US20200071718A1 - 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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US20200071718A1
US20200071718A1 US16/434,689 US201916434689A US2020071718A1 US 20200071718 A1 US20200071718 A1 US 20200071718A1 US 201916434689 A US201916434689 A US 201916434689A US 2020071718 A1 US2020071718 A1 US 2020071718A1
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rna
sequence
seq
disclosure
binding polypeptide
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David A. Nelles
Ranjan Batra
Eugene Yeo
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Locana Inc
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Locana Inc
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Priority to US16/723,079 priority patent/US10822617B2/en
Publication of US20200071718A1 publication Critical patent/US20200071718A1/en
Assigned to LOCANA, INC. reassignment LOCANA, INC. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: YEO, Eugene, BATRA, Ranjan, Nelles, David A.
Priority to US17/001,318 priority patent/US20210047654A1/en
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    • C12N2750/14011—Parvoviridae
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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
  • the scaffold sequence comprises or consists of the sequence
  • 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 NOB 1 polypeptide.
  • the NOB 1 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_200273 ipolypeptide.
  • 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 T7 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:
  • Cas13b Species Cas13b Accession 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.
  • 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. 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:
  • 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_contigl3552000311:
  • 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 meta enome conti 2643000492:
  • 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
  • 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 OCTW011587266.1:
  • 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 RNAse1l11 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.
  • Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, 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.
  • 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 NOB 1 polypeptide.
  • the NOB 1 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 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 IIC, 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 Pumilio 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
  • a PUF3 protein of the disclosure comprises or consists of the amino acid sequence of
  • a PUF5 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 (SIV SM ) vector, a modified sooty mangabey simian immunodeficiency virus (SIV SM ) vector, a African green monkey simian immunodeficiency virus (SIV AGM ) vector, a modified African green monkey simian immunodeficiency virus (SIV AGM ) vector, an HIV immunodeficiency virus (HIV) 1 vector, a modified human immunodeficiency virus (HIV) 1 vector, a human immunodeficiency virus (HIV) 2 vector, a modified human
  • 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
  • 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.
  • composition of embodiment 1, wherein the target sequence comprises at least one repeated sequence.
  • composition of embodiment 1 or 2 wherein the sequence comprising the gRNA comprises a promoter capable of expressing the gRNA in a eukaryotic cell.
  • composition of embodiment 3, wherein the eukaryotic cell is an animal cell.
  • composition of embodiment 4, wherein the animal cell is a mammalian cell.
  • composition of embodiment 5, wherein the animal cell is a human cell.
  • composition of any one of embodiments 1-6, wherein the promoter is a constitutively active promoter is a constitutively active promoter.
  • tRNA transfer RNA
  • 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.
  • composition of embodiment 10, wherein the promoter is isolated or derived from a valine tRNA promoter.
  • 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.
  • 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.
  • 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), GGGGCCGGGGCCGG
  • 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.
  • composition of embodiment 19, wherein the scaffold sequence comprises a stem-loop structure.
  • composition of embodiment 19 or 20, wherein the scaffold sequence comprises or consists of 90 nucleotides.
  • composition of embodiment 19 or 20, wherein the scaffold sequence comprises or consists of 93 nucleotides.
  • composition of embodiment 22, wherein the scaffold sequence comprises the sequence
  • 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).
  • composition of embodiment 19 or 24, wherein the scaffold sequence comprises a step-loop structure.
  • composition of embodiment 25, wherein the scaffold sequence comprises or consists of 85 nucleotides.
  • composition of embodiment 26, wherein the scaffold sequence comprises the sequence
  • 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.
  • composition of embodiment 28, wherein the sequence comprising the gRNA comprises a scaffold sequence that specifically binds to the first RNA binding protein.
  • composition of embodiment 29, wherein the scaffold sequence comprises a stem-loop structure.
  • composition of embodiment 29 or 30, wherein the scaffold sequence comprises or consists of 90 nucleotides.
  • composition of embodiment 30 or 31, wherein the scaffold sequence comprises or consists of 93 nucleotides.
  • composition of embodiment 32, wherein the scaffold sequence comprises the sequence
  • composition of embodiment 34, wherein an RNA genome or an RNA transcriptome comprises the RNA molecule.
  • composition of embodiment 36, wherein the CRISPR-Cas protein is a Type II CRISPR-Cas protein.
  • composition of embodiment 37 wherein the first RNA binding protein comprises a Cas9 polypeptide or an RNA-binding portion thereof.
  • composition of embodiment 36, wherein the CRISPR-Cas protein is a Type V CRISPR-Cas protein.
  • composition of embodiment 39 wherein the first RNA binding protein comprises a Cpf1 polypeptide or an RNA-binding portion thereof.
  • composition of embodiment 36, wherein the CRISPR-Cas protein is a Type VI CRISPR-Cas protein.
  • composition of embodiment 41, wherein the first RNA binding protein comprises a Cas13 polypeptide or an RNA-binding portion thereof.
  • composition of any one of embodiments 36-42, wherein the CRISPR-Cas protein comprises a native RNA nuclease activity comprises a native RNA nuclease activity.
  • composition of embodiment 43 wherein the native RNA nuclease activity is reduced or inhibited.
  • composition of embodiment 43 wherein the native RNA nuclease activity is increased or induced.
  • composition of embodiment 46, wherein the CRISPR-Cas protein comprises a mutation.
  • composition of embodiment 47, wherein a nuclease domain of the CRISPR-Cas protein comprises the mutation.
  • composition of embodiment 47 wherein the mutation occurs in a nucleic acid encoding the CRISPR-Cas protein.
  • composition of embodiment 47 wherein the mutation occurs in an amino acid encoding the CRISPR-Cas protein.
  • 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.
  • 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.
  • PEF Pumilio and FBF
  • composition of embodiment 53, wherein the first RNA binding protein comprises a Pumilio -based assembly (PUMBY) protein.
  • PUMBY Pumilio -based assembly
  • composition of any one of embodiments 1-54, wherein the first RNA binding protein does not require multimerization for RNA-binding activity does not require multimerization for RNA-binding activity.
  • 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.
  • composition of embodiment 60 wherein an RNA genome or an RNA transcriptome comprises the RNA molecule.
  • 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.
  • NLS nuclear localization signal
  • 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
  • composition of embodiment 64 wherein the first RNA binding protein comprises an NLS at a C-terminus of the protein.
  • 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.
  • 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.
  • composition of embodiment 69, wherein the sequence encoding the second RNA binding protein comprises or consists of an RNAse.
  • composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAse1.
  • composition of embodiment 71, wherein the RNAse1 protein comprises or consists of SEQ ID NO: 20.
  • composition of embodiment 72, wherein the second RNA binding protein comprises or consists of an RNAse4.
  • composition of embodiment 73, wherein the RNAse4 protein comprises or consists of: (SEQ ID NO: 21.
  • composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAse6.
  • composition of embodiment 75 wherein the RNAse6 protein comprises or consists of SEQ ID NO: 22.
  • composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAse7.
  • composition of embodiment 77, wherein the RNAse7 protein comprises or consists of SEQ ID NO: 23.
  • composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAse8.
  • composition of embodiment 79, wherein the RNAse8 protein comprises or consists of SEQ ID NO: 24.
  • composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAse2.
  • composition of embodiment 81, wherein the RNAse2 protein comprises or consists of SEQ ID NO: 25.
  • composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAse6PL.
  • composition of embodiment 83, wherein the RNAse6PL protein comprises or consists of SEQ ID NO: 26.
  • composition of embodiment 70 wherein the second RNA binding protein comprises or consists of an RNAseL.
  • composition of embodiment 85 wherein the RNAseL protein comprises or consists of SEQ ID NO: 27.
  • composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAseT2.
  • composition of embodiment 87, wherein the RNAseT2 protein comprises or consists of SEQ ID NO: 28.
  • composition of embodiment 70, wherein the second RNA binding protein comprises or consists of an RNAse11.
  • composition of embodiment 89, wherein the RNAse11 comprises or consists of SEQ ID NO: 29.
  • composition of embodiment 70 wherein the second RNA binding protein comprises or consists of an RNAseT2-like.
  • composition of embodiment 91, wherein the RNAseT2-like protein comprises or consists of SEQ ID NO: 30.
  • composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a NOB 1 polypeptide.
  • composition of embodiment 93, wherein the NOB 1 polypeptide comprises or consists of SEQ ID NO: 31.
  • composition of embodiment 69, wherein the second RNA binding protein comprises or consists of an endonuclease.
  • composition of embodiment 95, wherein the second RNA binding protein comprises or consists of an endonuclease V (ENDOV).
  • ENDOV endonuclease V
  • composition of embodiment 96, wherein the ENDOV protein comprises or consists of SEQ ID NO: 32.
  • composition of embodiment 95, wherein the second RNA binding protein comprises or consists of an endonuclease G (ENDOG).
  • ENDOG endonuclease G
  • composition of embodiment 98, wherein the ENDOG protein comprises or consists of SEQ ID NO: 33.
  • composition of embodiment 95, wherein the second RNA binding protein comprises or consists of an endonuclease D1 (ENDOD1).
  • ENDOD1 endonuclease D1
  • composition of embodiment 100, wherein the ENDOD1 protein comprises or consists of SEQ ID NO: 34.
  • composition of embodiment 95, wherein the second RNA binding protein comprises or consists of a Human flap endonuclease-1 (hFEN1).
  • composition of embodiment 102, wherein the hFEN1 protein comprises or consists of SEQ ID NO: 35.
  • composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a human Schlafen 14 (hSLFN14) polypeptide.
  • composition of embodiment 104, wherein the hSLFN14 polypeptide comprises or consists of SEQ ID NO: 36.
  • 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
  • composition of embodiment 106, wherein the hLACTB2 polypeptide comprises or consists of SEQ ID NO: 37.
  • 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
  • composition of embodiment 108, wherein the APEX2 polypeptide comprises or consists of SEQ ID NO: 38.
  • composition of embodiment 108, wherein the APEX2 polypeptide comprises or consists of: SEQ ID NO: 39.
  • composition of embodiment 69, wherein the second RNA binding protein comprises or consists of an angiogenin (ANG) polypeptide.
  • ANG angiogenin
  • composition of embodiment 111, wherein the ANG polypeptide comprises or consists of SEQ ID NO: 40.
  • 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
  • composition of embodiment 113, wherein the HRSP12 polypeptide comprises or consists of SEQ ID NO: 41.
  • composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a Zinc Finger CCCH-Type Containing 12A (ZC3H12A) polypeptide.
  • composition of embodiment 115, wherein the ZC3H12A polypeptide comprises or consists of SEQ ID NO: 42.
  • composition of embodiment 115, wherein the ZC3H12A polypeptide comprises or consists of SEQ ID NO: 43.
  • 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
  • composition of embodiment 118, wherein the RIDA polypeptide comprises or consists of SEQ ID NO: 44.
  • 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
  • composition of embodiment 120, wherein the PDL6 polypeptide comprises or consists of: (SEQ ID NO: 126.
  • 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
  • composition of embodiment 122, wherein the NTHL polypeptide comprises or consists of SEQ ID NO: 123.
  • composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a Mitochondrial ribonuclease P catalytic subunit (KIAA0391) polypeptide.
  • composition of embodiment 124, wherein the KIAA0391 polypeptide comprises or consists of SEQ ID NO: 127.
  • 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
  • composition of embodiment 126, wherein the APEX1 polypeptide comprises or consists of SEQ ID NO: 125.
  • composition of embodiment 69, wherein the second RNA binding protein comprises or consists of an argonaute 2 (AGO2) polypeptide.
  • composition of embodiment 128, wherein the AGO2 polypeptide comprises or consists of SEQ ID NO: 128.
  • composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a mitochondrial nuclease EXOG (EXOG) polypeptide.
  • EXOG mitochondrial nuclease EXOG
  • composition of embodiment 130, wherein the EXOG polypeptide comprises or consists of SEQ ID NO: 129.
  • composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a Zinc Finger CCCH-Type Containing 12D (ZC3H12D) polypeptide.
  • composition of embodiment 132, wherein the ZC3H12D polypeptide comprises or consists of SEQ ID NO: 130.
  • composition of embodiment 69, wherein the second RNA binding protein comprises or consists of an endoplasmic reticulum to nucleus signaling 2 (ERN2) polypeptide.
  • composition of embodiment 134, wherein the ERN2 polypeptide comprises or consists of SEQ ID NO: 131.
  • 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
  • composition of embodiment 136, wherein the PELO polypeptide comprises or consists of SEQ ID NO: 132.
  • composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a YBEY metallopeptidase (YBEY) polypeptide.
  • YBEY YBEY metallopeptidase
  • composition of embodiment 138, wherein the YBEY polypeptide comprises or consists of SEQ ID NO: 133.
  • 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
  • composition of embodiment 140, wherein the CPSF4L comprises or consists of SEQ ID NO: 134.
  • composition of embodiment 69, wherein the second RNA binding protein comprises or consists of an hCG_200273 ipolypeptide.
  • composition of embodiment 142, wherein the hCG_2002731 polypeptide comprises or consists of SEQ ID NO: 135.
  • composition of embodiment 142, wherein the hCG_2002731 polypeptide comprises or consists of SEQ ID NO: 136.
  • 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
  • composition of embodiment 145, wherein the ERCC1 polypeptide comprises or consists of SEQ ID NO: 137.
  • 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
  • composition of embodiment 147, wherein the RAC1 polypeptide comprises or consists of SEQ ID NO: 138.
  • composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a Ribonuclease A A1 (RAA1) polypeptide.
  • RAA1 Ribonuclease A A1
  • composition of embodiment 149, wherein the RAA1 polypeptide comprises or consists of SEQ ID NO: 139.
  • composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a Ras Related Protein (RAB1) polypeptide.
  • RAB1 Ras Related Protein
  • composition of embodiment 151, wherein the RAB1 polypeptide comprises or consists of SEQ ID NO: 140.
  • 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
  • composition of embodiment 153, wherein the DNA2 polypeptide comprises or consists of SEQ ID NO: 141.
  • composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a FLJ35220 polypeptide.
  • composition of embodiment 155, wherein the FLJ35220 polypeptide comprises or consists of SEQ ID NO: 142.
  • composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a FLJ13173 polypeptide.
  • composition of embodiment 157, wherein the FLJ13173 polypeptide comprises or consists of: (SEQ ID NO: 143.
  • 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
  • composition of embodiment 159, wherein the ERCC4 polypeptide comprises or consists of SEQ ID NO: 64.
  • composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(K41R)) polypeptide.
  • composition of embodiment 161, wherein the Rnase1(K41R) polypeptide comprises or consists of SEQ ID NO: 116.
  • composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(K41R, D121E)) polypeptide.
  • composition of embodiment 163, wherein the Rnase1 (Rnase1(K41R, D121E)) polypeptide comprises or consists of SEQ ID NO: 117.
  • composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(K41R, D121E, H119N)) polypeptide.
  • composition of embodiment 165, wherein the Rnase1 (Rnase1(K41R, D121E, H119N)) polypeptide comprises or consists of SEQ ID NO: 118.
  • composition of embodiment 69, wherein the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(H119N)) polypeptide.
  • composition of embodiment 167, wherein the Rnase1 (Rnase1(H119N)) polypeptide comprises or consists of SEQ ID NO: 119.
  • 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.
  • composition of embodiment 169, wherein the Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide comprises or consists of SEQ ID NO: 120.
  • 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.
  • 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.
  • 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.
  • composition of embodiment 173, wherein the Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D)) polypeptide comprises or consists of SEQ ID NO: 122.
  • 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
  • composition of embodiment 175, wherein the TENM1 polypeptide comprises or consists of SEQ ID NO: 144.
  • 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
  • composition of embodiment 177, wherein the TENM2 polypeptide comprises or consists of SEQ ID NO: 145.
  • 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.
  • composition of embodiment 179, wherein the first RNA-binding polypeptide or portion thereof is a PUF, PUMBY, or PPR polypeptide or portion thereof.
  • a method for modifying the level of expression of an RNA molecule or a protein encoded by the RNA molecule 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.
  • CTG-targeting spacer SEQ ID NO: 85 AGCAGCAGCAGCAGCAGCAG Non-targeting control spacer ( ⁇ 2) SEQ ID NO: 86 GTGATAAGTGGAATGCCATG sgRNA scaffold (N's indicate spacer) SEQ ID NO: 87 GNNNNNNNNNNNNNNNNNNNNGUUUAAGAGCUAUGCUGGAAACAGCAUAG CAAGUUUAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAG UCGGUGCUUUUUUUUU
  • 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 NTHL 1 (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.
  • NS5-targeting spacer 1 gcaatgatcttcatgttgggagc (SEQ ID NO: 196)
  • NS5-targeting spacer 2 gaaccttgttgatgaactcttc (SEQ ID NO: 197)
  • NS5-targeting spacer 3 gttggtgattagagcttcattc (SEQ ID NO: 198)
  • NS5-targeting spacer 4 gagtgatcctcgttcaagaatcc SEQ ID NO: 199)
  • Non-targeting control GTGATAAGTGGAATGCCATG SEQ ID NO: 200
  • spacer ⁇ 2
  • sgRNA scaffold N's GNNNNNNNNNNNNNNNNNNNNNNNNGUUUAAGAGCUAUG indicate spacer

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