues. The hydrogen bonding may occur by Watson-Crick base pairing, Hoogstein binding, or in any other sequence-specific manner. The complex may comprise two strands forming a duplex structure, three or more strands forming a multi-stranded complex, a single self-hybridizing strand, or any combination of these. A hybridization reaction may constitute a step in a more extensive process, such as the initiation of a PC reaction, or the enzymatic cleavage of a polynucleotide by a ribozyme.
  • Examples of stringent hybridization conditions include: incubation temperatures of about 25° C. to about 37° C.; hybridization buffer concentrations of about 6×SSC to about 10×SSC; formamide concentrations of about 0% to about 25%; and wash solutions from about 4×SSC to about 8×SSC. Examples of moderate hybridization conditions include: incubation temperatures of about 40° C. to about 50° C.; buffer concentrations of about 9×SSC to about 2×SSC; formamide concentrations of about 30% to about 50%; and wash solutions of about 5×SSC to about 2×SSC. Examples of high stringency conditions include: incubation temperatures of about 55° C. to about 68° C.; buffer concentrations of about 1×SSC to about 0.1×SSC; formamide concentrations of about 55% to about 75%; and wash solutions of about 1×SSC, 0.1×SSC, or deionized water. In general, hybridization incubation times are from 5 minutes to 24 hours, with 1, 2, or more washing steps, and wash incubation times are about 1, 2, or 15 minutes. SSC is 0.15 M NaCl and 15 mM citrate buffer. It is understood that equivalents of SSC using other buffer systems can be employed.
  • “Homology” or “identity” or “similarity” refers to sequence similarity between two peptides or between two nucleic acid molecules. Homology can be determined by comparing a position in each sequence which may be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same base or amino acid, then the molecules are homologous at that position. A degree of homology between sequences is a function of the number of matching or homologous positions shared by the sequences. An “unrelated” or “non-homologous”sequence shares less than 40% identity, or alternatively less than 25% identity, with one of the sequences of the present invention.
    • Cells
  • In some embodiments of the compositions and methods of the disclosure, a cell of the disclosure is a prokaryotic cell.
  • In some embodiments of the compositions and methods of the disclosure, a cell of the disclosure is a eukaryotic cell. In some embodiments, the cell is a mammalian cell. In some embodiments, the cell is a bovine, murine, feline, equine, porcine, canine, simian, or human cell. In some embodiments, the cell is a non-human mammalian cell such as a non-human primate cell.
  • In some embodiments, a cell of the disclosure is a somatic cell. In some embodiments, a cell of the disclosure is a germline cell. In some embodiments, a germline cell of the disclosure is not a human cell.
  • In some embodiments of the compositions and methods of the disclosure, a cell of the disclosure is a stem cell. In some embodiments, a cell of the disclosure is an embryonic stem cell. In some embodiments, an embryonic stem cell of the disclosure is not a human cell. In some embodiments, a cell of the disclosure is a multipotent stem cell or a pluripotent stem cell. In some embodiments, a cell of the disclosure is an adult stem cell. In some embodiments, a cell of the disclosure is an induced pluripotent stem cell (iPSC). In some embodiments, a cell of the disclosure is a hematopoietic stem cell (HSC).
  • In some embodiments of the compositions and methods of the disclosure, a somatic cell of the disclosure is an immune cell. In some embodiments, an immune cell of the disclosure is a lymphocyte. In some embodiments, an immune cell of the disclosure is a T lymphocyte (also referred to herein as a T-cell). Exemplary T-cells of the disclosure include, but are not limited to, naïve T cells, effector T cells, helper T cells, memory T cells, regulatory T cells (Tregs) and Gamma delta T cells. In some embodiments, an immune cell of the disclosure is a B lymphocyte. In some embodiments, an immune cell of the disclosure is a natural killer cell. In some embodiments, an immune cell of the disclosure is an antigen-presenting cell.
  • In some embodiments of the compositions and methods of the disclosure, a somatic cell of the disclosure is a muscle cell. In some embodiments, a muscle cell of the disclosure is a myoblast or a myocyte. In some embodiments, a muscle cell of the disclosure is a cardiac muscle cell, skeletal muscle cell or smooth muscle cell. In some embodiments, a muscle cell of the disclosure is a striated cell.
  • In some embodiments of the compositions and methods of the disclosure, a somatic cell of the disclosure is an epithelial cell. In some embodiments, an epithelial cell of the disclosure forms a squamous cell epithelium, a cuboidal cell epithelium, a columnar cell epithelium, a stratified cell epithelium, a pseudostratified columnar cell epithelium or a transitional cell epithelium. In some embodiments, an epithelial cell of the disclosure forms a gland including, but not limited to, a pineal gland, a thymus gland, a pituitary gland, a thyroid gland, an adrenal gland, an apocrine gland, a holocrine gland, a merocrine gland, a serous gland, a mucous gland and a sebaceous gland. In some embodiments, an epithelial cell of the disclosure contacts an outer surface of an organ including, but not limited to, a lung, a spleen, a stomach, a pancreas, a bladder, an intestine, a kidney, a gallbladder, a liver, a larynx or a pharynx. In some embodiments, an epithelial cell of the disclosure contacts an outer surface of a blood vessel or a vein.
  • In some embodiments of the compositions and methods of the disclosure, a somatic cell of the disclosure is a neuronal cell. In some embodiments, a neuron cell of the disclosure is a neuron of the central nervous system. In some embodiments, a neuron cell of the disclosure is a neuron of the brain or the spinal cord. In some embodiments, a neuron cell of the disclosure is a neuron of the retina. In some embodiments, a neuron cell of the disclosure is a neuron of a cranial nerve or an optic nerve. In some embodiments, a neuron cell of the disclosure is a neuron of the peripheral nervous system. In some embodiments, a neuron cell of the disclosure is a neuroglial or a glial cell. In some embodiments, a glial of the disclosure is a glial cell of the central nervous system including, but not limited to, oligodendrocytes, astrocytes, ependymal cells, and microglia. In some embodiments, a glial of the disclosure is a glial cell of the peripheral nervous system including, but not limited to, Schwann cells and satellite cells.
  • In some embodiments of the compositions and methods of the disclosure, a somatic cell of the disclosure is a primary cell.
  • In some embodiments of the compositions and methods of the disclosure, a somatic cell of the disclosure is a cultured cell.
  • In some embodiments of the compositions and methods of the disclosure, a somatic cell of the disclosure is in vivo, in vitro, ex vivo or in situ.
  • In some embodiments of the compositions and methods of the disclosure, a somatic cell of the disclosure is autologous or allogeneic.
    • Methods of Use
  • The disclosure provides a method of modifying level of expression of an RNA molecule of the disclosure or a protein encoded by the RNA molecule comprising contacting the composition and the RNA molecule under conditions suitable for binding of one or more of the guide RNA or the fusion protein (or a portion thereof) to the RNA molecule.
  • The disclosure provides a method of modifying an activity of a protein encoded by an RNA molecule comprising contacting the composition and the RNA molecule under conditions suitable for binding of one or more of the guide RNA or the fusion protein (or a portion thereof) to the RNA molecule.
  • The disclosure provides a method of modifying level of expression of an RNA molecule of the disclosure or a protein encoded by the RNA molecule comprising contacting the composition and a cell comprising the RNA molecule under conditions suitable for binding of one or more of the guide RNA or the fusion protein (or a portion thereof) to the RNA molecule. In some embodiments, the cell is in vivo, in vitro, ex vivo or in situ. In some embodiments, the composition comprises a vector comprising composition comprising a guide RNA of the disclosure and a fusion protein of the disclosure. In some embodiments, the vector is an AAV.
  • The disclosure provides a method of modifying an activity of a protein encoded by an RNA molecule comprising contacting the composition and a cell comprising the RNA molecule under conditions suitable for binding of one or more of the guide RNA or the fusion protein (or a portion thereof) to the RNA molecule. In some embodiments, the cell is in vivo, in vitro, ex vivo or in situ. In some embodiments, the composition comprises a vector comprising composition comprising a guide RNA or a single guide RNA of the disclosure and a fusion protein of the disclosure. In some embodiments, the vector is an AAV.
  • The disclosure provides a method of modifying level of expression of an RNA molecule of the disclosure or a protein encoded by the RNA molecule comprising contacting the composition and the RNA molecule under conditions suitable for RNA nuclease activity wherein the fusion protein induces a break in the RNA molecule.
  • The disclosure provides a method of modifying an activity of a protein encoded by an RNA molecule comprising contacting the composition and the RNA molecule under conditions suitable for RNA nuclease activity wherein the fusion protein induces a break in the RNA molecule.
  • The disclosure provides a method of modifying a level of expression of an RNA molecule of the disclosure or a protein encoded by the RNA molecule comprising contacting the composition and a cell comprising the RNA molecule under conditions suitable for RNA nuclease activity wherein the fusion protein induces a break in the RNA molecule. In some embodiments, the cell is in vivo, in vitro, ex vivo or in situ. In some embodiments, the composition comprises a vector comprising composition comprising a guide RNA of the disclosure and a fusion protein of the disclosure. In some embodiments, the vector is an AAV.
  • The disclosure provides a method of modifying an activity of a protein encoded by an RNA molecule comprising contacting the composition and a cell comprising the RNA molecule under conditions suitable for RNA nuclease activity wherein the fusion protein induces a break in the RNA molecule. In some embodiments, the cell is in vivo, in vitro, ex vivo or in situ. In some embodiments, the composition comprises a vector comprising composition comprising a guide RNA or a single guide RNA of the disclosure and a fusion protein of the disclosure. In some embodiments, the vector is an AAV.
  • The disclosure provides a method of treating a disease or disorder comprising administering to a subject a therapeutically effective amount of a composition of the disclosure.
  • The disclosure provides a method of treating a disease or disorder comprising administering to a subject a therapeutically effective amount of a composition of the disclosure, wherein the composition comprises a vector comprising composition comprising a guide RNA of the disclosure and a fusion protein of the disclosure and wherein the composition modifies a level of expression of an RNA molecule of the disclosure or a protein encoded by the RNA molecule.
  • The disclosure provides a method of treating a disease or disorder comprising administering to a subject a therapeutically effective amount of a composition of the disclosure, wherein the composition comprises a vector comprising composition comprising a guide RNA of the disclosure and a fusion protein of the disclosure and wherein the composition modifies an activity of a protein encoded by an RNA molecule.
  • In some embodiments of the compositions and methods of the disclosure, a disease or disorder of the disclosure includes, but is not limited to, a genetic disease or disorder. In some embodiments, the genetic disease or disorder is a single-gene disease or disorder. In some embodiments, the single-gene disease or disorder is an autosomal dominant disease or disorder, an autosomal recessive disease or disorder, an X-chromosome linked (X-linked) disease or disorder, an X-linked dominant disease or disorder, an X-linked recessive disease or disorder, a Y-linked disease or disorder or a mitochondrial disease or disorder. In some embodiments, the genetic disease or disorder is a multiple-gene disease or disorder. In some embodiments, the genetic disease or disorder is a multiple-gene disease or disorder. In some embodiments, the single-gene disease or disorder is an autosomal dominant disease or disorder including, but not limited to, Huntington's disease, neurofibromatosis type 1, neurofibromatosis type 2, Marfan syndrome, hereditary nonpolyposis colorectal cancer, hereditary multiple exostoses, Von Willebrand disease, and acute intermittent porphyria. In some embodiments, the single-gene disease or disorder is an autosomal recessive disease or disorder including, but not limited to, Albinism, Medium-chain acyl-CoA dehydrogenase deficiency, cystic fibrosis, sickle-cell disease, Tay-Sachs disease, Niemann-Pick disease, spinal muscular atrophy, and Roberts syndrome. In some embodiments, the single-gene disease or disorder is X-linked disease or disorder including, but not limited to, muscular dystrophy, Duchenne muscular dystrophy, Hemophilia, Adrenoleukodystrophy (ALD), Rett syndrome, and Hemophilia A. In some embodiments, the single-gene disease or disorder is a mitochondrial disorder including, but not limited to, Leber's hereditary optic neuropathy.
  • In some embodiments of the compositions and methods of the disclosure, a disease or disorder of the disclosure includes, but is not limited to, an immune disease or disorder. In some embodiments, the immune disease or disorder is an immunodeficiency disease or disorder including, but not limited to, B-cell deficiency, T-cell deficiency, neutropenia, asplenia, complement deficiency, acquired immunodeficiency syndrome (AIDS) and immunodeficiency due to medical intervention (immunosuppression as an intended or adverse effect of a medical therapy). In some embodiments, the immune disease or disorder is an autoimmune disease or disorder including, but not limited to, Achalasia, Addison's disease, Adult Still's disease, Agammaglobulinemia, Alopecia areata, Amyloidosis, Anti-GBM/Anti-TBM nephritis, Antiphospholipid syndrome, Autoimmune angioedema, Autoimmune dysautonomia, Autoimmune encephalomyelitis, Autoimmune hepatitis, Autoimmune inner ear disease (AIED), Autoimmune myocarditis, Autoimmune oophoritis, Autoimmune orchitis, Autoimmune pancreatitis, Autoimmune retinopathy, Autoimmune urticaria, Axonal & neuronal neuropathy (AMAN), Baló disease, Behcet's disease, Benign mucosal pemphigoid, Bullous pemphigoid, Castleman disease (CD), Celiac disease, Chagas disease, Chronic inflammatory demyelinating polyneuropathy (CIDP), Chronic recurrent multifocal osteomyelitis (CRMO), Churg-Strauss Syndrome (CSS) or Eosinophilic Granulomatosis (EGPA), Cicatricial pemphigoid, Cogan's syndrome, Cold agglutinin disease, Congenital heart block, Coxsackie myocarditis, CREST syndrome, Crohn's disease, Dermatitis herpetiformis, Dermatomyositis, Devic's disease (neuromyelitis optica), Discoid lupus, Dressler's syndrome, Endometriosis, Eosinophilic esophagitis (EoE), Eosinophilic fasciitis, Erythema nodosum, Essential mixed cryoglobulinemia, Evans syndrome, Fibromyalgia, Fibrosing alveolitis, Giant cell arteritis (temporal arteritis), Giant cell myocarditis, Glomerulonephritis, Goodpasture's syndrome, Granulomatosis with Polyangiitis, Graves' disease, Guillain-Barre syndrome, Hashimoto's thyroiditis, Hemolytic anemia, Henoch-Schonlein purpura (HSP), Herpes gestationis or pemphigoid gestationis (PG), Hidradenitis Suppurativa (HS) (Acne Inversa), Hypogammalglobulinemia, IgA Nephropathy, IgG4-related sclerosing disease, Immune thrombocytopenic purpura (ITP), Inclusion body myositis (IBM), Interstitial cystitis (IC), Juvenile arthritis, Juvenile diabetes (Type 1 diabetes), Juvenile myositis (JM), Kawasaki disease, Lambert-Eaton syndrome, Leukocytoclastic vasculitis, Lichen planus, Lichen sclerosus, Ligneous conjunctivitis, Linear IgA disease (LAD), Lupus, Lyme disease chronic, Meniere's disease, Microscopic polyangiitis (MPA), Mixed connective tissue disease (MCTD), Mooren's ulcer, Mucha-Habermann disease, Multifocal Motor Neuropathy (MMN) or MMNCB, Multiple sclerosis, Myasthenia gravis, Myositis, Narcolepsy, Neonatal Lupus, Neuromyelitis optica, Neutropenia, Ocular cicatricial pemphigoid, Optic neuritis, Palindromic rheumatism (PR), PANDAS, Paraneoplastic cerebellar degeneration (PCD), Paroxysmal nocturnal hemoglobinuria (PNH), Parry Romberg syndrome, Pars planitis (peripheral uveitis), Parsonnage-Turner syndrome, Pemphigus, Peripheral neuropathy, Perivenous encephalomyelitis, Pernicious anemia (PA), POEMS syndrome, Polyarteritis nodosa, Polyglandular syndromes type I, II, III, Polymyalgia rheumatica, Polymyositis, Postmyocardial infarction syndrome, Postpericardiotomy syndrome, Primary biliary cirrhosis, Primary sclerosing cholangitis, Progesterone dermatitis, Psoriasis, Psoriatic arthritis, Pure red cell aplasia (PRCA), Pyoderma gangrenosum, Raynaud's phenomenon, Reactive Arthritis, Reflex sympathetic dystrophy, Relapsing polychondritis, Restless legs syndrome (RLS), Retroperitoneal fibrosis, Rheumatic fever, Rheumatoid arthritis, Sarcoidosis, Schmidt syndrome, Scleritis, Scleroderma, Sjögren's syndrome, Sperm & testicular autoimmunity, Stiff person syndrome (SPS), Subacute bacterial endocarditis (SBE), Susac's syndrome, Sympathetic ophthalmia (SO), Takayasu's arteritis, Temporal arteritis/Giant cell arteritis, Thrombocytopenic purpura (TTP), Tolosa-Hunt syndrome (THS), Transverse myelitis, Type 1 diabetes, Ulcerative colitis (UC), Undifferentiated connective tissue disease (UCTD), Uveitis, Vasculitis, Vitiligo, Vogt-Koyanagi-Harada Disease, or Wegener's granulomatosis.
  • In some embodiments of the compositions and methods of the disclosure, a disease or disorder of the disclosure includes, but is not limited to, an inflammatory disease or disorder.
  • In some embodiments of the compositions and methods of the disclosure, a disease or disorder of the disclosure includes, but is not limited to, a metabolic disease or disorder.
  • In some embodiments of the compositions and methods of the disclosure, a disease or disorder of the disclosure includes, but is not limited to, a degenerative or a progressive disease or disorder. In some embodiments, the degenerative or a progressive disease or disorder includes, but is not limited to, amyotrophic lateral sclerosis (ALS), Huntington's disease, Alzheimer's disease, and aging.
  • In some embodiments of the compositions and methods of the disclosure, a disease or disorder of the disclosure includes, but is not limited to, an infectious disease or disorder.
  • In some embodiments of the compositions and methods of the disclosure, a disease or disorder of the disclosure includes, but is not limited to, a pediatric or a developmental disease or disorder.
  • In some embodiments of the compositions and methods of the disclosure, a disease or disorder of the disclosure includes, but is not limited to, a cardiovascular disease or disorder.
  • In some embodiments of the compositions and methods of the disclosure, a disease or disorder of the disclosure includes, but is not limited to, a proliferative disease or disorder. In some embodiments, the proliferative disease or disorder is a cancer. In some embodiments, the cancer includes, but is not limited to, Acute Lymphoblastic Leukemia (ALL), Acute Myeloid Leukemia (AML), Adrenocortical Carcinoma, AIDS-Related Cancers, Kaposi Sarcoma (Soft Tissue Sarcoma), AIDS-Related Lymphoma (Lymphoma), Primary CNS Lymphoma (Lymphoma), Anal Cancer, Appendix Cancer, Gastrointestinal Carcinoid Tumors, Astrocytomas, Atypical Teratoid/Rhabdoid Tumor, Central Nervous System (Brain Cancer), Basal Cell Carcinoma, Bile Duct Cancer, Bladder Cancer, Bone Cancer, Ewing Sarcoma, Osteosarcoma, Malignant Fibrous Histiocytoma, Brain Tumors, Breast Cancer, Burkitt Lymphoma, Carcinoid Tumor, Carcinoma, Cardiac (Heart) Tumors, Embryonal Tumors, Germ Cell Tumor, Primary CNS Lymphoma, Cervical Cancer, Cholangiocarcinoma, Chordoma, Chronic Lymphocytic Leukemia (CLL), Chronic Myelogenous Leukemia (CML), Chronic Myeloproliferative Neoplasms, Colorectal Cancer, Craniopharyngioma, Cutaneous T-Cell Lymphoma, Ductal Carcinoma In Situ, Embryonal Tumors, Endometrial Cancer (Uterine Cancer), Ependymoma, Esophageal Cancer, Esthesioneuroblastoma (Head and Neck Cancer), Ewing Sarcoma (Bone Cancer), Extracranial Germ Cell Tumor, Extragonadal Germ Cell Tumor, Eye Cancer, Childhood Intraocular Melanoma, Intraocular Melanoma, Retinoblastoma, Fallopian Tube Cancer, Fibrous Histiocytoma of Bone, Malignant, and Osteosarcoma, Gallbladder Cancer, Gastric (Stomach) Cancer, Gastrointestinal Carcinoid Tumor, Gastrointestinal Stromal Tumors (GIST) (Soft Tissue Sarcoma), Childhood Gastrointestinal Stromal Tumors, Germ Cell Tumors, Childhood Extracranial Germ Cell Tumors, Extragonadal Germ Cell Tumors, Ovarian Germ Cell Tumors, Testicular Cancer, Gestational Trophoblastic Disease, Hairy Cell Leukemia, Head and Neck Cancer, Heart Tumors, Hepatocellular (Liver) Cancer, Histiocytosis, Hodgkin Lymphoma, Hypopharyngeal Cancer (Head and Neck Cancer), Intraocular Melanoma, Islet Cell Tumors, Pancreatic Neuroendocrine Tumors, Kaposi Sarcoma (Soft Tissue Sarcoma), Kidney (Renal Cell) Cancer, Langerhans Cell Histiocytosis, Laryngeal Cancer (Head and Neck Cancer), Leukemia, Lip and Oral Cavity Cancer (Head and Neck Cancer), Liver Cancer, Lung Cancer (Non-Small Cell and Small Cell), Childhood Lung Cancer, Lymphoma, Male Breast Cancer, Malignant Fibrous Histiocytoma of Bone and Osteosarcoma, Melanoma, Merkel Cell Carcinoma (Skin Cancer), Mesothelioma, Metastatic Squamous Neck Cancer with Occult Primary (Head and Neck Cancer), Midline Tract Carcinoma With NUT Gene Changes, Mouth Cancer (Head and Neck Cancer), Multiple Endocrine Neoplasia Syndromes, Multiple Myeloma/Plasma Cell Neoplasms, Mycosis Fungoides (Lymphoma), Myelodysplastic Syndromes, Myelodysplastic/Myeloproliferative Neoplasms, Nasal Cavity and Paranasal Sinus Cancer (Head and Neck Cancer), Nasopharyngeal Cancer (Head and Neck Cancer), Neuroblastoma, Non-Hodgkin Lymphoma, Non-Small Cell Lung Cancer, Oral Cancer, Lip and Oral Cavity Cancer and Oropharyngeal Cancer, Osteosarcoma and Malignant Fibrous Histiocytoma of Bone, Ovarian Cancer, Pancreatic Cancer, Pancreatic Neuroendocrine Tumors (Islet Cell Tumors), Papillomatosis, Paraganglioma, Parathyroid Cancer, Penile Cancer, Pharyngeal Cancer (Head and Neck Cancer), Pheochromocytoma, Plasma Cell Neoplasm/Multiple Myeloma, Pleuropulmonary Blastoma, Pregnancy and Breast Cancer, Primary Central Nervous System (CNS) Lymphoma, Primary Peritoneal Cancer, Prostate Cancer, Rectal Cancer, Recurrent Cancer, Renal Cell (Kidney) Cancer, Retinoblastoma, Rhabdomyosarcoma, Childhood (Soft Tissue Sarcoma), Salivary Gland Cancer (Head and Neck Cancer), Sarcoma, Childhood Rhabdomyosarcoma (Soft Tissue Sarcoma), Childhood Vascular Tumors (Soft Tissue Sarcoma), Ewing Sarcoma (Bone Cancer), Kaposi Sarcoma (Soft Tissue Sarcoma), Osteosarcoma (Bone Cancer), Uterine Sarcoma, Sézary Syndrome, Lymphoma, Skin Cancer, Small Cell Lung Cancer, Small Intestine Cancer, Soft Tissue Sarcoma, Squamous Cell Carcinoma of the Skin, Squamous Neck Cancer, Stomach (Gastric) Cancer, T-Cell Lymphoma, Testicular Cancer, Throat Cancer (Head and Neck Cancer), Nasopharyngeal Cancer, Oropharyngeal Cancer, Hypopharyngeal Cancer, Thymoma and Thymic Carcinoma, Thyroid Cancer, Transitional Cell Cancer of the Renal Pelvis and Ureter, Renal Cell Cancer, Urethral Cancer, Uterine Sarcoma, Vaginal Cancer, Vascular Tumors (Soft Tissue Sarcoma), Vulvar Cancer, Wilms Tumor and Other Childhood Kidney Tumors.
  • In some embodiments of the methods of the disclosure, a subject of the disclosure has been diagnosed with the disease or disorder. In some embodiments, the subject of the disclosure presents at least one sign or symptom of the disease or disorder. In some embodiments, the subject has a biomarker predictive of a risk of developing the disease or disorder. In some embodiments, the biomarker is a genetic mutation.
  • In some embodiments of the methods of the disclosure, a subject of the disclosure is female. In some embodiments of the methods of the disclosure, a subject of the disclosure is male. In some embodiments, a subject of the disclosure has two XX or XY chromosomes. In some embodiments, a subject of the disclosure has two XX or XY chromosomes and a third chromosome, either an X or a Y.
  • In some embodiments of the methods of the disclosure, a subject of the disclosure is a neonate, an infant, a child, an adult, a senior adult, or an elderly adult. In some embodiments of the methods of the disclosure, a subject of the disclosure is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or 31 days old. In some embodiments of the methods of the disclosure, a subject of the disclosure is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12 months old. In some embodiments of the methods of the disclosure, a subject of the disclosure is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or any number of years or partial years in between of age.
  • In some embodiments of the methods of the disclosure, a subject of the disclosure is a mammal. In some embodiments, a subject of the disclosure is a non-human mammal.
  • In some embodiments of the methods of the disclosure, a subject of the disclosure is a human.
  • In some embodiments of the methods of the disclosure, a therapeutically effective amount comprises a single dose of a composition of the disclosure. In some embodiments, a therapeutically effective amount comprises a therapeutically effective amount comprises at least one dose of a composition of the disclosure. In some embodiments, a therapeutically effective amount comprises a therapeutically effective amount comprises one or more dose(s) of a composition of the disclosure.
  • In some embodiments of the methods of the disclosure, a therapeutically effective amount eliminates a sign or symptom of the disease or disorder. In some embodiments, a therapeutically effective amount reduces a severity of a sign or symptom of the disease or disorder.
  • In some embodiments of the methods of the disclosure, a therapeutically effective amount eliminates the disease or disorder.
  • In some embodiments of the methods of the disclosure, a therapeutically effective amount prevents an onset of a disease or disorder. In some embodiments, a therapeutically effective amount delays the onset of a disease or disorder. In some embodiments, a therapeutically effective amount reduces the severity of a sign or symptom of the disease or disorder. In some embodiments, a therapeutically effective amount improves a prognosis for the subject.
  • In some embodiments of the methods of the disclosure, a composition of the disclosure is administered to the subject systemically. In some embodiments, the composition of the disclosure is administered to the subject by an intravenous route. In some embodiments, the composition of the disclosure is administered to the subject by an injection or an infusion.
  • In some embodiments of the methods of the disclosure, a composition of the disclosure is administered to the subject locally. In some embodiments, the composition of the disclosure is administered to the subject by an intraosseous, intraocular, intracerebrospinal or intraspinal route. In some embodiments, the composition of the disclosure is administered directly to the cerebral spinal fluid of the central nervous system. In some embodiments, the composition of the disclosure is administered directly to a tissue or fluid of the eye and does not have bioavailability outside of ocular structures. In some embodiments, the composition of the disclosure is administered to the subject by an injection or an infusion.
  • In some embodiments, the compositions comprising the RNA-binding fusion proteins disclosed herein are formulated as pharmaceutical compositions. Briefly, pharmaceutical compositions for use as disclosed herein may comprise a fusion protein(s) or a polynucleotide encoding the fusion protein(s), optionally comprised in an AAV, which is optionally also immune orthogonal, in combination with one or more pharmaceutically or physiologically acceptable carriers, diluents or excipients. Such compositions may comprise buffers such as neutral buffered saline, phosphate buffered saline and the like; carbohydrates such as glucose, mannose, sucrose or dextrans, mannitol; proteins; polypeptides or amino acids such as glycine; antioxidants; chelating agents such as EDTA or glutathione; adjuvants (e.g., aluminum hydroxide); and preservatives. Compositions of the disclosure may be formulated for oral, intravenous, topical, enteral, intraocular, and/or parenteral administration. In certain embodiments, the compositions of the present disclosure are formulated for intravenous administration.
    • Example Embodiments
  • Embodiment 1. A composition comprising:
  • (a) a sequence comprising a guide RNA (gRNA) that specifically binds a target sequence within an RNA molecule and
  • (b) a sequence encoding a fusion protein, the sequence comprising a sequence encoding a first RNA-binding polypeptide and a sequence encoding a second RNA-binding polypeptide,
  • wherein neither the first RNA-binding polypeptide nor the second RNA-binding polypeptide comprises a significant DNA-nuclease activity,
  • wherein the first RNA-binding polypeptide and the second RNA-binding polypeptide are not identical, and
  • wherein the second RNA-binding polypeptide comprises an RNA-nuclease activity; or
  • a composition comprising nucleic acid sequence encoding a fusion protein, the fusion protein comprising a first RNA-binding polypeptide and a second RNA-binding polypeptide, wherein the first RNA-binding polypeptide is not a guided RNA-binding polypeptide, wherein the first RNA-binding polypeptide and the second RNA-binding polypeptide are not identical, and wherein the second RNA-binding polypeptide comprises an RNA-nuclease activity.
  • Embodiment 2. The composition of embodiment 1, wherein the target sequence comprises at least one repeated sequence.
  • Embodiment 3. The composition of embodiment 1 or 2, wherein the sequence comprising the gRNA comprises a promoter capable of expressing the gRNA in a eukaryotic cell.
  • Embodiment 4. The composition of embodiment 3, wherein the eukaryotic cell is an animal cell.
  • Embodiment 5. The composition of embodiment 4, wherein the animal cell is a mammalian cell.
  • Embodiment 6. The composition of embodiment 5, wherein the animal cell is a human cell.
  • Embodiment 7. The composition of any one of embodiments 1-6, wherein the promoter is a constitutively active promoter.
  • Embodiment 8. The composition of any one of embodiments 1-7, wherein the promoter is isolated or derived from a promoter capable of driving expression of an RNA polymerase.
  • Embodiment 9. The composition of embodiment 8, wherein the promoter is isolated or derived from a U6 promoter.
  • Embodiment 10. The composition of any one of embodiments 1-7, wherein the promoter is isolated or derived from a promoter capable of driving expression of a transfer RNA (tRNA).
  • Embodiment 11. The composition of embodiment 10, wherein the promoter is isolated or derived from an alanine tRNA promoter, an arginine tRNA promoter, an asparagine tRNA promoter, an aspartic acid tRNA promoter, a cysteine tRNA promoter, a glutamine tRNA promoter, a glutamic acid tRNA promoter, a glycine tRNA promoter, a histidine tRNA promoter, an isoleucine tRNA promoter, a leucine tRNA promoter, a lysine tRNA promoter, a methionine tRNA promoter, a phenylalanine tRNA promoter, a proline tRNA promoter, a serine tRNA promoter, a threonine tRNA promoter, a tryptophan tRNA promoter, a tyrosine tRNA promoter, or a valine tRNA promoter.
  • Embodiment 12. The composition of embodiment 10, wherein the promoter is isolated or derived from a valine tRNA promoter.
  • Embodiment 13. The composition of any one of embodiments 1-12, wherein the sequence comprising the gRNA comprises a spacer sequence that specifically binds to the target RNA sequence.
  • Embodiment 14. The composition of embodiment 13, wherein the spacer sequence has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 87%, 90%, 95%, 97%, 99% or any percentage in between of complementarity to the target RNA sequence.
  • Embodiment 15. The composition of embodiment 13, wherein the spacer sequence has 100% complementarity to the target RNA sequence.
  • Embodiment 16. The composition of any one of embodiments 13-15, wherein the spacer sequence comprises or consists of 20 nucleotides.
  • Embodiment 17. The composition of any one of embodiments 13-15, wherein the spacer sequence comprises or consists of 21 nucleotides.
  • Embodiment 18. The composition of embodiment 17, wherein the spacer sequence comprises the sequence UGGAGCGAGCAUCCCCCAAA (SEQ ID NO: 1), GUUUGGGGGAUGCUCGCUCCA (SEQ ID NO: 2), CCCUCACUGCUGGGGAGUCC (SEQ ID NO: 3), GGACUCCCCAGCAGUGAGGG (SEQ ID NO: 4), GCAACUGGAUCAAUUUGCUG (SEQ ID NO: 5), GCAGCAAAUUGAUCCAGUUGC (SEQ ID NO: 6), GCAUUCUUAUCUGGUCAGUGC (SEQ ID NO: 7), GCACUGACCAGAUAAGAAUG (SEQ ID NO: 8), GAGCAGCAGCAGCAGCAGCAG (SEQ ID NO: 9), GCAGGCAGGCAGGCAGGCAGG (SEQ ID NO: 10), GCCCCGGCCCCGGCCCCGGC (SEQ ID NO: 11), or GCTGCTGCTGCTGCTGCTGC (SEQ ID NO: 12), GGGGCCGGGGCCGGGGCCGG (SEQ ID NO: 74), GGGCCGGGGCCGGGGCCGGG (SEQ ID NO: 75), GGCCGGGGCCGGGGCCGGGG (SEQ ID NO: 76), GCCGGGGCCGGGGCCGGGGC (SEQ ID NO: 77), CCGGGGCCGGGGCCGGGGCC (SEQ ID NO: 78), CGGGGCCGGGGCCGGGGCCG (SEQ ID NO: 79).
  • Embodiment 19. The composition of any one of embodiments 1-18, wherein the sequence comprising the gRNA comprises a scaffold sequence that specifically binds to the first RNA binding protein.
  • Embodiment 20. The composition of embodiment 19, wherein the scaffold sequence comprises a stem-loop structure.
  • Embodiment 21. The composition of embodiment 19 or 20, wherein the scaffold sequence comprises or consists of 90 nucleotides.
  • Embodiment 22. The composition of embodiment 19 or 20, wherein the scaffold sequence comprises or consists of 93 nucleotides.
  • Embodiment 23. The composition of embodiment 22, wherein the scaffold sequence comprises the sequence
  • (SEQ ID NO: 13)
    GUUUAAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUC
    CGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUUUU.
  • Embodiment 24. The composition of embodiment 16, wherein the spacer sequence comprises the sequence GUGAUAAGUGGAAUGCCAUG (SEQ ID NO: 14), CUGGUGAACUUCCGAUAGUG (SEQ ID NO: 15), or GAGATATAGCCTGGTGGTTC (SEQ ID NO: 16).
  • Embodiment 25. The composition of embodiment 19 or 24, wherein the scaffold sequence comprises a step-loop structure.
  • Embodiment 26. The composition of embodiment 25, wherein the scaffold sequence comprises or consists of 85 nucleotides.
  • Embodiment 27. The composition of embodiment 26, wherein the scaffold sequence comprises the sequence
  • (SEQ ID NO: 17)
    GGACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAA
    GUGGCACCGAGUCGGUGCUUUUU.
  • Embodiment 28. The composition of embodiment 16, wherein the spacer sequence comprises the sequence at least 1, 2, 3, 4, 5, 6, or 7 repeats of the sequence CUG (SEQ ID NO: 18), CCUG (SEQ ID NO: 19), CAG (SEQ ID NO: 80), GGGGCC (SEQ ID NO: 81) or any combination thereof.
  • Embodiment 29. The composition of embodiment 28, wherein the sequence comprising the gRNA comprises a scaffold sequence that specifically binds to the first RNA binding protein.
  • Embodiment 30. The composition of embodiment 29, wherein the scaffold sequence comprises a stem-loop structure.
  • Embodiment 31. The composition of embodiment 29 or 30, wherein the scaffold sequence comprises or consists of 90 nucleotides.
  • Embodiment 32. The composition of embodiment 30 or 31, wherein the scaffold sequence comprises or consists of 93 nucleotides.
  • Embodiment 33. The composition of embodiment 32, wherein the scaffold sequence comprises the sequence
  • (SEQ ID NO: 82)
    GUUUAAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUC
    CGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUUUU
    or
    (SEQ ID NO: 83)
    GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAAC
    UUGAAAAAGUGGCACCGAGUCGGUGCU.
  • Embodiment 34. The composition of any one of embodiments 1-33, wherein the gRNA does not bind or does not selectively bind to a second sequence within the RNA molecule.
  • Embodiment 35. The composition of embodiment 34, wherein an RNA genome or an RNA transcriptome comprises the RNA molecule.
  • Embodiment 36. The composition of any one of embodiments 1-35, wherein the first RNA binding protein comprises a CRISPR-Cas protein.
  • Embodiment 37. The composition of embodiment 36, wherein the CRISPR-Cas protein is a Type II CRISPR-Cas protein.
  • Embodiment 38. The composition of embodiment 37, wherein the first RNA binding protein comprises a Cas9 polypeptide or an RNA-binding portion thereof.
  • Embodiment 39. The composition of embodiment 36, wherein the CRISPR-Cas protein is a Type V CRISPR-Cas protein.
  • Embodiment 40. The composition of embodiment 39, wherein the first RNA binding protein comprises a Cpf1 polypeptide or an RNA-binding portion thereof.
  • Embodiment 41. The composition of embodiment 36, wherein the CRISPR-Cas protein is a Type VI CRISPR-Cas protein.
  • Embodiment 42. The composition of embodiment 41, wherein the first RNA binding protein comprises a Cas13 polypeptide or an RNA-binding portion thereof.
  • Embodiment 43. The composition of any one of embodiments 36-42, wherein the CRISPR-Cas protein comprises a native RNA nuclease activity.
  • Embodiment 44. The composition of embodiment 43, wherein the native RNA nuclease activity is reduced or inhibited.
  • Embodiment 45. The composition of embodiment 43, wherein the native RNA nuclease activity is increased or induced.
  • Embodiment 46. The composition of any one of embodiments 36-45, wherein the CRISPR-Cas protein comprises a native DNA nuclease activity and wherein the native DNA nuclease activity is inhibited.
  • Embodiment 47. The composition of embodiment 46, wherein the CRISPR-Cas protein comprises a mutation.
  • Embodiment 48. The composition of embodiment 47, wherein a nuclease domain of the CRISPR-Cas protein comprises the mutation.
  • Embodiment 49. The composition of embodiment 47, wherein the mutation occurs in a nucleic acid encoding the CRISPR-Cas protein.
  • Embodiment 50. The composition of embodiment 47, wherein the mutation occurs in an amino acid encoding the CRISPR-Cas protein.
  • Embodiment 51. The composition of any one of embodiments 47-50, wherein the mutation comprises a substitution, an insertion, a deletion, a frameshift, an inversion, or a transposition.
  • Embodiment 52. The composition of any one of embodiments 47-50, wherein the mutation comprises a deletion of a nuclease domain, a binding site within the nuclease domain, an active site within the nuclease domain, or at least one essential amino acid residue within the nuclease domain.
  • Embodiment 53. The composition of any one of embodiments 1-35, wherein the first RNA binding protein comprises a Pumilio and FBF (PUF) protein.
  • Embodiment 54. The composition of embodiment 53, wherein the first RNA binding protein comprises a Pumilio-based assembly (PUMBY) protein.
  • Embodiment 55. The composition of any one of embodiments 1-54, wherein the first RNA binding protein does not require multimerization for RNA-binding activity.
  • Embodiment 56. The composition of embodiment 55, wherein the first RNA binding protein is not a monomer of a multimer complex
  • Embodiment 57. The composition of embodiment 55, wherein a multimer protein complex does not comprise the first RNA binding protein.
  • Embodiment 58. The composition of any one of embodiments 1-57, wherein the first RNA binding protein selectively binds to a target sequence within the RNA molecule.
  • Embodiment 59. The composition of embodiment 58, wherein the first RNA binding protein does not comprise an affinity for a second sequence within the RNA molecule.
  • Embodiment 60. The composition of embodiment 58 or 59, wherein the first RNA binding protein does not comprise a high affinity for or selectively bind a second sequence within the RNA molecule.
  • Embodiment 61. The composition of embodiment 60, wherein an RNA genome or an RNA transcriptome comprises the RNA molecule.
  • Embodiment 62. The composition of any one of embodiments 1-61, wherein the first RNA binding protein comprises between 2 and 1300 amino acids, inclusive of the endpoints.
  • Embodiment 63. The composition of any one of embodiments 1-62, wherein the sequence encoding the first RNA binding protein further comprises a sequence encoding a nuclear localization signal (NLS).
  • Embodiment 64. The composition of embodiment 63, wherein the sequence encoding a nuclear localization signal (NLS) is positioned 3′ to the sequence encoding the first RNA binding protein.
  • Embodiment 65. The composition of embodiment 64, wherein the first RNA binding protein comprises an NLS at a C-terminus of the protein.
  • Embodiment 66. The composition of any one of embodiments 1-62, wherein the sequence encoding the first RNA binding protein further comprises a first sequence encoding a first NLS and a second sequence encoding a second NLS.
  • Embodiment 67. The composition of embodiment 66, wherein the sequence encoding the first NLS or the second NLS is positioned 3′ to the sequence encoding the first RNA binding protein.
  • Embodiment 68. The composition of embodiment 67, wherein the first RNA binding protein comprises the first NLS or the second NLS at a C-terminus of the protein.
  • Embodiment 69. The composition of any one of embodiments 1-68, wherein the second RNA binding protein comprises or consists of a nuclease domain.
  • Embodiment 70. The composition of embodiment 69, wherein the sequence encoding the second RNA binding protein comprises or consists of an RNAse.
  • Embodiment 71. The composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAse1.
  • Embodiment 72. The composition of embodiment 71, wherein the RNAse1 protein comprises or consists of SEQ ID NO: 20.
  • Embodiment 73. The composition of embodiment 72, wherein the second RNA binding protein comprises or consists of an RNAse4.
  • Embodiment 74. The composition of embodiment 73, wherein the RNAse4 protein comprises or consists of: (SEQ ID NO: 21.
  • Embodiment 75. The composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAse6.
  • Embodiment 76. The composition of embodiment 75, wherein the RNAse6 protein comprises or consists of SEQ ID NO: 22.
  • Embodiment 77. The composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAse7.
  • Embodiment 78. The composition of embodiment 77, wherein the RNAse7 protein comprises or consists of SEQ ID NO: 23.
  • Embodiment 79. The composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAse8.
  • Embodiment 80. The composition of embodiment 79, wherein the RNAse8 protein comprises or consists of SEQ ID NO: 24.
  • Embodiment 81. The composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAse2.
  • Embodiment 82. The composition of embodiment 81, wherein the RNAse2 protein comprises or consists of SEQ ID NO: 25.
  • Embodiment 83. The composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAse6PL.
  • Embodiment 84. The composition of embodiment 83, wherein the RNAse6PL protein comprises or consists of SEQ ID NO: 26.
  • Embodiment 85. The composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAseL.
  • Embodiment 86. The composition of embodiment 85, wherein the RNAseL protein comprises or consists of SEQ ID NO: 27.
  • Embodiment 87. The composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAseT2.
  • Embodiment 88. The composition of embodiment 87, wherein the RNAseT2 protein comprises or consists of SEQ ID NO: 28.
  • Embodiment 89. The composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAse11.
  • Embodiment 90. The composition of embodiment 89, wherein the RNAse11 comprises or consists of SEQ ID NO: 29.
  • Embodiment 91. The composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAseT2-like.
  • Embodiment 92. The composition of embodiment 91, wherein the RNAseT2-like protein comprises or consists of SEQ ID NO: 30.
  • Embodiment 93. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a NOB1 polypeptide.
  • Embodiment 94. The composition of embodiment 93, wherein the NOB1 polypeptide comprises or consists of SEQ ID NO: 31.
  • Embodiment 95. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of an endonuclease.
  • Embodiment 96. The composition of embodiment 95, wherein the second RNA binding protein comprises or consists of an endonuclease V (ENDOV).
  • Embodiment 97. The composition of embodiment 96, wherein the ENDOV protein comprises or consists of SEQ ID NO: 32.
  • Embodiment 98. The composition of embodiment 95, wherein the second RNA binding protein comprises or consists of an endonuclease G (ENDOG).
  • Embodiment 99. The composition of embodiment 98, wherein the ENDOG protein comprises or consists of SEQ ID NO: 33.
  • Embodiment 100. The composition of embodiment 95, wherein the second RNA binding protein comprises or consists of an endonuclease D1 (ENDOD1).
  • Embodiment 101. The composition of embodiment 100, wherein the ENDOD1 protein comprises or consists of SEQ ID NO: 34.
  • Embodiment 102. The composition of embodiment 95, wherein the second RNA binding protein comprises or consists of a Human flap endonuclease-1 (hFEN1).
  • Embodiment 103. The composition of embodiment 102, wherein the hFEN1 protein comprises or consists of SEQ ID NO: 35.
  • Embodiment 104. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a human Schlafen 14 (hSLFN14) polypeptide.
  • Embodiment 105. The composition of embodiment 104, wherein the hSLFN14 polypeptide comprises or consists of SEQ ID NO: 36.
  • Embodiment 106. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a human beta-lactamase-like protein 2 (hLACTB2) polypeptide.
  • Embodiment 107. The composition of embodiment 106, wherein the hLACTB2 polypeptide comprises or consists of SEQ ID NO: 37.
  • Embodiment 108. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of an apurinic/apyrimidinic (AP) endodeoxyribonuclease (APEX2) polypeptide.
  • Embodiment 109. The composition of embodiment 108, wherein the APEX2 polypeptide comprises or consists of SEQ ID NO: 38.
  • Embodiment 110. The composition of embodiment 108, wherein the APEX2 polypeptide comprises or consists of: SEQ ID NO: 39.
  • Embodiment 111. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of an angiogenin (ANG) polypeptide.
  • Embodiment 112. The composition of embodiment 111, wherein the ANG polypeptide comprises or consists of SEQ ID NO: 40.
  • Embodiment 113. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a heat responsive protein 12 (HRSP12) polypeptide.
  • Embodiment 114. The composition of embodiment 113, wherein the HRSP12 polypeptide comprises or consists of SEQ ID NO: 41.
  • Embodiment 115. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a Zinc Finger CCCH-Type Containing 12A (ZC3H12A) polypeptide.
  • Embodiment 116. The composition of embodiment 115, wherein the ZC3H12A polypeptide comprises or consists of SEQ ID NO: 42.
  • Embodiment 117. The composition of embodiment 115, wherein the ZC3H12A polypeptide comprises or consists of SEQ ID NO: 43.
  • Embodiment 118. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a Reactive Intermediate Imine Deaminase A (RIDA) polypeptide.
  • Embodiment 119. The composition of embodiment 118, wherein the RIDA polypeptide comprises or consists of SEQ ID NO: 44.
  • Embodiment 120. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a Phospholipase D Family Member 6 (PDL6) polypeptide.
  • Embodiment 121. The composition of embodiment 120, wherein the PDL6 polypeptide comprises or consists of: (SEQ ID NO: 126.
  • Embodiment 122. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a Endonuclease III-like protein 1 (NTHL) polypeptide.
  • Embodiment 123. The composition of embodiment 122, wherein the NTHL polypeptide comprises or consists of SEQ ID NO: 123.
  • Embodiment 124. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a Mitochondrial ribonuclease P catalytic subunit (KIAA0391) polypeptide.
  • Embodiment 125. The composition of embodiment 124, wherein the KIAA0391 polypeptide comprises or consists of SEQ ID NO: 127.
  • Embodiment 126. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of an apurinic or apyrimidinic site lyase (APEX1) polypeptide.
  • Embodiment 127. The composition of embodiment 126, wherein the APEX1 polypeptide comprises or consists of SEQ ID NO: 125.
  • Embodiment 128. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of an argonaute 2 (AGO2) polypeptide.
  • Embodiment 129. The composition of embodiment 128, wherein the AGO2 polypeptide comprises or consists of SEQ ID NO: 128.
  • Embodiment 130. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a mitochondrial nuclease EXOG (EXOG) polypeptide.
  • Embodiment 131. The composition of embodiment 130, wherein the EXOG polypeptide comprises or consists of SEQ ID NO: 129.
  • Embodiment 132. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a Zinc Finger CCCH-Type Containing 12D (ZC3H12D) polypeptide.
  • Embodiment 133. The composition of embodiment 132, wherein the ZC3H12D polypeptide comprises or consists of SEQ ID NO: 130.
  • Embodiment 134. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of an endoplasmic reticulum to nucleus signaling 2 (ERN2) polypeptide.
  • Embodiment 135. The composition of embodiment 134, wherein the ERN2 polypeptide comprises or consists of SEQ ID NO: 131.
  • Embodiment 136. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a pelota mRNA surveillance and ribosome rescue factor (PELO) polypeptide.
  • Embodiment 137. The composition of embodiment 136, wherein the PELO polypeptide comprises or consists of SEQ ID NO: 132.
  • Embodiment 138. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a YBEY metallopeptidase (YBEY) polypeptide.
  • Embodiment 139. The composition of embodiment 138, wherein the YBEY polypeptide comprises or consists of SEQ ID NO: 133.
  • Embodiment 140. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a cleavage and polyadenylation specific factor 4 like (CPSF4L) polypeptide.
  • Embodiment 141. The composition of embodiment 140, wherein the CPSF4L comprises or consists of SEQ ID NO: 134.
  • Embodiment 142. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of an hCG_2002731 polypeptide.
  • Embodiment 143. The composition of embodiment 142, wherein the hCG_2002731 polypeptide comprises or consists of SEQ ID NO: 135.
  • Embodiment 144. The composition of embodiment 142, wherein the hCG_2002731 polypeptide comprises or consists of SEQ ID NO: 136.
  • Embodiment 145. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of an Excision Repair Cross-Complementation Group 1 (ERCC1) polypeptide.
  • Embodiment 146. The composition of embodiment 145, wherein the ERCC1 polypeptide comprises or consists of SEQ ID NO: 137.
  • Embodiment 147. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a ras-related C3 botulinum toxin substrate 1 isoform (RAC1) polypeptide.
  • Embodiment 148. The composition of embodiment 147, wherein the RAC1 polypeptide comprises or consists of SEQ ID NO: 138.
  • Embodiment 149. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a Ribonuclease A A1 (RAA1) polypeptide.
  • Embodiment 150. The composition of embodiment 149, wherein the RAA1 polypeptide comprises or consists of SEQ ID NO: 139.
  • Embodiment 151. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a Ras Related Protein (RAB1) polypeptide.
  • Embodiment 152. The composition of embodiment 151, wherein the RAB1 polypeptide comprises or consists of SEQ ID NO: 140.
  • Embodiment 153. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a DNA Replication Helicase/Nuclease 2 (DNA2) polypeptide.
  • Embodiment 154. The composition of embodiment 153, wherein the DNA2 polypeptide comprises or consists of SEQ ID NO: 141.
  • Embodiment 155. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a FLJ35220 polypeptide.
  • Embodiment 156. The composition of embodiment 155, wherein the FLJ35220 polypeptide comprises or consists of SEQ ID NO: 142.
  • Embodiment 157. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a FLJ13173 polypeptide.
  • Embodiment 158. The composition of embodiment 157, wherein the FLJ13173 polypeptide comprises or consists of: (SEQ ID NO: 143.
  • Embodiment 159. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a DNA repair endonuclease XPF (ERCC4) polypeptide.
  • Embodiment 160. The composition of embodiment 159, wherein the ERCC4 polypeptide comprises or consists of SEQ ID NO: 64.
  • Embodiment 161. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(K41R)) polypeptide.
  • Embodiment 162. The composition of embodiment 161, wherein the Rnase1(K41R) polypeptide comprises or consists of SEQ ID NO: 116.
  • Embodiment 163. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(K41R, D121E)) polypeptide.
  • Embodiment 164. The composition of embodiment 163, wherein the Rnase1 (Rnase1(K41R, D121E)) polypeptide comprises or consists of SEQ ID NO: 117.
  • Embodiment 165. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(K41R, D121E, H119N)) polypeptide.
  • Embodiment 166. The composition of embodiment 165, wherein the Rnase1 (Rnase1(K41R, D121E, H119N)) polypeptide comprises or consists of SEQ ID NO: 118.
  • Embodiment 167. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(H119N)) polypeptide.
  • Embodiment 168. The composition of embodiment 167, wherein the Rnase1 (Rnase1(H119N)) polypeptide comprises or consists of SEQ ID NO: 119.
  • Embodiment 169. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide.
  • Embodiment 170. The composition of embodiment 169, wherein the Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide comprises or consists of SEQ ID NO: 120.
  • Embodiment 171. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide.
  • Embodiment 172. The composition of embodiment 171, wherein the Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N, K41R, D121E)) polypeptide comprises or consists of SEQ ID NO: 121.
  • Embodiment 173. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide.
  • Embodiment 174. The composition of embodiment 173, wherein the Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D)) polypeptide comprises or consists of SEQ ID NO: 122.
  • Embodiment 175. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of Teneurin Transmembrane Protein 1 (TENM1) polypeptide.
  • Embodiment 176. The composition of embodiment 175, wherein the TENM1 polypeptide comprises or consists of SEQ ID NO: 144.
  • Embodiment 177. The composition of embodiment 69, wherein the second RNA binding protein comprises or consists of Teneurin Transmembrane Protein 2 (TENM2) polypeptide.
  • Embodiment 178. The composition of embodiment 177, wherein the TENM2 polypeptide comprises or consists of SEQ ID NO: 145.
  • Embodiment 179. A composition comprising a sequence encoding a target RNA-binding fusion protein comprising (a) a sequence encoding a first RNA-binding polypeptide or portion thereof; and (b) a sequence encoding a second RNA-binding polypeptide, wherein the first RNA-biding polypeptide binds a target RNA not guided by a gRNA sequence, and wherein the second RNA-binding polypeptide comprises RNA-nuclease activity.
  • Embodiment 180. The composition of embodiment 179, wherein the first RNA-binding polypeptide or portion thereof is a PUF, PUMBY, or PPR polypeptide or portion thereof.
  • Embodiment 181. A method for modifying the level of expression of an RNA molecule or a protein encoded by the RNA molecule, the method comprising contacting the composition of embodiments 1 or 179 and the RNA molecule under conditions suitable for binding of the fusion protein or a portion thereof to the RNA molecule.
    • EXAMPLES Example 1: Methods
  • HEK-293 cells were cultured in DMEM with 10% FBS and 1% penicillin/streptomycin (GIBCO) and passaged at 90%-100% confluency. Cells were seeded at 1×10{circumflex over ( )}5 cells per well of a 24-well plate for RNA isolation or 0.5×10{circumflex over ( )}5 cells per well of a 96-well plate for luciferase assays. RNA isolations were carried out with RNAeasy columns (Qiagen) according to the manufacturer's protocol. RNA quality and concentrations were estimated using the Nanodrop spectrophotometer. cDNA preparation was done using Superscript III (Thermo) with random primers according to the manufacturer's protocol. qPCR was carried out with primers in a sequence adjacent to the CTG repeat in the reporter plasmid using the following primers:
  •
    Forward TetCTG_DMPK_EIS_F TCGGAGCGG SEQ ID 
    Primer  TTGTGAACT NO: 83
    Reverse TetCTG_DMPK_EIS_R GTTCGCCGT SEQ ID 
    Primer  TGTTCTGTC NO: 84
  • Relative abundance of the CTG repeat reporter was determined by normalization to GAPDH. Next, levels of the CTG-targeting sgRNA were normalized to a non-targeting sgRNA to generate a final value reported in the associated data package.
  •
    CTG- AGCAGCAGCAGCAGCAGCAG SEQ ID
    targeting NO: 85
    spacer
    Non- GTGATAAGTGGAATGCCATG SEQ ID
    targeting NO: 86
    control
    spacer 
    (λ2)
    sgRNA GNNNNNNNNNNNNNNNNNNN SEQ ID
    scaffold NGUUUAAGAGCUAUGCUGGA NO: 87
    (N's AACAGCAUAGCAAGUUUAAA
    indicate UAAGGCUAGUCCGUUAUCAA
    spacer) CUUGAAAAAGUGGCACCGAG
    UCGGUGCUUUUUUU
  • Luciferase assays were conducted with the Promega Dual Luciferase kit according to manufacturer's directions. Reported values are a ratio of firefly and renilla luciferase luminescence readings.
    • Example 2: RNA-Guided Cleavage of Repetitive RNA Molecules and mRNA Molecules
  • Experimental Design: Various fusions of human proteins with annotated RNA endonuclease activity and Cas9 (Streptococcus pyogenes or Campylobacter jejuni) were constructed. Plasmids encoding the above fusions were co-transfected with either a repeat-containing plasmid or a luciferase assay plasmid (comprising an mRNA sequence encoding a luciferase protein). A level of CTG repeat-containing RNA was measured with qPCR in the condition in which an RNA endonuclease/Cas9 fusion was co-transfected with a repetitive RNA. A level of luciferase protein was measured using a luminescence assay in the condition in which an RNA endonuclease/Cas9 fusion was co-transfected with a luciferase assay plasmid. All measurements were normalized to a non-targeting sgRNA control construct (FIGS. 3A-5 and FIG. 9).
    • Example 3: RNA-Guided Cleavage of Viral RNA Molecules
  • A549 cells were cultured in DMEM with 10% FBS and 1% penicillin/streptomycin (GIBCO) and passaged at 90%-100% confluency. Cells were seeded at 1×10{circumflex over ( )}5 cells per well of a 24-well plate for RNA isolation or 0.5×10{circumflex over ( )}5 cells per well. Cells were transfected with plasmids encoding Campylobacter jejuni Cas9 (CjeCas9) fused to the gene NTHL1 (residues 31-312, E43) or CPSF4L (full length, E67) with plasmids encoding one of four sites in Zika NS5 RNA. CjeCas9 was driven by an EFS promoter while the guide RNAs were driven by U6 promoter. The sequences of the sgRNAs are presented in Table 1. The sequences of the constructs used in this study are presented below.
  • RNA isolations were carried out with RNAeasy columns (Qiagen) according to the manufacturer's protocol. RNA quality and concentrations were estimated using the Nanodrop spectrophotometer. cDNA preparation was done using Superscript III (Thermo) with random primers according to the manufacturer's protocol. qPCR was carried out with the following primers as listed in Table 2.
  • FIG. 7 shows expression levels of Zika NS5 assessed in the presence of both E43 and E67 endonucleases with sgRNAs containing the various NS5-targeting spacer sequences as indicated in Table 2. Zika NS5 expression is displayed as fold change relative to the endonuclease loaded with an sgRNA containing a control (Lambda) spacer sequence.
  • Immunofluorescence microscopy was used to visualize Zika NS5 expression in the presence of E43 or E67 endonucleases fused to CjeCas9. FIG. 8A shows a fluorescence microscopy image of cells transfected with CjeCas9-endonuclease fusions loaded with an sgRNA containing a Zika NS5-targeting spacer sequence. Expression of Zika NS5 is markedly decreased in the presence of CjeCas9-endonuclease fusions loaded with the appropriate Zika NS5-targeting sgRNA as compared to CjeCas9-endonuclease fusions loaded with a non-Zika NS5 targeting sgRNA (FIGS. 8A and 8B). FIG. 6 is a list of exemplary endonucleases for use in the compositions of the disclosure.
  • TABLE 1
    qPCR primers
    GAPDH_F CAGCCICAAGATCATCAGCAA
    (SEQ ID NO: 192) 
    GAPDH_R TGTGGTCATGAGTCCTTCCA
    (SEQ ID NO: 193) 
    NS5_F GAGGAGAGTGCCAGAGTTGT
    (SEQ ID NO: 194) 
    NS5_R TCTCTCTCCCCATCCAGTGA
    (SEQ ID NO: 195) 
  • TABLE 2
    sgRNA sequences
    NS5-targeting gcaatgatcttcatgttgggagc 
    spacer 1 (SEQ ID NO: 196)
    NS5-targeting gaaccttgttgatgaactcttc 
    spacer 2 (SEQ ID NO: 197)
    NS5-targeting gttggtgattagagatcattc 
    spacer 3 (SEQ ID NO: 198)
    NS5-targeting gagtgatcctcgttcaagaatcc 
    spacer 4 (SEQ ID NO: 199)
    Non-targeting GTGATAAGTGGAATGCCATG
    control spacer (SEQ ID NO: 200) 
    (λ2)
    sgRNA scaffold GNNNNNNNNGUUUAAGAGCUAUG 
    (N's indicate CUGGAAACAGCAUAGCAAGUUUA 
    spacer) AAUAAGGCUAGUCCGUUAUCAAC 
    UUGAAAAAGUGGCACCGAGUCGG 
    UGCUUUUUUU
    (SEQ ID NO: 201)
  • A E43-CjeCas9 and sgRNA plasmid may comprise or consist of the sequence (U6: N's=sgRNA spacer, E43, CjeCas9):
  • (SEQ ID NO: 202)
    gtttattacagggacagcagagatccagtttggttaattaaggtaccgag
    ggcctatttcccatgattccttcatatttgcatatacgatacaaggctgt
    tagagagataattagaattaatttgactgtaaacacaaagatattagtac
    aaaatacgtgacgtagaaagtaataatttcttgggtagtttgcagtttta
    aaattatgttttaaaatggactatcatatgcttaccgtaacttgaaagta
    tttcgatttcttggctttatatatcttGTGGAAAGGACGAAACACCGTTT
    TAGTCCCTGAAGGGACTAAAATAAAGAGTTTGCGGGACTCTGCGGGGTTA
    CAATCCCCTAAAACCGCTTTTTTTCCTGCAGCCCGGGGGATCCACTAGTT
    CTAGAGCGGCCGCCACCGCGGTGGAGCTCCAGCTTTTGTTCCCTTTAGTG
    AGGGTTAATTGCGCGAATTCGCTAGCTAGGTCTTGAAAGGAGTGGGAATT
    GGCTCCGGTGCCCGTCAGTGGGCAGAGCGCACATCGCCCACAGTCCCCGA
    GAAGTTGGGGGGAGGGGTCGGCAATTGATCCGGTGCCTAGAGAAGGTGGC
    GCGGGGTAAACTGGGAAAGTGATGTCGTGTACTGGCTCCGCCTTTTTCCC
    GAGGGTGGGGGAGAACCGTATATAAGTGCAGTAGTCGCCGTGAACGTTCT
    TTTTCGCAACGGGTTTGCCGCCAGAACACAGGACCGGTTCTAGAGCGCTA
    TTTAGAACCatgTGTTCTCCCCAAGAATCTGGCATGACCGCTCTTTCAGC
    GAGGATGTTGACGCGAAGCAGATCCCTGGGACCTGGGGCCGGGCCACGAG
    GGTGTCGGGAAGAACCAGGACCGTTGCGACGGAGGGAAGCAGCAGCGGAA
    GCTCGGAAATCCCATTCTCCGGTTAAACGACCCCGCAAGGCACAACGGCT
    CAGGGTTGCTTACGAGGGGAGCGATTCCGAAAAGGGTGAAGGAGCAGAGC
    CCTTGAAGGTTCCAGTATGGGAACCCCAGGATTGGCAGCAGCAGCTTGTA
    AACATCCGAGCAATGAGGAACAAAAAAGATGCACCTGTTGATCACCTCGG
    AACCGAACATTGTTATGATTCTAGTGCGCCGCCAAAAGTCCGCCGGTATC
    AGGTTCTGTTGAGTTTGATGCTGAGTAGTCAGACTAAGGACCAGGTTACG
    GCCGGAGCAATGCAACGGCTTCGGGCACGGGGACTCACGGTCGATAGCAT
    TTTGCAGACCGATGACGCAACATTGGGTAAACTCATATATCCAGTTGGCT
    TCTGGCGGAGCAAAGTGAAGTACATCAAGCAGACCTCAGCCATTCTCCAA
    CAACATTACGGAGGTGATATACCCGCAAGCGTAGCTGAACTGGTAGCACT
    GCCGGGCGTCGGTCCCAAAATGGCACATCTGGCTATGGCGGTTGCTTGGG
    GAACGGTGTCTGGTATCGCAGTTGATACGCATGTCCACCGCATCGCCAAT
    CGGCTGAGGTGGACTAAAAAAGCCACTAAGTCTCCTGAAGAAACACGGGC
    TGCTCTGGAAGAGTGGCTTCCACGAGAGCTGTGGCATGAAATCAATGGAT
    TGCTGGTTGGTTTCGGGCAGCAGACATGCTTGCCCGTGCACCCCCGGTGT
    CATGCTTGCTTGAACCAGGCTTTGTGCCCAGCTGCCCAGGGCCTGAGTGG
    AAGTGAGACACCGGGAACATCTGAGTCTGCGACCCCGGAGAGCacaaac G
    CGCGAATCCTGGCCTTCGcgATTGGCATTAGCAGCATCGGCTGGGCATTC
    TCTGAAAACGACGAACTGAAGGATTGCGGCGTGCGAATTTTCACTAAGGT
    CGAAAATCCCAAAACTGGTGAATCACTCGCTCTCCCTAGACGACTGGCAC
    GCTCCGCACGAAAGAGGCTTGCCCGCCGCAAGGCACGCTTGAACCATCTT
    AAACACCTTATTGCAAATGAGTTTAAACTGAATTATGAGGACTACCAATC
    CTTTGACGAGTCTCTTGCTAAAGCCTACAAAGGGAGCCTTATATCCCCGT
    ATGAGCTCCGGTTCAGAGCACTCAACGAACTGCTGTCCAAACAGGATTTT
    GCTCGCGTGATTCTCCACATAGCGAAGAGGCGAGGATACGATGACATTAA
    AAACAGTGATGATAAGGAAAAAGGGGCCATACTCAAAGCGATTAAGCAAA
    ATGAAGAGAAGCTCGCTAACTATCAATCAGTAGGGGAGTATCTCTATAAA
    GAGTACTTCCAGAAGTTCAAAGAAAATAGCAAGGAATTTACTAATGTCCG
    GAATAAAAAGGAGTCTTACGAAAGATGTATTGCGCAATCTTTCCTCAAGG
    ACGAGCTCAAATTGATTTTCAAGAAACAAAGGGAATTTGGGTTCAGCTTC
    TCAAAAAAATTTGAGGAAGAGGTTCTGAGCGTTGCCTTTTACAAACGCGC
    CCTTAAGGACTTCTCACATCTCGTAGGGAATTGTAGTTTCTTCACCGATG
    AAAAACGGGCGCCAAAAAATAGCCCTTTGGCTTTTATGTTTGTCGCTCTG
    ACTCGCATCATTAATCTGCTCAACAACCTTAAAAACACGGAAGGGATTCT
    GTACACAAAGGATGATCTGAACGCTCTGCTTAACGAAGTTTTGAAGAACG
    GGACTTTGACCTACAAACAAACCAAAAAGCTTCTTGGTCTCAGTGATGAC
    TACGAATTCAAGGGAGAAAAAGGGACATATTTCATCGAATTCAAGAAGTA
    TAAGGAGTTCATCAAAGCCTTGGGCGAGCACAACTTGTCTCAAGATGATC
    TCAACGAAATTGCTAAGGATATCACTCTGATTAAAGACGAGATCAAGCTC
    AAAAAGGCGTTGGCGAAGTATGACCTTAACCAAAACCAAATAGATAGCCT
    CAGCAAGTTGGAATTTAAAGATCACTTGAATATAAGTTTCAAGGCCCTTA
    AGTTGGTCACCCCCTTGATGCTTGAAGGAAAGAAATATGATGAGGCATGT
    AATGAGCTGAATCTCAAGGTTGCTATTAACGAAGACAAAAAAGATTTCCT
    CCCAGCTTTCAATGAGACTTACTATAAGGACGAGGTTACCAATCCTGTGG
    TGCTCCGAGCCATCAAAGAGTATCGAAAGGTCCTGAATGCTTTGCTCAAA
    AAATACGGTAAGGTACACAAAATAAATATTGAGCTCGCAAGGGAGGTCGG
    TAAGAACCACTCCCAGCGCGCCAAAATAGAAAAGGAACAGAATGAAAATT
    ACAAAGCGAAAAAGGACGCCGAGCTCGAGTGCGAAAAGCTGGGCCTGAAA
    ATAAACAGCAAGAACATTCTCAAACTCCGCCTCTTCAAAGAACAAAAAGA
    ATTTTGTGCTTATAGTGGTGAGAAAATAAAAATCTCCGATCTTCAAGACG
    AGAAGATGCTCGAAATAGACgcgATATATCCATATAGCAGGTCTTTTGAC
    GATTCTTACATGAATAAAGTGCTTGTTTTCACTAAGCAGAATCAGGAAAA
    GTTGAATCAGACCCCCTTTGAGGCCTTTGGCAACGACTCAGCAAAGTGGC
    AGAAGATCGAGGTCTTGGCTAAGAATCTTCCTACTAAGAAACAGAAAAGG
    ATATTGGATAAGAACTATAAAGACAAAGAACAAAAGAACTTTAAAGACCG
    CAACCTCAATGACACCAGATACATAGCAAGATTGGTTCTGAACTACACAA
    AAGATTATTTGGACTTCTTGCCGCTGTCTGATGATGAGAACACGAAACTC
    AACGACACGCAAAAGGGGTCTAAAGTCCACGTCGAAGCTAAATCTGGGAT
    GCTCACCTCAGCATTGAGGCATACGTGGGGATTCTCAGCAAAGGACCGAA
    ACAATCACCTGCACCATGCCATTGACGCAGTTATCATAGCGTATGCCAAT
    AATTCAATAGTAAAAGCGTTTAGCGACTTCAAGAAGGAACAAGAGTCCAA
    CAGCGCCGAGCTCTACGCAAAAAAGATTAGTGAACTCGACTACAAAAACA
    AAAGAAAATTCTTTGAGCCGTTCAGCGGATTTCGACAGAAGGTATTGGAT
    AAAATAGATGAAATTTTCGTGAGCAAACCCGAAAGGAAAAAGCCCTCAGG
    CGCCTTGCACGAAGAGACTTTCAGGAAGGAAGAGGAATTCTACCAAAGCT
    ACGGCGGAAAAGAGGGAGTTTTGAAGGCTCTCGAACTTGGAAAGATTAGG
    AAGGTGAACGGCAAGATAGTGAAAAACGGCGATATGTTCCGGGTTGATAT
    CTTCAAACATAAAAAAACGAATAAATTTTATGCTGTGCCTATATACACTA
    TGGACTTCGCACTTAAGGTCCTGCCGAATAAGGCGGTAGCCCGATCTAAA
    AAAGGCGAAATTAAGGACTGGATTTTGATGGATGAAAATTACGAGTTCTG
    CTTTTCTCTCTACAAGGATTCCCTTATATTGATACAGACGAAAGATATGC
    AGGAACCGGAATTCGTGTATTACAACGCTTTTACTTCCTCTACGGTATCT
    TTGATTGTCTCCAAACATGACAACAAATTCGAAACACTCAGTAAAAACCA
    AAAGATTCTCTTTAAAAATGCGAACGAGAAAGAAGTAATTGCAAAATCAA
    TTGGCATCCAAAATTTGAAAGTTTTTGAAAAATATATAGTATCTG CCCTC
    GGAGAGGTTACTAAAGCGGAATTTAGACAGCGAGAGGACTTCAAAAAATC
    AGGTCCACCCAAGAAAAAACGCAAGGTGGAAGATCCGAAGAAAAAGCGAA
    AAGTGGATGTGtaaCGTTTTCCGGGACGCCGGCTGGATGATCCTCCAGCG
    CGGGGATCTCATGCTGGAGTTCTTCGCCCACCCCAACTTGTTTATTGCAG
    CTTATAATGGTTACAAATAAAGCAATAGCATCACAAATTTCACAAATAAA
    GCATTTTTTTCACTGCATTCTAGTTGTGGTTTGTCCAAACTCATCAATGT
    ATCTTATCATGTCTGTATACCG.
  • A E67-CjeCas9 and sgRNA plasmid may comprise or consist of the sequence (U6: N's=sgRNA spacer, E67, CieCas9):
  • (SEQ ID NO: 203)
    gtttattacagggacagcagagatccagtttggttaattaaggtaccgag
    ggcctatttcccatgattccttcatatttgcatatacgatacaaggctgt
    tagagagataattagaattaatttgactgtaaacacaaagatattagtac
    aaaatacgtgacgtagaaagtaataatttcttgggtagtttgcagtttta
    aaattatgttttaaaatggactatcatatgcttaccgtaacttgaaagta
    tttcgatttcttggctttatatatcttGTGGAAAGGACGAAACACCGTTT
    TAGTCCCTGAAGGGACTAAAATAAAGAGTTTGCGGGACTCTGCGGGGTTA
    CAATCCCCTAAAACCGCTTTTTTTCCTGCAGCCCGGGGGATCCACTAGTT
    CTAGAGCGGCCGCCACCGCGGTGGAGCTCCAGCTTTTGTTCCCTTTAGTG
    AGGGTTAATTGCGCGAATTCGCTAGCTAGGTCTTGAAAGGAGTGGGAATT
    GGCTCCGGTGCCCGTCAGTGGGCAGAGCGCACATCGCCCACAGTCCCCGA
    GAAGTTGGGGGGAGGGGTCGGCAATTGATCCGGTGCCTAGAGAAGGTGGC
    GCGGGGTAAACTGGGAAAGTGATGTCGTGTACTGGCTCCGCCTTTTTCCC
    GAGGGTGGGGGAGAACCGTATATAAGTGCAGTAGTCGCCGTGAACGTTCT
    TTTTCGCAACGGGTTTGCCGCCAGAACACAGGACCGGTTCTAGAGCGCTA
    TTTAGAACCatgCAGGAGGTAATAGCGGGGCTTGAGCGATTTACCTTTGC
    CTTCGAAAAAGACGTAGAGATGCAGAAGGGAACCGGCCTGCTCCCATTTC
    AAGGTATGGACAAATCAGCATCTGCCGTGTGCAATTTTTTCACCAAGGGT
    CTGTGTGAAAAGGGGAAGCTCTGTCCATTTCGCCATGATCGCGGAGAGAA
    GATGGTGGTGTGTAAGCACTGGCTGAGAGGGCTTTGCAAAAAAGGCGACC
    ACTGCAAATTTCTTCACCAATATGACCTGACTCGAATGCCTGAGTGTTAT
    TTTTACAGTAAGTTCGGTGACTGTAGCAACAAAGAATGCAGCTTCTTGCA
    TGTCAAACCAGCATTCAAGTCACAGGATTGCCCGTGGTACGATCAGGGTT
    TTTGCAAGGACGGTCCCCTCTGCAAATATCGACACGTACCCAGAATTATG
    TGCCTTAATTACCTGGTCGGCTTCTGTCCTGAAGGGCCAAAATGTCAGTT
    TGCTCAAAAAATTCGCGAGTTCAAATTGCTCCCTGGGTCTAAAATTTGGG
    AACCCCAGGATTGGCAGCAGCAGCTTGTAAACATCCGAGCAATGAGGAAC
    AAAAAAGATGCACCTGTTGATCACCTCGGAACCGAACATTGTTATGATTC
    TAGTGCGCCGCCAAAAGTCCGCCGGTATCAGGTTCTGTTGAGTTTGATGC
    TGAGTAGTCAGACTAAGGACCAGGTTACGGCCGGAGCAATGCAACGGCTT
    CGGGCACGGGGACTCACGGTCGATAGCATTTTGCAGACCGATGACGCAAC
    ATTGGGTAAACTCATATATCCAGTTGGCTTCTGGCGGAGCAAAGTGAAGT
    ACATCAAGCAGACCTCAGCCATTCTCCAACAACATTACGGAGGTGATATA
    CCCGCAAGCGTAGCTGAACTGGTAGCACTGCCGGGCGTCGGTCCCAAAAT
    GGCACATCTGGCTATGGCGGTTGCTTGGGGAACGGTGTCTGGTATCGCAG
    TTGATACGCATGTCCACCGCATCGCCAATCGGCTGAGGTGGACTAAAAAA
    GCCACTAAGTCTCCTGAAGAAACACGGGCTGCTCTGGAAGAGTGGCTTCC
    ACGAGAGCTGTGGCATGAAATCAATGGATTGCTGGTTGGTTTCGGGCAGC
    AGACATGCTTGCCCGTGCACCCCCGGTGTCATGCTTGCTTGAACCAGGCT
    TTGTGCCCAGCTGCCCAGGGCCTGAGTGGAAGTGAGACACCGGGAACATC
    TGAGTCTGCGACCCCGGAGAGCacaaac GCGCGAATCCTGGCCTTCGcgA
    TTGGCATTAGCAGCATCGGCTGGGCATTCTCTGAAAACGACGAACTGAAG
    GATTGCGGCGTGCGAATTTTCACTAAGGTCGAAAATCCCAAAACTGGTGA
    ATCACTCGCTCTCCCTAGACGACTGGCACGCTCCGCACGAAAGAGGCTTG
    CCCGCCGCAAGGCACGCTTGAACCATCTTAAACACCTTATTGCAAATGAG
    TTTAAACTGAATTATGAGGACTACCAATCCTTTGACGAGTCTCTTGCTAA
    AGCCTACAAAGGGAGCCTTATATCCCCGTATGAGCTCCGGTTCAGAGCAC
    TCAACGAACTGCTGTCCAAACAGGATTTTGCTCGCGTGATTCTCCACATA
    GCGAAGAGGCGAGGATACGATGACATTAAAAACAGTGATGATAAGGAAAA
    AGGGGCCATACTCAAAGCGATTAAGCAAAATGAAGAGAAGCTCGCTAACT
    ATCAATCAGTAGGGGAGTATCTCTATAAAGAGTACTTCCAGAAGTTCAAA
    GAAAATAGCAAGGAATTTACTAATGTCCGGAATAAAAAGGAGTCTTACGA
    AAGATGTATTGCGCAATCTTTCCTCAAGGACGAGCTCAAATTGATTTTCA
    AGAAACAAAGGGAATTTGGGTTCAGCTTCTCAAAAAAATTTGAGGAAGAG
    GTTCTGAGCGTTGCCTTTTACAAACGCGCCCTTAAGGACTTCTCACATCT
    CGTAGGGAATTGTAGTTTCTTCACCGATGAAAAACGGGCGCCAAAAAATA
    GCCCTTTGGCTTTTATGTTTGTCGCTCTGACTCGCATCATTAATCTGCTC
    AACAACCTTAAAAACACGGAAGGGATTCTGTACACAAAGGATGATCTGAA
    CGCTCTGCTTAACGAAGTTTTGAAGAACGGGACTTTGACCTACAAACAAA
    CCAAAAAGCTTCTTGGTCTCAGTGATGACTACGAATTCAAGGGAGAAAAA
    GGGACATATTTCATCGAATTCAAGAAGTATAAGGAGTTCATCAAAGCCTT
    GGGCGAGCACAACTTGTCTCAAGATGATCTCAACGAAATTGCTAAGGATA
    TCACTCTGATTAAAGACGAGATCAAGCTCAAAAAGGCGTTGGCGAAGTAT
    GACCTTAACCAAAACCAAATAGATAGCCTCAGCAAGTTGGAATTTAAAGA
    TCACTTGAATATAAGTTTCAAGGCCCTTAAGTTGGTCACCCCCTTGATGC
    TTGAAGGAAAGAAATATGATGAGGCATGTAATGAGCTGAATCTCAAGGTT
    GCTATTAACGAAGACAAAAAAGATTTCCTCCCAGCTTTCAATGAGACTTA
    CTATAAGGACGAGGTTACCAATCCTGTGGTGCTCCGAGCCATCAAAGAGT
    ATCGAAAGGTCCTGAATGCTTTGCTCAAAAAATACGGTAAGGTACACAAA
    ATAAATATTGAGCTCGCAAGGGAGGTCGGTAAGAACCACTCCCAGCGCGC
    CAAAATAGAAAAGGAACAGAATGAAAATTACAAAGCGAAAAAGGACGCCG
    AGCTCGAGTGCGAAAAGCTGGGCCTGAAAATAAACAGCAAGAACATTCTC
    AAACTCCGCCTCTTCAAAGAACAAAAAGAATTTTGTGCTTATAGTGGTGA
    GAAAATAAAAATCTCCGATCTTCAAGACGAGAAGATGCTCGAAATAGACg
    cgATATATCCATATAGCAGGTCTTTTGACGATTCTTACATGAATAAAGTG
    CTTGTTTTCACTAAGCAGAATCAGGAAAAGTTGAATCAGACCCCCTTTGA
    GGCCTTTGGCAACGACTCAGCAAAGTGGCAGAAGATCGAGGTCTTGGCTA
    AGAATCTTCCTACTAAGAAACAGAAAAGGATATTGGATAAGAACTATAAA
    GACAAAGAACAAAAGAACTTTAAAGACCGCAACCTCAATGACACCAGATA
    CATAGCAAGATTGGTTCTGAACTACACAAAAGATTATTTGGACTTCTTGC
    CGCTGTCTGATGATGAGAACACGAAACTCAACGACACGCAAAAGGGGTCT
    AAAGTCCACGTCGAAGCTAAATCTGGGATGCTCACCTCAGCATTGAGGCA
    TACGTGGGGATTCTCAGCAAAGGACCGAAACAATCACCTGCACCATGCCA
    TTGACGCAGTTATCATAGCGTATGCCAATAATTCAATAGTAAAAGCGTTT
    AGCGACTTCAAGAAGGAACAAGAGTCCAACAGCGCCGAGCTCTACGCAAA
    AAAGATTAGTGAACTCGACTACAAAAACAAAAGAAAATTCTTTGAGCCGT
    TCAGCGGATTTCGACAGAAGGTATTGGATAAAATAGATGAAATTTTCGTG
    AGCAAACCCGAAAGGAAAAAGCCCTCAGGCGCCTTGCACGAAGAGACTTT
    CAGGAAGGAAGAGGAATTCTACCAAAGCTACGGCGGAAAAGAGGGAGTTT
    TGAAGGCTCTCGAACTTGGAAAGATTAGGAAGGTGAACGGCAAGATAGTG
    AAAAACGGCGATATGTTCCGGGTTGATATCTTCAAACATAAAAAAACGAA
    TAAATTTTATGCTGTGCCTATATACACTATGGACTTCGCACTTAAGGTCC
    TGCCGAATAAGGCGGTAGCCCGATCTAAAAAAGGCGAAATTAAGGACTGG
    ATTTTGATGGATGAAAATTACGAGTTCTGCTTTTCTCTCTACAAGGATTC
    CCTTATATTGATACAGACGAAAGATATGCAGGAACCGGAATTCGTGTATT
    ACAACGCTTTTACTTCCTCTACGGTATCTTTGATTGTCTCCAAACATGAC
    AACAAATTCGAAACACTCAGTAAAAACCAAAAGATTCTCTTTAAAAATGC
    GAACGAGAAAGAAGTAATTGCAAAATCAATTGGCATCCAAAATTTGAAAG
    TTTTTGAAAAATATATAGTATCTGCCCTCGGAGAGGTTACTAAAGCGGAA
    TTTAGACAGCGAGAGGACTTCAAAAAATCAGGTCCA CCCAAGAAAAAACG
    CAAGGTGGAAGATCCGAAGAAAAAGCGAAAAGTGGATGTGtaaCGTTTTC
    CGGGACGCCGGCTGGATGATCCTCCAGCGCGGGGATCTCATGCTGGAGTT
    CTTCGCCCACCCCAACTTGTTTATTGCAGCTTATAATGGTTACAAATAAA
    GCAATAGCATCACAAATTTCACAAATAAAGCATTTTTTTCACTGCATTCT
    AGTTGTGGTTTGTCCAAACTCATCAATGTATCTTATCATGTCTGTATACC
    G.
    • INCORPORATION BY REFERENCE
  • Every document cited herein, including any cross referenced or related patent or application is hereby incorporated herein by reference in its entirety unless expressly excluded or otherwise limited. The citation of any document is not an admission that it is prior art with respect to any invention disclosed or embodimented herein or that it alone, or in any combination with any other reference or references, teaches, suggests or discloses any such invention. Further, to the extent that any meaning or definition of a term in this document conflicts with any meaning or definition of the same term in a document incorporated by reference, the meaning or definition assigned to that term in this document shall govern.
    • OTHER EMBODIMENTS
  • While particular embodiments of the disclosure have been illustrated and described, various other changes and modifications can be made without departing from the spirit and scope of the disclosure. The scope of the appended claims includes all such changes and modifications that are within the scope of this disclosure.

Claims (20)

1. A composition comprising a nucleic acid encoding a fusion protein, the fusion protein comprising a first RNA-binding polypeptide and a second RNA-binding polypeptide, wherein the first RNA-binding polypeptide is a CRISPR/Cas polypeptide or RNA binding domain thereof, wherein the second RNA-binding polypeptide comprises RNA-nuclease activity, wherein the second RNA-binding polypeptide comprises a Zinc Finger CCCH-Type Containing 12A (ZC3H12A) polypeptide, and wherein the ZC3H12A polypeptide comprises SEQ ID NO: 42.
2. The composition of claim 1, wherein the ZC3H12A polypeptide comprises SEQ ID NO: 43.
3. (canceled)
4. (canceled)
5. (canceled)
6. The composition of claim 1, wherein the CRISPR/Cas polypeptide or RNA binding domain thereof is selected from the group consisting of Cas9, Cpf1, Cas13a, Cas13b, Cas13c and Cas13d, and wherein the CRISPR/Cas polypeptide or portion thereof has native, reduced or null activity.
7. The composition of claim 1, wherein the ZC3H12A polypeptide is capable of binding RNA.
8. The composition of claim 7, wherein the ZC3H12A polypeptide is capable of binding and cleaving RNA.
9. The composition of claim 1, wherein the nucleic acid comprises a promoter.
10. The composition of claim 9, wherein the promoter is a constitutive promoter or a tissue-specific promoter.
11. The composition of claim 1, wherein the nucleic acid further comprises a guide RNA (gRNA) sequence, wherein the gRNA sequence comprises a) a spacer sequence that specifically binds a target sequence within an RNA molecule, and b) a scaffold sequence that specifically binds to the first RNA-binding polypeptide.
12. The composition of claim 11, wherein the spacer sequence comprises a sequence comprising at least 1, 2, 3, 4, 5, 6, or 7 repeats of a sequence selected from the group consisting of: CUG (SEQ ID NO: 18), CCUG (SEQ ID NO: 19), CAG (SEQ ID NO: 80), GGGGCC (SEQ ID NO: 81), and a combination thereof.
13. The composition of claim 11, wherein the nucleic acid comprises a promoter which drives expression of the gRNA sequence.
14. The composition of claim 13, wherein the promoter is a polymerase III promoter.
15. The composition of claim 14, wherein the polymerase III promoter is a U6 promoter or a tRNA promoter.
16. The composition of claim 1, wherein the fusion protein comprises an NLS, NES or tag.
17. A vector comprising the composition of claim 1.
18. The vector of claim 17, wherein the vector is selected from the group consisting of: adeno-associated virus, retrovirus, lentivirus, adenovirus, nanoparticle, micelle, liposome, lipoplex, polymersome, polyplex, and dendrimer.
19. A cell comprising the vector of claim 17.
20. The composition of claim 11, wherein the scaffold sequence comprises a direct repeat sequence.
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