WO2022197839A1 - Crispr/cas effector-histone modifier fusion proteins and methods of use thereof - Google Patents

Crispr/cas effector-histone modifier fusion proteins and methods of use thereof Download PDF

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WO2022197839A1
WO2022197839A1 PCT/US2022/020603 US2022020603W WO2022197839A1 WO 2022197839 A1 WO2022197839 A1 WO 2022197839A1 US 2022020603 W US2022020603 W US 2022020603W WO 2022197839 A1 WO2022197839 A1 WO 2022197839A1
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polypeptide
cell
fusion polypeptide
crispr
nucleic acid
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WO2022197839A9 (en
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Jennifer A. Doudna
Enrique LIN-SHIAO
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The Regents Of The University Of California
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/102—Mutagenizing nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/62—DNA sequences coding for fusion proteins
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
    • C12N9/1003—Transferases (2.) transferring one-carbon groups (2.1)
    • C12N9/1007—Methyltransferases (general) (2.1.1.)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
    • C12N9/1025—Acyltransferases (2.3)
    • C12N9/1029—Acyltransferases (2.3) transferring groups other than amino-acyl groups (2.3.1)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/16—Hydrolases (3) acting on ester bonds (3.1)
    • C12N9/22—Ribonucleases RNAses, DNAses
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/80—Fusion polypeptide containing a DNA binding domain, e.g. Lacl or Tet-repressor
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/20—Type of nucleic acid involving clustered regularly interspaced short palindromic repeats [CRISPRs]
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y201/00—Transferases transferring one-carbon groups (2.1)
    • C12Y201/01—Methyltransferases (2.1.1)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y203/00—Acyltransferases (2.3)
    • C12Y203/01—Acyltransferases (2.3) transferring groups other than amino-acyl groups (2.3.1)
    • C12Y203/01048—Histone acetyltransferase (2.3.1.48)

Definitions

  • CRISPR clustered regularly interspaced palindromic repeat
  • Cas clustered regularly interspaced palindromic repeat
  • DSB targeted dsDNA breaks
  • NHEJ non-homologous end joining
  • MMEJ microhomology-mediated end joining
  • HDR homology directed repair
  • end joining either through NHEJ or MMEJ can lead to random insertions and deletions (indels), which allows for targeted knock out of specific genes.
  • Indels random insertions and deletions
  • bias toward HDR may be desired.
  • Approaches to bias repair pathways to HDR upon CRISPR mediated DSBs include: inhibiting canonical NHEJ pathways through the use of small molecule inhibitors; restricting Cas9 expression to specific phases of the cell cycle; fusions of Cas9 with proteins directly involved in HDR; designing guide RNAs following specific rules; and modifying the donor template DNA or linking template to Cas9.
  • the present disclosure provides a fusion polypeptide comprising: a) a CRISPR/Cas effector polypeptide; and b) a chromatin marker polypeptide that provides for modification of a histone polypeptide present in chromatin.
  • the present disclosure provides nucleic acids encoding the fusion polypeptide, and cells comprising the fusion polypeptide and/or the nucleic acids.
  • the present disclosure provides systems, kits, devices, and containers comprising a fusion polypeptide of the present disclosure or a nucleic acid encoding same.
  • the present disclosure provides methods for modifying a target nucleic acid, which methods comprise use of the fusion polypeptide.
  • FIG. 1A-1D depict HDR mediated by Cas9-PRDM9AC.
  • FIG. 2A-2B provide amino acid sequences of PRDM9 polypeptides.
  • FIG. 3A-3B provide amino acid sequences of Cas9-PRDM9AC fusion polypeptides.
  • FIG. 4A-4F provide amino acid sequences of SETD2 polypeptides.
  • FIG. 5A-5P provide amino acid sequences of CRISPR/Cas effector polypeptides.
  • FIG. 6A-6G provide amino acid sequences of SETMAR polypeptides.
  • FIG. 7 provides an amino acid sequence of a MOF polypeptide.
  • FIG. 8 provides an amino acid sequence of a ZMYND8 polypeptide.
  • FIG. 9 provides an amino acid sequence of a ZCWPW 1 polypeptide.
  • FIG. 10 provides the amino acid sequence of a PRDM9 polypeptide.
  • FIG. 11A-11H provide amino acid sequences of exemplary fusion polypeptides of the present disclosure.
  • FIG. 12A-12J provide amino acid sequences of exemplary fusion polypeptides of the present disclosure.
  • FIG. 13 provides an amino acid sequence of a HELLS chromatin remodeling polypeptide.
  • FIG. 14A-14D depict the effect of endogenous histone modifications on DNA repair pathway choice.
  • FIG. 15A-15E depict data showing that engineered CRISPR-Cas9 epigenetic fusions display higher HDR and HDRbndel ratios.
  • FIG. 16A-16D depict data showing that epigenetic fusions display increased HDR efficiency and HDRbndel ratios across multiple endogenous sites
  • FIG. 17A-17D depict data showing that PRDM9-Cas9 fusion displays increased
  • FIG. 18 provides a schematic depiction of fusion proteins comprising: i) CRISPR-Cas9; and ii) a lysine methyl transferase (KMT).
  • FIG. 19A-19E depict increased HDR and increased HDRdndel ratios with PRDM9-
  • FIG. 20A-20B depict increased HDR and increased HDRdndel ratios with PRDM9-
  • Heterologous means a nucleotide or polypeptide sequence that is not found in the native nucleic acid or protein, respectively.
  • a heterologous polypeptide e.g., a heterologous fusion partner
  • polynucleotide and “nucleic acid,” used interchangeably herein, refer to a polymeric form of nucleotides of any length, either ribonucleotides or deoxynucleotides. Thus, this term includes, but is not limited to, single-, double-, or multi-stranded DNA or RNA, genomic DNA, cDNA, DNA-RNA hybrids, or a polymer comprising purine and pyrimidine bases or other natural, chemically or biochemically modified, non-natural, or derivatized nucleotide bases.
  • polynucleotide and “nucleic acid” should be understood to include, as applicable to the embodiment being described, single- stranded (such as sense or antisense) and double-stranded polynucleotides.
  • polypeptide refers to a polymeric form of amino acids of any length, which can include genetically coded and nongene tically coded amino acids, chemically or biochemically modified or derivatized amino acids, and polypeptides having modified peptide backbones.
  • the term includes fusion proteins, including, but not limited to, fusion proteins with a heterologous amino acid sequence, fusions with heterologous and homologous leader sequences, with or without N-terminal methionine residues; immunologically tagged proteins; and the like.
  • nucleic acid refers to a nucleic acid, cell, protein, or organism that is found in nature.
  • isolated is meant to describe a polynucleotide, a polypeptide, or a cell that is in an environment different from that in which the polynucleotide, the polypeptide, or the cell naturally occurs.
  • An isolated genetically modified host cell may be present in a mixed population of genetically modified host cells.
  • Recombinant means that a particular nucleic acid (DNA or RNA) is the product of various combinations of cloning, restriction, and/or ligation steps resulting in a construct having a structural coding or non-coding sequence distinguishable from endogenous nucleic acids found in natural systems.
  • DNA sequences encoding the structural coding sequence can be assembled from cDNA fragments and short oligonucleotide linkers, or from a series of synthetic oligonucleotides, to provide a synthetic nucleic acid which is capable of being expressed from a recombinant transcriptional unit contained in a cell or in a cell-free transcription and translation system.
  • sequences can be provided in the form of an open reading frame uninterrupted by internal non- translated sequences, or introns, which are typically present in eukaryotic genes.
  • Genomic DNA comprising the relevant sequences can also be used in the formation of a recombinant gene or transcriptional unit. Sequences of non-translated DNA may be present 5’ or 3’ from the open reading frame, where such sequences do not interfere with manipulation or expression of the coding regions, and may indeed act to modulate production of a desired product by various mechanisms (see “DNA regulatory sequences”, below).
  • the term “recombinant” polynucleotide or “recombinant” nucleic acid refers to one which is not naturally occurring, e.g., is made by the artificial combination of two otherwise separated segments of sequence through human intervention.
  • This artificial combination is often accomplished by either chemical synthesis means, or by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques. Such is usually done to replace a codon with a redundant codon encoding the same or a conservative amino acid, while typically introducing or removing a sequence recognition site. Alternatively, it is performed to join together nucleic acid segments of desired functions to generate a desired combination of functions.
  • This artificial combination is often accomplished by either chemical synthesis means, or by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques.
  • polypeptide refers to a polypeptide which is not naturally occurring, e.g., is made by the artificial combination of two otherwise separated segments of amino sequence through human intervention.
  • a polypeptide that comprises a heterologous amino acid sequence is recombinant.
  • construct or “vector” is meant a recombinant nucleic acid, generally recombinant
  • DNA which has been generated for the purpose of the expression and/or propagation of a specific nucleotide sequence(s), or is to be used in the construction of other recombinant nucleotide sequences.
  • DNA regulatory sequences control elements
  • regulatory elements used interchangeably herein, refer to transcriptional and translational control sequences, such as promoters, enhancers, polyadenylation signals, terminators, protein degradation signals, and the like, that provide for and/or regulate expression of a coding sequence and/or production of an encoded polypeptide in a host cell.
  • transformation is used interchangeably herein with “genetic modification” and refers to a permanent or transient genetic change induced in a cell following introduction of new nucleic acid (e.g., DNA exogenous to the cell) into the cell.
  • Genetic change (“modification”) can be accomplished either by incorporation of the new nucleic acid into the genome of the host cell, or by transient or stable maintenance of the new nucleic acid as an episomal element.
  • a permanent genetic change is generally achieved by introduction of new DNA into the genome of the cell.
  • chromosomes In prokaryotic cells, permanent changes can be introduced into the chromosome or via extrachromosomal elements such as plasmids and expression vectors, which may contain one or more selectable markers to aid in their maintenance in the recombinant host cell.
  • Suitable methods of genetic modification include viral infection, transfection, conjugation, protoplast fusion, electroporation, particle gun technology, calcium phosphate precipitation, direct microinjection, and the like.
  • the choice of method is generally dependent on the type of cell being transformed and the circumstances under which the transformation is taking place (i.e. in vitro, ex vivo, or in vivo). A general discussion of these methods can be found in Ausubel, et al., Short Protocols in Molecular Biology, 3rd ed., Wiley & Sons, 1995.
  • “Operably linked” refers to a juxtaposition wherein the components so described are in a relationship permitting them to function in their intended manner.
  • a promoter is operably linked to a coding sequence if the promoter affects its transcription or expression.
  • heterologous promoter and “heterologous control regions” refer to promoters and other control regions that are not normally associated with a particular nucleic acid in nature.
  • a “transcriptional control region heterologous to a coding region” is a transcriptional control region that is not normally associated with the coding region in nature.
  • a “host cell,” as used herein, denotes an in vivo or in vitro eukaryotic cell, a prokaryotic cell, or a cell from a multicellular organism (e.g., a cell line) cultured as a unicellular entity, which eukaryotic or prokaryotic cells can be, or have been, used as recipients for a nucleic acid (e.g., an expression vector), and include the progeny of the original cell which has been genetically modified by the nucleic acid. It is understood that the progeny of a single cell may not necessarily be completely identical in morphology or in genomic or total DNA complement as the original parent, due to natural, accidental, or deliberate mutation.
  • a “recombinant host cell” (also referred to as a “genetically modified host cell”) is a host cell into which has been introduced a heterologous nucleic acid, e.g., an expression vector.
  • a subject eukaryotic host cell is a genetically modified eukaryotic host cell, by virtue of introduction into a suitable eukaryotic host cell of a heterologous nucleic acid, e.g., an exogenous nucleic acid that is foreign to the eukaryotic host cell, or a recombinant nucleic acid that is not normally found in the eukaryotic host cell.
  • a group of amino acids having aliphatic side chains consists of glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains consists of serine and threonine; a group of amino acids having amide-containing side chains consists of asparagine and glutamine; a group of amino acids having aromatic side chains consists of phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains consists of lysine, arginine, and histidine; and a group of amino acids having sulfur- containing side chains consists of cysteine and methionine.
  • Exemplary conservative amino acid substitution groups are: valine-leucine-isoleucine, phenylalanine-tyrosine, lysine-arginine,
  • a polynucleotide or polypeptide has a certain percent “sequence identity” to another polynucleotide or polypeptide, meaning that, when aligned, that percentage of bases or amino acids are the same, and in the same relative position, when comparing the two sequences. Sequence similarity can be determined in a number of different manners. To determine sequence identity, sequences can be aligned using the methods and computer programs, including BLAST, available over the world wide web at ncbi.nlm.nih.gov/BLAST. See, e.g., Altschul et al. (1990), J. Mol. Biol. 215:403-10.
  • LASTA is LASTA, available in the Genetics Computing Group (GCG) package, from Madison, Wisconsin, USA, a wholly owned subsidiary of Oxford Molecular Group, Inc.
  • GCG Genetics Computing Group
  • Other techniques for alignment are described in Methods in Enzymology, vol. 266: Computer Methods for Macromolecular Sequence Analysis (1996), ed. Doolittle, Academic Press, Inc., a division of Harcourt Brace & Co., San Diego, California, USA.
  • alignment programs that permit gaps in the sequence.
  • the Smith- Waterman is one type of algorithm that permits gaps in sequence alignments. See Meth. Mol. Biol. 70: 173-187 (1997).
  • the GAP program using the Needleman and Wunsch alignment method can be utilized to align sequences. See J. Mol. Biol.
  • treatment refers to obtaining a desired pharmacologic and/or physiologic effect.
  • the effect may be prophylactic in terms of completely or partially preventing a disease or symptom thereof and/or may be therapeutic in terms of a partial or complete cure for a disease and/or adverse effect attributable to the disease.
  • Treatment covers any treatment of a disease in a mammal, e.g., in a human, and includes: (a) preventing the disease from occurring in a subject which may be predisposed to the disease but has not yet been diagnosed as having it; (b) inhibiting the disease, i.e., arresting its development; and (c) relieving the disease, i.e., causing regression of the disease.
  • the terms "individual,” “subject,” “host,” and “patient,” used interchangeably herein, refer to an individual organism, e.g., a mammal, including, but not limited to, murines, simians, humans, non-human primates, mammalian farm animals, mammalian sport animals, and mammalian pets.
  • the present disclosure provides a fusion polypeptide comprising: a) a CRISPR/Cas effector polypeptide; and b) a chromatin marker polypeptide that provides for modification of a histone polypeptide present in chromatin.
  • the present disclosure provides nucleic acids encoding the fusion polypeptide, and cells comprising the fusion polypeptide and/or the nucleic acids.
  • the present disclosure provides systems, kits, devices, and containers comprising a fusion polypeptide of the present disclosure or a nucleic acid encoding same.
  • the present disclosure provides methods for modifying a target nucleic acid, which methods comprise use of the fusion polypeptide.
  • the present disclosure provides a fusion polypeptide comprising: a) a CRISPR/Cas effector polypeptide; and b) a chromatin marker polypeptide that provides for modification of a histone polypeptide present in chromatin. The modification marks the chromatin as a site for recombination.
  • a fusion polypeptide of the present disclosure when complexed with a guide nucleic acid, can modify a target nucleic acid.
  • a fusion polypeptide of the present disclosure is complexed with a guide nucleic acid, and when a donor template nucleic acid is provided, provides for an increased level of HDR, compared with the level of HDR that would occur using a CRISPR/Cas effector polypeptide not fused to the fusion partner present in the fusion polypeptide.
  • a fusion polypeptide of the present disclosure (comprising a CRISPR/Cas effector polypeptide and a chromatin marker polypeptide), a guide RNA, and a donor template DNA are introduced into a target eukaryotic cell, where such introducing results in a level of HDR that is at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100% (or two-fold), at least 2.5-fold, at least 3-fold, at least 4-fold, at least 5-fold, or at least 10-fold, or more than 10-fold, higher than the level of HDR that would occur if the CRISPR/Cas effector polypeptide (not fused to the chromatin marker polypeptide), the guide RNA, and the donor template DNA were introduced into the cell.
  • a fusion polypeptide of the present disclosure (comprising a CRISPR/Cas effector polypeptide and a chromatin marker polypeptide), a guide RNA, and a donor template DNA are introduced into a target eukaryotic cell, where such introducing results in modification of a target nucleic acid in the cell, wherein the ratio of HDR events to NHEJ events is at least 1.5:1, at least 2:1, at least 2.5:1, at least 3:1, at least 4:1, at least 5:1, at least 7.5:1, at least 10:1, at least 25:1, at least 50:1, or at least 100:1.
  • a fusion polypeptide of the present disclosure provides for an increased
  • the HDRdndel ratio compared to the HDRdndel ratio of a CRISPR/Cas effector polypeptide not fused to a chromatin modifying polypeptide.
  • the HDRdndel ratio is increased by at least 10%, at least 15%, at least 25%, at least 50%, at least 2-fold, at least 3-fold, or more than 3-fold, compared to the HDRdndel ratio obtained with a control CRISPR/Cas effector polypeptide (the CRISPR/Cas effector polypeptide not fused to the chromatin-modifying polypeptide).
  • a fusion polypeptide of the present disclosure provides for reduced incidence of chromosomal translocations or chromothripsis, compared to the incidence of chromosomal translocations or chromothripsis observed using a CRISPR-Cas effector polypeptide not fused to a chromatin marker polypeptide.
  • a fusion polypeptide of the present disclosure provides for reduced (e.g., at least 10% reduced, at least 15% reduced, at least 20% reduced, at least 25% reduced, at least 30% reduced, at least 35% reduced, at least 40% reduced, at least 45% reduced, or at least 50% reduced) incidence of chromosomal translocations or chromothripsis, compared to the incidence of chromosomal translocations or chromothripsis observed using a CRISPR-Cas effector polypeptide not fused to the SETMAR polypeptide.
  • a fusion polypeptide of the present disclosure comprises, in order from N- terminus to C-terminus: a) a CRISPR/Cas effector polypeptide; and b) a chromatin modifying polypeptide.
  • a fusion polypeptide of the present disclosure comprises, in order from N- terminus to C-terminus: a) a chromatin modifying polypeptide; and b) a CRISPR/Cas effector polypeptide.
  • a fusion polypeptide of the present disclosure comprises, in order from N- terminus to C-terminus: a) an N-terminal portion of a CRISPR/Cas effector polypeptide; b) a chromatin modifying polypeptide; and c) a C-terminal portion of the CRISPR/Cas effector polypeptide.
  • a fusion polypeptide of the present disclosure comprises, in order from N-terminus to C-terminus: a) a C-terminal portion of a CRISPR/Cas effector polypeptide; b) a chromatin modifying polypeptide; and c) an N-terminal portion of the CRISPR/Cas effector polypeptide.
  • the fusion polypeptide can comprise one or more NLSs, where the one or more NLSs can be located at one or more of: i) the N-terminus of the fusion polypeptide; ii) at the C-terminus of the fusion polypeptide; and iii) between the CRISPR/Cas effector polypeptide and the chromatin-modifying polypeptide.
  • the fusion polypeptide can comprise one or more peptide linkers, e.g., between the CRISPR/Cas effector polypeptide and the chromatin-modifying polypeptide.
  • a chromatin marker polypeptide that provides for modification of a histone polypeptide present in chromatin, that is suitable for inclusion in a fusion polypeptide of the present disclosure includes: a) a histone me thy ltransf erase; b) a histone acetyltransferase; c) a polypeptide that binds F13K4me3 and/or F13K36me3 and that recruits one or more polypeptides that promote F1DR to the chromatin; and d) a polypeptide that binds a PRDM9 polypeptide.
  • a chromatin marker polypeptide suitable for inclusion in a fusion polypeptide of the present disclosure does not bind DNA, e.g., lacks a domain (e.g., a sequence of amino acids) that bind to DNA, where such domains include Zn- finger DNA binding domains, transcription-activator like effector (TALE) DNA binding domains, transposases, recombinases, and the like.
  • a domain e.g., a sequence of amino acids
  • TALE transcription-activator like effector
  • the CRISPR/Cas polypeptide, together with a guide nucleic acid provide for binding to a target nucleic acid.
  • a MOF polypeptide acetylating lysine- 16 of histone 4 (H4) is specifically excluded.
  • Histone methyltransf erases HMTs
  • a chromatin marker polypeptide suitable for inclusion in a fusion polypeptide of the present disclosure is a histone methyltransferase (HMT).
  • HMT histone methyltransferase
  • a chromatin marker polypeptide suitable for inclusion in a fusion polypeptide of the present disclosure methylates one or more lysine resides in histone 3 (H3).
  • a chromatin marker polypeptide suitable for inclusion in a fusion polypeptide of the present disclosure methylates Iysine-4 (K4) of H3, such that K4 of H3 is mono-, di-, or trimethylated.
  • a chromatin marker polypeptide suitable for inclusion in a fusion polypeptide of the present disclosure methylates K4 of H3 such that K4 is trimethylated; such a methylated histone is referred to as H3K4me3.
  • a chromatin marker polypeptide suitable for inclusion in a fusion polypeptide of the present disclosure methylates lysine-36 (K36) of H3, such that K36 of H3 is mono-, di-, or trimethylated.
  • a chromatin marker polypeptide suitable for inclusion in a fusion polypeptide of the present disclosure methylates K36 of H3, such that K36 of H3 is trimethylated; such a methylated histone is referred to as H3K36me3.
  • Suitable HMTs include, but are not limited to, PRDM9, SETD2, and SETMAR. Where an HMT methylates a lysine residue, such an HMT is also referred to herein as a lysine methyltransferase (KMT).
  • a suitable PRDM9 PR domain zinc finger protein 9; minisatellite binding protein 3
  • polypeptide comprises a PR/SET domain and may further comprise one or both of a KRAB domain and an SSXRD domain.
  • a PRDM9 polypeptide suitable for including in a fusion polypeptide of the present disclosure does not include a zinc-finger (Zn-finger) DNA-binding domain.
  • a PRDM9 polypeptide suitable for including in a fusion polypeptide of the present disclosure comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the PRDM9 amino acid sequence depicted in FIG. 2A or FIG. 2B ; and has a length of from about 350 amino acids to about 400 amino acids (e.g., has a length of from about 350 amino acids (aa) to 360 aa, from 360 aa to 370 aa, from 370 aa to 380 aa, from 380 aa to 390 aa, or from 390 aa to 400 aa.
  • a PRDM9 polypeptide suitable for including in a fusion polypeptide of the present disclosure comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the PRDM9 amino acid sequence depicted in FIG. 2A; and has a length of 370 amino acids.
  • a PRDM9 polypeptide suitable for including in a fusion polypeptide of the present disclosure comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the PRDM9 amino acid sequence depicted in FIG. 2B; and has a length of 371 amino acids.
  • a PRDM9 polypeptide suitable for including in a fusion polypeptide of the present disclosure comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the PRDM9 amino acid sequence depicted in FIG.
  • a PRDM9 polypeptide suitable for including in a fusion polypeptide of the present disclosure comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the PRDM9 amino acid sequence depicted in FIG. 10; and has a length of 416 amino acids.
  • a suitable SETD2 (SET (Su(var)3-9, Enhancer of Zeste, and Trithorax) domain
  • a SETD2 polypeptide can comprise an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in any one of FIG. 4A-4E.
  • a SETD2 polypeptide lacks a WW domain.
  • a SETD2 polypeptide lacks an SRI domain.
  • a SETD2 polypeptide lacks both a WW domain and an SRI domain.
  • a suitable SETD2 polypeptide has a length of from about 1500 amino acids to 2000 amino acids.
  • a SETD2 polypeptide suitable for including in a fusion polypeptide of the present disclosure comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the SETD2 polypeptide depicted in FIG. 4F; and has a length of 196 amino acids.
  • a suitable SETMAR (SET domain and mariner transposase fusion gene; histone-lysine
  • N-methyltransferase SETMAR N-methyltransferase SETMAR
  • METNASE Marl
  • polypeptide can comprise an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in any one of FIG. 6A-6G, where the SETMAR polypeptide does not include a transposase domain.
  • a suitable SETMAR polypeptide comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to amino acids 1-346 of the amino acid sequence depicted in FIG. 6A; and has a length of from about 300 amino acids to about 350 amino acids.
  • a suitable SETMAR polypeptide comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to amino acids 1-362 of the amino acid sequence depicted in FIG. 6B; and has a length of from about 300 amino acids to about 360 amino acids.
  • a suitable SETMAR polypeptide comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to amino acids 1-268 of the amino acid sequence depicted in FIG.6C; and has a length of from about 225 amino acids to about 270 amino acids.
  • a suitable SETMAR polypeptide comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to amino acids 1-224 or amino acids 1-269 of the amino acid sequence depicted in FIG.6D; and has a length of from about 225 amino acids to about 270 amino acids.
  • a suitable SETMAR polypeptide comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to amino acids 1- 245 of the amino acid sequence depicted in FIG.6E; and has a length of from about 215 amino acids to about 245 amino acids.
  • a suitable SETMAR polypeptide comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to amino acids 1-213 of the amino acid sequence depicted in FIG.6F; and has a length of from about 190 amino acids to about 215 amino acids.
  • a suitable SETMAR polypeptide comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG.6G; and has a length of 263 amino acids.
  • a suitable MOT (MYST-1; KAT8; ZC2HC8) polypeptide can comprise an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 7.
  • a chromatin marker that is suitable for inclusion in a fusion polypeptide of the present disclosure is a polypeptide that: i) binds H3K4me3 and/or H3K36me3; and ii) recruits one or more polypeptides that promote HDR to the chromatin.
  • polypeptides include ZMYND8 and ZCWPWI.
  • a suitable ZMYND8 polypeptide comprises an amino acid sequence having at least
  • a suitable ZCWPW1 polypeptide comprises an amino acid sequence having at least
  • a polypeptide suitable for inclusion in a fusion polypeptide of the present disclosure is a chromatin remodeler polypeptide.
  • a suitable chromatin remodeler polypeptide is a helicase, lymphoid specific (HELLS) polypeptide.
  • HELLS polypeptide is a member of the SNF2 helicase family of chromatin remodeling proteins.
  • a suitable HELLS polypeptide comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 13.
  • any CRISPR/Cas effector polypeptide is suitable for inclusion in a fusion polypeptide of the present disclosure.
  • the CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure is a type II CRISPR/Cas effector polypeptide, a type V CRISPR/Cas effector polypeptide, or a type VI CRISPR/Cas effector polypeptide.
  • the CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure is a type II CRISPR/Cas effector polypeptide.
  • the CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure is a Cas9 polypeptide. In some cases, the CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure is a type V CRISPR/Cas effector polypeptide. In some cases, the CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure is a Casl2a, a Casl2b, a Casl2c, a Casl2d, or a Casl2e polypeptide.
  • the CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure is a type VI CRISPR/Cas effector polypeptide.
  • the CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure is a Casl3a, a Casl3b, a Casl3c, or a Casl3d polypeptide.
  • the CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure is a Casl4a, a Casl4b, or a Casl4c polypeptide. Amino acid sequences of a variety of CRISPR/Cas effector polypeptides are known.
  • a CRISPR/Cas effector polypeptide suitable for inclusion in a fusion polypeptide of the present disclosure comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in any one of FIG. 5A-5P.
  • a CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure is enzymatically active. In some cases, a CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure exhibits reduced enzymatic activity compared to a wild- type CRISPR/Cas effector polypeptide. In some cases, a CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure is a nickase.
  • a CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure comprises a substitution of D10 (e.g., D10A) or H840 (e.g., H840A) of the amino acid sequence depicted in FIG. 5A, or a corresponding amino acid of another CRISPR/Cas effector polypeptide.
  • a CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure is enzymatically inactive (a “dead” CRISPR/Cas effector polypeptide) but retains the ability to bind a target nucleic acid when complexed with a guide nucleic acid.
  • a CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure comprises a substitution of both D10 and H840 (e.g., D10A; and H840A) of the amino acid sequence depicted in FIG. 5A, or corresponding amino acids of another CRISPR/Cas effector polypeptide.
  • a fusion polypeptide of the present disclosure comprises one or more additional heterologous polypeptides at the N-terminus, the C-terminus, or both the N-terminus and the C-terminus of the fusion polypeptide.
  • a fusion polypeptide of the present disclosure includes (is fused to) a nuclear localization signal (NLS) (e.g., in some cases 2 or more, 3 or more, 4 or more, or 5 or more NLSs).
  • NLS nuclear localization signal
  • a fusion polypeptide of the present disclosure includes one or more NLSs (e.g., 2 or more, 3 or more, 4 or more, or 5 or more NLSs).
  • one or more NLSs (2 or more, 3 or more, 4 or more, or 5 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) the N-terminus and/or the C-terminus.
  • one or more NLSs (2 or more, 3 or more, 4 or more, or 5 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) the N-terminus. In some cases, one or more NLSs (2 or more, 3 or more, 4 or more, or 5 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) the C-terminus. In some cases, one or more NLSs (3 or more, 4 or more, or 5 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) both the N-terminus and the C-terminus.
  • an NLS is positioned at the N-terminus and an NLS is positioned at the C-terminus.
  • one or more NLSs (2 or more, 3 or more, 4 or more, or 5 or more NLSs) are positioned internally within a fusion polypeptide of the present disclosure.
  • Non-limiting examples of NLSs include an NLS sequence derived from: the NLS of the SV40 virus large T-antigen, having the amino acid sequence PKKKRKV (SEQ ID NO:37); the NLS from nucleoplasmin (e.g., the nucleoplasmin bipartite NLS with the sequence KRPAATKKAGQAKKKK (SEQ ID NO:61)); the c-myc NLS having the amino acid sequence PAAKRVKLD (SEQ ID NO:62) or RQRRNELKRSP (SEQ ID NO:63); the hRNPAl M9 NLS having the sequence NQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGY (SEQ ID NO:64); the sequence RMRIZFKNKGKDTAELRRRRVEVSVELRKAKKDEQILKRRNV (SEQ ID NO:65) of the IBB domain from importin-alpha; the sequences VSRKRPRP (SEQ ID NO:66) and
  • NLS are of sufficient strength to drive accumulation of the fusion protein in a detectable amount in the nucleus of a eukaryotic cell. Detection of accumulation in the nucleus may be performed by any suitable technique. For example, a detectable marker may be fused to the fusion protein such that location within a cell may be visualized. Cell nuclei may also be isolated from cells, the contents of which may then be analyzed by any suitable process for detecting protein, such as immunohistochemistry, Western blot, or enzyme activity assay. Accumulation in the nucleus may also be determined indirectly.
  • a fusion polypeptide of the present disclosure includes a "Protein Transduction Domain” or PTD (also known as a CPP - cell penetrating peptide), which refers to a polypeptide, polynucleotide, carbohydrate, or organic or inorganic compound that facilitates traversing a lipid bilayer, micelle, cell membrane, organelle membrane, or vesicle membrane.
  • PTD Protein Transduction Domain
  • a PTD attached to another molecule which can range from a small polar molecule to a large macromolecule and/or a nanoparticle, facilitates the molecule traversing a membrane, for example going from extracellular space to intracellular space, or cytosol to within an organelle.
  • a PTD is covalently linked to the carboxyl terminus of a fusion polypeptide of the present disclosure.
  • the PTD is inserted internally in a fusion polypeptide of the present disclosure at a suitable insertion site.
  • a fusion polypeptide of the present disclosure includes (is conjugated to, is fused to) one or more PTDs (e.g., two or more, three or more, four or more PTDs).
  • a PTD includes a nuclear localization signal (NLS) (e.g., in some cases 2 or more, 3 or more, 4 or more, or 5 or more NLSs).
  • NLS nuclear localization signal
  • a fusion polypeptide of the present disclosure includes one or more NLSs (e.g., 2 or more, 3 or more, 4 or more, or 5 or more NLSs).
  • PTDs include but are not limited to a minimal undecapeptide protein transduction domain (corresponding to residues 47-57 of HIV-1 TAT comprising YGRKKRRQRRR; SEQ ID NO:76); a polyarginine sequence comprising a number of arginines sufficient to direct entry into a cell (e.g., 3, 4, 5, 6, 7, 8, 9, 10, or 10-50 arginines); a VP22 domain (Zender et al. (2002) Cancer Gene Ther.
  • RRQRRTSKLMKR SEQ ID NO:77
  • Transportan GWTLNSAGYLLGKINLKALAALAKKIL SEQ ID NO:78
  • KALAWEAKLAKALAKALAKHLAKALAKALKCEA SEQ ID NO:79
  • RQIKIWF QNRRMKWKK SEQ ID NO: 80
  • Exemplary PTDs include but are not limited to, YGRKKRRQRRR (SEQ ID NO:76), RKKRRQRRR (SEQ ID NO:81); an arginine homopolymer of from 3 arginine residues to 50 arginine residues;
  • Exemplary PTD domain amino acid sequences include, but are not limited to, any of the following: YGRKKRRQRRR (SEQ ID NO:76); RKKRRQRR (SEQ ID NO:82); YARAAARQARA (SEQ ID NO:83); THRLPRRRRRR (SEQ ID NO:84); and GGRRARRRRRR (SEQ ID NO:85).
  • the PTD is an activatable CPP (ACPP) (Aguilera et al. (2009) Integr Biol ( Camb) June; 1(5-6): 371-381).
  • ACPPs comprise a polycationic CPP (e.g., Arg9 or “R9”) connected via a cleavable linker to a matching polyanion (e.g., Glu9 or ⁇ 9”), which reduces the net charge to nearly zero and thereby inhibits adhesion and uptake into cells.
  • a polyanion e.g., Glu9 or ⁇ 9
  • a fusion polypeptide of the present disclosure comprises one or more linker polypeptides; e.g., a linker polypeptide between the CRISPR/Cas effector polypeptide and the chromatin marker polypeptide.
  • the linker polypeptide may have any of a variety of amino acid sequences. Proteins can be joined by a spacer peptide, generally of a flexible nature, although other chemical linkages are not excluded. Suitable linkers include polypeptides of between 4 amino acids and 40 amino acids in length, or between 4 amino acids and 25 amino acids in length.
  • linkers can be produced by using synthetic, linker-encoding oligonucleotides to couple the proteins, or can be encoded by a nucleic acid sequence encoding the fusion protein.
  • Peptide linkers with a degree of flexibility can be used.
  • the linking peptides may have virtually any amino acid sequence, bearing in mind that the preferred linkers will have a sequence that results in a generally flexible peptide.
  • small amino acids, such as glycine and alanine are of use in creating a flexible peptide. The creation of such sequences is routine to those of skill in the art.
  • a variety of different linkers are commercially available and are considered suitable for use.
  • linker polypeptides include glycine polymers (G) n , glycine-serine polymers (including, for example, (GS)neig, GSGGS n (SEQ ID NO:86), (GGS)n, GGSGGS n (SEQ ID NO:87), (GGGGS)n (SEQ ID NO:88), and GGGS n (SEQ ID NO:89), where n is an integer of at least one; glycine-alanine polymers, alanine-serine polymers.
  • Exemplary linkers can comprise amino acid sequences including, but not limited to, GGSG (SEQ ID NO:90), GGSGG (SEQ ID NO:91), GSGSG (SEQ ID NO:92), GSGGG (SEQ ID NO:93), GGGSG (SEQ ID NO:94), GSSSG (SEQ ID NO:95), and the like.
  • Exemplary linkers include (GGGGS)n (SEQ ID NO:96), where n is an integer from 1 to 20.
  • Exemplary linkers include (GGGGS)n (SEQ ID NO:97), where n is 1, 2, 3, 4, 5, 6, or 7.
  • Exemplary linkers include (GGS)n (SEQ ID NO:98), where n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • design of a peptide conjugated to any desired element can include linkers that are all or partially flexible, such that the linker can include a flexible linker as well as one or more portions that confer less flexible structure.
  • a fusion polypeptide of the present disclosure comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 3A. In some cases, a fusion polypeptide of the present disclosure comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 3B.
  • a fusion polypeptide of the present disclosure comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 11 A-l 1H.
  • linkers of various lengths can be used; for example, a (GGGGS)n (SEQ ID NO:99) linker (where n is an integer from 1 to 10) can be used.
  • A-l 1H can be substituted with an NLS of a different amino acid sequence, or a different number of NLSs can be used.
  • the FLAG-tag included in the fusion polypeptides can be omitted, or a different epitope tag can be used.
  • a fusion polypeptide of the present disclosure comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 12A-12J.
  • linkers of various lengths can be used; for example, a (GGGGS)n (SEQ ID NO:99) linker (where n is an integer from 1 to 10) can be used.
  • 12A-12J can be substituted with an NLS of a different amino acid sequence, or a different number of NLSs can be used.
  • the FLAG-tag included in the fusion polypeptides can be omitted, or a different epitope tag can be used.
  • the present disclosure provides a nucleic acid comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure.
  • the present disclosure provides one or more nucleic acids comprising one or more of: a donor polynucleotide, a nucleotide sequence encoding a fusion polypeptide of the present disclosure, a guide nucleic acid (e.g., a guide RNA), and a nucleotide sequence encoding a guide nucleic acid (e.g., a guide RNA).
  • the present disclosure provides a nucleic acid comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure.
  • the present disclosure provides a recombinant expression vector that comprises a nucleotide sequence encoding a fusion polypeptide of the present disclosure.
  • the present disclosure provides a recombinant expression vector that comprises: a) a nucleotide sequence encoding a fusion polypeptide of the present disclosure; and b) a nucleotide sequence encoding a guide RNA(s).
  • the nucleotide sequence encoding the fusion polypeptide of the present disclosure and/or the nucleotide sequence encoding the guide RNA is operably linked to a promoter that is operable in a cell type of choice (e.g., a eukaryotic cell; such as a plant cell, an animal cell, a mammalian cell, a non-human primate cell, a rodent cell, a human cell, an insect cell, an arachnid cell, a yeast cell, etc.).
  • a cell type of choice e.g., a eukaryotic cell; such as a plant cell, an animal cell, a mammalian cell, a non-human primate cell, a rodent cell, a human cell, an insect cell, an arachnid cell, a yeast cell, etc.
  • a nucleotide sequence encoding a fusion polypeptide of the present disclosure is codon optimized. This type of optimization can entail a mutation of a fusion polypeptide- encoding nucleotide sequence to mimic the codon preferences of the intended host organism or cell while encoding the same protein. Thus, the codons can be changed, but the encoded protein remains unchanged. For example, if the intended target cell was a human cell, a human codon-optimized fusion polypeptide-encoding nucleotide sequence could be used. As another non-limiting example, if the intended host cell were a mouse cell, then a mouse codon-optimized fusion polypeptide-encoding nucleotide sequence could be generated.
  • the intended host cell were a plant cell, then a plant codon-optimized fusion polypeptide-encoding nucleotide sequence could be generated.
  • a plant codon-optimized fusion polypeptide-encoding nucleotide sequence could be generated.
  • an insect codon-optimized fusion polypeptide-encoding nucleotide sequence could be generated.
  • Codon usage tables are readily available, for example, at the "Codon Usage Database" available at www[dot]kazusa[dot]or[dot]jp[forwardslash]codon.
  • a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a eukaryotic cell.
  • a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in an animal cell.
  • a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a fungus cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a plant cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a monocotyledonous plant species. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptideencoding nucleotide sequence that is codon optimized for expression in a dicotyledonous plant species.
  • a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a gymnosperm plant species. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in an angiosperm plant species. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a corn cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a soybean cell.
  • a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a rice cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a wheat cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a cotton cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptideencoding nucleotide sequence that is codon optimized for expression in a sorghum cell.
  • a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in an alfalfa cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a sugar cane cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in an Arabidopsis cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a tomato cell.
  • a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a cucumber cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a potato cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptideencoding nucleotide sequence that is codon optimized for expression in an algae cell.
  • the present disclosure provides one or more recombinant expression vectors that include (in different recombinant expression vectors in some cases, and in the same recombinant expression vector in some cases): (i) a nucleotide sequence of a donor template nucleic acid (where the donor template comprises a nucleotide sequence having homology to a target sequence of a target nucleic acid (e.g., a target genome)); (ii) a nucleotide sequence that encodes a guide RNA that hybridizes to a target sequence of the target locus of the targeted genome (e.g., operably linked to a promoter that is operable in a target cell such as a eukaryotic cell); and (iii) a nucleotide sequence encoding a fusion polypeptide of the present disclosure (e.g., operably linked to a promoter that is operable in a target cell such as a eukaryotic cell).
  • the present disclosure provides one or more recombinant expression vectors that include (in separate recombinant expression vectors in some cases, and in the same recombinant expression vector in some cases): (i) a nucleotide sequence of a donor template nucleic acid (where the donor template comprises a nucleotide sequence having homology to a target sequence of a target nucleic acid (e.g., a target genome)); and (ii) a nucleotide sequence that encodes a guide RNA that hybridizes to a target sequence of the target locus of the targeted genome (e.g., operably linked to a promoter that is operable in a target cell such as a eukaryotic cell).
  • a nucleotide sequence of a donor template nucleic acid where the donor template comprises a nucleotide sequence having homology to a target sequence of a target nucleic acid (e.g., a target genome)
  • the present disclosure provides one or more recombinant expression vectors that include (in separate recombinant expression vectors in some cases, and in the same recombinant expression vector in some cases): (i) a nucleotide sequence that encodes a guide RNA that hybridizes to a target sequence of the target locus of the targeted genome (e.g., operably linked to a promoter that is operable in a target cell such as a eukaryotic cell); and (ii) a nucleotide sequence encoding a fusion polypeptide of the present disclosure (e.g., operably linked to a promoter that is operable in a target cell such as a eukaryotic cell).
  • a nucleotide sequence that encodes a guide RNA that hybridizes to a target sequence of the target locus of the targeted genome e.g., operably linked to a promoter that is operable in a target cell such as a eukaryotic cell
  • Suitable expression vectors include viral expression vectors (e.g. viral vectors based on vaccinia virus; poliovirus; adenovirus (see, e.g., Li et al., Invest Opthalmol Vis Sci 35:25432549, 1994; Borras et al., Gene Ther 6:515 524, 1999; Li and Davidson, PNAS 92:77007704, 1995; Sakamoto et al., H Gene Ther 5:1088 1097, 1999; WO 94/12649, WO 93/03769; WO 93/19191; WO 94/28938; WO 95/11984 and WO 95/00655); adeno-associated virus (AAV) (see, e.g., Ali et al., Hum Gene Ther 9:81 86, 1998, Flannery et al., PNAS 94:6916 6921, 1997; Bennett et al., Invest Opthalmol Vis
  • SV40 herpes simplex virus
  • human immunodeficiency virus see, e.g., Miyoshi et al., PNAS 94:1031923, 1997; Takahashi et al., J Virol 73:78127816, 1999
  • a retroviral vector e.g., Murine Leukemia Virus, spleen necrosis virus, and vectors derived from retroviruses such as Rous Sarcoma Virus, Harvey Sarcoma Virus, avian leukosis virus, a lentivirus, human immunodeficiency virus, myeloproliferative sarcoma virus, and mammary tumor virus
  • retroviral vector e.g., Murine Leukemia Virus, spleen necrosis virus, and vectors derived from retroviruses such as Rous Sarcoma Virus, Harvey Sarcoma Virus, avian leukosis virus, a lentivirus, human immunodeficiency virus, myeloprol
  • a recombinant expression vector of the present disclosure is a recombinant adeno-associated virus (AAV) vector.
  • a recombinant expression vector of the present disclosure is a recombinant lentivirus vector.
  • a recombinant expression vector of the present disclosure is a recombinant retroviral vector.
  • viral vectors based on Tobamoviruses, Potexviruses, Potyviruses, Tobraviruses, Tombusviruses, Geminiviruses, Bromoviruses, Carmoviruses, Alfamoviruses, or Cucumoviruses can be used. See, e.g., Peyret and Lomonossoff (2015) Plant Biotechnol. J. 13:1121.
  • Suitable Tobamovirus vectors include, for example, a tomato mosaic virus (ToMV) vector, a tobacco mosaic virus (TMV) vector, a tobacco mild green mosaic virus (TMGMV) vector, a pepper mild mottle virus (PMMoV) vector, a paprika mild mottle virus (PaMMV) vector, a cucumber green mottle mosaic virus (CGMMV) vector, a kyuri green mottle mosaic virus (KGMMV) vector, a hibiscus latent fort pierce virus (HLFPV) vector, an odontoglossum ringspot virus (ORSV) vector, a rehmannia mosaic virus (ReMV) vector, a Sammon's opuntia virus (SOV) vector, a wasabi mottle virus (WMoV) vector, a youcai mosaic virus (YoMV) vector, a sunn-hemp mosaic virus (SHMV) vector, and the like.
  • ToMV tomato mosaic virus
  • TMV tobacco mosaic virus
  • TMV
  • Suitable Potexvirus vectors include, for example, a potato virus X (PVX) vector, a potato aucubamosaicvirus (PAMV) vector, an Alstroemeria virus X (AlsVX) vector, a cactus virus X (CVX) vector, a Cymbidium mosaic virus (CymMV) vector, a hosta virus X (HVX) vector, a lily virus X (LVX) vector, a Narcissus mosaic virus (NMV) vector, a Nerine virus X (NVX) vector, a Plantago asiatica mosaic virus (P1AMV) vector, a strawberry mild yellow edge virus (SMYEV) vector, a tulip virus X (TVX) vector, a white clover mosaic virus (WC1MV) vector, a bamboo mosaic virus (BaMV) vector, and the like.
  • PVX potato virus X
  • PAMV potato aucubamosaicvirus
  • Suitable Potyvirus vectors include, for example, a potato virus Y (PVY) vector, a bean common mosaic virus (BCMV) vector, a clover yellow vein virus (C1YVV) vector, an East Asian Passiflora virus (EAPV) vector, a Freesia mosaic virus (FreMV) vector, a Japanese yam mosaic virus (JYMV) vector, a lettuce mosaic virus (LMV) vector, a Maize dwarf mosaic virus (MDMV) vector, an onion yellow dwarf virus (OYDV) vector, a papaya ringspot virus (PRSV) vector, a pepper mottle virus (PepMoV) vector, a Perilla mottle virus (PerMoV) vector, a plum pox virus (PPV) vector, a potato virus A (PVA) vector, a sorghum mosaic virus (SrMV) vector, a soybean mosaic virus (SMV) vector, a sugarcane mosaic virus (SCMV) vector, a tulip mosaic virus (TulMV
  • Suitable Tobravirus vectors include, for example, a tobacco rattle virus (TRV) vector and the like.
  • Suitable Tombusvirus vectors include, for example, a tomato bushy stunt virus (TBSV) vector, an eggplant mottled crinkle virus (EMCV) vector, a grapevine Jamaican latent virus (GALV) vector, and the like.
  • Suitable Cucumovirus vectors include, for example, a cucumber mosaic virus (CMV) vector, a peanut stunt virus (PSV) vector, a tomato aspermy virus (TAV) vector, and the like.
  • Suitable Bromovirus vectors include, for example, a brome mosaic virus (BMV) vector, a cowpea chlorotic mottle virus (CCMV) vector, and the like.
  • Suitable Carmovirus vectors include, for example, a carnation mottle virus (CarMV) vector, a melon necrotic spot virus (MNSV) vector, a pea stem necrotic virus (PSNV) vector, a turnip crinkle virus (TCV) vector, and the like.
  • Suitable Alfamovirus vectors include, for example, an alfalfa mosaic virus (AMV) vector, and the like.
  • any of a number of suitable transcription and translation control elements including constitutive and inducible promoters, transcription enhancer elements, transcription terminators, etc. may be used in the expression vector.
  • a nucleotide sequence encoding a guide RNA is operably linked to a control element, e.g., a transcriptional control element, such as a promoter.
  • a nucleotide sequence encoding a fusion polypeptide of the present disclosure is operably linked to a control element, e.g., a transcriptional control element, such as a promoter.
  • the transcriptional control element can be a promoter.
  • the promoter is a constitutively active promoter.
  • the promoter is a regulatable promoter.
  • the promoter is an inducible promoter.
  • the promoter is a tissue-specific promoter.
  • the promoter is a cell type-specific promoter.
  • the transcriptional control element e.g., the promoter
  • the transcriptional control element is functional in a targeted cell type or targeted cell population.
  • the transcriptional control element can be functional in eukaryotic cells, e.g., hematopoietic stem cells (e.g., mobilized peripheral blood (mPB) CD34(+) cell, bone marrow (BM) CD34(+) cell, etc.).
  • eukaryotic promoters include EFla, those from cytomegalovirus (CMV) immediate early, herpes simplex virus (HSV) thymidine kinase, early and late SV40, long terminal repeats (LTRs) from retrovirus, and mouse metallothionein-I.
  • the expression vector may also contain a ribosome binding site for translation initiation and a transcription terminator.
  • the expression vector may also include appropriate sequences for amplifying expression.
  • the expression vector may also include nucleotide sequences encoding protein tags (e.g., 6xHis tag, hemagglutinin tag, fluorescent protein, etc.) that can be fused a fusion polypeptide of the present disclosure.
  • a nucleotide sequence encoding a guide RNA and/or a fusion polypeptide of the present disclosure is operably linked to an inducible promoter. In some embodiments, a nucleotide sequence encoding a guide RNA and/or a fusion polypeptide of the present disclosure is operably linked to a constitutive promoter.
  • a promoter can be a constitutively active promoter (i.e., a promoter that is constitutively in an active/”ON” state), it may be an inducible promoter (i.e., a promoter whose state, active/”ON” or inactive/ 4 OFF”, is controlled by an external stimulus, e.g., the presence of a particular temperature, compound, or protein.), it may be a spatially restricted promoter (i.e., transcriptional control element, enhancer, etc.)(e.g., tissue specific promoter, cell type specific promoter, etc.), and it may be a temporally restricted promoter (i.e., the promoter is in the “ON” state or “OFF” state during specific stages of embryonic development or during specific stages of a biological process, e.g., hair follicle cycle in mice).
  • a constitutively active promoter i.e., a promoter that is constitutively in an active/”ON” state
  • it may be an inducible
  • Suitable promoters can be derived from viruses and can therefore be referred to as viral promoters, or they can be derived from any organism, including prokaryotic or eukaryotic organisms. Suitable promoters can be used to drive expression by any RNA polymerase (e.g., pol I, pol II, pol III).
  • RNA polymerase e.g., pol I, pol II, pol III
  • Exemplary promoters include, but are not limited to the SV40 early promoter, mouse mammary tumor virus long terminal repeat (LTR) promoter; adenovirus major late promoter (Ad MLP); a herpes simplex virus (F1SV) promoter, a cytomegalovirus (CMV) promoter such as the CMV immediate early promoter region (CMVIE), a rous sarcoma virus (RSV) promoter, a human U6 small nuclear promoter (U6) (Miyagishi et al., Nature Biotechnology 20, 497 - 500 (2002)), an enhanced U6 promoter (e.g., Xia et al., Nucleic Acids Res. 2003 Sep 1 ;31 (17)), a human HI promoter (HI), and the like.
  • LTR mouse mammary tumor virus long terminal repeat
  • Ad MLP adenovirus major late promoter
  • F1SV herpes simplex virus
  • CMV cytomegalovirus
  • CMVIE
  • a nucleotide sequence encoding a guide RNA is operably linked to (under the control of) a promoter operable in a eukaryotic cell (e.g., a U6 promoter, an enhanced U6 promoter, an HI promoter, and the like).
  • a promoter operable in a eukaryotic cell e.g., a U6 promoter, an enhanced U6 promoter, an HI promoter, and the like.
  • a promoter operable in a eukaryotic cell e.g., a U6 promoter, an enhanced U6 promoter, an HI promoter, and the like.
  • a promoter operable in a eukaryotic cell e.g., a U6 promoter, an enhanced U6 promoter, an HI promoter, and the like.
  • the RNA may need to be mutated if there are several Ts in a row (coding for Us in the RNA).
  • a nucleotide sequence encoding a fusion polypeptide of the present disclosure is operably linked to a promoter operable in a eukaryotic cell (e.g., a CMV promoter, an EFla promoter, an estrogen receptor-regulated promoter, and the like).
  • a promoter operable in a eukaryotic cell e.g., a CMV promoter, an EFla promoter, an estrogen receptor-regulated promoter, and the like.
  • nucleic acid e.g., a nucleic acid comprising a donor polynucleotide sequence, one or more nucleic acids encoding a fusion polypeptide of the present disclosure and/or a guide RNA, and the like
  • a nucleic acid e.g., an expression construct
  • Suitable methods include e.g., viral infection, transfection, lipofection, electroporation, calcium phosphate precipitation, polyethyleneimine (PEI)-mediated transfection, DEAE-dextran mediated transfection, liposome-mediated transfection, particle gun technology, calcium phosphate precipitation, direct microinjection, nanoparticle -mediated nucleic acid delivery, and the like.
  • PEI polyethyleneimine
  • Introducing the recombinant expression vector into cells can occur in any culture media and under any culture conditions that promote the survival of the cells. Introducing the recombinant expression vector into a target cell can be carried out in vivo or ex vivo. Introducing the recombinant expression vector into a target cell can be carried out in vitro.
  • a guide RNA (or a nucleic acid comprising a nucleotide sequence encoding same) and/or a fusion polypeptide of the present disclosure (or a nucleic acid comprising a nucleotide sequence encoding same) and/or a donor polynucleotide (donor template) can be introduced into a host cell by any of a variety of well-known methods.
  • a system of the present disclosure comprises: a) a fusion polypeptide of the present disclosure; and a CRISPR/Cas guide nucleic acid; b) a fusion polypeptide of the present disclosure; a CRISPR/Cas guide nucleic acid, and a DNA donor template; c) a fusion polypeptide of the present disclosure; and a CRISPR/Cas guide RNA; d) a fusion polypeptide of the present disclosure; a CRISPR/Cas guide RNA, and a DNA donor template; e) an mRNA encoding a fusion polypeptide of the present disclosure; and a CRISPR/Cas guide nucleic acid; f) an mRNA encoding a fusion polypeptide of the present disclosure; a CRISPR/Cas guide nucleic acid, and a DNA donor template
  • Methods of introducing a nucleic acid into a host cell are known in the art, and any convenient method can be used to introduce a subject nucleic acid (e.g., an expression construct/vector) into a target cell (e.g., prokaryotic cell, eukaryotic cell, plant cell, animal cell, mammalian cell, human cell, and the like).
  • a subject nucleic acid e.g., an expression construct/vector
  • a target cell e.g., prokaryotic cell, eukaryotic cell, plant cell, animal cell, mammalian cell, human cell, and the like.
  • Suitable methods include, e.g., viral infection, transfection, conjugation, protoplast fusion, lipofection, electroporation, calcium phosphate precipitation, polyethyleneimine (PEI) -mediated transfection, DEAE-dextran mediated transfection, liposome-mediated transfection, particle gun technology, calcium phosphate precipitation, direct micro injection, nanoparticle-mediated nucleic acid delivery (see, e.g., Panyam et., al Adv Drug Deliv Rev. 2012 Sep 13. pii: S0169-409X(12)00283-9. doi: 10.1016/j.addr.2012.09.023 ), and the like.
  • PKI polyethyleneimine
  • a fusion polypeptide of the present disclosure is provided as a nucleic acid (e.g., an mRNA, a DNA, a plasmid, an expression vector, a viral vector, etc.) that encodes the fusion polypeptide.
  • a fusion polypeptide of the present disclosure is provided directly as a protein (e.g., without an associated guide RNA or with an associate guide RNA, i.e., as a ribonucleoprotein complex).
  • a fusion polypeptide of the present disclosure can be introduced into a cell (provided to the cell) by any convenient method; such methods are known to those of ordinary skill in the art.
  • a fusion polypeptide of the present disclosure can be injected directly into a cell (e.g., with or without a guide RNA or nucleic acid encoding a guide RNA, and with or without a donor polynucleotide).
  • a preformed complex of a fusion polypeptide of the present disclosure and a guide RNA can be introduced into a cell (e.g., a eukaryotic cell) (e.g., via injection, via nucleofection; via a protein transduction domain (PTD) conjugated to one or more components, e.g., conjugated to the fusion polypeptide of the present disclosure, conjugated to a guide RNA, conjugated to a fusion polypeptide of the present disclosure and a guide RNA; etc.).
  • a cell e.g., a eukaryotic cell
  • PTD protein transduction domain
  • a nucleic acid e.g., a guide RNA; a nucleic acid comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure; etc.
  • a cell e.g., a target host cell
  • a polypeptide e.g., a fusion polypeptide of the present disclosure
  • a system of the present disclosure is delivered to a cell in a particle, or associated with a particle.
  • the terms “particle” and “nanoparticle” can be used interchangeably, as appropriate.
  • a recombinant expression vector comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure and/or a guide RNA, an mRNA comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure, and guide RNA may be delivered simultaneously using particles or lipid envelopes; for instance, a fusion polypeptide of the present disclosure and a guide RNA, e.g., as a complex (e.g., a ribonucleoprotein (RNP) complex), can be delivered via a particle, e.g., a delivery particle comprising lipid or lipidoid and hydrophilic polymer, e.g., a cationic lipid and a hydrophilic polymer, for instance wherein the cationic lipid comprises 1,2- dioleoyl-3-trimethylammonium-propane (DOTAP) or 1 ,2-ditetradecanoyl-sn-glycero-3-phosphocholine (
  • a particle can be formed using a multistep process in which a fusion polypeptide of the present disclosure and a guide RNA are mixed together, e.g., at a 1:1 molar ratio, e.g., at room temperature, e.g., for 30 minutes, e.g., in sterile, nuclease free 1 x phosphate-buffered saline (PBS); and separately, DOTAP, DMPC, PEG, and cholesterol as applicable for the formulation are dissolved in alcohol, e.g., 100% ethanol; and, the two solutions are mixed together to form particles containing the complexes).
  • PBS nuclease free 1 x phosphate-buffered saline
  • a fusion polypeptide of the present disclosure (or an mRNA comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure; or a recombinant expression vector comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure) and/or guide RNA (or a nucleic acid such as one or more expression vectors encoding the guide RNA) may be delivered simultaneously using particles or lipid envelopes.
  • a biodegradable core-shell structured nanoparticle with a poly (b-amino ester) (PBAE) core enveloped by a phospholipid bilayer shell can be used.
  • particles/nanoparticles based on self assembling bioadhesive polymers are used; such particles/nanoparticles may be applied to oral delivery of peptides, intravenous delivery of peptides and nasal delivery of peptides, e.g., to the brain.
  • Other embodiments, such as oral absorption and ocular delivery of hydrophobic drugs are also contemplated.
  • a molecular envelope technology which involves an engineered polymer envelope which is protected and delivered to the site of the disease, can be used. Doses of about 5 mg/kg can be used, with single or multiple doses, depending on various factors, e.g., the target tissue.
  • Lipidoid compounds are also useful in the administration of polynucleotides, and can be used to deliver fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure
  • the aminoalcohol lipidoid compounds are combined with an agent to be delivered to a cell or a subject to form microparticles, nanoparticles, liposomes, or micelles.
  • the aminoalcohol lipidoid compounds may be combined with other aminoalcohol lipidoid compounds, polymers (synthetic or natural), surfactants, cholesterol, carbohydrates, proteins, lipids, etc. to form the particles. These particles may then optionally be combined with a pharmaceutical excipient to form a pharmaceutical composition.
  • a poly(beta-amino alcohol) can be used to deliver a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell.
  • US Patent Publication No. 20130302401 relates to a class of poly(beta-amino alcohols) (PBAAs) that has been prepared using combinatorial polymerization.
  • Sugar-based particles may be used, for example GalNAc, as described with reference to
  • WO2014118272 (incorporated herein by reference) and Nair, J K et al., 2014, Journal of the American Chemical Society 136 (49), 16958-16961) can be used to deliver a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell.
  • lipid nanoparticles are used to deliver a fusion polypeptide of the present disclosure an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell.
  • Negatively charged polymers such as RNA may be loaded into LNPs at low pH values (e.g., pH 4) where the ionizable lipids display a positive charge.
  • pH values e.g., pH 4
  • the LNPs exhibit a low surface charge compatible with longer circulation times.
  • ionizable cationic lipids Four species of ionizable cationic lipids have been focused upon, namely l,2-dilineoyl-3- dimethylammonium-propane (DLinDAP), l,2-dilinoleyloxy-3-N,N-dimethylaminopropane (DLinDMA),
  • DLinKDMA 1.2-dilinoleyloxy-keto-N,N-dimethyl-3-aminopropane
  • DLinKC2-DMA 1 ,2-dilinoleyl-4-(2- dimethylaminoethyl)-[l,3]-dioxolane
  • DLinK-DMA 1.2-dilinoleyloxyketo-N,N-dimethyl-3-aminopropane
  • DLinKC2-DMA 1 ,2-dilinoleyl-4-(2- dimethylaminoethyl)-[l,3]-dioxolane
  • DLinKC2-DMA 3-o-[2"-(methoxypolyethyleneglycol 2000) succinoyl]-l,2-dimyristoyl-sn-glycol
  • R-3-[(.omega.-methoxy-poly(ethylene glycol)2000) carbamoyl]-l,2-dimyristyloxlpropyl-3-amine (PEG-C-DOMG) may be used.
  • a nucleic acid (e.g., a guide RNA; a nucleic acid of the present disclosure; etc.) may be encapsulated in LNPs containing DLinDAP, DLinDMA, DLinK-DMA, and DLinKC2-DMA (cationic lipid:DSPC:CHOL: PEGS-DMG or PEG-C-DOMG at 40:10:40:10 molar ratios). In some cases, 0.2% SP-DiOC18 is incorporated.
  • Spherical Nucleic Acid (SNATM) constructs and other nanoparticles can be used to deliver a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell.
  • SNATM Spherical Nucleic Acid
  • Self-assembling nanoparticles with RNA may be constructed with polyethyleneimine
  • PEI polyethylene glycol
  • nanoparticle refers to any particle having a diameter of less than 1000 nm.
  • nanoparticles suitable for use in delivering a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell have a diameter of 500 nm or less, e.g., from 25 nm to 35 nm, from 35 nm to 50 nm, from 50 nm to 75 nm, from 75 nm to 100 nm, from 100 nm to 150 nm, from 150 nm to 200 nm, from 200 nm to 300 nm, from 300 nm to 400 nm, or from 400 nm to 500 nm.
  • nanoparticles suitable for use in delivering a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell have a diameter of from 25 nm to 200 nm.
  • nanoparticles suitable for use in delivering a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell have a diameter of 100 nm or less
  • nanoparticles suitable for use in delivering a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell have a diameter of from 35 nm to 60 nm.
  • Nanoparticles suitable for use in delivering a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell may be provided in different forms, e.g., as solid nanoparticles (e.g., metal such as silver, gold, iron, titanium), non-metal, lipid-based solids, polymers), suspensions of nanoparticles, or combinations thereof.
  • Metal, dielectric, and semiconductor nanoparticles may be prepared, as well as hybrid structures (e.g., core-shell nanoparticles).
  • Nanoparticles made of semiconducting material may also be labeled quantum dots if they are small enough (typically below 10 nm) that quantization of electronic energy levels occurs. Such nanoscale particles are used in biomedical applications as drug carriers or imaging agents and may be adapted for similar purposes in the present disclosure.
  • Semi-solid and soft nanoparticles are also suitable for use in delivering fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell.
  • a prototype nanoparticle of semi-solid nature is the liposome.
  • an exosome is used to deliver a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell.
  • Exosomes are endogenous nano-vesicles that transport RNAs and proteins, and which can deliver RNA to the brain and other target organs.
  • a liposome is used to deliver a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell.
  • Liposomes are spherical vesicle structures composed of a uni- or multilamellar lipid bilayer surrounding internal aqueous compartments and a relatively impermeable outer lipophilic phospholipid bilayer. Liposomes can be made from several different types of lipids; however, phospholipids are most commonly used to generate liposomes.
  • liposome formation is spontaneous when a lipid film is mixed with an aqueous solution, it can also be expedited by applying force in the form of shaking by using a homogenizer, sonicator, or an extrusion apparatus.
  • Several other additives may be added to liposomes in order to modify their structure and properties. Lor instance, either cholesterol or sphingomyelin may be added to the liposomal mixture in order to help stabilize the liposomal structure and to prevent the leakage of the liposomal inner cargo.
  • a liposome formulation may be mainly comprised of natural phospholipids and lipids such as l,2-distearoryl-sn-glycero-3- phosphatidyl choline (DSPC), sphingomyelin, egg phosphatidylcholines and monosialoganglioside.
  • DSPC l,2-distearoryl-sn-glycero-3- phosphatidyl choline
  • sphingomyelin sphingomyelin
  • egg phosphatidylcholines monosialoganglioside.
  • a stable nucleic-acid-lipid particle SNALP
  • SNALP stable nucleic-acid-lipid particle
  • the SNALP formulation may contain the lipids 3-N- [(methoxypoly(ethylene glycol) 2000) carbamoyl] -1,2-dimyristyloxy-propylamine (PEG-C-DMA), 1,2- dilinoleyloxy-N,N-dimethyl-3-aminopropane (DLinDMA), l,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) and cholesterol, in a 2:40:10:48 molar percent ratio.
  • PEG-C-DMA 1,2- dilinoleyloxy-N,N-dimethyl-3-aminopropane
  • DSPC l,2-distearoyl-sn-glycero-3-phosphocholine
  • cholesterol in a 2:40:10:48 molar percent ratio.
  • the SNALP liposomes may be prepared by formulating D-Lin-DMA and PEG-C-DMA with distearoylphosphatidylcholine (DSPC), Cholesterol and siRNA using a 25:1 lipid/siRNA ratio and a 48/40/10/2 molar ratio of Cholesterol/D-Lin- DMA/DSPC/PEG-C-DMA.
  • DSPC distearoylphosphatidylcholine
  • Cholesterol and siRNA using a 25:1 lipid/siRNA ratio and a 48/40/10/2 molar ratio of Cholesterol/D-Lin- DMA/DSPC/PEG-C-DMA.
  • the resulting SNALP liposomes can be about 80-100 nm in size.
  • a SNALP may comprise synthetic cholesterol (Sigma-Aldrich, St Louis, Mo., USA), dipalmitoylphosphatidylcholine (Avanti Polar Lipids, Alabaster, Ala., USA), 3-N-[(w-methoxy poly(ethylene glycol)2000)carbamoyl]-l,2-dimyrestyloxypropylamine, and cationic l,2-dilinoleyloxy-3- N,Ndimethylaminopropane.
  • a SNALP may comprise synthetic cholesterol (Sigma-Aldrich), 1,2- distearoyl-sn-glycero-3-phosphocholine (DSPC; Avanti Polar Lipids Inc.), PEG-cDMA, and 1,2- dilinoleyloxy-3-(N ;N-dimethyl)aminopropane (DLinDMA).
  • DSPC 1,2- distearoyl-sn-glycero-3-phosphocholine
  • PEG-cDMA 1,2- dilinoleyloxy-3-(N ;N-dimethyl)aminopropane
  • cationic lipids such as amino lipid 2,2-dilinoleyl-4-dimethylaminoethyl-[l,3]- dioxolane (DLin-KC2-DMA) can be used to deliver a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell.
  • DLin-KC2-DMA amino lipid 2,2-dilinoleyl-4-dimethylaminoethyl-[l,3]- dioxolane
  • a preformed vesicle with the following lipid composition may be contemplated: amino lipid, distearoylphosphatidylcholine (DSPC), cholesterol and (R)-2,3- bis(octadecyloxy) propyl- l-(methoxy poly(ethylene glycol)2000)propylcarbamate (PEG-lipid) in the molar ratio 40/10/40/10, respectively, and a FVII siRNA/total lipid ratio of approximately 0.05 (w/w).
  • the particles may be extruded up to three times through 80 nm membranes prior to adding the guide RNA.
  • Particles containing the highly potent amino lipid 16 may be used, in which the molar ratio of the four lipid components 16, DSPC, cholesterol and PEG-lipid (50/10/38.5/1.5) which may be further optimized to enhance in vivo activity.
  • Lipids may be formulated with a system of the present disclosure or component(s) thereof or nucleic acids encoding the same to form lipid nanoparticles (LNPs).
  • Suitable lipids include, but are not limited to, DLin-KC2-DMA4, C12-200 and colipids disteroylphosphatidyl choline, cholesterol, and PEG-DMG may be formulated with a system, or component thereof, of the present disclosure, using a spontaneous vesicle formation procedure.
  • the component molar ratio may be about 50/10/38.5/1.5 (DLin-KC2-DMA or C12-200/disteroylphosphatidyl choline/cholesterol/PEG-DMG).
  • a system of the present disclosure, or a component thereof may be delivered encapsulated in PLGA microspheres such as that further described in US published applications 20130252281 and 20130245107 and 20130244279.
  • Supercharged proteins can be used to deliver a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell.
  • Supercharged proteins are a class of engineered or naturally occurring proteins with unusually high positive or negative net theoretical charge. Both supernegatively and superpositively charged proteins exhibit the ability to withstand thermally or chemically induced aggregation. Superpositively charged proteins are also able to penetrate mammalian cells. Associating cargo with these proteins, such as plasmid DNA, RNA, or other proteins, can enable the functional delivery of these macromolecules into mammalian cells both in vitro and in vivo.
  • CPPs Cell Penetrating Peptides
  • CPPs can be used to deliver a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell.
  • CPPs typically have an amino acid composition that either contains a high relative abundance of positively charged amino acids such as lysine or arginine or has sequences that contain an alternating pattern of polar/charged amino acids and non-polar, hydrophobic amino acids.
  • An implantable device can be used to deliver a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure (e.g., a guide RNA, a nucleic acid encoding a guide RNA, a nucleic acid encoding a fusion polypeptide of the present disclosure, a donor template, and the like), or a system of the present disclosure, to a target cell (e.g., a target cell in vivo, where the target cell is a target cell in circulation, a target cell in a tissue, a target cell in an organ, etc.).
  • a target cell e.g., a target cell in vivo, where the target cell is a target cell in circulation, a target cell in a tissue, a target cell in an organ, etc.
  • An implantable device suitable for use in delivering a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell can include a container (e.g., a reservoir, a matrix, etc.) that comprises the fusion polypeptide of the present disclosure, the RNP, or the system (or component thereof, e.g., a nucleic acid of the present disclosure).
  • a suitable implantable device can comprise a polymeric substrate, such as a matrix for example, that is used as the device body, and in some cases additional scaffolding materials, such as metals or additional polymers, and materials to enhance visibility and imaging.
  • An implantable delivery device can be advantageous in providing release locally and over a prolonged period, where the polypeptide and/or nucleic acid to be delivered is released directly to a target site, e.g., the extracellular matrix (ECM), the vasculature surrounding a tumor, a diseased tissue, etc.
  • ECM extracellular matrix
  • Suitable implantable delivery devices include devices suitable for use in delivering to a cavity such as the abdominal cavity and/or any other type of administration in which the drug delivery system is not anchored or attached, comprising a biostable and/or degradable and/or bioabsorbable polymeric substrate, which may for example optionally be a matrix.
  • a suitable implantable drug delivery device comprises degradable polymers, wherein the main release mechanism is bulk erosion.
  • a suitable implantable drug delivery device comprises non degradable, or slowly degraded polymers, wherein the main release mechanism is diffusion rather than bulk erosion, so that the outer part functions as membrane, and its internal part functions as a drug reservoir, which practically is not affected by the surroundings for an extended period (for example from about a week to about a few months).
  • the main release mechanism is diffusion rather than bulk erosion, so that the outer part functions as membrane, and its internal part functions as a drug reservoir, which practically is not affected by the surroundings for an extended period (for example from about a week to about a few months).
  • Combinations of different polymers with different release mechanisms may also optionally be used.
  • the concentration gradient at the can be maintained effectively constant during a significant period of the total releasing period, and therefore the diffusion rate is effectively constant (termed "zero mode" diffusion).
  • constant it is meant a diffusion rate that is maintained above the lower threshold of therapeutic effectiveness, but which may still optionally feature an initial burst and/or may fluctuate, for example increasing and decreasing to a certain degree.
  • the diffusion rate can be so maintained for a prolonged period, and it can be considered constant to a certain level to optimize the therapeutically effective period, for example the effective silencing period.
  • the implantable delivery system is designed to shield the nucleotide based therapeutic agent from degradation, whether chemical in nature or due to attack from enzymes and other factors in the body of the subject.
  • the site for implantation of the device, or target site can be selected for maximum therapeutic efficacy.
  • a delivery device can be implanted within or in the proximity of a tumor environment, or the blood supply associated with a tumor.
  • the target location can be, e.g.: 1) the brain at degenerative sites like in Parkinson or Alzheimer disease at the basal ganglia, white and gray matter; 2) the spine, as in the case of amyotrophic lateral sclerosis (ALS); 3) uterine cervix; 4) active and chronic inflammatory joints; 5) dermis as in the case of psoriasis; 7) sympathetic and sensoric nervous sites for analgesic effect; 7) a bone; 8) a site of acute or chronic infection; 9) Intra vaginal; 10) Inner ear- -auditory system, labyrinth of the inner ear, vestibular system; 11) Intra tracheal; 12) Intra-cardiac; coronary, epicardiac; 13)
  • the method of insertion may optionally already be used for other types of tissue implantation and/or for insertions and/or for sampling tissues, optionally without modifications, or alternatively optionally only with non-major modifications in such methods.
  • Such methods optionally include but are not limited to brachytherapy methods, biopsy, endoscopy with and/or without ultrasound, such as stereotactic methods into the brain tissue, laparoscopy, including implantation with a laparoscope into joints, abdominal organs, the bladder wall and body cavities.
  • the present disclosure provides a cell (a “modified cell”) comprising a fusion polypeptide of the present disclosure.
  • the present disclosure provides a cell (a “modified cell”) comprising a nucleic acid of the present disclosure (e.g., a nucleic acid comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure).
  • the present disclosure provides a modified cell comprising a fusion polypeptide of the present disclosure and/or a nucleic acid comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure.
  • the present disclosure provides a modified cell comprising a fusion polypeptide of the present disclosure, where the modified cell is a cell that does not normally comprise a fusion polypeptide of the present disclosure.
  • the present disclosure provides a modified cell (e.g., a genetically modified cell) comprising nucleic acid comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure.
  • the present disclosure provides a genetically modified cell that is genetically modified with an mRNA comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure.
  • the present disclosure provides a genetically modified cell that is genetically modified with a recombinant expression vector comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure.
  • the present disclosure provides a genetically modified cell that is genetically modified with a recombinant expression vector comprising: a) a nucleotide sequence encoding a fusion polypeptide of the present disclosure; and b) a nucleotide sequence encoding a guide RNA of the present disclosure.
  • the present disclosure provides a genetically modified cell that is genetically modified with a recombinant expression vector comprising: a) a nucleotide sequence encoding a fusion polypeptide of the present disclosure; b) a nucleotide sequence encoding a guide RNA of the present disclosure; and c) a nucleotide sequence encoding a donor template.
  • a cell that serves as a recipient for a fusion polypeptide of the present disclosure and/or a nucleic acid comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure and/or a guide RNA and/or a donor template can be any of a variety of eukaryotic cells, including, e.g., in vitro cells; in vivo cells; ex vivo cells; primary cells; cancer cells; animal cells; plant cells; algal cells; fungal cells; etc.
  • a cell that serves as a recipient for a fusion polypeptide of the present disclosure and/or a nucleic acid comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure and/or a guide RNA is referred to as a “host cell” or a “target cell.”
  • a host cell or a target cell can be a recipient of a system of the present disclosure, or a component of a system of the present disclosure.
  • a host cell or a target cell can be a recipient of an RNP of the present disclosure.
  • a host cell or a target cell can be a recipient of a single component of a system of the present disclosure.
  • Non-limiting examples of cells include: a prokaryotic cell, eukaryotic cell, a bacterial cell, an archaeal cell, a cell of a single-cell eukaryotic organism, a protozoa cell, a cell from a plant (e.g., cells from plant crops, fruits, vegetables, grains, soy bean, corn, maize, wheat, seeds, tomatoes, rice, cassava, sugarcane, pumpkin, hay, potatoes, cotton, cannabis, tobacco, flowering plants, conifers, gymnosperms, angiosperms, ferns, clubmosses, hornworts, liverworts, mosses, dicotyledons, monocotyledons, etc.), an algal cell, (e.g., Botryococcus braunii, Chlamydomonas reinhardtii, Nannochloropsis gaditana, Chlorella pyrenoidosa, Sargassum patens, C.
  • a prokaryotic cell
  • seaweeds e.g. kelp
  • a fungal cell e.g., a yeast cell, a cell from a mushroom
  • an animal cell e.g., a cell from an invertebrate animal (e.g., fruit fly, cnidarian, echinoderm, nematode, etc.)
  • a cell from a vertebrate animal e.g., fish, amphibian, reptile, bird, mammal
  • a cell from a mammal e.g., an ungulate (e.g., a pig, a cow, a goat, a sheep); a rodent (e.g., a rat, a mouse); a non-human primate; a human; a feline (e.g., a cat); a canine (e.g., a dog); etc.), and the like.
  • the cell is a cell that does not originate from a natural organism (e.g., the cell can be a synthetically made cell; also referred to as an artificial cell).
  • a cell can be an in vitro cell (e.g., established cultured cell line).
  • a cell can be an ex vivo cell (cultured cell from an individual).
  • a cell can be and in vivo cell (e.g., a cell in an individual).
  • a cell can be an isolated cell.
  • a cell can be a cell inside of an organism.
  • a cell can be an organism.
  • a cell can be a cell in a cell culture (e.g., in vitro cell culture).
  • a cell can be one of a collection of cells.
  • a cell can be a eukaryotic cell or derived from a eukaryotic cell.
  • a cell can be a plant cell or derived from a plant cell.
  • a cell can be an animal cell or derived from an animal cell.
  • a cell can be an invertebrate cell or derived from an invertebrate cell.
  • a cell can be a vertebrate cell or derived from a vertebrate cell.
  • a cell can be a mammalian cell or derived from a mammalian cell.
  • a cell can be a rodent cell or derived from a rodent cell.
  • a cell can be a human cell or derived from a human cell.
  • a cell can be a fungi cell or derived from a fungi cell.
  • a cell can be an insect cell.
  • a cell can be an arthropod cell.
  • a cell can be a protozoan cell.
  • a cell can be a helminth cell.
  • Suitable cells include a stem cell (e.g. an embryonic stem (ES) cell, an induced pluripotent stem (iPS) cell; a germ cell (e.g., an oocyte, a sperm, an oogonia, a spermatogonia, etc.); a somatic cell, e.g. a fibroblast, an oligodendrocyte, a glial cell, a hematopoietic cell, a neuron, a muscle cell, a bone cell, a hepatocyte, a pancreatic cell, etc.
  • ES embryonic stem
  • iPS induced pluripotent stem
  • germ cell e.g., an oocyte, a sperm, an oogonia, a spermatogonia, etc.
  • a somatic cell e.g. a fibroblast, an oligodendrocyte, a glial cell, a hematopoietic cell,
  • Suitable cells include human embryonic stem cells, fetal cardiomyocytes, myofibroblasts, mesenchymal stem cells, cardiomyocytes, adipocytes, totipotent cells, pluripotent cells, blood stem cells, myoblasts, adult stem cells, bone marrow cells, mesenchymal cells, embryonic stem cells, parenchymal cells, epithelial cells, endothelial cells, mesothelial cells, fibroblasts, osteoblasts, chondrocytes, exogenous cells, endogenous cells, stem cells, hematopoietic stem cells, bone-marrow derived progenitor cells, myocardial cells, skeletal cells, fetal cells, undifferentiated cells, multi-potent progenitor cells, unipotent progenitor cells, monocytes, cardiac myoblasts, skeletal myoblasts, macrophages, capillary endothelial cells, xenogeneic cells, allogenic cells, and post-
  • the cell is an immune cell, a neuron, an epithelial cell, and endothelial cell, or a stem cell.
  • the immune cell is a T cell, a B cell, a monocyte, a natural killer cell, a dendritic cell, or a macrophage.
  • the immune cell is a cytotoxic T cell.
  • the immune cell is a helper T cell.
  • the immune cell is a regulatory T cell (Treg).
  • the cell is a stem cell.
  • Stem cells include adult stem cells.
  • Adult stem cells are also referred to as somatic stem cells.
  • Adult stem cells are resident in differentiated tissue, but retain the properties of selfrenewal and ability to give rise to multiple cell types, usually cell types typical of the tissue in which the stem cells are found.
  • somatic stem cells include muscle stem cells; hematopoietic stem cells; epithelial stem cells; neural stem cells; mesenchymal stem cells; mammary stem cells; intestinal stem cells; mesodermal stem cells; endothelial stem cells; olfactory stem cells; neural crest stem cells; and the like.
  • Stem cells of interest include mammalian stem cells, where the term “mammalian” refers to any animal classified as a mammal, including humans; non-human primates; domestic and farm animals; and zoo, laboratory, sports, or pet animals, such as dogs, horses, cats, cows, mice, rats, rabbits, etc.
  • the stem cell is a human stem cell.
  • the stem cell is a rodent (e.g., a mouse; a rat) stem cell.
  • the stem cell is a non-human primate stem cell.
  • Stem cells can express one or more stem cell markers, e.g., SOX9, KRT19, KRT7,
  • LGR5 LGR5, CA9, FXYD2, CDH6, CLDN18, TSPAN8, BPIFB1, OLFM4, CDH17, and PPARGC1A.
  • the stem cell is a hematopoietic stem cell (HSC).
  • HSCs are mesoderm-derived cells that can be isolated from bone marrow, blood, cord blood, fetal liver and yolk sac. HSCs are characterized as CD34 + and CD3 . HSCs can repopulate the erythroid, neutrophil- macrophage, megakaryocyte and lymphoid hematopoietic cell lineages in vivo. In vitro, HSCs can be induced to undergo at least some self-renewing cell divisions and can be induced to differentiate to the same lineages as is seen in vivo. As such, HSCs can be induced to differentiate into one or more of erythroid cells, megakaryocytes, neutrophils, macrophages, and lymphoid cells.
  • the stem cell is a neural stem cell (NSC).
  • NSC neural stem cell
  • NSCs are capable of differentiating into neurons, and glia (including oligodendrocytes, and astrocytes).
  • a neural stem cell is a multipotent stem cell which is capable of multiple divisions, and under specific conditions can produce daughter cells which are neural stem cells, or neural progenitor cells that can be neuroblasts or glioblasts, e.g., cells committed to become one or more types of neurons and glial cells respectively.
  • Methods of obtaining NSCs are known in the art.
  • the stem cell is a mesenchymal stem cell (MSC).
  • MSCs originally derived from the embryonal mesoderm and isolated from adult bone marrow, can differentiate to form muscle, bone, cartilage, fat, marrow stroma, and tendon. Methods of isolating MSC are known in the art; and any known method can be used to obtain MSC. See, e.g., U.S. Pat. No. 5,736,396, which describes isolation of human MSC.
  • a cell is in some cases a plant cell.
  • a plant cell can be a cell of a monocotyledon.
  • a cell can be a cell of a dicotyledon.
  • the cell is a plant cell.
  • the cell can be a cell of a major agricultural plant, e.g., Barley, Beans (Dry Edible), Canola, Corn, Cotton (Pima), Cotton (Upland), Flaxseed, Hay (Alfalfa), Hay (Non- Alfalfa), Oats, Peanuts, Rice, Sorghum, Soybeans, Sugarbeets, Sugarcane, Sunflowers (Oil), Sunflowers (Non-Oil), Sweet Potatoes , Tobacco (Burley), Tobacco (Flue- cured), Tomatoes, Wheat (Durum), Wheat (Spring), Wheat (Winter), and the like.
  • a major agricultural plant e.g., Barley, Beans (Dry Edible), Canola, Corn, Cotton (Pima), Cotton (Upland), Flaxseed, Hay (Alfalfa), Hay (Non- Alfalfa), Oats, Peanuts, Rice, S
  • the cell is a cell of a vegetable crops which include but are not limited to, e.g., alfalfa sprouts, aloe leaves, arrow root, arrowhead, artichokes, asparagus, bamboo shoots, banana flowers, bean sprouts, beans, beet tops, beets, bittermelon, bok choy, broccoli, broccoli rabe (rappini), brussels sprouts, cabbage, cabbage sprouts, cactus leaf (nopales), calabaza, cardoon, carrots, cauliflower, celery, chayote, Chinese artichoke (crosnes), Chinese cabbage, Chinese celery, Chinese chives, choy sum, chrysanthemum leaves (tung ho), collard greens, corn stalks, corn-sweet, cucumbers, daikon, dandelion greens, dasheen, dau mue (pea tips), donqua (winter melon), eggplant, endive, escarole, fiddle head ferns,
  • the plant cell is a cell of a plant component such as a leaf, a stem, a root, a seed, a flower, pollen, an anther, an ovule, a pedicel, a fruit, a meristem, a cotyledon, a hypocotyl, a pod, an embryo, endosperm, an explant, a callus, or a shoot.
  • a plant component such as a leaf, a stem, a root, a seed, a flower, pollen, an anther, an ovule, a pedicel, a fruit, a meristem, a cotyledon, a hypocotyl, a pod, an embryo, endosperm, an explant, a callus, or a shoot.
  • a cell is in some cases an arthropod cell.
  • the cell can be a cell of a suborder, a family, a sub-family, a group, a sub-group, or a species of, e.g., Chelicerata, Myriapodia, Hexipodia, Arachnida, Insecta, Archaeognatha, Thysanura, Palaeoptera, Ephemeroptera, Odonata, Anisoptera, Zygoptera, Neoptera, Exopterygota, Plecoptera , Embioptera , Orthoptera, Zoraptera , Dermaptera, Dictyoptera, Notoptera, Grylloblattidae, Mantophasmatidae, Phasmatodea , Blattaria, Isoptera, Mantodea, Parapneuroptera, Psocoptera, Thysanoptera, Phthiraptera, Hemi
  • a cell is in some cases an insect cell.
  • the cell is a cell of a mosquito, a grasshopper, a true bug, a fly, a flea, a bee, a wasp, an ant, a louse, a moth, or a beetle.
  • the present disclosure provides a composition comprising a fusion polypeptide of the present disclosure.
  • the composition may comprise a pharmaceutically acceptable excipient, a variety of which are known in the art and need not be discussed in detail herein.
  • Pharmaceutically acceptable excipients have been amply described in a variety of publications, including, for example, “Remington: The Science and Practice of Pharmacy”, 19 th Ed. (1995), or latest edition, Mack Publishing Co; A. Gennaro (2000) “Remington: The Science and Practice of Pharmacy", 20th edition, Lippincott, Williams, & Wilkins; Pharmaceutical Dosage Forms and Drug Delivery Systems (1999) H.C.
  • a composition of the present disclosure can include: a) one or more of: i) a fusion polypeptide of the present disclosure; ii) a guide nucleic acid (e.g., a guide RNA); and iii) a donor template; and b) one or more of: a buffer, a surfactant, an antioxidant, a hydrophilic polymer, a dextrin, a chelating agent, a suspending agent, a solubilizer, a thickening agent, a stabilizer, a bacteriostatic agent, a wetting agent, and a preservative.
  • a buffer a surfactant, an antioxidant, a hydrophilic polymer, a dextrin, a chelating agent, a suspending agent, a solubilizer, a thickening agent, a stabilizer, a bacteriostatic agent, a wetting agent, and a preservative.
  • Suitable buffers include, but are not limited to, (such as N,N-bis(2-hydroxyethyl)-2- aminoethanesulfonic acid (BES), bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane (BIS-Tris), N- (2-hydroxyethyl)piperazine-N'3-propanesulfonic acid (EPPS or HEPPS), glycylglycine, N-2- hydroxyehtylpiperazine-N'-2-ethanesulfonic acid (HEPES), 3-(N-morpholino)propane sulfonic acid (MOPS), piperazine-N,N'-bis(2-ethane-sulfonic acid) (PIPES), sodium bicarbonate, 3-(N- tris(hydroxymethyl)-methyl-amino)-2-hydroxy-propanesulfonic acid) TAPSO, (N- tris(hydroxymethyl)methyl-2-aminoethanesulfonic
  • a composition of the present disclosure can include: a) a system of the present disclosure; and b) one or more of: a buffer, a surfactant, an antioxidant, a hydrophilic polymer, a dextrin, a chelating agent, a suspending agent, a solubilizer, a thickening agent, a stabilizer, a bacteriostatic agent, a wetting agent, and a preservative.
  • Suitable buffers include, but are not limited to, (such as N,N-bis(2- hydroxyethyl)-2-aminoethanesulfonic acid (BES), bis(2-hydroxyethyl)amino- tris(hydroxymethyl)methane (BIS-Tris), N-(2-hydroxyethyl)piperazine-N'3-propanesulfonic acid (EPPS or HEPPS), glycylglycine, N-2-hydroxyehtylpiperazine-N'-2-ethanesulfonic acid (HEPES), 3-(N- morpholino)propane sulfonic acid (MOPS), piperazine-N,N'-bis(2-ethane-sulfonic acid) (PIPES), sodium bicarbonate, 3-(N-tris(hydroxymethyl)-methyl-amino)-2-hydroxy-propanesulfonic acid) TAPSO, (N- tris(hydroxymethyl)methyl-2-aminoethanes
  • the composition is sterile. In some cases, the composition is suitable for administration to a human subject, e.g., where the composition is sterile and is free of detectable pyrogens and/or other toxins.
  • a composition of the present disclosure may include other components, such as pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium, carbonate, and the like.
  • the compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions such as pH adjusting and buffering agents, toxicity adjusting agents and the like, for example, sodium acetate, sodium chloride, potassium chloride, calcium chloride, sodium lactate, hydrochloride, sulfate salts, solvates (e.g., mixed ionic salts, water, organics), hydrates (e.g., water), and the like.
  • a composition of the present disclosure comprises saline.
  • the present disclosure provides a system comprising a fusion polypeptide of the present disclosure.
  • the present disclosure provides a system comprising one of: a) a fusion polypeptide of the present disclosure; and a CRISPR/Cas guide nucleic acid; b) a fusion polypeptide of the present disclosure; a CRISPR/Cas guide nucleic acid, and a DNA donor template; c) a fusion polypeptide of the present disclosure; and a CRISPR/Cas guide RNA; d) a fusion polypeptide of the present disclosure; a CRISPR/Cas guide RNA, and a DNA donor template; e) an mRNA encoding a fusion polypeptide of the present disclosure; and a CRISPR/Cas guide nucleic acid; f) an mRNA encoding a fusion polypeptide of the present disclosure; a CRISPR/Cas guide nucleic acid, and a DNA donor template; g) an mRNA encoding a fusion polypeptide of the present disclosure; and a DNA donor template
  • a guide nucleic acid suitable for inclusion in a system of the present disclosure can include: i) a first segment (referred to herein as a “targeting segment”); and ii) a second segment (referred to herein as a “protein-binding segment”).
  • a segment it is meant a segment/section/region of a molecule, e.g., a contiguous stretch of nucleotides in a nucleic acid molecule.
  • a segment can also mean a region/section of a complex such that a segment may comprise regions of more than one molecule.
  • the “targeting segment” is also referred to herein as a “variable region” of a guide RNA.
  • the “protein-binding segment” is also referred to herein as a “constant region” of a guide RNA.
  • the first segment (targeting segment) of a guide RNA includes a nucleotide sequence (a guide sequence) that is complementary to (and therefore hybridizes with) a specific sequence (a target site) within a target nucleic acid (e.g., a target ssRNA, a target ssDNA, the complementary strand of a double stranded target DNA, etc.).
  • the protein-binding segment (or “protein-binding sequence”) interacts with (binds to) a CRISPR/Cas effector polypeptide.
  • the protein-binding segment of a guide RNA includes two complementary stretches of nucleotides that hybridize to one another to form a double stranded RNA duplex (dsRNA duplex).
  • Site-specific binding and/or cleavage of a target nucleic acid can occur at locations (e.g., target sequence of a target locus) determined by base-pairing complementarity between the guide RNA (the guide sequence of the guide RNA) and the target nucleic acid.
  • a guide RNA and a CRISPR/Cas effector polypeptide form a complex (e.g., bind via non- covalent interactions).
  • the guide RNA provides target specificity to the complex by including a targeting segment, which includes a guide sequence (a nucleotide sequence that is complementary to a sequence of a target nucleic acid).
  • the CRISPR/Cas effector polypeptide of the complex provides the site-specific activity (e.g., cleavage activity or an activity provided by the CRISPR/Cas effector polypeptide when the CRISPR/Cas effector polypeptide is a CRISPR/Cas effector polypeptide fusion polypeptide, i.e., has a fusion partner).
  • the CRISPR/Cas effector polypeptide is guided to a target nucleic acid sequence (e.g. a target sequence in a chromosomal nucleic acid, e.g., a chromosome; a target sequence in an extrachromosomal nucleic acid, e.g. an episomal nucleic acid, a minicircle, an ssRNA, an ssDNA, etc.; a target sequence in a mitochondrial nucleic acid; a target sequence in a chloroplast nucleic acid; a target sequence in a plasmid; a target sequence in a viral nucleic acid; etc.) by virtue of its association with the guide RNA.
  • a target nucleic acid sequence e.g. a target sequence in a chromosomal nucleic acid, e.g., a chromosome
  • a target sequence in an extrachromosomal nucleic acid e.g. an episomal nucleic acid,
  • the guide RNA (e.g., a single-molecule guide RNA) has a length of from about 15 nucleotides to about 50 nucleotides; e.g., in some cases, the guide RNA (e.g., a single -molecule guide RNA) has a length of from about 15 nucleotides to about 20 nucleotides, from about 20 nucleotides to about 25 nucleotides, from about 25 nucleotides to about 30 nucleotides, or from about 30 nucleotides to about 50 nucleotides.
  • the guide RNA (e.g., a single-molecule guide RNA) has a length of from about 14 nucleotides to about 16 nucleotides.
  • the “guide sequence” also referred to as the “targeting sequence” of a guide RNA can be modified so that the guide RNA can target a CRISPR/Cas effector polypeptide to any desired sequence of any desired target nucleic acid, with the exception that the protospacer adjacent motif (PAM) sequence can be taken into account.
  • PAM protospacer adjacent motif
  • a guide RNA can have a targeting segment with a sequence (a guide sequence) that has complementarity with (e.g., can hybridize to) a sequence in a nucleic acid in a eukaryotic cell, e.g., a viral nucleic acid, a eukaryotic nucleic acid (e.g., a eukaryotic chromosome, chromosomal sequence, a eukaryotic RNA, etc.), and the like.
  • a eukaryotic cell e.g., a viral nucleic acid, a eukaryotic nucleic acid (e.g., a eukaryotic chromosome, chromosomal sequence, a eukaryotic RNA, etc.), and the like.
  • a guide RNA includes two separate nucleic acid molecules: an “activator” and a “targeter” and is referred to herein as a “dual guide RNA”, a “double-molecule guide RNA”, or a “two- molecule guide RNA” a “dual guide RNA”, or a “dgRNA.”
  • the activator and targeter are covalently linked to one another (e.g., via intervening nucleotides) and the guide RNA is referred to as a “single guide RNA”, a “Cas single guide RNA”, a “single-molecule Cas guide RNA,” or a “one -molecule Cas guide RNA”, or simply “sgRNA.”
  • Examples of various CRISPR/Cas effector polypeptides and guide RNAs can be found in the art, for example, see Jinek et al., Science. 2012 Aug 17;337(6096):816-21; Chylinski et al., RNA Biol. 2013 May;10(5):726-37; Ma et al., Biomed Res Int. 2013;2013:270805; Hou et al., Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15644-9; Jinek et al., Elife.
  • Jinek et al. Science. 2012 Aug 17;337(6096):816-21
  • Chylinski et al. RNA Biol. 2013 May;10(5):726-37
  • Ma et al. Biomed Res Int. 2013;2013:270805
  • Hou et al. Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):156
  • a guide nucleic acid comprises ribonucleotides only, deoxyribonucleotides only, or a mixture of ribonucleotides and deoxyribonucleotides.
  • a guide nucleic acid comprises ribonucleotides only, and is referred to herein as a “guide RNA.”
  • a guide nucleic acid comprises deoxyribonucleotides only, and is referred to herein as a “guide DNA.”
  • a guide nucleic acid comprises both ribonucleotides and deoxyribonucleotides.
  • a guide nucleic acid can comprise combinations of ribonucleotide bases, deoxyribonucleotide bases, nucleotide analogs, modified nucleotides, and the like; and may further include naturally-occurring backbone residues and/or linkages and/or non-naturally-occurring backbone residues and/or linkages.
  • Donor DNA template can comprise combinations of ribonucleotide bases, deoxyribonucleotide bases, nucleotide analogs, modified nucleotides, and the like; and may further include naturally-occurring backbone residues and/or linkages and/or non-naturally-occurring backbone residues and/or linkages.
  • a system of the present disclosure comprises a donor nucleic acid.
  • donor nucleic acid or “donor sequence” or “donor polynucleotide” or “donor template” it is meant a nucleic acid sequence to be inserted at the site cleaved by a CRISPR/Cas effector protein present in a fusion polypeptide of the present disclosure (e.g., after dsDNA cleavage, after nicking a target DNA, after dual nicking a target DNA, and the like).
  • the donor polynucleotide can contain sufficient homology to a genomic sequence at the target site, e.g. 70%, 80%, 85%, 90%, 95%, or 100% homology with the nucleotide sequences flanking the target site, e.g.
  • Donor polynucleotides can be of any length, e.g.
  • Donor polynucleotides can be from 25 nucleotides to 50 nucleotides, from 50 nucleotides to 100 nucleotides, from 100 nucleotides to 500 nucleotides, from 500 nucleotides to 1000 nucleotides, from 1000 nucleotides to 5000 nucleotides, or from 5000 nucleotides to 10,000 nucleotides, or more than 10,000 nucleotides, in length.
  • the donor sequence is typically not identical to the genomic sequence that it replaces. Rather, the donor sequence may contain at least one or more single base changes, insertions, deletions, inversions or rearrangements with respect to the genomic sequence, so long as sufficient homology is present to support homology-directed repair (e.g., for gene correction, e.g., to convert a disease-causing base pair or a non disease-causing base pair).
  • the donor sequence comprises a non-homologous sequence flanked by two regions of homology, such that homology-directed repair between the target DNA region and the two flanking sequences results in insertion of the non- homologous sequence at the target region.
  • Donor sequences may also comprise a vector backbone containing sequences that are not homologous to the DNA region of interest and that are not intended for insertion into the DNA region of interest.
  • the homologous region(s) of a donor sequence will have at least 50% sequence identity to a genomic sequence with which recombination is desired. In certain embodiments, 60%, 70%, 80%, 90%, 95%, 98%, 99%, or 99.9% sequence identity is present.
  • the donor sequence may comprise certain sequence differences as compared to the genomic sequence, e.g. restriction sites, nucleotide polymorphisms, selectable markers (e.g., drug resistance genes, fluorescent proteins, enzymes etc.), etc., which may be used to assess for successful insertion of the donor sequence at the cleavage site or in some cases may be used for other purposes (e.g., to signify expression at the targeted genomic locus).
  • selectable markers e.g., drug resistance genes, fluorescent proteins, enzymes etc.
  • sequence differences may include flanking recombination sequences such as FLPs, loxP sequences, or the like, that can be activated at a later time for removal of the marker sequence.
  • the donor sequence is provided to the cell as single-stranded DNA. In some cases, the donor sequence is provided to the cell as double-stranded DNA. It may be introduced into a cell in linear or circular form. If introduced in linear form, the ends of the donor sequence may be protected (e.g., from exonucleolytic degradation) by any convenient method and such methods are known to those of skill in the art. For example, one or more dideoxynucleotide residues can be added to the 3' terminus of a linear molecule and/or self-complementary oligonucleotides can be ligated to one or both ends. See, for example, Chang et al. (1987) Proc. Natl.
  • Additional methods for protecting exogenous polynucleotides from degradation include, but are not limited to, addition of terminal amino group(s) and the use of modified internucleotide linkages such as, for example, phosphorothioates, phosphor amidates, and O-methyl ribose or deoxyribose residues.
  • additional lengths of sequence may be included outside of the regions of homology that can be degraded without impacting recombination.
  • a donor sequence can be introduced into a cell as part of a vector molecule having additional sequences such as, for example, replication origins, promoters and genes encoding antibiotic resistance.
  • a fusion polypeptide of the present disclosure finds use in a variety of methods, which are provided herein.
  • the present disclosure provides a method of modifying a target nucleic acid, the method comprising contacting the target nucleic acid with: a) a fusion polypeptide of the present disclosure; and b) a guide nucleic acid that comprises: i) a guide sequence that hybridizes to a target sequence of the target nucleic acid; and ii) an activator sequence that binds to the CRISPR/Cas effector polypeptide.
  • a method of the present disclosure comprises contacting a target nucleic acid with: a) a fusion polypeptide of the present disclosure; b) a guide nucleic acid that comprises: i) a guide sequence that hybridizes to a target sequence of the target nucleic acid; and ii) an activator sequence that binds to the CRISPR/Cas effector polypeptide; and c) a donor DNA template.
  • the contacting step results in modification of the target nucleic acid by the CRISPR/Cas effector polypeptide.
  • the modification comprises cleaving the target nucleic acid.
  • the modification comprises replacing all or part of a target nucleic acid with a donor nucleic acid.
  • a method of the present disclosure can provide for increased homology-directed repair
  • a method of the present disclosure for modifying a target nucleic acid comprises contacting the target nucleic acid with: a) a fusion polypeptide of the present disclosure; and b) a guide nucleic acid, wherein said contacting results in modification of the target nucleic acid by the CRISPR/Cas effector polypeptide.
  • a method of the present disclosure for modifying a target nucleic acid comprises contacting the target nucleic acid with: a) a fusion polypeptide of the present disclosure; b) a guide nucleic acid; and c) a donor template DNA, wherein said contacting results in modification of the target nucleic acid by the CRISPR/Cas effector polypeptide.
  • the target nucleic acid is present in chromatin.
  • the contacting step takes place in vitro outside of a cell. In some cases, the contacting step takes place inside of a cell in in vitro culture. In some cases, the contacting step takes place inside of a eukaryotic cell in vivo.
  • the present disclosure provides a method of modifying a target nucleic acid present in chromatin in a eukaryotic cell, the method comprising: a) contacting the chromatin with a first fusion polypeptide comprising: i) an enzymatically inactive CRISPR/Cas effector polypeptide; and ii) a chromatin marker polypeptide that modifies a histone polypeptide present in chromatin, wherein the modification marks the chromatin as a site for recombination; and b) contacting the marked chromatin with: i) a complex comprising an enzymatically active CRISPR/Cas effector polypeptide and a guide nucleic acid; and ii) a donor template DNA.
  • the present disclosure provides a method of modifying chromatin in a eukaryotic cell, the method comprising contacting the chromatin with a fusion polypeptide of the present disclosure.
  • the cell is in vitro.
  • the cell is in vivo (e.g., in a multicellular organism).
  • a target nucleic acid is present in chromatin.
  • a target nucleic acid is typically double stranded DNA (e.g., a chromosome (genomic DNA), derived from a chromosome, chromosomal DNA, extracellular, intracellular, mitochondrial, chloroplast, linear, circular, etc.) and can be from any organism (e.g., as long as the guide RNA comprises a nucleotide sequence that hybridizes to a target sequence in a target nucleic acid, such that the target nucleic acid can be targeted).
  • a chromosome genomic DNA
  • derived from a chromosome derived from a chromosome, chromosomal DNA, extracellular, intracellular, mitochondrial, chloroplast, linear, circular, etc.
  • a target nucleic acid can be located anywhere, for example, outside of a cell in vitro, inside of a cell in vitro, inside of a cell in vivo, inside of a cell ex vivo.
  • Suitable target cells include, but are not limited to: a bacterial cell; an archaeal cell; a cell of a single-cell eukaryotic organism; a plant cell; an algal cell, e.g., Botryococcus braunii, Chlamydomonas reinhardtii, Nannochloropsis gaditana, Chlorella pyrenoidosa, Sargassum patens, C.
  • a fungal cell e.g., a yeast cell
  • an animal cell e.g. fruit fly, a cnidarian, an echinoderm, a nematode, etc.
  • a cell of an insect e.g., a mosquito; a bee; an agricultural pest; etc.
  • a cell of an arachnid e.g., a spider; a tick; etc.
  • a cell from a vertebrate animal e.g., a fish, an amphibian, a reptile, a bird, a mammal
  • a cell from a mammal e.g., a cell from a rodent; a cell from a human; a cell of a non-human mammal; a cell of a rodent (e.g., a mouse, a rat); a cell of a lagomorph (e.g.,
  • a stem cell e.g. an embryonic stem (ES) cell, an induced pluripotent stem (iPS) cell, a germ cell (e.g., an oocyte, a sperm, an oogonia, a spermatogonia, etc.), an adult stem cell, a somatic cell, e.g. a fibroblast, a hematopoietic cell, a neuron, a muscle cell, a bone cell, a hepatocyte, a pancreatic cell; an in vitro or in vivo embryonic cell of an embryo at any stage, e.g., a 1-cell, 2-cell, 4-cell, 8-cell, etc.
  • ES embryonic stem
  • iPS induced pluripotent stem
  • a germ cell e.g., an oocyte, a sperm, an oogonia, a spermatogonia, etc.
  • a somatic cell e.g. a fibroblast,
  • Cells may be from established cell lines or they may be primary cells, where “primary cells”, “primary cell lines”, and “primary cultures” are used interchangeably herein to refer to cells and cells cultures that have been derived from a subject and allowed to grow in vitro for a limited number of passages of the culture.
  • primary cultures are cultures that may have been passaged 0 times, 1 time, 2 times, 4 times, 5 times, 10 times, or 15 times, but not enough times go through the crisis stage.
  • the primary cell lines are maintained for fewer than 10 passages in vitro.
  • Target cells can be unicellular organisms and/or can be grown in culture. If the cells are primary cells, they may be harvest from an individual by any convenient method.
  • leukocytes may be conveniently harvested by apheresis, leukocytapheresis, density gradient separation, etc., while cells from tissues such as skin, muscle, bone marrow, spleen, liver, pancreas, lung, intestine, stomach, etc. can be conveniently harvested by biopsy.
  • the subject methods may be employed to induce target nucleic acid cleavage, target nucleic acid modification, and/or to bind target nucleic acids (e.g., for visualization, for collecting and/or analyzing, etc.) in mitotic or post-mitotic cells in vivo and/or ex vivo and/or in vitro (e.g., to disrupt production of a protein encoded by a targeted mRNA, to cleave or otherwise modify target DNA, to genetically modify a target cell, and the like).
  • a mitotic and/or post-mitotic cell of interest in the disclosed methods may include a cell from any organism (e.g.
  • a cell of a single-cell eukaryotic organism a plant cell, an algal cell, e.g., Botryococcus braunii, Chlamydomonas reinhardtii, Nannochloropsis gaditana, Chlorella pyrenoidosa, Sargassum patens, C. agardh, and the like, a fungal cell (e.g., a yeast cell), an animal cell, a cell from an invertebrate animal (e.g.
  • fruit fly cnidarian, echinoderm, nematode, etc.
  • a cell from a vertebrate animal e.g., fish, amphibian, reptile, bird, mammal
  • a cell from a mammal e.g., a cell from a rodent, a cell from a human, etc.
  • a fusion polypeptide of the present disclosure (and/or nucleic acid encoding the protein such as DNA and/or RNA), and/or guide RNA (and/or a DNA encoding the guide RNA), and/or donor template, and/or RNP can be introduced into an individual (i.e., the target cell can be in vivo ) (e.g., a mammal, a rat, a mouse, a pig, a primate, a non-human primate, a human, etc.).
  • an administration can be for the purpose of treating and/or preventing a disease, e.g., by editing the genome of targeted cells.
  • the present disclosure provides a method of modifying chromatin in a gamete, the method comprising contacting the chromatin in the gamete with: a) a fusion polypeptide of the present disclosure; and b) a guide nucleic acid comprising a nucleotide sequence that hybridizes to a target nucleic acid in the chromatin, thereby generating a gamete comprising chromatin comprising a modification.
  • the modification generates a recombination hotspot.
  • the modification generates a meiotic recombination hotspot.
  • a “recombination hotspot” is a region in a genome that exhibits elevated rates of recombination relative to a neutral expectation, e.g., relative to a surrounding region in the genome.
  • the rate of recombination at a recombination hotspot is from 10-fold to 25-fold, from 25-fold to 50-fold, from 50-fold to 100-fold, from 100-fold to 250-fold, from 250-fold to 500-fold, from 500-fold to 10 3 -fold, from 10 3 -fold to 5 x 10 3 -fold, or more than 5 x 10 3 - fold, higher than the rate of recombination in an adjacent region in the genome.
  • the gamete is a sperm. In some cases, the gamete is an oocyte. Gametes can be from a mammal (e.g., a human, a non-human primate, a rodent, an ungulate (e.g., a camel, a horse, a cow, a goat, a sheep, etc.), a non-mammalian vertebrate, an amphibian, a reptile, an arachnid, an insect, a plant, etc.
  • a mammal e.g., a human, a non-human primate, a rodent, an ungulate (e.g., a camel, a horse, a cow, a goat, a sheep, etc.), a non-mammalian vertebrate, an amphibian, a reptile, an arachnid, an insect, a plant, etc.
  • the chromatin in the gamete is contacted with a fusion polypeptide of the present disclosure and a guide nucleic acid (e.g., a guide RNA), where the CRISPR/Cas effector polypeptide present in the fusion polypeptide is a nickase.
  • the chromatin in the gamete is contacted with a fusion polypeptide of the present disclosure, where the CRISPR/Cas effector polypeptide present in the fusion polypeptide is enzymatically inactive.
  • a donor template is not used in the method; in other words, in some cases, a composition comprising a fusion polypeptide of the present disclosure and a guide nucleic acid (e.g., a guide RNA) is introduced into a gamete, where the composition does not include a donor template.
  • a guide nucleic acid e.g., a guide RNA
  • a composition comprising: a) a fusion polypeptide of the present disclosure (e.g., where the CRISPR/Cas effector polypeptide present in the fusion polypeptide is a nickase or is enzymatically inactive); and b) a guide nucleic acid (e.g., a guide RNA) is introduced into a gamete using any of a variety of known methods.
  • a fusion polypeptide of the present disclosure e.g., where the CRISPR/Cas effector polypeptide present in the fusion polypeptide is a nickase or is enzymatically inactive
  • a guide nucleic acid e.g., a guide RNA
  • composition comprising: a) a fusion polypeptide of the present disclosure (e.g., where the CRISPR/Cas effector polypeptide present in the fusion polypeptide is a nickase or is enzymatically inactive); and b) a guide nucleic acid (e.g., a guide RNA) is injected into a gamete.
  • a fusion polypeptide of the present disclosure e.g., where the CRISPR/Cas effector polypeptide present in the fusion polypeptide is a nickase or is enzymatically inactive
  • a guide nucleic acid e.g., a guide RNA
  • a nucleic acid e.g., a recombinant expression vector
  • a nucleic acid comprising nucleotide sequences encoding: a) a fusion polypeptide of the present disclosure (e.g., where the CRISPR/Cas effector polypeptide present in the fusion polypeptide is a nickase or is enzymatically inactive); and b) a guide nucleic acid (e.g., a guide RNA), is introduced into a gamete.
  • a recombinant expression vector comprising nucleotide sequences encoding: a) a fusion polypeptide of the present disclosure (e.g., where the CRISPR/Cas effector polypeptide present in the fusion polypeptide is a nickase or is enzymatically inactive); and b) a guide nucleic acid (e.g., a guide RNA), is introduced into a gamete, where expression of the nucleotide sequences encoding the fusion polypeptide and the guide RNA is Cre-mediated.
  • a guide nucleic acid e.g., a guide RNA
  • a recombinant expression vector comprising nucleotide sequences encoding: a) a fusion polypeptide of the present disclosure (e.g., where the CRISPR/Cas effector polypeptide present in the fusion polypeptide is a nickase or is enzymatically inactive); and b) a guide nucleic acid (e.g., a guide RNA), is introduced into a gamete, where expression of the nucleotide sequences encoding the fusion polypeptide and the guide RNA is Cre-mediated.
  • the gamete is in a Spoll-eGFP-Cre transgenic mouse.
  • Spoll-eGFP-Cre transgenic mice have the mouse Spoil (SPOl 1 meiotic protein covalently bound to DSB) gene promoter driving Cre recombinase expression in spermatocytes that have initiated meiosis.
  • the method is useful for creating non-human animal models, e.g., non-human animal models of diseases.
  • the dominant negative allele in an organism that has a dominant negative allele (e.g. mutation in p53, for example R172H substitution mutation in mice) and a wild type counterpart of the dominant negative allele, the dominant negative allele can be marked for recombination during meiosis, such that gene conversion is enhanced at that site, such that the dominant negative allele is replaced with a copy of the wild-type allele.
  • a dominant negative allele e.g. mutation in p53, for example R172H substitution mutation in mice
  • the dominant negative allele can be marked for recombination during meiosis, such that gene conversion is enhanced at that site, such that the dominant negative allele is replaced with a copy of the wild-type allele.
  • a fusion polypeptide comprising: a) a CRISPR/Cas effector polypeptide; and b) a chromatin marker polypeptide that provides for modification of a histone polypeptide present in chromatin, wherein the modification marks the chromatin as a site for recombination.
  • Aspect 2 The fusion polypeptide of aspect 1, wherein the chromatin marker polypeptide is a histone methyltransferase (HMT).
  • HMT histone methyltransferase
  • Aspect 3 The fusion polypeptide of aspect 2, wherein the HMT methylates Lys4 or
  • Aspect 4 The fusion polypeptide of aspect 3, wherein the HMT is a PRDM9 polypeptide, a SETD2 polypeptide, or a SETMAR polypeptide.
  • Aspect 5 The fusion polypeptide of aspect 1, wherein the chromatin marker polypeptide is a histone acetyltransferase.
  • Aspect 6 The fusion polypeptide of aspect 5, wherein the histone acetyltransferase acetylates Lysl6 of histone H4.
  • Aspect 7 The fusion polypeptide of aspect 6, wherein the histone acetyltransferase is a
  • Aspect 8 The fusion polypeptide of aspect 4, wherein the PRDM9 polypeptide comprises a KRAB domain, an SSXRD domain, and a PR/SET domain, and does not include a zinc finger DNA-binding domain.
  • Aspect 9 The fusion polypeptide of aspect 8, wherein the PRDM9 polypeptide has a length of from about 350 amino acids to about 390 amino acids, and wherein the PRDM9 polypeptide comprises an amino acid sequence having at least 85% amino acid sequence identity to amino acids 1- 370 of the amino acid sequence of the PRDM9 polypeptide depicted in FIG. 2A or at least 85% amino acid sequence identity to amino acids 1-371 of the amino acid sequence of the PRDM9 polypeptide depicted in FIG. 2B.
  • Aspect 10 The fusion polypeptide of aspect 1, wherein the fusion polypeptide comprises an amino acid sequence having at least 85% amino acid sequence identity to the amino acid sequence depicted in FIG. 3 A or FIG. 3B.
  • Aspect 11 The fusion polypeptide of aspect 1 , wherein the chromatin marker polypeptide binds H3K4me3 and/or H3K36me3.
  • Aspect 12 The fusion polypeptide of aspect 11, wherein the chromatin marker polypeptide is a ZMYND8 polypeptide of a ZCWPWI polypeptide.
  • Aspect 13 The fusion polypeptide of aspect 1, wherein the chromatin marker polypeptide is a PRDM9-binding polypeptide.
  • Aspect 14 The fusion polypeptide of aspect 13, wherein the PRDM9-binding polypeptide is EWSR1 or PREC8.
  • Aspect 15 The fusion polypeptide of any one of aspects 1-14, wherein the CRISPR/Cas effector polypeptide is a type II CRISPR/Cas effector polypeptide, a type V CRISPR/Cas effector polypeptide, or a type VI CRISPR/Cas effector polypeptide.
  • Aspect 16 The fusion polypeptide of any one of aspects 1-14, wherein the CRISPR/Cas effector polypeptide is a type II CRISPR/Cas effector polypeptide.
  • Aspect 17 The fusion polypeptide of aspect 16, wherein the type II CRISPR/Cas effector polypeptide is a Cas9 polypeptide.
  • Aspect 18 The fusion polypeptide of any one of aspects 1-14, wherein the CRISPR/Cas effector polypeptide is a type V CRISPR/Cas effector polypeptide.
  • Aspect 19 The fusion polypeptide of aspect 18, wherein the type V CRISPR/Cas effector polypeptide is a Casl2a, a Casl2b, a Casl2c, a Casl2d, or a Casl2e polypeptide.
  • Aspect 20 The fusion polypeptide of any one of aspects 1-14, wherein the CRISPR/Cas effector polypeptide is a type VI CRISPR/Cas effector polypeptide.
  • Aspect 21 The fusion polypeptide of aspect 20, wherein the type VI CRISPR/Cas effector polypeptide is a Casl3a, a Casl3b, a Casl3c, or a Casl3d polypeptide.
  • Aspect 22 The fusion polypeptide of any one of aspects 1-14, wherein the CRISPR/Cas effector polypeptide is a Casl4a, a Casl4b, or a Casl4c polypeptide.
  • Aspect 23 The fusion polypeptide of any one of aspects 1-22, wherein the CRISPR/Cas effector polypeptide is enzymatically active.
  • Aspect 24 The fusion polypeptide of any one of aspects 1-22, wherein the CRISPR/Cas effector polypeptide exhibits reduced enzymatic activity.
  • Aspect 25 The fusion polypeptide of any one of aspects 1-22, wherein the CRISPR/Cas effector polypeptide exhibits nickase activity.
  • Aspect 26 The fusion polypeptide of aspect 25, wherein the CRISPR/Cas effector polypeptide comprises a D10A substitution or an H840A substitution, based on the amino acid numbering of Streptococcus pyogenes Cas9, or a corresponding amino acid in another Cas9 polypeptide.
  • Aspect 27 The fusion polypeptide of any one of aspects 1-22, wherein the CRISPR/Cas effector polypeptide is enzymatically inactive.
  • Aspect 28 The fusion polypeptide of aspect 27, wherein the CRISPR/Cas effector polypeptide comprises a D10A substitution and an H840A substitution, based on the amino acid numbering of Streptococcus pyogenes Cas9, or the corresponding amino acids in another Cas9 polypeptide.
  • Aspect 29 The fusion polypeptide of any one of aspects 1-28, wherein the fusion polypeptide comprises, in order from N-terminus to C-terminus: a) the CRISPR/Cas effector polypeptide; and b) the chromatin modifying polypeptide.
  • Aspect 30 The fusion polypeptide of any one of aspects 1-28, wherein the fusion polypeptide comprises, in order from N-terminus to C-terminus: a) the chromatin modifying polypeptide; and b) the CRISPR/Cas effector polypeptide.
  • Aspect 31 The fusion polypeptide of any one of aspects 1-28, wherein the fusion polypeptide comprises, in order from N-terminus to C-terminus: a) an N-terminal portion of the CRISPR/Cas effector polypeptide; b) the chromatin modifying polypeptide; and c) a C-terminal portion of the CRISPR/Cas effector polypeptide.
  • Aspect 32 The fusion polypeptide of any one of aspects 1-28, wherein the fusion polypeptide comprises, in order from N-terminus to C-terminus: a) a C-terminal portion of the CRISPR/Cas effector polypeptide; b) the chromatin modifying polypeptide; and c) an N-terminal portion of the CRISPR/Cas effector polypeptide.
  • Aspect 33 The fusion polypeptide of any one of aspects 1-32, further comprising one or more nuclear localization signals.
  • Aspect 34 A nucleic acid comprising a nucleotide sequence encoding the fusion polypeptide of any one of aspects 1-33.
  • Aspect 35 The nucleic acid of aspect 34, wherein the nucleotide sequence is operably linked to a promoter that is functional in a eukaryotic cell.
  • Aspect 36 The nucleic acid of aspect 35, wherein the promoter is functional in one or more of: a plant cell, a fungal cell, an animal cell, cell of an invertebrate, a fly cell, a cell of a vertebrate, a mammalian cell, a primate cell, a non-human primate cell, and a human cell.
  • Aspect 37 The nucleic acid of aspect 35 or 36, wherein the promoter is a constitutive promoter, an inducible promoter, a cell type-specific promoter, or a tissue-specific promoter.
  • Aspect 38 A recombinant expression vector comprising the nucleic acid of any one of aspects 34-37.
  • Aspect 39 The recombinant expression vector of aspect 38, wherein the recombinant expression vector is a recombinant adenoassociated viral vector, a recombinant retroviral vector, or a recombinant lentiviral vector.
  • Aspect 40 A eukaryotic cell comprising the fusion polypeptide of any one of aspects 1-
  • Aspect 41 The eukaryotic cell of aspect 40, further comprising a CRISPR/Cas guide nucleic acid, or a nucleic acid comprising a nucleotide sequence encoding a CRISPR/Cas guide nucleic acid.
  • Aspect 42 The eukaryotic cell of aspect 40 or aspect 41, further comprising a donor
  • Aspect 43 The eukaryotic cell of any one of aspects 40-42, wherein the eukaryotic cell is a plant cell, a mammalian cell, an insect cell, an arachnid cell, a yeast cell, a fungal cell, a bird cell, a reptile cell, an amphibian cell, an invertebrate cell, a mouse cell, a rat cell, a primate cell, a non-human primate cell, or a human cell.
  • the eukaryotic cell is a plant cell, a mammalian cell, an insect cell, an arachnid cell, a yeast cell, a fungal cell, a bird cell, a reptile cell, an amphibian cell, an invertebrate cell, a mouse cell, a rat cell, a primate cell, a non-human primate cell, or a human cell.
  • a composition comprising: a) the fusion polypeptide of any one of aspects 1-
  • a composition comprising: a) the fusion polypeptide of any one of aspects 1-
  • a CRISPR/Cas guide nucleic acid or one or more DNA molecules comprising a nucleotide sequence(s) encoding the CRISPR/Cas guide nucleic acid.
  • Aspect 46 The composition of aspect 45, wherein the CRISPR/Cas guide nucleic acid is an RNA, a DNA, or an RNA/DNA hybrid.
  • Aspect 47 The composition of aspect 44 or aspect 45, wherein the composition comprises a lipid.
  • Aspect 48 The composition of aspect 44 or aspect 45, wherein a) and b) are within a liposome.
  • Aspect 49 The composition of any one of aspects 44-47, wherein a) and b) are within a particle.
  • Aspect 50 The composition of any one of aspects 44-49, comprising one or more of: a buffer, a nuclease inhibitor, and a protease inhibitor.
  • Aspect 51 The composition of any one of aspects 44-50, further comprising a DNA donor template.
  • a system comprising one of: a) a fusion polypeptide of any one of aspects 1-33; and a CRISPR/Cas guide nucleic acid; b) a fusion polypeptide of any one of aspects 1-33; a CRISPR/Cas guide nucleic acid, and a DNA donor template; c) a fusion polypeptide of any one of aspects 1-33; and a CRISPR/Cas guide RNA; d) a fusion polypeptide of any one of aspects 1-33; a CRISPR/Cas guide RNA, and a DNA donor template; e) an mRNA encoding a fusion polypeptide of any one of aspects 1-33; and a CRISPR/Cas guide nucleic acid; f) an mRNA encoding a fusion polypeptide of any one of aspects 1-33; a CRISPR/Cas guide nucleic acid, and a DNA donor template; g) an mRNA encoding a fusion poly
  • Aspect 53 The system of aspect 52, wherein the donor template nucleic acid has a length of from 8 nucleotides to 10,000 nucleotides.
  • Aspect 54 The system of aspect 52, wherein the donor template nucleic acid has a length of from 25 nucleotides to 5,000 nucleotides.
  • Aspect 55 A kit comprising the system of any one of aspects 52-54.
  • Aspect 56 The kit of aspect 55, wherein the components of the kit are in the same container.
  • Aspect 57 The kit of aspect 55, wherein the components of the kit are in separate containers.
  • Aspect 58 A sterile container comprising the system of any one of aspects 52-54.
  • Aspect 59 The sterile container of aspect 58, wherein the sterile container is a syringe.
  • Aspect 60 An implantable device comprising the system of any one of aspects 52-54.
  • Aspect 61 The device of aspect 60, wherein the system is within a matrix.
  • Aspect 62 The device of aspect 60, wherein the system is in a reservoir.
  • Aspect 63 The device of any one of aspects 60-62, wherein the device comprises a catheter.
  • Aspect 64 The device of any one of aspects 60-63, wherein the device provides for controlled release of the system.
  • a method of modifying a target nucleic acid comprising contacting the target nucleic acid with: a) the fusion polypeptide of any one of aspects 1-33; and b) a guide nucleic acid that comprises: i) a guide sequence that hybridizes to a target sequence of the target nucleic acid; and ii) an activator sequence that binds to the CRISPR/Cas effector polypeptide, wherein said contacting results in modification of the target nucleic acid by the CRISPR/Cas effector polypeptide.
  • Aspect 66 The method of aspect 65, wherein said modification comprises cleavage of the target nucleic acid.
  • Aspect 67 The method of aspect 65 or aspect 66, wherein said modification comprises homology-directed repair of the target nucleic acid.
  • Aspect 68 The method of any one of aspects 65-67, wherein the target nucleic acid is present in chromatin.
  • Aspect 69 The method of any one of aspects 65-68, wherein said contacting takes place in vitro outside of a cell.
  • Aspect 70 The method of any one of aspects 65-68, wherein said contacting takes place inside of a cell in in vitro culture.
  • Aspect 71 The method of any one of aspects 65-68, wherein said contacting takes place inside of a eukaryotic cell in vivo.
  • Aspect 72 The method of aspect 70 or aspect 71, wherein the cell is selected from: a plant cell, a fungal cell, a mammalian cell, a reptile cell, an insect cell, an avian cell, a fish cell, a parasite cell, an arthropod cell, a cell of an invertebrate, a cell of a vertebrate, a rodent cell, a mouse cell, a rat cell, a primate cell, a non-human primate cell, and a human cell.
  • the cell is selected from: a plant cell, a fungal cell, a mammalian cell, a reptile cell, an insect cell, an avian cell, a fish cell, a parasite cell, an arthropod cell, a cell of an invertebrate, a cell of a vertebrate, a rodent cell, a mouse cell, a rat cell, a primate cell, a non-human primate cell, and a human cell.
  • Aspect 73 The method of aspect any one of aspects 65-72, wherein said contacting comprises: introducing into a cell: (a) the fusion polypeptide, or a nucleic acid comprising a nucleotide sequence encoding the fusion polypeptide, and (b) the guide nucleic acid, or a nucleic acid comprising a nucleotide sequence encoding the guide nucleic acid.
  • Aspect 74 The method of any one of aspects 65-73, wherein said contacting further comprises: introducing a DNA donor template into the cell.
  • a method of modifying a target nucleic acid present in chromatin in a eukaryotic cell comprising: a) contacting the chromatin with a first fusion polypeptide comprising: i) an enzymatically inactive CRISPR/Cas effector polypeptide; and ii) a chromatin marker polypeptide that modifies a histone polypeptide present in chromatin, wherein the modification marks the chromatin as a site for recombination; and b) contacting the marked chromatin with: i) a complex comprising an enzymatically active CRISPR/Cas effector polypeptide and a guide nucleic acid; and ii) a donor template DNA.
  • Aspect 76 A method of modifying chromatin in a eukaryotic cell, the method comprising contacting the chromatin with the fusion polypeptide of any one of aspects 1-33.
  • a method of modifying chromatin in a gamete comprising contacting the chromatin in the gamete with: a) the fusion polypeptide of any one of aspects 1-33; and b) a guide nucleic acid comprising a nucleotide sequence that hybridizes to a target nucleic acid in the chromatin, thereby a gamete comprising chromatin comprising a modification.
  • Aspect 78 The method of aspect 77, wherein the gamete is a sperm.
  • Aspect 79 The method of aspect 77, wherein the game is an oocyte.
  • Aspect 80 The method of any one of aspects 77-79, wherein the modification generates a recombination hotspot.
  • Standard abbreviations may be used, e.g., bp, base pair(s); kb, kilobase(s); pi, picoliter(s); s or sec, second(s); min, minute(s); h or hr, hour(s); aa, amino acid(s); kb, kilobase(s); bp, base pair(s); nt, nucleotide(s); i.m., intramuscular(ly); i.p., intraperitoneal(ly); s.c., subcutaneous(ly); and the like.
  • Target sites were selected based on narrow-peak calls for H3K4me3 and H3K36me3 in
  • HEK293 cells Call sets were obtained from the ENCODE portal with the following identifier: ENCSR372WXC. https:(//)www(dot)encodeproject(dot)org/reference-epigenomes/ENCSR372WXC/. Plasmid construction
  • the Cas9 expression plasmid pCAGGS was used. Cas9 was amplified from the expression plasmid using CloneAmp HiFi polymerase chain reaction (PCR) Premix (Takara Bio) for 35 cycles (98°C for 10 s, 55°C for 15 s, and 72°C for 10 s; then 72°C for 1 min). PRDM9 and PRDM9dC was amplified from human cDNA purchased from GenScript (ORF Clone ID OFiu03253).
  • SETD2 was amplified from SETD2-GFP (Addgene plasmid # 80653; http://n2t.net/addgene:80653), and SETMAR was amplified from SETMAR (3B05) (Addgene plasmid # 25250; http://n2t.net/addgene:25250).
  • SETMAR was amplified from SETMAR (3B05) (Addgene plasmid # 25250; http://n2t.net/addgene:25250).
  • Takara Bio was used to clone PRDM9-Cas9, PRDM9dC-Cas9, SETD2-Cas9, and SETMAR-Cas9 into the pCAGGS expression vector. All Cas9 variants were confirmed by Sanger sequencing.
  • DMEM fetal bovine serum
  • P/S Penicillin/Streptomycin
  • All cells were cultured at 37°C in a 5% C02 air incubator. Lipofection was performed using Lipofectamine 3000 (Thermo Fisher Scientific) according to the manufacturer’s instructions. 50,000 cells per well were seeded in 24-weII plates 24 hours prior to lipofection. Cells were transfected with 500 ng Cas nuclease expression plasmid, 150 ng sgRNA expression plasmid, and 1.5 pmol single-stranded oligodeoxynucleotide (ssODN) template (IDT) per well.
  • ssODN oligodeoxynucleotide
  • BFP-GFP blue fluorescent protein-green fluorescent protein reporter cell line
  • the cell line expresses blue fluorescent protein (BFP) constitutively.
  • the cells can be edited using CRISPR-Cas9 and an asymmetric single stranded DNA template donor, as described in (Richardson et al., 2016, supra). If the double stranded break (DSB) is repaired via homology directed repair (HDR), the cells start expressing Enhanced Green Fluorescent Protein (EGFP) and no longer express BFP.
  • HDR homology directed repair
  • EGFP Enhanced Green Fluorescent Protein
  • the cells lose all fluorescence, if the DSBs caused by CRISPR-Cas9 introduce insertions and deletions (indels), typical when repair happens through non homologous end joining (NHEJ).
  • 20,000 HEK293T BFP to EGFP cells were seeded in 24-weII plates. The next day, cells were transfected with 1.5m1 of Lipofectamine 3000, Im ⁇ of p300 enhancer, 500ng of nuclease (Cas9 or Cas9-PRDM9 ⁇ C), 150ng of sgRNA and 1.5 pmol of DNA template ordered from IDT.
  • the sequence of the ssDNA template was: [00270] GCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGC CCGTGCCCTGGCCCACCCTCGTGACCACCCTGACGTACGGCGTGCAGTGCTTCAGCCGCTAC
  • the protospacer targeted with the sgRNA was: GCTGAAGCACTGCACGCCAT (SEQ ID NO: 1]
  • Imaging was performed using the Odyssey imaging system (LI-COR). Double bands were caused by incomplete cleavage at the self-cleaving P2A peptide, leading to an uncleaved byproduct (Kim et al., (2011) PLOS ONE, 6(4), el8556. https://doi.org/10.1371/journal.pone.0018556 Chromatin immunoprecipitation
  • Chromatin immunoprecipitation was performed. Briefly, cells were cross! inked for 5 min in 1% formaldehyde, and the reaction was quenched by the addition of glycine to 125 mM and incubation for 5 min. Cells were washed twice with lysis buffer 1 and 2, respectively. Then, cells were resuspended in lysis buffer 3 and sheared by sonication (30s on/30s off) using a Covaris S2 (UC Berkeley Functional Genomics Laboratory).
  • IP Protein G Magnetic Beads
  • 200,000 HEK293T BFP to GFP cells were seeded in 10cm plates. The next day, cells were transfected with 15m1 Lipofectamine 3000, 10m1 of p300 enhancer, 5ug of nuclease (dCas9 or dCas9-PRDM9 ⁇ C), 1.5pg of sgRNA and 15 pmol of DNA template ordered from Integrated DNA Technologies (IDT).
  • the target site was: chr20:32761950 -32761969.
  • the protospacer targeted with sgRNA was: GGCACTGCGGCTGGAGGTGG (SEQ ID NO:
  • the ssDNA template was:
  • the cells were cross-linked with a final concentration of 1 % formaldehyde by shaking at
  • Immunoprecipitations were performed using 500 mg of sheared chromatin lysate and 2 pg of antibodies preconjugated to protein G beads (Invitrogen): H3K4me3 (ab8580, Abeam), H3K36me3 (61101, Active Motif) and rabbit anti-mouse IgG control (ab46540, Abeam).
  • ChIP reactions were incubated for 16 hours at 4°C with rotation and then washed four times in wash buffer [50 mM Hepes-HCl (pH 8), 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, and 0.5% A-laurylsarcosine] , followed by one wash in ChIP final wash buffer (lx tris- EDTA (TE) Buffer and 50 mM NaCl).
  • Immunoprecipitated DNA was eluted from washed beads and reverse cross-linked overnight. DNA was then purified by phenohchloroform extraction and ethanol precipitation and resuspended in lx TE buffer.
  • qPCR was carried out with Power SYBR (Applied Biosystems) using primers for the target site on chromosome 20 or an upstream control.
  • Upstream control [00284] fwd: AGTAGAAACGGGGTGTCTCCA (SEQ ID NO: 106) rev: TTGGGAGGCTGAGGTGGG (SEQ ID NO: 107).
  • qPCR-F CGCCTGTGATGGGCTAATTG (SEQ ID NO: 108)
  • qPCR-F CCACATTGGCTCCACCCATC (SEQ ID NO: 110)
  • FIG. 1A provides a schematic model of how a
  • PRDM9AC/Cas9 fusion protein decorates adjacent nucleosomes with H3K4me3 (yellow) and H3K36me3 (orange) during donor template-mediated HDR, to improve HDR rates.
  • FIG. IB HEK293T BFP-EGFP reporter cell line expresses EGFP upon HDR and loses fluorescence if DNA repair proceeds through NHEJ.
  • Flow cytometry of 20,000 cells precondition shows Cas9-PRDM9AC (with guide RNA + donor DNA template) provides for increased HDR and decreased NHEJ, compared to Cas9 (not fused to PRDM9AC) and control.
  • FIG. 1C The first cell line.
  • FIG. ID. ChIP-qPCR experiments show dCas9-PRDM9AC selectively decorates target sites with H3K4me3 and H3K36me3. Endogenous chromatin architecture mediates DNA repair pathway choice
  • endogenous chromatin architecture affects Cas9 activity and DNA repair pathway choice
  • endogenous loci with varying chromatin modifications were identified based on publicly available ENCODE-ChIP-seq data from human embryonic kidney 293 cells (HEK293T).
  • H3K4me3 and H3K36me3 enrichment were selected (FIG. 14A), including disease-relevant sites (HBB and LDLR) as CRISPR-Cas9 precise editing at these sites can be a powerful strategy to introduce desired sequence alterations for clinical applications.
  • HDR frequencies at the selected sites were examined by transfecting HEK293T cells with Cas9 and single guide RNA (sgRNA) expression plasmids along with an ssODN donor template encoding a point mutation upstream of the PAM.
  • sgRNA single guide RNA
  • the HDRdndel ratios were significantly higher at sites highly enriched with both H3K4me3 and H3K36me3 marks compared to unenriched sites (FIG. 14B).
  • the HDRdndel ratio (0.77 ⁇ 0.04) at site 5, which is heavily decorated with histone marks, is 4-fold higher compared to sites without H3K4me3 and H3K36me3 enrichment.
  • Engineered CRISPR-Cas9 epigenetic fusions deposit histone modifications in a site-specific manner
  • Epigenetic fusion nucleases were engineered, and it was tested whether newly deposited histone modifications could increase HDR frequency and HDRdndel ratio (FIG. 14C).
  • Four fusion constructs were constructed by fusing histone methyltransferases at the N-terminus of Cas9 in the pCAGGS expression vector (FIG. 14C).
  • the PRDM9-Cas9 fusion comprises the KRAB domain which recruits additional proteins to facilitate recombination, the PR/SET domain which catalyzes methyltransf erase activity, and a post-SET single zinc finger (ZnF) (Thibault-Sennett et al., (2016) Genetics, 209(2), 475-487. https://doi.org/10.1534/genetics.118.300565). Additionally, the N-terminal domains of PRDM9 may be important for mediating interactions with HEEES and forming a pioneer complex to open chromatin.
  • PRDM9dC-Cas9 is a truncated version lacking the post- SET ZnF involved in negative autoregulation of methyltransferase activity and is thus predicted to show higher methylation activity.
  • SETD2-Cas9 includes a SET domain which deposits H3K36me3 marks. Additionally, a SETMAR-Cas9 fusion was generated, which consists of a SET domain which deposits H3K36me2 marks shown to be important for NHEJ repair.
  • the PRDM9 fusions also effectively deposited H3K4me3 marks at site 9 (100-fold enrichment by PRDM9-Cas9 and 30-fold enrichment by PRDM9dC-Cas9), although they only increased H3K36me3 by up to 4.6-fold.
  • SETD2-dCas9 increased H3K36me3 by 42-fold at site 7 and 15-fold at site 9 (FIG. 14D).
  • SETMAR-dCas9 only achieved a 1.7-fold increase in H3K36me2 at site 7 and a 1.3-fold increase at site 9 compared to dCas9 (FIG. 14D).
  • PRDM9-Cas9 fusions display higher HDR and HDRdndel ratios
  • HEK293T cells stably expressing a BFP reporter was evaluated (Richardson et al., (2016) supra).
  • Cells were transfected with a sgRNA targeting the BFP gene and an ssODN template encoding a three- nucleotide change.
  • Cells express GFP if the Cas9-induced DSB is repaired via HDR; on the other hand, cells lose BFP expression if the cut is repaired via NHEJ (FIG. 15A).
  • BFP-/GFP+ (HDR) and BFP- /GFP- (NHEJ) cells were gated relative to cells transfected with a non-targeting control sgRNA (FIG. 15B).
  • PRDM9-Cas9 displayed a 2- fold higher HDRdndel ratio (0.28 ⁇ 0.02) compared to Cas9 (0.14 ⁇ 0.01). Together, these data provide evidence that the Cas9 epigenetic fusions improve HDR while decreasing indel formation. PRDM9-Cas9 fusions display increased HDRdndel ratios across multiple endogenous sites and different cell types
  • HEK293T cells were transfected with the previously described sgRNAs and ssODN templates (FIG. 14A) and measured the extent of genome modification by next-generation sequencing.
  • PRDM9-Cas9, PRDM9dC-Cas9, and SETD2-Cas9 all achieved higher HDR efficiency than unmodified Cas9 at both sites (FIG. 16A-16B).
  • PRDM9-Cas9 displayed HDR frequencies of 10.99 ⁇ 0.18% and 9.17 ⁇ 0.57% at sites 7 and 9, compared to 5.82 ⁇ 0.50% and 5.56 ⁇ 0.23% with Cas9 at the respective sites.
  • PRDM9-Cas9 and SETD2-Cas9 improved HDRdndel ratios by 3-fold or more compared to unmodified Cas9.
  • PRDM9-Cas9 offered the highest HDR frequency at both sites, we sought to test this fusion at additional endogenous sites.
  • the results showed that the HDR frequencies of PRDM9-Cas9 were up to 2-fold higher than Cas9 at sites 6-9, which lacked endogenous histone modifications (FIG. 16C).
  • the fusion did not display enhanced HDR efficiencies at 2 additional highly characterized sites 10 (HEK2) and 11 (exon in SERPINA). Endogenous H3K4me3 or H3K36me3 enrichment was not detected at these two sites based on the analysis of ENCODE data, which suggests that other factors beyond chromatin architecture are also important in DNA repair pathway choice.
  • PRDM9-Cas9 also showed higher HDRdndel ratios compared to Cas9 at sites 6-9, but only achieved modest improvements in HDRdndel ratios at sites 10 and 11. Given that the fusions can modify adjacent chromatin, it was then examined whether this can lead to higher off-target editing by evaluating their editing activity at 6 potential off-target sites predicted from 2 sgRNAs. The results showed that PRDM9- Cas9 does not lead to higher off-target effects compared to Cas9 (FIG. 16D). Together, these data highlight the ability of PRDM9-Cas9 to significantly improve Cas9-mediated HDR efficiency and HDRdndel ratio via de novo modifications of chromatin architecture in response to a targeted DSB.
  • PAM influences the pattern of indels following Cas9-mediated DSBs (Shen et al., (2016) Nature, 567(7733), 646-651. https://doi.org/10.1038/s41586-018-0686-x; Taheri-Ghahfarokhi et al., (2016) Nucleic Acids Research, 46(16), 8417-8434. https://doi.org/10.1093/nar/gky653; Tatiossian et al., (2021) Molecular Therapy: The Journal of the American Society of Gene Therapy, 29(3), 1057-1069. https://doi.org/10.1016/j-ymthe.2020.10.006).
  • a guanine at position 4 shows the lowest frequency of single nucleotide indels and promotes the formation of primarily deletions (Taheri-Ghahfarokhi et al., (2016) supra). It was investigated whether position 4 nucleotide identity predicts indel patterns using either Cas9 or PRDM9-Cas9 without a donor template at sites 6-11. The frequencies of NHEJ were quantified as deletions of less than 3bp and insertions, and MMEJ as deletions of more than 3bp (Tatiossian et al., (2021) supra). The results did not show a significant correlation between the nucleotide identity at position 4 and the relative frequency of NHEJ and MMEJ. Importantly, Cas9 and PRDM9- Cas9 showed the same indel patterns at each target site.
  • PRDM9-Cas9 can improve HDR efficiency in other cell types.
  • HBB high-binding protein
  • LDLR low-density lipoprotein
  • a consistent increase in HDR frequency by PRDM9-Cas9 was not observed in these cell types, which may be due to differences in histone modifications and DNA repair processes that are cell type-specific (FIG. 17C- 17D). Nonetheless, PRDM9-Cas9 enhanced HDRtindel ratios by up to 2-fold across all three target sites in both cell types.
  • PRDM9-Cas9 improves the relative frequency of HDR to indel at multiple endogenous sites across different mammalian cell lines.
  • FIG. 14A-14D Endogenous histone modifications mediate DNA repair pathway choice.
  • FIG. 14A Endogenous trimethylation of H3K4 and H3K36 at target sites based on reanalyzed ENCODE ChIP-seq data in HEK293T cells.
  • FIG. 14C Schematic of a novel strategy to decorate chromatin to increase HDR efficiency using 4 distinct epigenetic writer fusions.
  • FIG. 15A-15E Engineered CRISPR-Cas9 epigenetic fusions display higher HDR and
  • FIG. 15 A Schematic of BFP-to-GFP reporter assay.
  • BFP+/GFP- cells can be converted to BFP-/GFP+ cells via HDR or to BFP-/GFP- via NHEJ.
  • FIG. 15B Frequency of HDR (lower right quadrant) and NHEJ (upper left quadrant) measured by flow cytometry in BFP-to-GFP reporter cells transfected with the fusions and sgRNA with ssODN template.
  • FIG. 15C Editing activity of epigenetic fusions in the absence of ssODN template measured by flow cytometry in BFP-to-GFP reporter cells.
  • FIG. 15D Editing activity of epigenetic fusions in the absence of ssODN template measured by flow cytometry in BFP-to-GFP reporter cells.
  • FIG. 15E HDR:indel ratio measured by flow cytometry in BFP-to-GFP reporter cells transfected with the fusions and sgRNA with ssODN template.
  • FIG. 16A-16D Epigenetic fusions display increased FiDR efficiency and HDR:indel ratios across multiple endogenous sites.
  • FIG. 16A FiDR frequency and HDR:indel ratio measured by NGS at an intergenic genomic locus (site 7) in FIEK293T cells transfected with the fusions and sgRNA with ssODN template.
  • FIG. 16B FiDR frequency and HDR:indel ratio measured by NGS at an exonic disease-relevant genomic locus (site 9) in FIEK293T cells transfected with the fusions and sgRNA with ssODN template.
  • FIG. 16C FiDR frequency and HDR:indel ratio measured by NGS at an exonic disease-relevant genomic locus
  • FIG. 16D Off-target activity of PRDM9-Cas9 measured by NGS at 6 off-target sites predicted from 2 sgRNAs.
  • FIG. 17A-17D PRDM9-Cas9 fusion displays increased HDR:indel ratios across different cell types.
  • FIG. 17A FiDR frequency measured by NGS at multiple genomic loci (sites 7, 9, 10) in FIEK293T cells transfected with PRDM9-Cas9 and sgRNA with ssODN templates either with or without a mutation at the PAM site.
  • FIG. 17B HDR:indel ratio measured by NGS at multiple genomic loci (sites 7, 9, 10) in FIEK293T cells transfected with PRDM9-Cas9 and sgRNA with ssODN templates either with or without a mutation at the PAM site.
  • FIG. 17C The HDR:indel ratio measured by NGS at multiple genomic loci (sites 7, 9, 10) in FIEK293T cells transfected with PRDM9-Cas9 and sgRNA with ssODN templates either with or without a mutation at the PAM site.
  • FIG. 17C
  • FIG. 17D FiDR frequency and HDR:indel ratio measured by NGS at multiple genomic loci (sites 7-9) in U20S cells transfected with PRDM9-Cas9 and sgRNA with ssODN template.
  • FIG. 1A provides a schematic showing CRISPR-Cas9 fused with a lysine methyl transferase (KMT) deposits methyl marks to increase homology directed repair.
  • KMT lysine methyl transferase
  • FIG. 18 provides a schematic depiction of CRISPR-Cas9 fusions that were generated and tested.
  • the CRISPR-Cas9 fusions were as follows: PRDM9 (416aa; amino acids 1-416)-Cas9; ii) PRDM9dC (371aa; amino acids 1-371)-Cas9; iii) SETD2 (196 aa; amino acids 1494-1690)-Cas9; and iv) SETMAR (263 aa; amino acids 14-277)-Cas9.
  • the CRISPR-Cas fusions were tested, as described in Example 1, using a BFP-to-GFP conversion assay. The data are shown in FIG. 19A-19E and in FIG.
  • FIG. 19A-19E PRDM9 fusions show increased HDR and increased HDRdndel ratios compared to Cas9 alone.
  • D) PRDM9 fusions show up to 50% more HDR compared to Cas9 alone.
  • PRDM9 fusions show up to 3 fold HDRdndel ratios compared to Cas9 alone.
  • FIG. 20A-20B PRDM9-Cas9 fusion showed up to 2-fold increased HDR and 3-fold increased HDRdndel ratio across 6 endogenous sites tested, including 2 disease specific mutations on genes (HBB and LDLR).

Abstract

The present disclosure provides a fusion polypeptide comprising: a) a CRISPR/Cas effector polypeptide; and b) a chromatin marker polypeptide that provides for modification of a histone polypeptide present in chromatin. The present disclosure provides nucleic acids encoding the fusion polypeptide, and cells comprising the fusion polypeptide and/or the nucleic acids. The present disclosure provides systems, kits, devices, and containers comprising a fusion polypeptide of the present disclosure or a nucleic acid encoding same. The present disclosure provides methods for modifying a target nucleic acid, which methods comprise use of the fusion polypeptide.

Description

CRISPR/CAS EFFECTOR-HISTONE MODIFIER FUSION PROTEINS AND METHODS OF USE THEREOF
CROSS -REFERENCE
[0001] This application claims the benefit of U.S. Provisional Patent Application No.
63/162,874, filed March 18, 2021, which application is incorporated herein by reference in its entirety.
STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH [0002] This invention was made with government support under 1244557 awarded by the
National Science Foundation. The government has certain rights in the invention
INCORPORATION BY REFERENCE OF SEQUENCE LISTING PROVIDED AS A TEXT FILE [0003] A Sequence Listing is provided herewith as a text file, “BERK-
441WO_SEQ_LIST_ST25.txt” created on March 15, 2022 and having a size of 648 KB. The contents of the text file are incorporated by reference herein in their entirety.
INTRODUCTION
[0004] The development of genome editing based on clustered regularly interspaced palindromic repeat (CRISPR) associated (Cas) systems has revolutionized biology. CRISPR/Cas systems provide for the introduction of targeted dsDNA breaks (DSB) which can then be repaired through 4 main mechanisms: 1) re-ligation, 2) non-homologous end joining (NHEJ), 3) microhomology-mediated end joining (MMEJ); or 4) homology directed repair (HDR) if a donor template is provided.
[0005] In some eukaryotic cells, end joining either through NHEJ or MMEJ can lead to random insertions and deletions (indels), which allows for targeted knock out of specific genes. In some instances, bias toward HDR may be desired.
[0006] Approaches to bias repair pathways to HDR upon CRISPR mediated DSBs, include: inhibiting canonical NHEJ pathways through the use of small molecule inhibitors; restricting Cas9 expression to specific phases of the cell cycle; fusions of Cas9 with proteins directly involved in HDR; designing guide RNAs following specific rules; and modifying the donor template DNA or linking template to Cas9.
[0007] There is a need in the art for compositions and methods for increasing HDR.
SUMMARY
[0008] The present disclosure provides a fusion polypeptide comprising: a) a CRISPR/Cas effector polypeptide; and b) a chromatin marker polypeptide that provides for modification of a histone polypeptide present in chromatin. The present disclosure provides nucleic acids encoding the fusion polypeptide, and cells comprising the fusion polypeptide and/or the nucleic acids. The present disclosure provides systems, kits, devices, and containers comprising a fusion polypeptide of the present disclosure or a nucleic acid encoding same. The present disclosure provides methods for modifying a target nucleic acid, which methods comprise use of the fusion polypeptide.
BRIEF DESCRIPTION OF THE DRAWINGS [0009] FIG. 1A-1D depict HDR mediated by Cas9-PRDM9AC.
[0010] FIG. 2A-2B provide amino acid sequences of PRDM9 polypeptides.
[0011] FIG. 3A-3B provide amino acid sequences of Cas9-PRDM9AC fusion polypeptides.
[0012] FIG. 4A-4F provide amino acid sequences of SETD2 polypeptides.
[0013] FIG. 5A-5P provide amino acid sequences of CRISPR/Cas effector polypeptides.
[0014] FIG. 6A-6G provide amino acid sequences of SETMAR polypeptides.
[0015] FIG. 7 provides an amino acid sequence of a MOF polypeptide.
[0016] FIG. 8 provides an amino acid sequence of a ZMYND8 polypeptide.
[0017] FIG. 9 provides an amino acid sequence of a ZCWPW 1 polypeptide.
[0018] FIG. 10 provides the amino acid sequence of a PRDM9 polypeptide.
[0019] FIG. 11A-11H provide amino acid sequences of exemplary fusion polypeptides of the present disclosure.
[0020] FIG. 12A-12J provide amino acid sequences of exemplary fusion polypeptides of the present disclosure.
[0021] FIG. 13 provides an amino acid sequence of a HELLS chromatin remodeling polypeptide.
[0022] FIG. 14A-14D depict the effect of endogenous histone modifications on DNA repair pathway choice.
[0023] FIG. 15A-15E depict data showing that engineered CRISPR-Cas9 epigenetic fusions display higher HDR and HDRbndel ratios.
[0024] FIG. 16A-16D depict data showing that epigenetic fusions display increased HDR efficiency and HDRbndel ratios across multiple endogenous sites
[0025] FIG. 17A-17D depict data showing that PRDM9-Cas9 fusion displays increased
HDRdndel ratios across different cell types.
[0026] FIG. 18 provides a schematic depiction of fusion proteins comprising: i) CRISPR-Cas9; and ii) a lysine methyl transferase (KMT).
[0027] FIG. 19A-19E depict increased HDR and increased HDRdndel ratios with PRDM9-
Cas9 fusion proteins, compared to Cas9 alone. [0028] FIG. 20A-20B depict increased HDR and increased HDRdndel ratios with PRDM9-
Cas9 fusion proteins.
DEFINITIONS
[0029] “Heterologous,” as used herein, means a nucleotide or polypeptide sequence that is not found in the native nucleic acid or protein, respectively. For example, relative to a CRISPR/Cas effector polypeptide, a heterologous polypeptide (e.g., a heterologous fusion partner) comprises an amino acid sequence from a protein other than the CRISPR/Cas effector polypeptide.
[0030] The terms “polynucleotide” and “nucleic acid,” used interchangeably herein, refer to a polymeric form of nucleotides of any length, either ribonucleotides or deoxynucleotides. Thus, this term includes, but is not limited to, single-, double-, or multi-stranded DNA or RNA, genomic DNA, cDNA, DNA-RNA hybrids, or a polymer comprising purine and pyrimidine bases or other natural, chemically or biochemically modified, non-natural, or derivatized nucleotide bases. The terms “polynucleotide” and “nucleic acid” should be understood to include, as applicable to the embodiment being described, single- stranded (such as sense or antisense) and double-stranded polynucleotides.
[0031] The terms "polypeptide," "peptide," and "protein", are used interchangeably herein, refer to a polymeric form of amino acids of any length, which can include genetically coded and nongene tically coded amino acids, chemically or biochemically modified or derivatized amino acids, and polypeptides having modified peptide backbones. The term includes fusion proteins, including, but not limited to, fusion proteins with a heterologous amino acid sequence, fusions with heterologous and homologous leader sequences, with or without N-terminal methionine residues; immunologically tagged proteins; and the like.
[0032] The term “naturally-occurring” as used herein as applied to a nucleic acid, a protein, a cell, or an organism, refers to a nucleic acid, cell, protein, or organism that is found in nature.
[0033] As used herein the term “isolated” is meant to describe a polynucleotide, a polypeptide, or a cell that is in an environment different from that in which the polynucleotide, the polypeptide, or the cell naturally occurs. An isolated genetically modified host cell may be present in a mixed population of genetically modified host cells.
[0034] “Recombinant,” as used herein, means that a particular nucleic acid (DNA or RNA) is the product of various combinations of cloning, restriction, and/or ligation steps resulting in a construct having a structural coding or non-coding sequence distinguishable from endogenous nucleic acids found in natural systems. Generally, DNA sequences encoding the structural coding sequence can be assembled from cDNA fragments and short oligonucleotide linkers, or from a series of synthetic oligonucleotides, to provide a synthetic nucleic acid which is capable of being expressed from a recombinant transcriptional unit contained in a cell or in a cell-free transcription and translation system. Such sequences can be provided in the form of an open reading frame uninterrupted by internal non- translated sequences, or introns, which are typically present in eukaryotic genes. Genomic DNA comprising the relevant sequences can also be used in the formation of a recombinant gene or transcriptional unit. Sequences of non-translated DNA may be present 5’ or 3’ from the open reading frame, where such sequences do not interfere with manipulation or expression of the coding regions, and may indeed act to modulate production of a desired product by various mechanisms (see “DNA regulatory sequences”, below).
[0035] Thus, e.g., the term “recombinant” polynucleotide or “recombinant” nucleic acid refers to one which is not naturally occurring, e.g., is made by the artificial combination of two otherwise separated segments of sequence through human intervention. This artificial combination is often accomplished by either chemical synthesis means, or by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques. Such is usually done to replace a codon with a redundant codon encoding the same or a conservative amino acid, while typically introducing or removing a sequence recognition site. Alternatively, it is performed to join together nucleic acid segments of desired functions to generate a desired combination of functions. This artificial combination is often accomplished by either chemical synthesis means, or by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques.
[0036] Similarly, the term “recombinant” polypeptide refers to a polypeptide which is not naturally occurring, e.g., is made by the artificial combination of two otherwise separated segments of amino sequence through human intervention. Thus, e.g., a polypeptide that comprises a heterologous amino acid sequence is recombinant.
[0037] By “construct” or “vector” is meant a recombinant nucleic acid, generally recombinant
DNA, which has been generated for the purpose of the expression and/or propagation of a specific nucleotide sequence(s), or is to be used in the construction of other recombinant nucleotide sequences. [0038] The terms “DNA regulatory sequences,” “control elements,” and “regulatory elements,” used interchangeably herein, refer to transcriptional and translational control sequences, such as promoters, enhancers, polyadenylation signals, terminators, protein degradation signals, and the like, that provide for and/or regulate expression of a coding sequence and/or production of an encoded polypeptide in a host cell.
[0039] The term “transformation” is used interchangeably herein with “genetic modification” and refers to a permanent or transient genetic change induced in a cell following introduction of new nucleic acid (e.g., DNA exogenous to the cell) into the cell. Genetic change (“modification”) can be accomplished either by incorporation of the new nucleic acid into the genome of the host cell, or by transient or stable maintenance of the new nucleic acid as an episomal element. Where the cell is a eukaryotic cell, a permanent genetic change is generally achieved by introduction of new DNA into the genome of the cell. In prokaryotic cells, permanent changes can be introduced into the chromosome or via extrachromosomal elements such as plasmids and expression vectors, which may contain one or more selectable markers to aid in their maintenance in the recombinant host cell. Suitable methods of genetic modification include viral infection, transfection, conjugation, protoplast fusion, electroporation, particle gun technology, calcium phosphate precipitation, direct microinjection, and the like. The choice of method is generally dependent on the type of cell being transformed and the circumstances under which the transformation is taking place (i.e. in vitro, ex vivo, or in vivo). A general discussion of these methods can be found in Ausubel, et al., Short Protocols in Molecular Biology, 3rd ed., Wiley & Sons, 1995.
[0040] “Operably linked” refers to a juxtaposition wherein the components so described are in a relationship permitting them to function in their intended manner. For instance, a promoter is operably linked to a coding sequence if the promoter affects its transcription or expression. As used herein, the terms “heterologous promoter” and “heterologous control regions” refer to promoters and other control regions that are not normally associated with a particular nucleic acid in nature. For example, a “transcriptional control region heterologous to a coding region” is a transcriptional control region that is not normally associated with the coding region in nature.
[0041] A “host cell,” as used herein, denotes an in vivo or in vitro eukaryotic cell, a prokaryotic cell, or a cell from a multicellular organism (e.g., a cell line) cultured as a unicellular entity, which eukaryotic or prokaryotic cells can be, or have been, used as recipients for a nucleic acid (e.g., an expression vector), and include the progeny of the original cell which has been genetically modified by the nucleic acid. It is understood that the progeny of a single cell may not necessarily be completely identical in morphology or in genomic or total DNA complement as the original parent, due to natural, accidental, or deliberate mutation. A “recombinant host cell” (also referred to as a “genetically modified host cell”) is a host cell into which has been introduced a heterologous nucleic acid, e.g., an expression vector. For example, a subject eukaryotic host cell is a genetically modified eukaryotic host cell, by virtue of introduction into a suitable eukaryotic host cell of a heterologous nucleic acid, e.g., an exogenous nucleic acid that is foreign to the eukaryotic host cell, or a recombinant nucleic acid that is not normally found in the eukaryotic host cell.
[0042] The term “conservative amino acid substitution” refers to the interchangeability in proteins of amino acid residues having similar side chains. For example, a group of amino acids having aliphatic side chains consists of glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains consists of serine and threonine; a group of amino acids having amide-containing side chains consists of asparagine and glutamine; a group of amino acids having aromatic side chains consists of phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains consists of lysine, arginine, and histidine; and a group of amino acids having sulfur- containing side chains consists of cysteine and methionine. Exemplary conservative amino acid substitution groups are: valine-leucine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine- valine, and asparagine-glutamine.
[0043] A polynucleotide or polypeptide has a certain percent “sequence identity” to another polynucleotide or polypeptide, meaning that, when aligned, that percentage of bases or amino acids are the same, and in the same relative position, when comparing the two sequences. Sequence similarity can be determined in a number of different manners. To determine sequence identity, sequences can be aligned using the methods and computer programs, including BLAST, available over the world wide web at ncbi.nlm.nih.gov/BLAST. See, e.g., Altschul et al. (1990), J. Mol. Biol. 215:403-10. Another alignment algorithm is LASTA, available in the Genetics Computing Group (GCG) package, from Madison, Wisconsin, USA, a wholly owned subsidiary of Oxford Molecular Group, Inc. Other techniques for alignment are described in Methods in Enzymology, vol. 266: Computer Methods for Macromolecular Sequence Analysis (1996), ed. Doolittle, Academic Press, Inc., a division of Harcourt Brace & Co., San Diego, California, USA. Of particular interest are alignment programs that permit gaps in the sequence. The Smith- Waterman is one type of algorithm that permits gaps in sequence alignments. See Meth. Mol. Biol. 70: 173-187 (1997). Also, the GAP program using the Needleman and Wunsch alignment method can be utilized to align sequences. See J. Mol. Biol. 48: 443-453 (1970). [0044] As used herein, the terms "treatment," "treating," and the like, refer to obtaining a desired pharmacologic and/or physiologic effect. The effect may be prophylactic in terms of completely or partially preventing a disease or symptom thereof and/or may be therapeutic in terms of a partial or complete cure for a disease and/or adverse effect attributable to the disease. "Treatment," as used herein, covers any treatment of a disease in a mammal, e.g., in a human, and includes: (a) preventing the disease from occurring in a subject which may be predisposed to the disease but has not yet been diagnosed as having it; (b) inhibiting the disease, i.e., arresting its development; and (c) relieving the disease, i.e., causing regression of the disease.
[0045] The terms "individual," "subject," "host," and "patient," used interchangeably herein, refer to an individual organism, e.g., a mammal, including, but not limited to, murines, simians, humans, non-human primates, mammalian farm animals, mammalian sport animals, and mammalian pets.
[0046] Before the present invention is further described, it is to be understood that this invention is not limited to particular embodiments described, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only by the appended claims. [0047] Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range, is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges, and are also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the invention.
[0048] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the present invention, the preferred methods and materials are now described. All publications mentioned herein are incorporated herein by reference to disclose and describe the methods and/or materials in connection with which the publications are cited.
[0049] It must be noted that as used herein and in the appended claims, the singular forms “a,”
“an,” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a histone modifier polypeptide” includes a plurality of such histone modifier polypeptides and reference to “the CRISPR/Cas effector polypeptide” includes reference to one or more CRISPR/Cas effector polypeptides and equivalents thereof known to those skilled in the art, and so forth. It is further noted that the claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as “solely,” “only” and the like in connection with the recitation of claim elements, or use of a “negative” limitation.
[0050] It is appreciated that certain features of the invention, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the invention, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable sub-combination. All combinations of the embodiments pertaining to the invention are specifically embraced by the present invention and are disclosed herein just as if each and every combination was individually and explicitly disclosed. In addition, all sub-combinations of the various embodiments and elements thereof are also specifically embraced by the present invention and are disclosed herein just as if each and every such subcombination was individually and explicitly disclosed herein.
[0051] The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. Further, the dates of publication provided may be different from the actual publication dates which may need to be independently confirmed.
DETAILED DESCRIPTION
[0052] The present disclosure provides a fusion polypeptide comprising: a) a CRISPR/Cas effector polypeptide; and b) a chromatin marker polypeptide that provides for modification of a histone polypeptide present in chromatin. The present disclosure provides nucleic acids encoding the fusion polypeptide, and cells comprising the fusion polypeptide and/or the nucleic acids. The present disclosure provides systems, kits, devices, and containers comprising a fusion polypeptide of the present disclosure or a nucleic acid encoding same. The present disclosure provides methods for modifying a target nucleic acid, which methods comprise use of the fusion polypeptide.
FUSION POLYPEPTIDES
[0053] The present disclosure provides a fusion polypeptide comprising: a) a CRISPR/Cas effector polypeptide; and b) a chromatin marker polypeptide that provides for modification of a histone polypeptide present in chromatin. The modification marks the chromatin as a site for recombination. [0054] A fusion polypeptide of the present disclosure, when complexed with a guide nucleic acid, can modify a target nucleic acid. In some cases, e.g., where a fusion polypeptide of the present disclosure is complexed with a guide nucleic acid, and when a donor template nucleic acid is provided, provides for an increased level of HDR, compared with the level of HDR that would occur using a CRISPR/Cas effector polypeptide not fused to the fusion partner present in the fusion polypeptide. For example, in some cases, a fusion polypeptide of the present disclosure (comprising a CRISPR/Cas effector polypeptide and a chromatin marker polypeptide), a guide RNA, and a donor template DNA are introduced into a target eukaryotic cell, where such introducing results in a level of HDR that is at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100% (or two-fold), at least 2.5-fold, at least 3-fold, at least 4-fold, at least 5-fold, or at least 10-fold, or more than 10-fold, higher than the level of HDR that would occur if the CRISPR/Cas effector polypeptide (not fused to the chromatin marker polypeptide), the guide RNA, and the donor template DNA were introduced into the cell. In some cases, a fusion polypeptide of the present disclosure (comprising a CRISPR/Cas effector polypeptide and a chromatin marker polypeptide), a guide RNA, and a donor template DNA are introduced into a target eukaryotic cell, where such introducing results in modification of a target nucleic acid in the cell, wherein the ratio of HDR events to NHEJ events is at least 1.5:1, at least 2:1, at least 2.5:1, at least 3:1, at least 4:1, at least 5:1, at least 7.5:1, at least 10:1, at least 25:1, at least 50:1, or at least 100:1.
[0055] In some cases, a fusion polypeptide of the present disclosure provides for an increased
HDRdndel ratio, compared to the HDRdndel ratio of a CRISPR/Cas effector polypeptide not fused to a chromatin modifying polypeptide. For example, in some cases, the HDRdndel ratio is increased by at least 10%, at least 15%, at least 25%, at least 50%, at least 2-fold, at least 3-fold, or more than 3-fold, compared to the HDRdndel ratio obtained with a control CRISPR/Cas effector polypeptide (the CRISPR/Cas effector polypeptide not fused to the chromatin-modifying polypeptide).
[0056] In some cases, a fusion polypeptide of the present disclosure provides for reduced incidence of chromosomal translocations or chromothripsis, compared to the incidence of chromosomal translocations or chromothripsis observed using a CRISPR-Cas effector polypeptide not fused to a chromatin marker polypeptide. For example, where the fusion partner is a SETMAR polypeptide, a fusion polypeptide of the present disclosure provides for reduced (e.g., at least 10% reduced, at least 15% reduced, at least 20% reduced, at least 25% reduced, at least 30% reduced, at least 35% reduced, at least 40% reduced, at least 45% reduced, or at least 50% reduced) incidence of chromosomal translocations or chromothripsis, compared to the incidence of chromosomal translocations or chromothripsis observed using a CRISPR-Cas effector polypeptide not fused to the SETMAR polypeptide.
[0057] In some cases, a fusion polypeptide of the present disclosure comprises, in order from N- terminus to C-terminus: a) a CRISPR/Cas effector polypeptide; and b) a chromatin modifying polypeptide. In some cases, a fusion polypeptide of the present disclosure comprises, in order from N- terminus to C-terminus: a) a chromatin modifying polypeptide; and b) a CRISPR/Cas effector polypeptide. In some cases, a fusion polypeptide of the present disclosure comprises, in order from N- terminus to C-terminus: a) an N-terminal portion of a CRISPR/Cas effector polypeptide; b) a chromatin modifying polypeptide; and c) a C-terminal portion of the CRISPR/Cas effector polypeptide. In some cases, a fusion polypeptide of the present disclosure comprises, in order from N-terminus to C-terminus: a) a C-terminal portion of a CRISPR/Cas effector polypeptide; b) a chromatin modifying polypeptide; and c) an N-terminal portion of the CRISPR/Cas effector polypeptide. In any of these embodiments, the fusion polypeptide can comprise one or more NLSs, where the one or more NLSs can be located at one or more of: i) the N-terminus of the fusion polypeptide; ii) at the C-terminus of the fusion polypeptide; and iii) between the CRISPR/Cas effector polypeptide and the chromatin-modifying polypeptide. In addition, in any of the above embodiments, the fusion polypeptide can comprise one or more peptide linkers, e.g., between the CRISPR/Cas effector polypeptide and the chromatin-modifying polypeptide. Chromatin marker polypeptides
[0058] A chromatin marker polypeptide that provides for modification of a histone polypeptide present in chromatin, that is suitable for inclusion in a fusion polypeptide of the present disclosure includes: a) a histone me thy ltransf erase; b) a histone acetyltransferase; c) a polypeptide that binds F13K4me3 and/or F13K36me3 and that recruits one or more polypeptides that promote F1DR to the chromatin; and d) a polypeptide that binds a PRDM9 polypeptide. In some cases, a chromatin marker polypeptide suitable for inclusion in a fusion polypeptide of the present disclosure does not bind DNA, e.g., lacks a domain (e.g., a sequence of amino acids) that bind to DNA, where such domains include Zn- finger DNA binding domains, transcription-activator like effector (TALE) DNA binding domains, transposases, recombinases, and the like. Instead, the CRISPR/Cas polypeptide, together with a guide nucleic acid, provide for binding to a target nucleic acid. In some cases, a MOF polypeptide (acetylating lysine- 16 of histone 4 (H4) is specifically excluded.
Histone methyltransf erases (HMTs)
[0059] In some cases, a chromatin marker polypeptide suitable for inclusion in a fusion polypeptide of the present disclosure is a histone methyltransferase (HMT). For example, a chromatin marker polypeptide suitable for inclusion in a fusion polypeptide of the present disclosure methylates one or more lysine resides in histone 3 (H3). In some cases, a chromatin marker polypeptide suitable for inclusion in a fusion polypeptide of the present disclosure methylates Iysine-4 (K4) of H3, such that K4 of H3 is mono-, di-, or trimethylated. In some cases, a chromatin marker polypeptide suitable for inclusion in a fusion polypeptide of the present disclosure methylates K4 of H3 such that K4 is trimethylated; such a methylated histone is referred to as H3K4me3. In some cases, a chromatin marker polypeptide suitable for inclusion in a fusion polypeptide of the present disclosure methylates lysine-36 (K36) of H3, such that K36 of H3 is mono-, di-, or trimethylated. In some cases, a chromatin marker polypeptide suitable for inclusion in a fusion polypeptide of the present disclosure methylates K36 of H3, such that K36 of H3 is trimethylated; such a methylated histone is referred to as H3K36me3. Suitable HMTs include, but are not limited to, PRDM9, SETD2, and SETMAR. Where an HMT methylates a lysine residue, such an HMT is also referred to herein as a lysine methyltransferase (KMT).
PRDM9
[0060] A suitable PRDM9 (PR domain zinc finger protein 9; minisatellite binding protein 3
(115 kD); histone-Iysine-N-methyltransferase PRDM9; PR domain containing 9; PFM6; PR/SET domain 9) polypeptide comprises a PR/SET domain and may further comprise one or both of a KRAB domain and an SSXRD domain. A PRDM9 polypeptide suitable for including in a fusion polypeptide of the present disclosure does not include a zinc-finger (Zn-finger) DNA-binding domain.
[0061] In some cases, a PRDM9 polypeptide suitable for including in a fusion polypeptide of the present disclosure comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the PRDM9 amino acid sequence depicted in FIG. 2A or FIG. 2B ; and has a length of from about 350 amino acids to about 400 amino acids (e.g., has a length of from about 350 amino acids (aa) to 360 aa, from 360 aa to 370 aa, from 370 aa to 380 aa, from 380 aa to 390 aa, or from 390 aa to 400 aa. In some cases, a PRDM9 polypeptide suitable for including in a fusion polypeptide of the present disclosure comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the PRDM9 amino acid sequence depicted in FIG. 2A; and has a length of 370 amino acids. In some cases, a PRDM9 polypeptide suitable for including in a fusion polypeptide of the present disclosure comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the PRDM9 amino acid sequence depicted in FIG. 2B; and has a length of 371 amino acids.
[0062] In some cases, a PRDM9 polypeptide suitable for including in a fusion polypeptide of the present disclosure comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the PRDM9 amino acid sequence depicted in FIG. 10; and has a length of from about 400 amino acids to about 430 amino acids (e.g., has a length of from about 400 amino acids (aa) to 405 aa, from about 405 aa to about 410 aa, from about 410 aa to about 415 aa, from about 415 aa to about 420 aa, from about 420 aa to about 425 aa, or from about 425 aa to about 430 aa). In some cases, a PRDM9 polypeptide suitable for including in a fusion polypeptide of the present disclosure comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the PRDM9 amino acid sequence depicted in FIG. 10; and has a length of 416 amino acids.
SETD2
[0063] A suitable SETD2 (SET (Su(var)3-9, Enhancer of Zeste, and Trithorax) domain
(catalytic domain of histone methyltransferase) domain containing 2, histone lysine methyltransferase) polypeptide can comprise an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in any one of FIG. 4A-4E. In some cases, a SETD2 polypeptide lacks a WW domain. In some cases, a SETD2 polypeptide lacks an SRI domain. In some cases, a SETD2 polypeptide lacks both a WW domain and an SRI domain. In some cases, a suitable SETD2 polypeptide has a length of from about 1500 amino acids to 2000 amino acids.
[0064] In some cases, a SETD2 polypeptide suitable for including in a fusion polypeptide of the present disclosure comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the SETD2 polypeptide depicted in FIG. 4F; and has a length of 196 amino acids.
SETMAR
[0065] A suitable SETMAR (SET domain and mariner transposase fusion gene; histone-lysine
N-methyltransferase SETMAR); METNASE; Marl) polypeptide can comprise an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in any one of FIG. 6A-6G, where the SETMAR polypeptide does not include a transposase domain. For example, in some cases, a suitable SETMAR polypeptide comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to amino acids 1-346 of the amino acid sequence depicted in FIG. 6A; and has a length of from about 300 amino acids to about 350 amino acids. As another example, in some cases, a suitable SETMAR polypeptide comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to amino acids 1-362 of the amino acid sequence depicted in FIG. 6B; and has a length of from about 300 amino acids to about 360 amino acids. As another example, in some cases, a suitable SETMAR polypeptide comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to amino acids 1-268 of the amino acid sequence depicted in FIG.6C; and has a length of from about 225 amino acids to about 270 amino acids. As another example, in some cases, a suitable SETMAR polypeptide comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to amino acids 1-224 or amino acids 1-269 of the amino acid sequence depicted in FIG.6D; and has a length of from about 225 amino acids to about 270 amino acids. As another example, in some cases, a suitable SETMAR polypeptide comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to amino acids 1- 245 of the amino acid sequence depicted in FIG.6E; and has a length of from about 215 amino acids to about 245 amino acids. As another example, in some cases, a suitable SETMAR polypeptide comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to amino acids 1-213 of the amino acid sequence depicted in FIG.6F; and has a length of from about 190 amino acids to about 215 amino acids.
[0066] In some cases, a suitable SETMAR polypeptide comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG.6G; and has a length of 263 amino acids.
Histone acetyltransferases
[0067] A suitable MOT (MYST-1; KAT8; ZC2HC8) polypeptide can comprise an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 7.
ZMYND8: ZCWPWI
[0068] In some cases, a chromatin marker that is suitable for inclusion in a fusion polypeptide of the present disclosure is a polypeptide that: i) binds H3K4me3 and/or H3K36me3; and ii) recruits one or more polypeptides that promote HDR to the chromatin. Examples of such polypeptides include ZMYND8 and ZCWPWI.
[0069] A suitable ZMYND8 polypeptide comprises an amino acid sequence having at least
85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 8. [0070] A suitable ZCWPW1 polypeptide comprises an amino acid sequence having at least
85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 9.
Chromatin remodeler polypeptides
[0071] In some cases, a polypeptide suitable for inclusion in a fusion polypeptide of the present disclosure is a chromatin remodeler polypeptide. For example, a suitable chromatin remodeler polypeptide is a helicase, lymphoid specific (HELLS) polypeptide. A HELLS polypeptide is a member of the SNF2 helicase family of chromatin remodeling proteins. A suitable HELLS polypeptide comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 13.
CRISPR/Cas effector polypeptides
[0072] Any CRISPR/Cas effector polypeptide is suitable for inclusion in a fusion polypeptide of the present disclosure. In some cases, the CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure is a type II CRISPR/Cas effector polypeptide, a type V CRISPR/Cas effector polypeptide, or a type VI CRISPR/Cas effector polypeptide. In some cases, the CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure is a type II CRISPR/Cas effector polypeptide. In some cases, the CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure is a Cas9 polypeptide. In some cases, the CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure is a type V CRISPR/Cas effector polypeptide. In some cases, the CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure is a Casl2a, a Casl2b, a Casl2c, a Casl2d, or a Casl2e polypeptide. In some cases, the CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure is a type VI CRISPR/Cas effector polypeptide. In some cases, the CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure is a Casl3a, a Casl3b, a Casl3c, or a Casl3d polypeptide. In some cases, the CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure is a Casl4a, a Casl4b, or a Casl4c polypeptide. Amino acid sequences of a variety of CRISPR/Cas effector polypeptides are known.
[0073] Examples of various Cas9 proteins (and Cas9 domain structure) and Cas9 guide RNAs (as well as information regarding requirements related to protospacer adjacent motif (PAM) sequences present in targeted nucleic acids) can be found in the art, for example, see Jinek et al., Science. 2012 Aug 17;337(6096):816-21; Chylinski et al., RNA Biol. 2013 May;10(5):726-37; Ma et al., Biomed Res Int. 2013;2013:270805; Hou et al., Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15644-9; Jinek et al., Elife. 2013;2:e00471; Pattanayak et al., Nat Biotechnol. 2013 Sep;31(9):839-43; Qi et al., Cell. 2013 Feb 28 ; 152(5): 1173-83; Wang et al., Cell. 2013 May 9;153(4):910-8; Auer et al., Genome Res. 2013 Oct 31; Chen et al., Nucleic Acids Res. 2013 Nov l;41(20):el9; Cheng et al., Cell Res. 2013 Oct;23(10):1163- 71; Cho et al., Genetics. 2013 Nov;195(3):1177-80; DiCarlo et al., Nucleic Acids Res. 2013 Apr;41(7):4336-43; Dickinson et al., Nat Methods. 2013 Oct;10(10):1028-34; Ebina et al., Sci Rep. 2013;3:2510; Fujii et al., Nucleic Acids Res. 2013 Nov l;41(20):el87; Hu et al., Cell Res. 2013 Nov;23(ll):1322-5; Jiang et al., Nucleic Acids Res. 2013 Nov l;41(20):el88; Larson et al., Nat Protoc. 2013 Nov;8(ll):2180-96; Mali et al., Nat Methods. 2013 Oct;10(10):957-63; Nakayama et al.,
Genesis. 2013 Dec;51(12):835-43; Ran et al., Nat Protocols 2013 Nov;8(ll):2281-308; Ran et al., Cell. 2013 Sep 12;154(6):1380-9; Upadhyay et al., G3 (Bethesda). 2013 Dec 9;3(12):2233-8; Walsh et al.,
Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15514-5; Xie et al., Mol Plant. 2013 Oct 9; Yang et al., Cell. 2013 Sep 12;154(6):1370-9; Briner et al., Mol Cell. 2014 Oct 23;56(2):333-9; Shmakov et al., Nat Rev Microbiol. 2017 Mar;15(3):169-182; and U.S. patents and patent applications: 8,906,616; 8,895,308; 8,889,418; 8,889,356; 8,871,445; 8,865,406; 8,795,965; 8,771,945; 8,697,359; 20140068797; 20140170753; 20140179006; 20140179770; 20140186843; 20140186919; 20140186958; 20140189896; 20140227787; 20140234972; 20140242664; 20140242699; 20140242700; 20140242702; 20140248702; 20140256046; 20140273037; 20140273226; 20140273230; 20140273231; 20140273232; 20140273233; 20140273234; 20140273235; 20140287938; 20140295556; 20140295557; 20140298547; 20140304853; 20140309487; 20140310828; 20140310830; 20140315985; 20140335063; 20140335620; 20140342456; 20140342457; 20140342458; 20140349400; 20140349405; 20140356867; 20140356956; 20140356958; 20140356959; 20140357523; 20140357530; 20140364333; and 20140377868; each of which is hereby incorporated by reference in its entirety.
[0074] In some cases, a CRISPR/Cas effector polypeptide suitable for inclusion in a fusion polypeptide of the present disclosure comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in any one of FIG. 5A-5P.
[0075] In some cases, a CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure is enzymatically active. In some cases, a CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure exhibits reduced enzymatic activity compared to a wild- type CRISPR/Cas effector polypeptide. In some cases, a CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure is a nickase. For example, in some cases, a CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure comprises a substitution of D10 (e.g., D10A) or H840 (e.g., H840A) of the amino acid sequence depicted in FIG. 5A, or a corresponding amino acid of another CRISPR/Cas effector polypeptide. In some cases, a CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure is enzymatically inactive (a “dead” CRISPR/Cas effector polypeptide) but retains the ability to bind a target nucleic acid when complexed with a guide nucleic acid. For example, in some cases, a CRISPR/Cas effector polypeptide present in a fusion polypeptide of the present disclosure comprises a substitution of both D10 and H840 (e.g., D10A; and H840A) of the amino acid sequence depicted in FIG. 5A, or corresponding amino acids of another CRISPR/Cas effector polypeptide.
Additional polypeptides
[0076] In some cases, a fusion polypeptide of the present disclosure comprises one or more additional heterologous polypeptides at the N-terminus, the C-terminus, or both the N-terminus and the C-terminus of the fusion polypeptide.
[0077] In some cases, a fusion polypeptide of the present disclosure includes (is fused to) a nuclear localization signal (NLS) (e.g., in some cases 2 or more, 3 or more, 4 or more, or 5 or more NLSs). Thus, in some cases, a fusion polypeptide of the present disclosure includes one or more NLSs (e.g., 2 or more, 3 or more, 4 or more, or 5 or more NLSs). In some cases, one or more NLSs (2 or more, 3 or more, 4 or more, or 5 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) the N-terminus and/or the C-terminus. In some cases, one or more NLSs (2 or more, 3 or more, 4 or more, or 5 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) the N-terminus. In some cases, one or more NLSs (2 or more, 3 or more, 4 or more, or 5 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) the C-terminus. In some cases, one or more NLSs (3 or more, 4 or more, or 5 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) both the N-terminus and the C-terminus. In some cases, an NLS is positioned at the N-terminus and an NLS is positioned at the C-terminus. In some cases, one or more NLSs (2 or more, 3 or more, 4 or more, or 5 or more NLSs) are positioned internally within a fusion polypeptide of the present disclosure.
[0078] Non-limiting examples of NLSs include an NLS sequence derived from: the NLS of the SV40 virus large T-antigen, having the amino acid sequence PKKKRKV (SEQ ID NO:37); the NLS from nucleoplasmin (e.g., the nucleoplasmin bipartite NLS with the sequence KRPAATKKAGQAKKKK (SEQ ID NO:61)); the c-myc NLS having the amino acid sequence PAAKRVKLD (SEQ ID NO:62) or RQRRNELKRSP (SEQ ID NO:63); the hRNPAl M9 NLS having the sequence NQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGY (SEQ ID NO:64); the sequence RMRIZFKNKGKDTAELRRRRVEVSVELRKAKKDEQILKRRNV (SEQ ID NO:65) of the IBB domain from importin-alpha; the sequences VSRKRPRP (SEQ ID NO:66) and PPKKARED (SEQ ID NO:67) of the myoma T protein; the sequence PQPKKKPL (SEQ ID NO:68) of human p53; the sequence SALIKKKKKMAP (SEQ ID NO:69) of mouse c-abl IV; the sequences DRLRR (SEQ ID NO:71) and PKQKKRK (SEQ ID NO:70) of the influenza virus NS1; the sequence RKLKKKIKKL (SEQ ID NO:72) of the Hepatitis virus delta antigen; the sequence REKKKFLKRR (SEQ ID NO:73) of the mouse Mxl protein; the sequence KRKGDEVDGVDEVAKKKSKK (SEQ ID NO:74) of the human poly(ADP-ribose) polymerase; and the sequence RKCLQAGMNLEARKTKK (SEQ ID NO:75) of the steroid hormone receptors (human) glucocorticoid. In general, NLS (or multiple NLSs) are of sufficient strength to drive accumulation of the fusion protein in a detectable amount in the nucleus of a eukaryotic cell. Detection of accumulation in the nucleus may be performed by any suitable technique. For example, a detectable marker may be fused to the fusion protein such that location within a cell may be visualized. Cell nuclei may also be isolated from cells, the contents of which may then be analyzed by any suitable process for detecting protein, such as immunohistochemistry, Western blot, or enzyme activity assay. Accumulation in the nucleus may also be determined indirectly.
[0079] In some cases, a fusion polypeptide of the present disclosure includes a "Protein Transduction Domain" or PTD (also known as a CPP - cell penetrating peptide), which refers to a polypeptide, polynucleotide, carbohydrate, or organic or inorganic compound that facilitates traversing a lipid bilayer, micelle, cell membrane, organelle membrane, or vesicle membrane. A PTD attached to another molecule, which can range from a small polar molecule to a large macromolecule and/or a nanoparticle, facilitates the molecule traversing a membrane, for example going from extracellular space to intracellular space, or cytosol to within an organelle. In some cases, a PTD is covalently linked to the carboxyl terminus of a fusion polypeptide of the present disclosure. In some cases, the PTD is inserted internally in a fusion polypeptide of the present disclosure at a suitable insertion site. In some cases, a fusion polypeptide of the present disclosure includes (is conjugated to, is fused to) one or more PTDs (e.g., two or more, three or more, four or more PTDs). In some cases, a PTD includes a nuclear localization signal (NLS) (e.g., in some cases 2 or more, 3 or more, 4 or more, or 5 or more NLSs). Thus, in some cases, a fusion polypeptide of the present disclosure includes one or more NLSs (e.g., 2 or more, 3 or more, 4 or more, or 5 or more NLSs). Examples of PTDs include but are not limited to a minimal undecapeptide protein transduction domain (corresponding to residues 47-57 of HIV-1 TAT comprising YGRKKRRQRRR; SEQ ID NO:76); a polyarginine sequence comprising a number of arginines sufficient to direct entry into a cell (e.g., 3, 4, 5, 6, 7, 8, 9, 10, or 10-50 arginines); a VP22 domain (Zender et al. (2002) Cancer Gene Ther. 9(6):489-96); an Drosophila Antennapedia protein transduction domain (Noguchi et al. (2003) Diabetes 52(7): 1732-1737); a truncated human calcitonin peptide (Trehin et al. (2004) Pharm. Research 21:1248-1256); polylysine (Wender et al. (2000) Proc. Natl. Acad. Sci. USA 97:13003-13008); RRQRRTSKLMKR (SEQ ID NO:77); Transportan GWTLNSAGYLLGKINLKALAALAKKIL (SEQ ID NO:78); KALAWEAKLAKALAKALAKHLAKALAKALKCEA (SEQ ID NO:79); and RQIKIWF QNRRMKWKK (SEQ ID NO: 80). Exemplary PTDs include but are not limited to, YGRKKRRQRRR (SEQ ID NO:76), RKKRRQRRR (SEQ ID NO:81); an arginine homopolymer of from 3 arginine residues to 50 arginine residues; Exemplary PTD domain amino acid sequences include, but are not limited to, any of the following: YGRKKRRQRRR (SEQ ID NO:76); RKKRRQRR (SEQ ID NO:82); YARAAARQARA (SEQ ID NO:83); THRLPRRRRRR (SEQ ID NO:84); and GGRRARRRRRR (SEQ ID NO:85). In some embodiments, the PTD is an activatable CPP (ACPP) (Aguilera et al. (2009) Integr Biol ( Camb) June; 1(5-6): 371-381). ACPPs comprise a polycationic CPP (e.g., Arg9 or “R9”) connected via a cleavable linker to a matching polyanion (e.g., Glu9 or Έ9”), which reduces the net charge to nearly zero and thereby inhibits adhesion and uptake into cells. Upon cleavage of the linker, the polyanion is released, locally unmasking the polyarginine and its inherent adhesiveness, thus “activating” the ACPP to traverse the membrane.
Linkers
[0080] In some embodiments, a fusion polypeptide of the present disclosure comprises one or more linker polypeptides; e.g., a linker polypeptide between the CRISPR/Cas effector polypeptide and the chromatin marker polypeptide. The linker polypeptide may have any of a variety of amino acid sequences. Proteins can be joined by a spacer peptide, generally of a flexible nature, although other chemical linkages are not excluded. Suitable linkers include polypeptides of between 4 amino acids and 40 amino acids in length, or between 4 amino acids and 25 amino acids in length. These linkers can be produced by using synthetic, linker-encoding oligonucleotides to couple the proteins, or can be encoded by a nucleic acid sequence encoding the fusion protein. Peptide linkers with a degree of flexibility can be used. The linking peptides may have virtually any amino acid sequence, bearing in mind that the preferred linkers will have a sequence that results in a generally flexible peptide. The use of small amino acids, such as glycine and alanine, are of use in creating a flexible peptide. The creation of such sequences is routine to those of skill in the art. A variety of different linkers are commercially available and are considered suitable for use.
[0081] Examples of linker polypeptides include glycine polymers (G)n, glycine-serine polymers (including, for example, (GS)„, GSGGSn (SEQ ID NO:86), (GGS)n, GGSGGSn (SEQ ID NO:87), (GGGGS)n (SEQ ID NO:88), and GGGSn (SEQ ID NO:89), where n is an integer of at least one; glycine-alanine polymers, alanine-serine polymers. Exemplary linkers can comprise amino acid sequences including, but not limited to, GGSG (SEQ ID NO:90), GGSGG (SEQ ID NO:91), GSGSG (SEQ ID NO:92), GSGGG (SEQ ID NO:93), GGGSG (SEQ ID NO:94), GSSSG (SEQ ID NO:95), and the like. Exemplary linkers include (GGGGS)n (SEQ ID NO:96), where n is an integer from 1 to 20. Exemplary linkers include (GGGGS)n (SEQ ID NO:97), where n is 1, 2, 3, 4, 5, 6, or 7. Exemplary linkers include (GGS)n (SEQ ID NO:98), where n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. The ordinarily skilled artisan will recognize that design of a peptide conjugated to any desired element can include linkers that are all or partially flexible, such that the linker can include a flexible linker as well as one or more portions that confer less flexible structure.
Exemplary fusion polypeptides
[0082] In some cases, a fusion polypeptide of the present disclosure comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 3A. In some cases, a fusion polypeptide of the present disclosure comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 3B.
[0083] In some cases, a fusion polypeptide of the present disclosure comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 11 A-l 1H. As an alternative to the (GGS)5 (SEQ ID NO:38) linker depicted in FIG. 11 A-l 1H, linkers of various lengths can be used; for example, a (GGGGS)n (SEQ ID NO:99) linker (where n is an integer from 1 to 10) can be used. Similarly, the NLS depicted in FIG. 11 A-l 1H can be substituted with an NLS of a different amino acid sequence, or a different number of NLSs can be used. Furthermore, the FLAG-tag included in the fusion polypeptides can be omitted, or a different epitope tag can be used.
[0084] In some cases, a fusion polypeptide of the present disclosure comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence depicted in FIG. 12A-12J. As an alternative to the (GGS)5 (SEQ ID NO:38) linker depicted in FIG. 12A-12J, linkers of various lengths can be used; for example, a (GGGGS)n (SEQ ID NO:99) linker (where n is an integer from 1 to 10) can be used. Similarly, the NLS depicted in FIG. 12A-12J can be substituted with an NLS of a different amino acid sequence, or a different number of NLSs can be used. Furthermore, the FLAG-tag included in the fusion polypeptides can be omitted, or a different epitope tag can be used.
NUCLEIC ACIDS
[0085] The present disclosure provides a nucleic acid comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure. The present disclosure provides one or more nucleic acids comprising one or more of: a donor polynucleotide, a nucleotide sequence encoding a fusion polypeptide of the present disclosure, a guide nucleic acid (e.g., a guide RNA), and a nucleotide sequence encoding a guide nucleic acid (e.g., a guide RNA). The present disclosure provides a nucleic acid comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure. The present disclosure provides a recombinant expression vector that comprises a nucleotide sequence encoding a fusion polypeptide of the present disclosure. The present disclosure provides a recombinant expression vector that comprises: a) a nucleotide sequence encoding a fusion polypeptide of the present disclosure; and b) a nucleotide sequence encoding a guide RNA(s). In some cases, the nucleotide sequence encoding the fusion polypeptide of the present disclosure and/or the nucleotide sequence encoding the guide RNA is operably linked to a promoter that is operable in a cell type of choice (e.g., a eukaryotic cell; such as a plant cell, an animal cell, a mammalian cell, a non-human primate cell, a rodent cell, a human cell, an insect cell, an arachnid cell, a yeast cell, etc.).
[0086] In some cases, a nucleotide sequence encoding a fusion polypeptide of the present disclosure is codon optimized. This type of optimization can entail a mutation of a fusion polypeptide- encoding nucleotide sequence to mimic the codon preferences of the intended host organism or cell while encoding the same protein. Thus, the codons can be changed, but the encoded protein remains unchanged. For example, if the intended target cell was a human cell, a human codon-optimized fusion polypeptide-encoding nucleotide sequence could be used. As another non-limiting example, if the intended host cell were a mouse cell, then a mouse codon-optimized fusion polypeptide-encoding nucleotide sequence could be generated. As another non-limiting example, if the intended host cell were a plant cell, then a plant codon-optimized fusion polypeptide-encoding nucleotide sequence could be generated. As another non-limiting example, if the intended host cell were an insect cell, then an insect codon-optimized fusion polypeptide-encoding nucleotide sequence could be generated.
[0087] Codon usage tables are readily available, for example, at the "Codon Usage Database" available at www[dot]kazusa[dot]or[dot]jp[forwardslash]codon. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a eukaryotic cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in an animal cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a fungus cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a plant cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a monocotyledonous plant species. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptideencoding nucleotide sequence that is codon optimized for expression in a dicotyledonous plant species.
In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a gymnosperm plant species. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in an angiosperm plant species. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a corn cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a soybean cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a rice cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a wheat cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a cotton cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptideencoding nucleotide sequence that is codon optimized for expression in a sorghum cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in an alfalfa cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a sugar cane cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in an Arabidopsis cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a tomato cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a cucumber cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptide-encoding nucleotide sequence that is codon optimized for expression in a potato cell. In some cases, a nucleic acid of the present disclosure comprises a fusion polypeptideencoding nucleotide sequence that is codon optimized for expression in an algae cell.
[0088] The present disclosure provides one or more recombinant expression vectors that include (in different recombinant expression vectors in some cases, and in the same recombinant expression vector in some cases): (i) a nucleotide sequence of a donor template nucleic acid (where the donor template comprises a nucleotide sequence having homology to a target sequence of a target nucleic acid (e.g., a target genome)); (ii) a nucleotide sequence that encodes a guide RNA that hybridizes to a target sequence of the target locus of the targeted genome (e.g., operably linked to a promoter that is operable in a target cell such as a eukaryotic cell); and (iii) a nucleotide sequence encoding a fusion polypeptide of the present disclosure (e.g., operably linked to a promoter that is operable in a target cell such as a eukaryotic cell). The present disclosure provides one or more recombinant expression vectors that include (in separate recombinant expression vectors in some cases, and in the same recombinant expression vector in some cases): (i) a nucleotide sequence of a donor template nucleic acid (where the donor template comprises a nucleotide sequence having homology to a target sequence of a target nucleic acid (e.g., a target genome)); and (ii) a nucleotide sequence that encodes a guide RNA that hybridizes to a target sequence of the target locus of the targeted genome (e.g., operably linked to a promoter that is operable in a target cell such as a eukaryotic cell). The present disclosure provides one or more recombinant expression vectors that include (in separate recombinant expression vectors in some cases, and in the same recombinant expression vector in some cases): (i) a nucleotide sequence that encodes a guide RNA that hybridizes to a target sequence of the target locus of the targeted genome (e.g., operably linked to a promoter that is operable in a target cell such as a eukaryotic cell); and (ii) a nucleotide sequence encoding a fusion polypeptide of the present disclosure (e.g., operably linked to a promoter that is operable in a target cell such as a eukaryotic cell).
[0089] Suitable expression vectors include viral expression vectors (e.g. viral vectors based on vaccinia virus; poliovirus; adenovirus (see, e.g., Li et al., Invest Opthalmol Vis Sci 35:25432549, 1994; Borras et al., Gene Ther 6:515 524, 1999; Li and Davidson, PNAS 92:77007704, 1995; Sakamoto et al., H Gene Ther 5:1088 1097, 1999; WO 94/12649, WO 93/03769; WO 93/19191; WO 94/28938; WO 95/11984 and WO 95/00655); adeno-associated virus (AAV) (see, e.g., Ali et al., Hum Gene Ther 9:81 86, 1998, Flannery et al., PNAS 94:6916 6921, 1997; Bennett et al., Invest Opthalmol Vis Sci 38:28572863, 1997; Jomary et al., Gene Ther 4:683 690, 1997, Rolling et al., Hum Gene Ther 10:641 648, 1999; Ali et al., Hum Mol Genet 5:591 594, 1996; Srivastava in WO 93/09239, Samulski et al., J. Vir. (1989) 63:3822-3828; Mendelson et al., Virol. (1988) 166:154-165; and Flotte et al., PNAS (1993) 90:10613-10617); SV40; herpes simplex virus; human immunodeficiency virus (see, e.g., Miyoshi et al., PNAS 94:1031923, 1997; Takahashi et al., J Virol 73:78127816, 1999); a retroviral vector (e.g., Murine Leukemia Virus, spleen necrosis virus, and vectors derived from retroviruses such as Rous Sarcoma Virus, Harvey Sarcoma Virus, avian leukosis virus, a lentivirus, human immunodeficiency virus, myeloproliferative sarcoma virus, and mammary tumor virus); and the like. In some cases, a recombinant expression vector of the present disclosure is a recombinant adeno-associated virus (AAV) vector. In some cases, a recombinant expression vector of the present disclosure is a recombinant lentivirus vector. In some cases, a recombinant expression vector of the present disclosure is a recombinant retroviral vector.
[0090] For plant applications, viral vectors based on Tobamoviruses, Potexviruses, Potyviruses, Tobraviruses, Tombusviruses, Geminiviruses, Bromoviruses, Carmoviruses, Alfamoviruses, or Cucumoviruses can be used. See, e.g., Peyret and Lomonossoff (2015) Plant Biotechnol. J. 13:1121. Suitable Tobamovirus vectors include, for example, a tomato mosaic virus (ToMV) vector, a tobacco mosaic virus (TMV) vector, a tobacco mild green mosaic virus (TMGMV) vector, a pepper mild mottle virus (PMMoV) vector, a paprika mild mottle virus (PaMMV) vector, a cucumber green mottle mosaic virus (CGMMV) vector, a kyuri green mottle mosaic virus (KGMMV) vector, a hibiscus latent fort pierce virus (HLFPV) vector, an odontoglossum ringspot virus (ORSV) vector, a rehmannia mosaic virus (ReMV) vector, a Sammon's opuntia virus (SOV) vector, a wasabi mottle virus (WMoV) vector, a youcai mosaic virus (YoMV) vector, a sunn-hemp mosaic virus (SHMV) vector, and the like. Suitable Potexvirus vectors include, for example, a potato virus X (PVX) vector, a potato aucubamosaicvirus (PAMV) vector, an Alstroemeria virus X (AlsVX) vector, a cactus virus X (CVX) vector, a Cymbidium mosaic virus (CymMV) vector, a hosta virus X (HVX) vector, a lily virus X (LVX) vector, a Narcissus mosaic virus (NMV) vector, a Nerine virus X (NVX) vector, a Plantago asiatica mosaic virus (P1AMV) vector, a strawberry mild yellow edge virus (SMYEV) vector, a tulip virus X (TVX) vector, a white clover mosaic virus (WC1MV) vector, a bamboo mosaic virus (BaMV) vector, and the like. Suitable Potyvirus vectors include, for example, a potato virus Y (PVY) vector, a bean common mosaic virus (BCMV) vector, a clover yellow vein virus (C1YVV) vector, an East Asian Passiflora virus (EAPV) vector, a Freesia mosaic virus (FreMV) vector, a Japanese yam mosaic virus (JYMV) vector, a lettuce mosaic virus (LMV) vector, a Maize dwarf mosaic virus (MDMV) vector, an onion yellow dwarf virus (OYDV) vector, a papaya ringspot virus (PRSV) vector, a pepper mottle virus (PepMoV) vector, a Perilla mottle virus (PerMoV) vector, a plum pox virus (PPV) vector, a potato virus A (PVA) vector, a sorghum mosaic virus (SrMV) vector, a soybean mosaic virus (SMV) vector, a sugarcane mosaic virus (SCMV) vector, a tulip mosaic virus (TulMV) vector, a turnip mosaic virus (TuMV) vector, a watermelon mosaic virus (WMV) vector, a zucchini yellow mosaic virus (ZYMV) vector, a tobacco etch virus (TEV) vector, and the like. Suitable Tobravirus vectors include, for example, a tobacco rattle virus (TRV) vector and the like. Suitable Tombusvirus vectors include, for example, a tomato bushy stunt virus (TBSV) vector, an eggplant mottled crinkle virus (EMCV) vector, a grapevine Algerian latent virus (GALV) vector, and the like. Suitable Cucumovirus vectors include, for example, a cucumber mosaic virus (CMV) vector, a peanut stunt virus (PSV) vector, a tomato aspermy virus (TAV) vector, and the like. Suitable Bromovirus vectors include, for example, a brome mosaic virus (BMV) vector, a cowpea chlorotic mottle virus (CCMV) vector, and the like. Suitable Carmovirus vectors include, for example, a carnation mottle virus (CarMV) vector, a melon necrotic spot virus (MNSV) vector, a pea stem necrotic virus (PSNV) vector, a turnip crinkle virus (TCV) vector, and the like. Suitable Alfamovirus vectors include, for example, an alfalfa mosaic virus (AMV) vector, and the like.
[0091] Depending on the host/vector system utilized, any of a number of suitable transcription and translation control elements, including constitutive and inducible promoters, transcription enhancer elements, transcription terminators, etc. may be used in the expression vector.
[0092] In some cases, a nucleotide sequence encoding a guide RNA is operably linked to a control element, e.g., a transcriptional control element, such as a promoter. In some cases, a nucleotide sequence encoding a fusion polypeptide of the present disclosure is operably linked to a control element, e.g., a transcriptional control element, such as a promoter.
[0093] The transcriptional control element can be a promoter. In some cases, the promoter is a constitutively active promoter. In some cases, the promoter is a regulatable promoter. In some cases, the promoter is an inducible promoter. In some cases, the promoter is a tissue-specific promoter. In some cases, the promoter is a cell type-specific promoter. In some cases, the transcriptional control element (e.g., the promoter) is functional in a targeted cell type or targeted cell population. For example, in some cases, the transcriptional control element can be functional in eukaryotic cells, e.g., hematopoietic stem cells (e.g., mobilized peripheral blood (mPB) CD34(+) cell, bone marrow (BM) CD34(+) cell, etc.). [0094] Non-limiting examples of eukaryotic promoters (promoters functional in a eukaryotic cell) include EFla, those from cytomegalovirus (CMV) immediate early, herpes simplex virus (HSV) thymidine kinase, early and late SV40, long terminal repeats (LTRs) from retrovirus, and mouse metallothionein-I. Selection of the appropriate vector and promoter is well within the level of ordinary skill in the art. The expression vector may also contain a ribosome binding site for translation initiation and a transcription terminator. The expression vector may also include appropriate sequences for amplifying expression. The expression vector may also include nucleotide sequences encoding protein tags (e.g., 6xHis tag, hemagglutinin tag, fluorescent protein, etc.) that can be fused a fusion polypeptide of the present disclosure.
[0095] In some cases, a nucleotide sequence encoding a guide RNA and/or a fusion polypeptide of the present disclosure is operably linked to an inducible promoter. In some embodiments, a nucleotide sequence encoding a guide RNA and/or a fusion polypeptide of the present disclosure is operably linked to a constitutive promoter.
[0096] A promoter can be a constitutively active promoter (i.e., a promoter that is constitutively in an active/”ON” state), it may be an inducible promoter (i.e., a promoter whose state, active/”ON” or inactive/4 OFF”, is controlled by an external stimulus, e.g., the presence of a particular temperature, compound, or protein.), it may be a spatially restricted promoter (i.e., transcriptional control element, enhancer, etc.)(e.g., tissue specific promoter, cell type specific promoter, etc.), and it may be a temporally restricted promoter (i.e., the promoter is in the “ON” state or “OFF” state during specific stages of embryonic development or during specific stages of a biological process, e.g., hair follicle cycle in mice).
[0097] Suitable promoters can be derived from viruses and can therefore be referred to as viral promoters, or they can be derived from any organism, including prokaryotic or eukaryotic organisms. Suitable promoters can be used to drive expression by any RNA polymerase (e.g., pol I, pol II, pol III). Exemplary promoters include, but are not limited to the SV40 early promoter, mouse mammary tumor virus long terminal repeat (LTR) promoter; adenovirus major late promoter (Ad MLP); a herpes simplex virus (F1SV) promoter, a cytomegalovirus (CMV) promoter such as the CMV immediate early promoter region (CMVIE), a rous sarcoma virus (RSV) promoter, a human U6 small nuclear promoter (U6) (Miyagishi et al., Nature Biotechnology 20, 497 - 500 (2002)), an enhanced U6 promoter (e.g., Xia et al., Nucleic Acids Res. 2003 Sep 1 ;31 (17)), a human HI promoter (HI), and the like.
[0098] In some cases, a nucleotide sequence encoding a guide RNA is operably linked to (under the control of) a promoter operable in a eukaryotic cell (e.g., a U6 promoter, an enhanced U6 promoter, an HI promoter, and the like). As would be understood by one of ordinary skill in the art, when expressing an RNA (e.g., a guide RNA) from a nucleic acid (e.g., an expression vector) using a U6 promoter (e.g., in a eukaryotic cell), or another PolIII promoter, the RNA may need to be mutated if there are several Ts in a row (coding for Us in the RNA). This is because a string of Ts (e.g., 5 Ts) in DNA can act as a terminator for polymerase III (PolIII). Thus, in order to ensure transcription of a guide RNA in a eukaryotic cell it may sometimes be necessary to modify the sequence encoding the guide RNA to eliminate runs of Ts. In some cases, a nucleotide sequence encoding a fusion polypeptide of the present disclosure is operably linked to a promoter operable in a eukaryotic cell (e.g., a CMV promoter, an EFla promoter, an estrogen receptor-regulated promoter, and the like).
[0099] Methods of introducing a nucleic acid (e.g., a nucleic acid comprising a donor polynucleotide sequence, one or more nucleic acids encoding a fusion polypeptide of the present disclosure and/or a guide RNA, and the like) into a host cell are known in the art, and any convenient method can be used to introduce a nucleic acid (e.g., an expression construct) into a cell. Suitable methods include e.g., viral infection, transfection, lipofection, electroporation, calcium phosphate precipitation, polyethyleneimine (PEI)-mediated transfection, DEAE-dextran mediated transfection, liposome-mediated transfection, particle gun technology, calcium phosphate precipitation, direct microinjection, nanoparticle -mediated nucleic acid delivery, and the like.
[00100] Introducing the recombinant expression vector into cells can occur in any culture media and under any culture conditions that promote the survival of the cells. Introducing the recombinant expression vector into a target cell can be carried out in vivo or ex vivo. Introducing the recombinant expression vector into a target cell can be carried out in vitro.
Introducing components into a target cell
[00101] A guide RNA (or a nucleic acid comprising a nucleotide sequence encoding same) and/or a fusion polypeptide of the present disclosure (or a nucleic acid comprising a nucleotide sequence encoding same) and/or a donor polynucleotide (donor template) can be introduced into a host cell by any of a variety of well-known methods. Any of a variety of compounds and methods can be used to deliver to a target cell a system of the present disclosure (e.g., where a system of the present disclosure comprises: a) a fusion polypeptide of the present disclosure; and a CRISPR/Cas guide nucleic acid; b) a fusion polypeptide of the present disclosure; a CRISPR/Cas guide nucleic acid, and a DNA donor template; c) a fusion polypeptide of the present disclosure; and a CRISPR/Cas guide RNA; d) a fusion polypeptide of the present disclosure; a CRISPR/Cas guide RNA, and a DNA donor template; e) an mRNA encoding a fusion polypeptide of the present disclosure; and a CRISPR/Cas guide nucleic acid; f) an mRNA encoding a fusion polypeptide of the present disclosure; a CRISPR/Cas guide nucleic acid, and a DNA donor template; g) an mRNA encoding a fusion polypeptide of the present disclosure; and a CRISPR/Cas guide RNA; h) an mRNA encoding a fusion polypeptide of the present disclosure; a CRISPR/Cas guide RNA, and a DNA donor template; i) one or more recombinant expression vectors comprising: i) a nucleotide sequence encoding a fusion polypeptide of the present disclosure; and ii) a nucleotide sequence encoding a CRISPR/Cas guide nucleic acid; j) one or more recombinant expression vectors comprising: i) a nucleotide sequence encoding a fusion polypeptide of the present disclosure; ii) a nucleotide sequence encoding a CRISPR/Cas guide nucleic acid; and iii) a DNA donor template; k) one or more recombinant expression vectors comprising: i) a nucleotide sequence encoding a fusion polypeptide of the present disclosure; and ii) a nucleotide sequence encoding a CRISPR/Cas guide RNA; or 1) one or more recombinant expression vectors comprising: i) a nucleotide sequence encoding a fusion polypeptide of the present disclosure; ii) a nucleotide sequence encoding a CRISPR/Cas guide RNA; and a DNA donor template; or some variation of one of (a) through (1). As a non-limiting example, a system of the present disclosure can be combined with a lipid. As another non-limiting example, a system of the present disclosure can be combined with a particle, or formulated into a particle.
[00102] Methods of introducing a nucleic acid into a host cell are known in the art, and any convenient method can be used to introduce a subject nucleic acid (e.g., an expression construct/vector) into a target cell (e.g., prokaryotic cell, eukaryotic cell, plant cell, animal cell, mammalian cell, human cell, and the like). Suitable methods include, e.g., viral infection, transfection, conjugation, protoplast fusion, lipofection, electroporation, calcium phosphate precipitation, polyethyleneimine (PEI) -mediated transfection, DEAE-dextran mediated transfection, liposome-mediated transfection, particle gun technology, calcium phosphate precipitation, direct micro injection, nanoparticle-mediated nucleic acid delivery (see, e.g., Panyam et., al Adv Drug Deliv Rev. 2012 Sep 13. pii: S0169-409X(12)00283-9. doi: 10.1016/j.addr.2012.09.023 ), and the like.
[00103] In some cases, a fusion polypeptide of the present disclosure is provided as a nucleic acid (e.g., an mRNA, a DNA, a plasmid, an expression vector, a viral vector, etc.) that encodes the fusion polypeptide. In some cases, a fusion polypeptide of the present disclosure is provided directly as a protein (e.g., without an associated guide RNA or with an associate guide RNA, i.e., as a ribonucleoprotein complex). A fusion polypeptide of the present disclosure can be introduced into a cell (provided to the cell) by any convenient method; such methods are known to those of ordinary skill in the art. As an illustrative example, a fusion polypeptide of the present disclosure can be injected directly into a cell (e.g., with or without a guide RNA or nucleic acid encoding a guide RNA, and with or without a donor polynucleotide). As another example, a preformed complex of a fusion polypeptide of the present disclosure and a guide RNA (an RNP) can be introduced into a cell (e.g., a eukaryotic cell) (e.g., via injection, via nucleofection; via a protein transduction domain (PTD) conjugated to one or more components, e.g., conjugated to the fusion polypeptide of the present disclosure, conjugated to a guide RNA, conjugated to a fusion polypeptide of the present disclosure and a guide RNA; etc.).
[00104] In some cases, a nucleic acid (e.g., a guide RNA; a nucleic acid comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure; etc.) is delivered to a cell (e.g., a target host cell) and/or a polypeptide (e.g., a fusion polypeptide of the present disclosure) in a particle, or associated with a particle. In some cases, a system of the present disclosure is delivered to a cell in a particle, or associated with a particle. The terms “particle” and “nanoparticle” can be used interchangeably, as appropriate. A recombinant expression vector comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure and/or a guide RNA, an mRNA comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure, and guide RNA may be delivered simultaneously using particles or lipid envelopes; for instance, a fusion polypeptide of the present disclosure and a guide RNA, e.g., as a complex (e.g., a ribonucleoprotein (RNP) complex), can be delivered via a particle, e.g., a delivery particle comprising lipid or lipidoid and hydrophilic polymer, e.g., a cationic lipid and a hydrophilic polymer, for instance wherein the cationic lipid comprises 1,2- dioleoyl-3-trimethylammonium-propane (DOTAP) or 1 ,2-ditetradecanoyl-sn-glycero-3-phosphocholine (DMPC) and/or wherein the hydrophilic polymer comprises ethylene glycol or polyethylene glycol (PEG); and/or wherein the particle further comprises cholesterol (e.g., particle from formulation l=DOTAP 100, DMPC 0, PEG 0, Cholesterol 0; formulation number 2=DOTAP 90, DMPC 0, PEG 10, Cholesterol 0; formulation number 3=DOTAP 90, DMPC 0, PEG 5, Cholesterol 5). For example, a particle can be formed using a multistep process in which a fusion polypeptide of the present disclosure and a guide RNA are mixed together, e.g., at a 1:1 molar ratio, e.g., at room temperature, e.g., for 30 minutes, e.g., in sterile, nuclease free 1 x phosphate-buffered saline (PBS); and separately, DOTAP, DMPC, PEG, and cholesterol as applicable for the formulation are dissolved in alcohol, e.g., 100% ethanol; and, the two solutions are mixed together to form particles containing the complexes).
[00105] A fusion polypeptide of the present disclosure (or an mRNA comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure; or a recombinant expression vector comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure) and/or guide RNA (or a nucleic acid such as one or more expression vectors encoding the guide RNA) may be delivered simultaneously using particles or lipid envelopes. For example, a biodegradable core-shell structured nanoparticle with a poly (b-amino ester) (PBAE) core enveloped by a phospholipid bilayer shell can be used. In some cases, particles/nanoparticles based on self assembling bioadhesive polymers are used; such particles/nanoparticles may be applied to oral delivery of peptides, intravenous delivery of peptides and nasal delivery of peptides, e.g., to the brain. Other embodiments, such as oral absorption and ocular delivery of hydrophobic drugs are also contemplated. A molecular envelope technology, which involves an engineered polymer envelope which is protected and delivered to the site of the disease, can be used. Doses of about 5 mg/kg can be used, with single or multiple doses, depending on various factors, e.g., the target tissue.
[00106] Lipidoid compounds (e.g., as described in US patent application 20110293703) are also useful in the administration of polynucleotides, and can be used to deliver fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure In one aspect, the aminoalcohol lipidoid compounds are combined with an agent to be delivered to a cell or a subject to form microparticles, nanoparticles, liposomes, or micelles. The aminoalcohol lipidoid compounds may be combined with other aminoalcohol lipidoid compounds, polymers (synthetic or natural), surfactants, cholesterol, carbohydrates, proteins, lipids, etc. to form the particles. These particles may then optionally be combined with a pharmaceutical excipient to form a pharmaceutical composition.
[00107] A poly(beta-amino alcohol) (PBAA) can be used to deliver a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell. US Patent Publication No. 20130302401 relates to a class of poly(beta-amino alcohols) (PBAAs) that has been prepared using combinatorial polymerization.
[00108] Sugar-based particles may be used, for example GalNAc, as described with reference to
WO2014118272 (incorporated herein by reference) and Nair, J K et al., 2014, Journal of the American Chemical Society 136 (49), 16958-16961) can be used to deliver a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell.
[00109] In some cases, lipid nanoparticles (LNPs) are used to deliver a fusion polypeptide of the present disclosure an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell. Negatively charged polymers such as RNA may be loaded into LNPs at low pH values (e.g., pH 4) where the ionizable lipids display a positive charge. However, at physiological pH values, the LNPs exhibit a low surface charge compatible with longer circulation times. Four species of ionizable cationic lipids have been focused upon, namely l,2-dilineoyl-3- dimethylammonium-propane (DLinDAP), l,2-dilinoleyloxy-3-N,N-dimethylaminopropane (DLinDMA),
1.2-dilinoleyloxy-keto-N,N-dimethyl-3-aminopropane (DLinKDMA), and 1 ,2-dilinoleyl-4-(2- dimethylaminoethyl)-[l,3]-dioxolane (DLinKC2-DMA). Preparation of LNPs and is described in, e.g., Rosin et al. (2011) Molecular Therapy 19:1286-2200). The cationic lipids l,2-dilineoyl-3- dimethylammonium-propane (DLinDAP), l,2-dilinoleyloxy-3-N,N-dimethylaminopropane (DLinDMA),
1.2-dilinoleyloxyketo-N,N-dimethyl-3-aminopropane (DLinK-DMA), 1 ,2-dilinoleyl-4-(2- dimethylaminoethyl)-[l,3]-dioxolane (DLinKC2-DMA), (3-o-[2"-(methoxypolyethyleneglycol 2000) succinoyl]-l,2-dimyristoyl-sn-glycol (PEG-S-DMG), and R-3-[(.omega.-methoxy-poly(ethylene glycol)2000) carbamoyl]-l,2-dimyristyloxlpropyl-3-amine (PEG-C-DOMG) may be used. A nucleic acid (e.g., a guide RNA; a nucleic acid of the present disclosure; etc.) may be encapsulated in LNPs containing DLinDAP, DLinDMA, DLinK-DMA, and DLinKC2-DMA (cationic lipid:DSPC:CHOL: PEGS-DMG or PEG-C-DOMG at 40:10:40:10 molar ratios). In some cases, 0.2% SP-DiOC18 is incorporated.
[00110] Spherical Nucleic Acid (SNA™) constructs and other nanoparticles (particularly gold nanoparticles) can be used to deliver a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell.. See, e.g., Cutler et al., J. Am. Chem. Soc. 2011 133:9254-9257, Hao et al., Small. 2011 7:3158-3162, Zhang et al., ACS Nano. 2011 5:6962-6970, Cutler et al., J. Am. Chem. Soc. 2012 134:1376-1391, Young et al., Nano Lett. 2012 12:3867-71, Zheng et al., Proc. Natl. Acad. Sci. USA. 2012 109:11975-80, Mirkin, Nanomedicine 20127:635-638 Zhang et al., J. Am. Chem. Soc. 2012 134:16488-1691, Weintraub, Nature 2013 495:S14-S16, Choi et al., Proc. Natl. Acad. Sci. USA. 2013 110(19): 7625-7630, Jensen et al., Sci. Transl. Med. 5, 209ral52 (2013) and Mirkin, et al., Small, 10:186-192.
[00111] Self-assembling nanoparticles with RNA may be constructed with polyethyleneimine
(PEI) that is PEGylated with an Arg-Gly-Asp (RGD) peptide ligand attached at the distal end of the polyethylene glycol (PEG).
[00112] In general, a "nanoparticle" refers to any particle having a diameter of less than 1000 nm. In some cases, nanoparticles suitable for use in delivering a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell have a diameter of 500 nm or less, e.g., from 25 nm to 35 nm, from 35 nm to 50 nm, from 50 nm to 75 nm, from 75 nm to 100 nm, from 100 nm to 150 nm, from 150 nm to 200 nm, from 200 nm to 300 nm, from 300 nm to 400 nm, or from 400 nm to 500 nm. In some cases, nanoparticles suitable for use in delivering a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell have a diameter of from 25 nm to 200 nm. In some cases, nanoparticles suitable for use in delivering a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell have a diameter of 100 nm or less In some cases, nanoparticles suitable for use in delivering a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell have a diameter of from 35 nm to 60 nm.
[00113] Nanoparticles suitable for use in delivering a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell may be provided in different forms, e.g., as solid nanoparticles (e.g., metal such as silver, gold, iron, titanium), non-metal, lipid-based solids, polymers), suspensions of nanoparticles, or combinations thereof. Metal, dielectric, and semiconductor nanoparticles may be prepared, as well as hybrid structures (e.g., core-shell nanoparticles). Nanoparticles made of semiconducting material may also be labeled quantum dots if they are small enough (typically below 10 nm) that quantization of electronic energy levels occurs. Such nanoscale particles are used in biomedical applications as drug carriers or imaging agents and may be adapted for similar purposes in the present disclosure.
[00114] Semi-solid and soft nanoparticles are also suitable for use in delivering fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell. A prototype nanoparticle of semi-solid nature is the liposome.
[00115] In some cases, an exosome is used to deliver a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell. Exosomes are endogenous nano-vesicles that transport RNAs and proteins, and which can deliver RNA to the brain and other target organs.
[00116] In some cases, a liposome is used to deliver a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell. Liposomes are spherical vesicle structures composed of a uni- or multilamellar lipid bilayer surrounding internal aqueous compartments and a relatively impermeable outer lipophilic phospholipid bilayer. Liposomes can be made from several different types of lipids; however, phospholipids are most commonly used to generate liposomes. Although liposome formation is spontaneous when a lipid film is mixed with an aqueous solution, it can also be expedited by applying force in the form of shaking by using a homogenizer, sonicator, or an extrusion apparatus. Several other additives may be added to liposomes in order to modify their structure and properties. Lor instance, either cholesterol or sphingomyelin may be added to the liposomal mixture in order to help stabilize the liposomal structure and to prevent the leakage of the liposomal inner cargo. A liposome formulation may be mainly comprised of natural phospholipids and lipids such as l,2-distearoryl-sn-glycero-3- phosphatidyl choline (DSPC), sphingomyelin, egg phosphatidylcholines and monosialoganglioside. [00117] A stable nucleic-acid-lipid particle (SNALP) can be used to deliver a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell. The SNALP formulation may contain the lipids 3-N- [(methoxypoly(ethylene glycol) 2000) carbamoyl] -1,2-dimyristyloxy-propylamine (PEG-C-DMA), 1,2- dilinoleyloxy-N,N-dimethyl-3-aminopropane (DLinDMA), l,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) and cholesterol, in a 2:40:10:48 molar percent ratio. The SNALP liposomes may be prepared by formulating D-Lin-DMA and PEG-C-DMA with distearoylphosphatidylcholine (DSPC), Cholesterol and siRNA using a 25:1 lipid/siRNA ratio and a 48/40/10/2 molar ratio of Cholesterol/D-Lin- DMA/DSPC/PEG-C-DMA. The resulting SNALP liposomes can be about 80-100 nm in size. A SNALP may comprise synthetic cholesterol (Sigma-Aldrich, St Louis, Mo., USA), dipalmitoylphosphatidylcholine (Avanti Polar Lipids, Alabaster, Ala., USA), 3-N-[(w-methoxy poly(ethylene glycol)2000)carbamoyl]-l,2-dimyrestyloxypropylamine, and cationic l,2-dilinoleyloxy-3- N,Ndimethylaminopropane. A SNALP may comprise synthetic cholesterol (Sigma-Aldrich), 1,2- distearoyl-sn-glycero-3-phosphocholine (DSPC; Avanti Polar Lipids Inc.), PEG-cDMA, and 1,2- dilinoleyloxy-3-(N ;N-dimethyl)aminopropane (DLinDMA). [00118] Other cationic lipids, such as amino lipid 2,2-dilinoleyl-4-dimethylaminoethyl-[l,3]- dioxolane (DLin-KC2-DMA) can be used to deliver a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell. A preformed vesicle with the following lipid composition may be contemplated: amino lipid, distearoylphosphatidylcholine (DSPC), cholesterol and (R)-2,3- bis(octadecyloxy) propyl- l-(methoxy poly(ethylene glycol)2000)propylcarbamate (PEG-lipid) in the molar ratio 40/10/40/10, respectively, and a FVII siRNA/total lipid ratio of approximately 0.05 (w/w). To ensure a narrow particle size distribution in the range of 70-90 nm and a low polydispersity index of 0.11.+-.0.04 (n=56), the particles may be extruded up to three times through 80 nm membranes prior to adding the guide RNA. Particles containing the highly potent amino lipid 16 may be used, in which the molar ratio of the four lipid components 16, DSPC, cholesterol and PEG-lipid (50/10/38.5/1.5) which may be further optimized to enhance in vivo activity.
[00119] Lipids may be formulated with a system of the present disclosure or component(s) thereof or nucleic acids encoding the same to form lipid nanoparticles (LNPs). Suitable lipids include, but are not limited to, DLin-KC2-DMA4, C12-200 and colipids disteroylphosphatidyl choline, cholesterol, and PEG-DMG may be formulated with a system, or component thereof, of the present disclosure, using a spontaneous vesicle formation procedure. The component molar ratio may be about 50/10/38.5/1.5 (DLin-KC2-DMA or C12-200/disteroylphosphatidyl choline/cholesterol/PEG-DMG). [00120] A system of the present disclosure, or a component thereof, may be delivered encapsulated in PLGA microspheres such as that further described in US published applications 20130252281 and 20130245107 and 20130244279.
[00121] Supercharged proteins can be used to deliver a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell. Supercharged proteins are a class of engineered or naturally occurring proteins with unusually high positive or negative net theoretical charge. Both supernegatively and superpositively charged proteins exhibit the ability to withstand thermally or chemically induced aggregation. Superpositively charged proteins are also able to penetrate mammalian cells. Associating cargo with these proteins, such as plasmid DNA, RNA, or other proteins, can enable the functional delivery of these macromolecules into mammalian cells both in vitro and in vivo.
[00122] Cell Penetrating Peptides (CPPs) can be used to deliver a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell. CPPs typically have an amino acid composition that either contains a high relative abundance of positively charged amino acids such as lysine or arginine or has sequences that contain an alternating pattern of polar/charged amino acids and non-polar, hydrophobic amino acids.
[00123] An implantable device can be used to deliver a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure (e.g., a guide RNA, a nucleic acid encoding a guide RNA, a nucleic acid encoding a fusion polypeptide of the present disclosure, a donor template, and the like), or a system of the present disclosure, to a target cell (e.g., a target cell in vivo, where the target cell is a target cell in circulation, a target cell in a tissue, a target cell in an organ, etc.). An implantable device suitable for use in delivering a fusion polypeptide of the present disclosure, an RNP of the present disclosure, a nucleic acid of the present disclosure, or a system of the present disclosure, to a target cell (e.g., a target cell in vivo, where the target cell is a target cell in circulation, a target cell in a tissue, a target cell in an organ, etc.) can include a container (e.g., a reservoir, a matrix, etc.) that comprises the fusion polypeptide of the present disclosure, the RNP, or the system (or component thereof, e.g., a nucleic acid of the present disclosure).
[00124] A suitable implantable device can comprise a polymeric substrate, such as a matrix for example, that is used as the device body, and in some cases additional scaffolding materials, such as metals or additional polymers, and materials to enhance visibility and imaging. An implantable delivery device can be advantageous in providing release locally and over a prolonged period, where the polypeptide and/or nucleic acid to be delivered is released directly to a target site, e.g., the extracellular matrix (ECM), the vasculature surrounding a tumor, a diseased tissue, etc. Suitable implantable delivery devices include devices suitable for use in delivering to a cavity such as the abdominal cavity and/or any other type of administration in which the drug delivery system is not anchored or attached, comprising a biostable and/or degradable and/or bioabsorbable polymeric substrate, which may for example optionally be a matrix. In some cases, a suitable implantable drug delivery device comprises degradable polymers, wherein the main release mechanism is bulk erosion. In some cases, a suitable implantable drug delivery device comprises non degradable, or slowly degraded polymers, wherein the main release mechanism is diffusion rather than bulk erosion, so that the outer part functions as membrane, and its internal part functions as a drug reservoir, which practically is not affected by the surroundings for an extended period (for example from about a week to about a few months). Combinations of different polymers with different release mechanisms may also optionally be used. The concentration gradient at the can be maintained effectively constant during a significant period of the total releasing period, and therefore the diffusion rate is effectively constant (termed "zero mode" diffusion). By the term "constant" it is meant a diffusion rate that is maintained above the lower threshold of therapeutic effectiveness, but which may still optionally feature an initial burst and/or may fluctuate, for example increasing and decreasing to a certain degree. The diffusion rate can be so maintained for a prolonged period, and it can be considered constant to a certain level to optimize the therapeutically effective period, for example the effective silencing period.
[00125] In some cases, the implantable delivery system is designed to shield the nucleotide based therapeutic agent from degradation, whether chemical in nature or due to attack from enzymes and other factors in the body of the subject.
[00126] The site for implantation of the device, or target site, can be selected for maximum therapeutic efficacy. For example, a delivery device can be implanted within or in the proximity of a tumor environment, or the blood supply associated with a tumor. The target location can be, e.g.: 1) the brain at degenerative sites like in Parkinson or Alzheimer disease at the basal ganglia, white and gray matter; 2) the spine, as in the case of amyotrophic lateral sclerosis (ALS); 3) uterine cervix; 4) active and chronic inflammatory joints; 5) dermis as in the case of psoriasis; 7) sympathetic and sensoric nervous sites for analgesic effect; 7) a bone; 8) a site of acute or chronic infection; 9) Intra vaginal; 10) Inner ear- -auditory system, labyrinth of the inner ear, vestibular system; 11) Intra tracheal; 12) Intra-cardiac; coronary, epicardiac; 13) urinary tract or bladder; 14) biliary system; 15) parenchymal tissue including and not limited to the kidney, liver, spleen; 16) lymph nodes; 17) salivary glands; 18) dental gums; 19) Intra-articular (into joints); 20) Intra-ocular; 21) Brain tissue; 22) Brain ventricles; 23) Cavities, including abdominal cavity (for example but without limitation, for ovary cancer); 24) Intra esophageal; and 25) Intra rectal; and 26) into the vasculature.
[00127] The method of insertion, such as implantation, may optionally already be used for other types of tissue implantation and/or for insertions and/or for sampling tissues, optionally without modifications, or alternatively optionally only with non-major modifications in such methods. Such methods optionally include but are not limited to brachytherapy methods, biopsy, endoscopy with and/or without ultrasound, such as stereotactic methods into the brain tissue, laparoscopy, including implantation with a laparoscope into joints, abdominal organs, the bladder wall and body cavities.
CELLS
[00128] The present disclosure provides a cell (a “modified cell”) comprising a fusion polypeptide of the present disclosure. The present disclosure provides a cell (a “modified cell”) comprising a nucleic acid of the present disclosure (e.g., a nucleic acid comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure).
[00129] The present disclosure provides a modified cell comprising a fusion polypeptide of the present disclosure and/or a nucleic acid comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure. The present disclosure provides a modified cell comprising a fusion polypeptide of the present disclosure, where the modified cell is a cell that does not normally comprise a fusion polypeptide of the present disclosure. The present disclosure provides a modified cell (e.g., a genetically modified cell) comprising nucleic acid comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure. The present disclosure provides a genetically modified cell that is genetically modified with an mRNA comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure. The present disclosure provides a genetically modified cell that is genetically modified with a recombinant expression vector comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure. The present disclosure provides a genetically modified cell that is genetically modified with a recombinant expression vector comprising: a) a nucleotide sequence encoding a fusion polypeptide of the present disclosure; and b) a nucleotide sequence encoding a guide RNA of the present disclosure. The present disclosure provides a genetically modified cell that is genetically modified with a recombinant expression vector comprising: a) a nucleotide sequence encoding a fusion polypeptide of the present disclosure; b) a nucleotide sequence encoding a guide RNA of the present disclosure; and c) a nucleotide sequence encoding a donor template.
[00130] A cell that serves as a recipient for a fusion polypeptide of the present disclosure and/or a nucleic acid comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure and/or a guide RNA and/or a donor template, can be any of a variety of eukaryotic cells, including, e.g., in vitro cells; in vivo cells; ex vivo cells; primary cells; cancer cells; animal cells; plant cells; algal cells; fungal cells; etc. A cell that serves as a recipient for a fusion polypeptide of the present disclosure and/or a nucleic acid comprising a nucleotide sequence encoding a fusion polypeptide of the present disclosure and/or a guide RNA is referred to as a “host cell” or a “target cell.” A host cell or a target cell can be a recipient of a system of the present disclosure, or a component of a system of the present disclosure. A host cell or a target cell can be a recipient of an RNP of the present disclosure. A host cell or a target cell can be a recipient of a single component of a system of the present disclosure.
[00131] Non-limiting examples of cells (target cells) include: a prokaryotic cell, eukaryotic cell, a bacterial cell, an archaeal cell, a cell of a single-cell eukaryotic organism, a protozoa cell, a cell from a plant (e.g., cells from plant crops, fruits, vegetables, grains, soy bean, corn, maize, wheat, seeds, tomatoes, rice, cassava, sugarcane, pumpkin, hay, potatoes, cotton, cannabis, tobacco, flowering plants, conifers, gymnosperms, angiosperms, ferns, clubmosses, hornworts, liverworts, mosses, dicotyledons, monocotyledons, etc.), an algal cell, (e.g., Botryococcus braunii, Chlamydomonas reinhardtii, Nannochloropsis gaditana, Chlorella pyrenoidosa, Sargassum patens, C. agardh, and the like), seaweeds (e.g. kelp) a fungal cell (e.g., a yeast cell, a cell from a mushroom), an animal cell, a cell from an invertebrate animal (e.g., fruit fly, cnidarian, echinoderm, nematode, etc.), a cell from a vertebrate animal (e.g., fish, amphibian, reptile, bird, mammal), a cell from a mammal (e.g., an ungulate (e.g., a pig, a cow, a goat, a sheep); a rodent (e.g., a rat, a mouse); a non-human primate; a human; a feline (e.g., a cat); a canine (e.g., a dog); etc.), and the like. In some cases, the cell is a cell that does not originate from a natural organism (e.g., the cell can be a synthetically made cell; also referred to as an artificial cell). [00132] A cell can be an in vitro cell (e.g., established cultured cell line). A cell can be an ex vivo cell (cultured cell from an individual). A cell can be and in vivo cell (e.g., a cell in an individual). A cell can be an isolated cell. A cell can be a cell inside of an organism. A cell can be an organism. A cell can be a cell in a cell culture (e.g., in vitro cell culture). A cell can be one of a collection of cells. A cell can be a eukaryotic cell or derived from a eukaryotic cell. A cell can be a plant cell or derived from a plant cell. A cell can be an animal cell or derived from an animal cell. A cell can be an invertebrate cell or derived from an invertebrate cell. A cell can be a vertebrate cell or derived from a vertebrate cell. A cell can be a mammalian cell or derived from a mammalian cell. A cell can be a rodent cell or derived from a rodent cell. A cell can be a human cell or derived from a human cell. A cell can be a fungi cell or derived from a fungi cell. A cell can be an insect cell. A cell can be an arthropod cell. A cell can be a protozoan cell. A cell can be a helminth cell.
[00133] Suitable cells include a stem cell (e.g. an embryonic stem (ES) cell, an induced pluripotent stem (iPS) cell; a germ cell (e.g., an oocyte, a sperm, an oogonia, a spermatogonia, etc.); a somatic cell, e.g. a fibroblast, an oligodendrocyte, a glial cell, a hematopoietic cell, a neuron, a muscle cell, a bone cell, a hepatocyte, a pancreatic cell, etc.
[00134] Suitable cells include human embryonic stem cells, fetal cardiomyocytes, myofibroblasts, mesenchymal stem cells, cardiomyocytes, adipocytes, totipotent cells, pluripotent cells, blood stem cells, myoblasts, adult stem cells, bone marrow cells, mesenchymal cells, embryonic stem cells, parenchymal cells, epithelial cells, endothelial cells, mesothelial cells, fibroblasts, osteoblasts, chondrocytes, exogenous cells, endogenous cells, stem cells, hematopoietic stem cells, bone-marrow derived progenitor cells, myocardial cells, skeletal cells, fetal cells, undifferentiated cells, multi-potent progenitor cells, unipotent progenitor cells, monocytes, cardiac myoblasts, skeletal myoblasts, macrophages, capillary endothelial cells, xenogeneic cells, allogenic cells, and post-natal stem cells. [00135] In some cases, the cell is an immune cell, a neuron, an epithelial cell, and endothelial cell, or a stem cell. In some cases, the immune cell is a T cell, a B cell, a monocyte, a natural killer cell, a dendritic cell, or a macrophage. In some cases, the immune cell is a cytotoxic T cell. In some cases, the immune cell is a helper T cell. In some cases, the immune cell is a regulatory T cell (Treg).
[00136] In some cases, the cell is a stem cell. Stem cells include adult stem cells. Adult stem cells are also referred to as somatic stem cells.
[00137] Adult stem cells are resident in differentiated tissue, but retain the properties of selfrenewal and ability to give rise to multiple cell types, usually cell types typical of the tissue in which the stem cells are found. Numerous examples of somatic stem cells are known to those of skill in the art, including muscle stem cells; hematopoietic stem cells; epithelial stem cells; neural stem cells; mesenchymal stem cells; mammary stem cells; intestinal stem cells; mesodermal stem cells; endothelial stem cells; olfactory stem cells; neural crest stem cells; and the like.
[00138] Stem cells of interest include mammalian stem cells, where the term “mammalian” refers to any animal classified as a mammal, including humans; non-human primates; domestic and farm animals; and zoo, laboratory, sports, or pet animals, such as dogs, horses, cats, cows, mice, rats, rabbits, etc. In some cases, the stem cell is a human stem cell. In some cases, the stem cell is a rodent (e.g., a mouse; a rat) stem cell. In some cases, the stem cell is a non-human primate stem cell.
[00139] Stem cells can express one or more stem cell markers, e.g., SOX9, KRT19, KRT7,
LGR5, CA9, FXYD2, CDH6, CLDN18, TSPAN8, BPIFB1, OLFM4, CDH17, and PPARGC1A.
[00140] In some embodiments, the stem cell is a hematopoietic stem cell (HSC). HSCs are mesoderm-derived cells that can be isolated from bone marrow, blood, cord blood, fetal liver and yolk sac. HSCs are characterized as CD34+ and CD3 . HSCs can repopulate the erythroid, neutrophil- macrophage, megakaryocyte and lymphoid hematopoietic cell lineages in vivo. In vitro, HSCs can be induced to undergo at least some self-renewing cell divisions and can be induced to differentiate to the same lineages as is seen in vivo. As such, HSCs can be induced to differentiate into one or more of erythroid cells, megakaryocytes, neutrophils, macrophages, and lymphoid cells.
[00141] In other embodiments, the stem cell is a neural stem cell (NSC). Neural stem cells
(NSCs) are capable of differentiating into neurons, and glia (including oligodendrocytes, and astrocytes). A neural stem cell is a multipotent stem cell which is capable of multiple divisions, and under specific conditions can produce daughter cells which are neural stem cells, or neural progenitor cells that can be neuroblasts or glioblasts, e.g., cells committed to become one or more types of neurons and glial cells respectively. Methods of obtaining NSCs are known in the art.
[00142] In other embodiments, the stem cell is a mesenchymal stem cell (MSC). MSCs originally derived from the embryonal mesoderm and isolated from adult bone marrow, can differentiate to form muscle, bone, cartilage, fat, marrow stroma, and tendon. Methods of isolating MSC are known in the art; and any known method can be used to obtain MSC. See, e.g., U.S. Pat. No. 5,736,396, which describes isolation of human MSC.
[00143] A cell is in some cases a plant cell. A plant cell can be a cell of a monocotyledon. A cell can be a cell of a dicotyledon.
[00144] In some cases, the cell is a plant cell. For example, the cell can be a cell of a major agricultural plant, e.g., Barley, Beans (Dry Edible), Canola, Corn, Cotton (Pima), Cotton (Upland), Flaxseed, Hay (Alfalfa), Hay (Non- Alfalfa), Oats, Peanuts, Rice, Sorghum, Soybeans, Sugarbeets, Sugarcane, Sunflowers (Oil), Sunflowers (Non-Oil), Sweet Potatoes , Tobacco (Burley), Tobacco (Flue- cured), Tomatoes, Wheat (Durum), Wheat (Spring), Wheat (Winter), and the like. As another example, the cell is a cell of a vegetable crops which include but are not limited to, e.g., alfalfa sprouts, aloe leaves, arrow root, arrowhead, artichokes, asparagus, bamboo shoots, banana flowers, bean sprouts, beans, beet tops, beets, bittermelon, bok choy, broccoli, broccoli rabe (rappini), brussels sprouts, cabbage, cabbage sprouts, cactus leaf (nopales), calabaza, cardoon, carrots, cauliflower, celery, chayote, Chinese artichoke (crosnes), Chinese cabbage, Chinese celery, Chinese chives, choy sum, chrysanthemum leaves (tung ho), collard greens, corn stalks, corn-sweet, cucumbers, daikon, dandelion greens, dasheen, dau mue (pea tips), donqua (winter melon), eggplant, endive, escarole, fiddle head ferns, field cress, frisee, gai choy (Chinese mustard), gallon, galanga (siam, thai ginger), garlic, ginger root, gobo, greens, hanover salad greens, huauzontle, jerusalem artichokes, jicama, kale greens, kohlrabi, lamb's quarters (quilete), lettuce (bibb), lettuce (boston), lettuce (boston red), lettuce (green leaf), lettuce (iceberg), lettuce (lolla rossa), lettuce (oak leaf - green), lettuce (oak leaf - red), lettuce (processed), lettuce (red leaf), lettuce (romaine), lettuce (ruby romaine), lettuce (russian red mustard), linkok, lo bok, long beans, lotus root, mache, maguey (agave) leaves, malanga, mesculin mix, mizuna, moap (smooth luffa), moo, moqua (fuzzy squash), mushrooms, mustard, nagaimo, okra, ong choy, onions green, opo (long squash), ornamental corn, ornamental gourds, parsley, parsnips, peas, peppers (bell type), peppers, pumpkins, radicchio, radish sprouts, radishes, rape greens, rape greens, rhubarb, romaine (baby red), rutabagas, salicornia (sea bean), sinqua (angled/ridged luffa), spinach, squash, straw bales, sugarcane, sweet potatoes, swiss chard, tamarindo, taro, taro leaf, taro shoots, tatsoi, tepeguaje (guaje), tindora, tomatillos, tomatoes, tomatoes (cherry), tomatoes (grape type), tomatoes (plum type), tumeric, turnip tops greens, turnips, water chestnuts, yampi, yams (names), yu choy, yuca (cassava), and the like.
[00145] In some cases, the plant cell is a cell of a plant component such as a leaf, a stem, a root, a seed, a flower, pollen, an anther, an ovule, a pedicel, a fruit, a meristem, a cotyledon, a hypocotyl, a pod, an embryo, endosperm, an explant, a callus, or a shoot.
[00146] A cell is in some cases an arthropod cell. For example, the cell can be a cell of a suborder, a family, a sub-family, a group, a sub-group, or a species of, e.g., Chelicerata, Myriapodia, Hexipodia, Arachnida, Insecta, Archaeognatha, Thysanura, Palaeoptera, Ephemeroptera, Odonata, Anisoptera, Zygoptera, Neoptera, Exopterygota, Plecoptera , Embioptera , Orthoptera, Zoraptera , Dermaptera, Dictyoptera, Notoptera, Grylloblattidae, Mantophasmatidae, Phasmatodea , Blattaria, Isoptera, Mantodea, Parapneuroptera, Psocoptera, Thysanoptera, Phthiraptera, Hemiptera, Endopterygota or Holometabola , Hymenoptera , Coleoptera, Strepsiptera, Raphidioptera, Megaloptera, Neuroptera , Mecoptera , Siphonaptera, Diptera, Trichoptera, or Lepidoptera.
[00147] A cell is in some cases an insect cell. For example, in some cases, the cell is a cell of a mosquito, a grasshopper, a true bug, a fly, a flea, a bee, a wasp, an ant, a louse, a moth, or a beetle. COMPOSITIONS
[00148] The present disclosure provides a composition comprising a fusion polypeptide of the present disclosure. The composition may comprise a pharmaceutically acceptable excipient, a variety of which are known in the art and need not be discussed in detail herein. Pharmaceutically acceptable excipients have been amply described in a variety of publications, including, for example, “Remington: The Science and Practice of Pharmacy”, 19th Ed. (1995), or latest edition, Mack Publishing Co; A. Gennaro (2000) "Remington: The Science and Practice of Pharmacy", 20th edition, Lippincott, Williams, & Wilkins; Pharmaceutical Dosage Forms and Drug Delivery Systems (1999) H.C. Ansel et al., eds 7th ed., Lippincott, Williams, & Wilkins; and Handbook of Pharmaceutical Excipients (2000) A.H. Kibbe et al., eds., 3rd ed. Amer. Pharmaceutical Assoc.
[00149] A composition of the present disclosure can include: a) one or more of: i) a fusion polypeptide of the present disclosure; ii) a guide nucleic acid (e.g., a guide RNA); and iii) a donor template; and b) one or more of: a buffer, a surfactant, an antioxidant, a hydrophilic polymer, a dextrin, a chelating agent, a suspending agent, a solubilizer, a thickening agent, a stabilizer, a bacteriostatic agent, a wetting agent, and a preservative. Suitable buffers include, but are not limited to, (such as N,N-bis(2-hydroxyethyl)-2- aminoethanesulfonic acid (BES), bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane (BIS-Tris), N- (2-hydroxyethyl)piperazine-N'3-propanesulfonic acid (EPPS or HEPPS), glycylglycine, N-2- hydroxyehtylpiperazine-N'-2-ethanesulfonic acid (HEPES), 3-(N-morpholino)propane sulfonic acid (MOPS), piperazine-N,N'-bis(2-ethane-sulfonic acid) (PIPES), sodium bicarbonate, 3-(N- tris(hydroxymethyl)-methyl-amino)-2-hydroxy-propanesulfonic acid) TAPSO, (N- tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid (TES), N-tris(hydroxymethyl)methyl-glycine (Tricine), tris(hydroxymethyl)-aminomethane (Tris), etc.). Suitable salts include, e.g., NaCl, MgC12,
KC1, MgSOzt, etc.
[00150] A composition of the present disclosure can include: a) a system of the present disclosure; and b) one or more of: a buffer, a surfactant, an antioxidant, a hydrophilic polymer, a dextrin, a chelating agent, a suspending agent, a solubilizer, a thickening agent, a stabilizer, a bacteriostatic agent, a wetting agent, and a preservative. Suitable buffers include, but are not limited to, (such as N,N-bis(2- hydroxyethyl)-2-aminoethanesulfonic acid (BES), bis(2-hydroxyethyl)amino- tris(hydroxymethyl)methane (BIS-Tris), N-(2-hydroxyethyl)piperazine-N'3-propanesulfonic acid (EPPS or HEPPS), glycylglycine, N-2-hydroxyehtylpiperazine-N'-2-ethanesulfonic acid (HEPES), 3-(N- morpholino)propane sulfonic acid (MOPS), piperazine-N,N'-bis(2-ethane-sulfonic acid) (PIPES), sodium bicarbonate, 3-(N-tris(hydroxymethyl)-methyl-amino)-2-hydroxy-propanesulfonic acid) TAPSO, (N- tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid (TES), N-tris(hydroxymethyl)methyl-glycine (Tricine), tris(hydroxymethyl)-aminomethane (Tris), etc.). Suitable salts include, e.g., NaC1, MgC12,
KC1, MgSO4 , etc. [00151] In some cases, the composition is sterile. In some cases, the composition is suitable for administration to a human subject, e.g., where the composition is sterile and is free of detectable pyrogens and/or other toxins.
[00152] A composition of the present disclosure may include other components, such as pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium, carbonate, and the like. The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions such as pH adjusting and buffering agents, toxicity adjusting agents and the like, for example, sodium acetate, sodium chloride, potassium chloride, calcium chloride, sodium lactate, hydrochloride, sulfate salts, solvates (e.g., mixed ionic salts, water, organics), hydrates (e.g., water), and the like. In some cases, a composition of the present disclosure comprises saline.
SYSTEMS
[00153] The present disclosure provides a system comprising a fusion polypeptide of the present disclosure.
[00154] The present disclosure provides a system comprising one of: a) a fusion polypeptide of the present disclosure; and a CRISPR/Cas guide nucleic acid; b) a fusion polypeptide of the present disclosure; a CRISPR/Cas guide nucleic acid, and a DNA donor template; c) a fusion polypeptide of the present disclosure; and a CRISPR/Cas guide RNA; d) a fusion polypeptide of the present disclosure; a CRISPR/Cas guide RNA, and a DNA donor template; e) an mRNA encoding a fusion polypeptide of the present disclosure; and a CRISPR/Cas guide nucleic acid; f) an mRNA encoding a fusion polypeptide of the present disclosure; a CRISPR/Cas guide nucleic acid, and a DNA donor template; g) an mRNA encoding a fusion polypeptide of the present disclosure; and a CRISPR/Cas guide RNA; h) an mRNA encoding a fusion polypeptide of the present disclosure; a CRISPR/Cas guide RNA, and a DNA donor template; i) one or more recombinant expression vectors comprising: i) a nucleotide sequence encoding a fusion polypeptide of the present disclosure; and ii) a nucleotide sequence encoding a CRISPR/Cas guide nucleic acid; j) one or more recombinant expression vectors comprising: i) a nucleotide sequence encoding a fusion polypeptide of the present disclosure; ii) a nucleotide sequence encoding a CRISPR/Cas guide nucleic acid; and iii) a DNA donor template; k) one or more recombinant expression vectors comprising: i) a nucleotide sequence encoding a fusion polypeptide of the present disclosure; and ii) a nucleotide sequence encoding a CRISPR/Cas guide RNA; and 1) one or more recombinant expression vectors comprising: i) a nucleotide sequence encoding a fusion polypeptide of the present disclosure; ii) a nucleotide sequence encoding a CRISPR/Cas guide RNA; and a DNA donor template; or some variation of one or (a) through (1). Guide nucleic acid
[00155] A guide nucleic acid suitable for inclusion in a system of the present disclosure can include: i) a first segment (referred to herein as a “targeting segment”); and ii) a second segment (referred to herein as a “protein-binding segment”). By “segment” it is meant a segment/section/region of a molecule, e.g., a contiguous stretch of nucleotides in a nucleic acid molecule. A segment can also mean a region/section of a complex such that a segment may comprise regions of more than one molecule. The “targeting segment” is also referred to herein as a “variable region” of a guide RNA. The “protein-binding segment” is also referred to herein as a “constant region” of a guide RNA. The first segment (targeting segment) of a guide RNA includes a nucleotide sequence (a guide sequence) that is complementary to (and therefore hybridizes with) a specific sequence (a target site) within a target nucleic acid (e.g., a target ssRNA, a target ssDNA, the complementary strand of a double stranded target DNA, etc.). The protein-binding segment (or “protein-binding sequence”) interacts with (binds to) a CRISPR/Cas effector polypeptide. The protein-binding segment of a guide RNA includes two complementary stretches of nucleotides that hybridize to one another to form a double stranded RNA duplex (dsRNA duplex). Site- specific binding and/or cleavage of a target nucleic acid (e.g., genomic DNA) can occur at locations (e.g., target sequence of a target locus) determined by base-pairing complementarity between the guide RNA (the guide sequence of the guide RNA) and the target nucleic acid.
[00156] A guide RNA and a CRISPR/Cas effector polypeptide form a complex (e.g., bind via non- covalent interactions). The guide RNA provides target specificity to the complex by including a targeting segment, which includes a guide sequence (a nucleotide sequence that is complementary to a sequence of a target nucleic acid). The CRISPR/Cas effector polypeptide of the complex provides the site-specific activity (e.g., cleavage activity or an activity provided by the CRISPR/Cas effector polypeptide when the CRISPR/Cas effector polypeptide is a CRISPR/Cas effector polypeptide fusion polypeptide, i.e., has a fusion partner). In other words, the CRISPR/Cas effector polypeptide is guided to a target nucleic acid sequence (e.g. a target sequence in a chromosomal nucleic acid, e.g., a chromosome; a target sequence in an extrachromosomal nucleic acid, e.g. an episomal nucleic acid, a minicircle, an ssRNA, an ssDNA, etc.; a target sequence in a mitochondrial nucleic acid; a target sequence in a chloroplast nucleic acid; a target sequence in a plasmid; a target sequence in a viral nucleic acid; etc.) by virtue of its association with the guide RNA.
[00157] In some cases, the guide RNA (e.g., a single-molecule guide RNA) has a length of from about 15 nucleotides to about 50 nucleotides; e.g., in some cases, the guide RNA (e.g., a single -molecule guide RNA) has a length of from about 15 nucleotides to about 20 nucleotides, from about 20 nucleotides to about 25 nucleotides, from about 25 nucleotides to about 30 nucleotides, or from about 30 nucleotides to about 50 nucleotides. In some cases, the guide RNA (e.g., a single-molecule guide RNA) has a length of from about 14 nucleotides to about 16 nucleotides. [00158] The “guide sequence” also referred to as the “targeting sequence” of a guide RNA can be modified so that the guide RNA can target a CRISPR/Cas effector polypeptide to any desired sequence of any desired target nucleic acid, with the exception that the protospacer adjacent motif (PAM) sequence can be taken into account. Thus, for example, a guide RNA can have a targeting segment with a sequence (a guide sequence) that has complementarity with (e.g., can hybridize to) a sequence in a nucleic acid in a eukaryotic cell, e.g., a viral nucleic acid, a eukaryotic nucleic acid (e.g., a eukaryotic chromosome, chromosomal sequence, a eukaryotic RNA, etc.), and the like.
[00159] In some cases, a guide RNA includes two separate nucleic acid molecules: an “activator” and a “targeter” and is referred to herein as a “dual guide RNA”, a “double-molecule guide RNA”, or a “two- molecule guide RNA” a “dual guide RNA”, or a “dgRNA.” In some embodiments, the activator and targeter are covalently linked to one another (e.g., via intervening nucleotides) and the guide RNA is referred to as a “single guide RNA”, a “Cas single guide RNA”, a “single-molecule Cas guide RNA,” or a “one -molecule Cas guide RNA”, or simply “sgRNA.”
[00160] Examples of various CRISPR/Cas effector polypeptides and guide RNAs (as well as information regarding requirements related to protospacer adjacent motif (PAM) sequences present in targeted nucleic acids) can be found in the art, for example, see Jinek et al., Science. 2012 Aug 17;337(6096):816-21; Chylinski et al., RNA Biol. 2013 May;10(5):726-37; Ma et al., Biomed Res Int. 2013;2013:270805; Hou et al., Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15644-9; Jinek et al., Elife. 2013;2:e00471; Pattanayak et al., Nat Biotechnol. 2013 Sep;31(9):839-43; Qi et al., Cell. 2013 Feb 28 ; 152(5): 1173-83; Wang et al., Cell. 2013 May 9;153(4):910-8; Auer et al., Genome Res. 2013 Oct 31; Chen et al., Nucleic Acids Res. 2013 Nov l;41(20):el9; Cheng et al., Cell Res. 2013 Oct;23(10):1163- 71; Cho et al., Genetics. 2013 Nov;195(3):1177-80; DiCarlo et al., Nucleic Acids Res. 2013 Apr;41(7):4336-43; Dickinson et al., Nat Methods. 2013 Oct;10(10):1028-34; Ebina et al., Sci Rep. 2013;3:2510; Fujii et al., Nucleic Acids Res. 2013 Nov l;41(20):el87; Hu et al., Cell Res. 2013 Nov;23(ll):1322-5; Jiang et al., Nucleic Acids Res. 2013 Nov l;41(20):el88; Larson et al., Nat Protoc. 2013 Nov;8(ll):2180-96; Mali et al., Nat Methods. 2013 Oct;10(10):957-63; Nakayama et al.,
Genesis. 2013 Dec;51(12):835-43; Ran et al., Nat Protoc. 2013 Nov;8(ll):2281-308; Ran et al., Cell. 2013 Sep 12;154(6):1380-9; Upadhyay et al., G3 (Bethesda). 2013 Dec 9;3(12):2233-8; Walsh et al.,
Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15514-5; Xie et al., Mol Plant. 2013 Oct 9; Yang et al., Cell. 2013 Sep 12;154(6):1370-9; Briner et al., Mol Cell. 2014 Oct 23;56(2):333-9; Shmakov et al., Nat Rev Microbiol. 2017 Mar;15(3):169-182; and U.S. patents and patent applications: 8,906,616; 8,895,308; 8,889,418; 8,889,356; 8,871,445; 8,865,406; 8,795,965; 8,771,945; 8,697,359; 20140068797; 20140170753; 20140179006; 20140179770; 20140186843; 20140186919; 20140186958; 20140189896; 20140227787; 20140234972; 20140242664; 20140242699; 20140242700; 20140242702; 20140248702; 20140256046; 20140273037; 20140273226; 20140273230; 20140273231; 20140273232; 20140273233; 20140273234; 20140273235; 20140287938; 20140295556; 20140295557; 20140298547; 20140304853; 20140309487; 20140310828; 20140310830; 20140315985; 20140335063; 20140335620; 20140342456; 20140342457; 20140342458; 20140349400; 20140349405; 20140356867; 20140356956; 20140356958; 20140356959; 20140357523; 20140357530; 20140364333; and 20140377868; each of which is hereby incorporated by reference in its entirety.
[00161] In some cases, a guide nucleic acid comprises ribonucleotides only, deoxyribonucleotides only, or a mixture of ribonucleotides and deoxyribonucleotides. In some cases, a guide nucleic acid comprises ribonucleotides only, and is referred to herein as a “guide RNA.” In some cases, a guide nucleic acid comprises deoxyribonucleotides only, and is referred to herein as a “guide DNA.” In some cases, a guide nucleic acid comprises both ribonucleotides and deoxyribonucleotides. A guide nucleic acid can comprise combinations of ribonucleotide bases, deoxyribonucleotide bases, nucleotide analogs, modified nucleotides, and the like; and may further include naturally-occurring backbone residues and/or linkages and/or non-naturally-occurring backbone residues and/or linkages. Donor DNA template
[00162] In some cases, a system of the present disclosure comprises a donor nucleic acid. By a
“donor nucleic acid” or “donor sequence” or “donor polynucleotide” or “donor template” it is meant a nucleic acid sequence to be inserted at the site cleaved by a CRISPR/Cas effector protein present in a fusion polypeptide of the present disclosure (e.g., after dsDNA cleavage, after nicking a target DNA, after dual nicking a target DNA, and the like). The donor polynucleotide can contain sufficient homology to a genomic sequence at the target site, e.g. 70%, 80%, 85%, 90%, 95%, or 100% homology with the nucleotide sequences flanking the target site, e.g. within about 50 bases or less of the target site, e.g. within about 30 bases, within about 15 bases, within about 10 bases, within about 5 bases, or immediately flanking the target site, to support homology-directed repair between it and the genomic sequence to which it bears homology. Approximately 25, 50, 100, or 200 nucleotides, or more than 200 nucleotides, of sequence homology between a donor and a genomic sequence (or any integral value between 10 and 200 nucleotides, or more) can support homology-directed repair. Donor polynucleotides can be of any length, e.g. 10 nucleotides or more, 50 nucleotides or more, 100 nucleotides or more, 250 nucleotides or more, 500 nucleotides or more, 1000 nucleotides or more, 5000 nucleotides or more, etc. Donor polynucleotides can be from 25 nucleotides to 50 nucleotides, from 50 nucleotides to 100 nucleotides, from 100 nucleotides to 500 nucleotides, from 500 nucleotides to 1000 nucleotides, from 1000 nucleotides to 5000 nucleotides, or from 5000 nucleotides to 10,000 nucleotides, or more than 10,000 nucleotides, in length.
[00163] The donor sequence is typically not identical to the genomic sequence that it replaces. Rather, the donor sequence may contain at least one or more single base changes, insertions, deletions, inversions or rearrangements with respect to the genomic sequence, so long as sufficient homology is present to support homology-directed repair (e.g., for gene correction, e.g., to convert a disease-causing base pair or a non disease-causing base pair). In some embodiments, the donor sequence comprises a non-homologous sequence flanked by two regions of homology, such that homology-directed repair between the target DNA region and the two flanking sequences results in insertion of the non- homologous sequence at the target region. Donor sequences may also comprise a vector backbone containing sequences that are not homologous to the DNA region of interest and that are not intended for insertion into the DNA region of interest. Generally, the homologous region(s) of a donor sequence will have at least 50% sequence identity to a genomic sequence with which recombination is desired. In certain embodiments, 60%, 70%, 80%, 90%, 95%, 98%, 99%, or 99.9% sequence identity is present.
Any value between 1% and 100% sequence identity can be present, depending upon the length of the donor polynucleotide.
[00164] The donor sequence may comprise certain sequence differences as compared to the genomic sequence, e.g. restriction sites, nucleotide polymorphisms, selectable markers (e.g., drug resistance genes, fluorescent proteins, enzymes etc.), etc., which may be used to assess for successful insertion of the donor sequence at the cleavage site or in some cases may be used for other purposes (e.g., to signify expression at the targeted genomic locus). In some cases, if located in a coding region, such nucleotide sequence differences will not change the amino acid sequence, or will make silent amino acid changes (i.e., changes which do not affect the structure or function of the protein). Alternatively, these sequences differences may include flanking recombination sequences such as FLPs, loxP sequences, or the like, that can be activated at a later time for removal of the marker sequence.
[00165] In some cases, the donor sequence is provided to the cell as single-stranded DNA. In some cases, the donor sequence is provided to the cell as double-stranded DNA. It may be introduced into a cell in linear or circular form. If introduced in linear form, the ends of the donor sequence may be protected (e.g., from exonucleolytic degradation) by any convenient method and such methods are known to those of skill in the art. For example, one or more dideoxynucleotide residues can be added to the 3' terminus of a linear molecule and/or self-complementary oligonucleotides can be ligated to one or both ends. See, for example, Chang et al. (1987) Proc. Natl. Acad Sci USA 84:4959-4963; Nehls et al. (1996) Science 272:886-889. Additional methods for protecting exogenous polynucleotides from degradation include, but are not limited to, addition of terminal amino group(s) and the use of modified internucleotide linkages such as, for example, phosphorothioates, phosphor amidates, and O-methyl ribose or deoxyribose residues. As an alternative to protecting the termini of a linear donor sequence, additional lengths of sequence may be included outside of the regions of homology that can be degraded without impacting recombination. A donor sequence can be introduced into a cell as part of a vector molecule having additional sequences such as, for example, replication origins, promoters and genes encoding antibiotic resistance. METHODS
[00166] A fusion polypeptide of the present disclosure finds use in a variety of methods, which are provided herein.
[00167] For examples of suitable methods, see, for example, Jinek et al., Science. 2012 Aug
17;337(6096):816-21; Chylinski et al., RNA Biol. 2013 May;10(5):726-37; Ma et al., Biomed Res Int. 2013;2013:270805; Hou et al., Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15644-9; Jinek et al., Elife. 2013;2:e00471; Pattanayak et al., Nat Biotechnol. 2013 Sep;31(9):839-43; Qi et al, Cell. 2013 Feb 28 ; 152(5): 1173-83; Wang et al., Cell. 2013 May 9;153(4):910-8; Auer et al., Genome Res. 2013 Oct 31; Chen et al., Nucleic Acids Res. 2013 Nov l;41(20):el9; Cheng et al., Cell Res. 2013 Oct;23(10):1163- 71; Cho et al., Genetics. 2013 Nov;195(3):1177-80; DiCarlo et al., Nucleic Acids Res. 2013 Apr;41(7):4336-43; Dickinson et al., Nat Methods. 2013 Oct;10(10):1028-34; Ebina et al., Sci Rep. 2013;3:2510; Fujii et al, Nucleic Acids Res. 2013 Nov l;41(20):el87; Hu et al., Cell Res. 2013 Nov;23(ll):1322-5; Jiang et al., Nucleic Acids Res. 2013 Nov l;41(20):el88; Larson et al., Nat Protoc. 2013 Nov;8(ll):2180-96; Mali et. at., Nat Methods. 2013 Oct;10(10):957-63; Nakayama et al.,
Genesis. 2013 Dec;51(12):835-43; Ran et al., Nat Protoc. 2013 Nov;8(ll):2281-308; Ran et al., Cell. 2013 Sep 12;154(6):1380-9; Upadhyay et al., G3 (Bethesda). 2013 Dec 9;3(12):2233-8; Walsh et al., Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15514-5; Xie et al., Mol Plant. 2013 Oct 9; Yang et al., Cell. 2013 Sep 12;154(6):1370-9; and U.S. patents and patent applications: 8,906,616; 8,895,308; 8,889,418; 8,889,356; 8,871,445; 8,865,406; 8,795,965; 8,771,945; 8,697,359; 20140068797; 20140170753; 20140179006; 20140179770; 20140186843; 20140186919; 20140186958; 20140189896; 20140227787; 20140234972; 20140242664; 20140242699; 20140242700; 20140242702; 20140248702; 20140256046; 20140273037; 20140273226; 20140273230; 20140273231; 20140273232; 20140273233; 20140273234; 20140273235; 20140287938; 20140295556; 20140295557; 20140298547; 20140304853; 20140309487; 20140310828; 20140310830; 20140315985; 20140335063; 20140335620; 20140342456; 20140342457; 20140342458; 20140349400; 20140349405; 20140356867; 20140356956; 20140356958; 20140356959; 20140357523; 20140357530; 20140364333; and 20140377868; each of which is hereby incorporated by reference in its entirety.
[00168] The present disclosure provides a method of modifying a target nucleic acid, the method comprising contacting the target nucleic acid with: a) a fusion polypeptide of the present disclosure; and b) a guide nucleic acid that comprises: i) a guide sequence that hybridizes to a target sequence of the target nucleic acid; and ii) an activator sequence that binds to the CRISPR/Cas effector polypeptide. In some cases, a method of the present disclosure comprises contacting a target nucleic acid with: a) a fusion polypeptide of the present disclosure; b) a guide nucleic acid that comprises: i) a guide sequence that hybridizes to a target sequence of the target nucleic acid; and ii) an activator sequence that binds to the CRISPR/Cas effector polypeptide; and c) a donor DNA template. The contacting step results in modification of the target nucleic acid by the CRISPR/Cas effector polypeptide. In some cases, the modification comprises cleaving the target nucleic acid. In some cases, the modification comprises replacing all or part of a target nucleic acid with a donor nucleic acid.
[00169] A method of the present disclosure can provide for increased homology-directed repair
(HDR) compared to non-homologous end joining (NHEJ). In some cases, a method of the present disclosure for modifying a target nucleic acid comprises contacting the target nucleic acid with: a) a fusion polypeptide of the present disclosure; and b) a guide nucleic acid, wherein said contacting results in modification of the target nucleic acid by the CRISPR/Cas effector polypeptide. In some cases, a method of the present disclosure for modifying a target nucleic acid comprises contacting the target nucleic acid with: a) a fusion polypeptide of the present disclosure; b) a guide nucleic acid; and c) a donor template DNA, wherein said contacting results in modification of the target nucleic acid by the CRISPR/Cas effector polypeptide. Generally, the target nucleic acid is present in chromatin. In some cases, the contacting step takes place in vitro outside of a cell. In some cases, the contacting step takes place inside of a cell in in vitro culture. In some cases, the contacting step takes place inside of a eukaryotic cell in vivo.
[00170] The present disclosure provides a method of modifying a target nucleic acid present in chromatin in a eukaryotic cell, the method comprising: a) contacting the chromatin with a first fusion polypeptide comprising: i) an enzymatically inactive CRISPR/Cas effector polypeptide; and ii) a chromatin marker polypeptide that modifies a histone polypeptide present in chromatin, wherein the modification marks the chromatin as a site for recombination; and b) contacting the marked chromatin with: i) a complex comprising an enzymatically active CRISPR/Cas effector polypeptide and a guide nucleic acid; and ii) a donor template DNA.
[00171] The present disclosure provides a method of modifying chromatin in a eukaryotic cell, the method comprising contacting the chromatin with a fusion polypeptide of the present disclosure. In some cases, the cell is in vitro. In some cases, the cell is in vivo (e.g., in a multicellular organism). [00172] A target nucleic acid is present in chromatin. A target nucleic acid is typically double stranded DNA (e.g., a chromosome (genomic DNA), derived from a chromosome, chromosomal DNA, extracellular, intracellular, mitochondrial, chloroplast, linear, circular, etc.) and can be from any organism (e.g., as long as the guide RNA comprises a nucleotide sequence that hybridizes to a target sequence in a target nucleic acid, such that the target nucleic acid can be targeted).
[00173] A target nucleic acid can be located anywhere, for example, outside of a cell in vitro, inside of a cell in vitro, inside of a cell in vivo, inside of a cell ex vivo. Suitable target cells (which can comprise target nucleic acids such as genomic DNA) include, but are not limited to: a bacterial cell; an archaeal cell; a cell of a single-cell eukaryotic organism; a plant cell; an algal cell, e.g., Botryococcus braunii, Chlamydomonas reinhardtii, Nannochloropsis gaditana, Chlorella pyrenoidosa, Sargassum patens, C. agardh, and the like; a fungal cell (e.g., a yeast cell); an animal cell; a cell from an invertebrate animal (e.g. fruit fly, a cnidarian, an echinoderm, a nematode, etc.); a cell of an insect (e.g., a mosquito; a bee; an agricultural pest; etc.); a cell of an arachnid (e.g., a spider; a tick; etc.); a cell from a vertebrate animal (e.g., a fish, an amphibian, a reptile, a bird, a mammal); a cell from a mammal (e.g., a cell from a rodent; a cell from a human; a cell of a non-human mammal; a cell of a rodent (e.g., a mouse, a rat); a cell of a lagomorph (e.g., a rabbit); a cell of an ungulate (e.g., a cow, a horse, a camel, a llama, a vicuna, a sheep, a goat, etc.); a cell of a marine mammal (e.g., a whale, a seal, an elephant seal, a dolphin, a sea lion; etc.) and the like. Any type of cell may be of interest (e.g. a stem cell, e.g. an embryonic stem (ES) cell, an induced pluripotent stem (iPS) cell, a germ cell (e.g., an oocyte, a sperm, an oogonia, a spermatogonia, etc.), an adult stem cell, a somatic cell, e.g. a fibroblast, a hematopoietic cell, a neuron, a muscle cell, a bone cell, a hepatocyte, a pancreatic cell; an in vitro or in vivo embryonic cell of an embryo at any stage, e.g., a 1-cell, 2-cell, 4-cell, 8-cell, etc. stage zebrafish embryo; etc.). [00174] Cells may be from established cell lines or they may be primary cells, where “primary cells”, “primary cell lines”, and “primary cultures” are used interchangeably herein to refer to cells and cells cultures that have been derived from a subject and allowed to grow in vitro for a limited number of passages of the culture. For example, primary cultures are cultures that may have been passaged 0 times, 1 time, 2 times, 4 times, 5 times, 10 times, or 15 times, but not enough times go through the crisis stage. Typically, the primary cell lines are maintained for fewer than 10 passages in vitro. Target cells can be unicellular organisms and/or can be grown in culture. If the cells are primary cells, they may be harvest from an individual by any convenient method. For example, leukocytes may be conveniently harvested by apheresis, leukocytapheresis, density gradient separation, etc., while cells from tissues such as skin, muscle, bone marrow, spleen, liver, pancreas, lung, intestine, stomach, etc. can be conveniently harvested by biopsy.
[00175] In some of the above applications, the subject methods may be employed to induce target nucleic acid cleavage, target nucleic acid modification, and/or to bind target nucleic acids (e.g., for visualization, for collecting and/or analyzing, etc.) in mitotic or post-mitotic cells in vivo and/or ex vivo and/or in vitro (e.g., to disrupt production of a protein encoded by a targeted mRNA, to cleave or otherwise modify target DNA, to genetically modify a target cell, and the like). Because the guide RNA provides specificity by hybridizing to target nucleic acid, a mitotic and/or post-mitotic cell of interest in the disclosed methods may include a cell from any organism (e.g. a cell of a single-cell eukaryotic organism, a plant cell, an algal cell, e.g., Botryococcus braunii, Chlamydomonas reinhardtii, Nannochloropsis gaditana, Chlorella pyrenoidosa, Sargassum patens, C. agardh, and the like, a fungal cell (e.g., a yeast cell), an animal cell, a cell from an invertebrate animal (e.g. fruit fly, cnidarian, echinoderm, nematode, etc.), a cell from a vertebrate animal (e.g., fish, amphibian, reptile, bird, mammal), a cell from a mammal, a cell from a rodent, a cell from a human, etc.). In some cases, a fusion polypeptide of the present disclosure (and/or nucleic acid encoding the protein such as DNA and/or RNA), and/or guide RNA (and/or a DNA encoding the guide RNA), and/or donor template, and/or RNP can be introduced into an individual (i.e., the target cell can be in vivo ) (e.g., a mammal, a rat, a mouse, a pig, a primate, a non-human primate, a human, etc.). In some case, such an administration can be for the purpose of treating and/or preventing a disease, e.g., by editing the genome of targeted cells.
Methods of generating recombination hotspots in gametes
[00176] The present disclosure provides a method of modifying chromatin in a gamete, the method comprising contacting the chromatin in the gamete with: a) a fusion polypeptide of the present disclosure; and b) a guide nucleic acid comprising a nucleotide sequence that hybridizes to a target nucleic acid in the chromatin, thereby generating a gamete comprising chromatin comprising a modification. In some cases, the modification generates a recombination hotspot. In some cases, the modification generates a meiotic recombination hotspot. A “recombination hotspot” is a region in a genome that exhibits elevated rates of recombination relative to a neutral expectation, e.g., relative to a surrounding region in the genome. In some cases, the rate of recombination at a recombination hotspot is from 10-fold to 25-fold, from 25-fold to 50-fold, from 50-fold to 100-fold, from 100-fold to 250-fold, from 250-fold to 500-fold, from 500-fold to 103-fold, from 103-fold to 5 x 103-fold, or more than 5 x 103- fold, higher than the rate of recombination in an adjacent region in the genome.
[00177] In some cases, the gamete is a sperm. In some cases, the gamete is an oocyte. Gametes can be from a mammal (e.g., a human, a non-human primate, a rodent, an ungulate (e.g., a camel, a horse, a cow, a goat, a sheep, etc.), a non-mammalian vertebrate, an amphibian, a reptile, an arachnid, an insect, a plant, etc.
[00178] In some cases, the chromatin in the gamete is contacted with a fusion polypeptide of the present disclosure and a guide nucleic acid (e.g., a guide RNA), where the CRISPR/Cas effector polypeptide present in the fusion polypeptide is a nickase. In some cases, the chromatin in the gamete is contacted with a fusion polypeptide of the present disclosure, where the CRISPR/Cas effector polypeptide present in the fusion polypeptide is enzymatically inactive. In some cases, a donor template is not used in the method; in other words, in some cases, a composition comprising a fusion polypeptide of the present disclosure and a guide nucleic acid (e.g., a guide RNA) is introduced into a gamete, where the composition does not include a donor template.
[00179] A composition comprising: a) a fusion polypeptide of the present disclosure (e.g., where the CRISPR/Cas effector polypeptide present in the fusion polypeptide is a nickase or is enzymatically inactive); and b) a guide nucleic acid (e.g., a guide RNA) is introduced into a gamete using any of a variety of known methods. For example, a composition comprising: a) a fusion polypeptide of the present disclosure (e.g., where the CRISPR/Cas effector polypeptide present in the fusion polypeptide is a nickase or is enzymatically inactive); and b) a guide nucleic acid (e.g., a guide RNA) is injected into a gamete. In some cases, a nucleic acid (e.g., a recombinant expression vector) comprising nucleotide sequences encoding: a) a fusion polypeptide of the present disclosure (e.g., where the CRISPR/Cas effector polypeptide present in the fusion polypeptide is a nickase or is enzymatically inactive); and b) a guide nucleic acid (e.g., a guide RNA), is introduced into a gamete. In some cases, a recombinant expression vector comprising nucleotide sequences encoding: a) a fusion polypeptide of the present disclosure (e.g., where the CRISPR/Cas effector polypeptide present in the fusion polypeptide is a nickase or is enzymatically inactive); and b) a guide nucleic acid (e.g., a guide RNA), is introduced into a gamete, where expression of the nucleotide sequences encoding the fusion polypeptide and the guide RNA is Cre-mediated.
[00180] As an example, a recombinant expression vector comprising nucleotide sequences encoding: a) a fusion polypeptide of the present disclosure (e.g., where the CRISPR/Cas effector polypeptide present in the fusion polypeptide is a nickase or is enzymatically inactive); and b) a guide nucleic acid (e.g., a guide RNA), is introduced into a gamete, where expression of the nucleotide sequences encoding the fusion polypeptide and the guide RNA is Cre-mediated. For example, the gamete is in a Spoll-eGFP-Cre transgenic mouse. Spoll-eGFP-Cre transgenic mice have the mouse Spoil (SPOl 1 meiotic protein covalently bound to DSB) gene promoter driving Cre recombinase expression in spermatocytes that have initiated meiosis.
[00181] The method is useful for creating non-human animal models, e.g., non-human animal models of diseases.
[00182] As another example, in an organism that has a dominant negative allele (e.g. mutation in p53, for example R172H substitution mutation in mice) and a wild type counterpart of the dominant negative allele, the dominant negative allele can be marked for recombination during meiosis, such that gene conversion is enhanced at that site, such that the dominant negative allele is replaced with a copy of the wild-type allele.
Examples of Non-Limiting Aspects of the Disclosure
[00183] Aspects, including embodiments, of the present subject matter described above may be beneficial alone or in combination, with one or more other aspects or embodiments. Without limiting the foregoing description, certain non-limiting aspects of the disclosure numbered 1-80 are provided below. As will be apparent to those of skill in the art upon reading this disclosure, each of the individually numbered aspects may be used or combined with any of the preceding or following individually numbered aspects. This is intended to provide support for all such combinations of aspects and is not limited to combinations of aspects explicitly provided below: [00184] Aspect 1. A fusion polypeptide comprising: a) a CRISPR/Cas effector polypeptide; and b) a chromatin marker polypeptide that provides for modification of a histone polypeptide present in chromatin, wherein the modification marks the chromatin as a site for recombination.
[00185] Aspect 2. The fusion polypeptide of aspect 1, wherein the chromatin marker polypeptide is a histone methyltransferase (HMT).
[00186] Aspect 3. The fusion polypeptide of aspect 2, wherein the HMT methylates Lys4 or
Lys36 of histone H3.
[00187] Aspect 4. The fusion polypeptide of aspect 3, wherein the HMT is a PRDM9 polypeptide, a SETD2 polypeptide, or a SETMAR polypeptide.
[00188] Aspect 5. The fusion polypeptide of aspect 1, wherein the chromatin marker polypeptide is a histone acetyltransferase.
[00189] Aspect 6. The fusion polypeptide of aspect 5, wherein the histone acetyltransferase acetylates Lysl6 of histone H4.
[00190] Aspect 7. The fusion polypeptide of aspect 6, wherein the histone acetyltransferase is a
MOF polypeptide.
[00191] Aspect 8. The fusion polypeptide of aspect 4, wherein the PRDM9 polypeptide comprises a KRAB domain, an SSXRD domain, and a PR/SET domain, and does not include a zinc finger DNA-binding domain.
[00192] Aspect 9. The fusion polypeptide of aspect 8, wherein the PRDM9 polypeptide has a length of from about 350 amino acids to about 390 amino acids, and wherein the PRDM9 polypeptide comprises an amino acid sequence having at least 85% amino acid sequence identity to amino acids 1- 370 of the amino acid sequence of the PRDM9 polypeptide depicted in FIG. 2A or at least 85% amino acid sequence identity to amino acids 1-371 of the amino acid sequence of the PRDM9 polypeptide depicted in FIG. 2B.
[00193] Aspect 10. The fusion polypeptide of aspect 1, wherein the fusion polypeptide comprises an amino acid sequence having at least 85% amino acid sequence identity to the amino acid sequence depicted in FIG. 3 A or FIG. 3B.
[00194] Aspect 11. The fusion polypeptide of aspect 1 , wherein the chromatin marker polypeptide binds H3K4me3 and/or H3K36me3.
[00195] Aspect 12. The fusion polypeptide of aspect 11, wherein the chromatin marker polypeptide is a ZMYND8 polypeptide of a ZCWPWI polypeptide.
[00196] Aspect 13. The fusion polypeptide of aspect 1, wherein the chromatin marker polypeptide is a PRDM9-binding polypeptide. [00197] Aspect 14. The fusion polypeptide of aspect 13, wherein the PRDM9-binding polypeptide is EWSR1 or PREC8.
[00198] Aspect 15. The fusion polypeptide of any one of aspects 1-14, wherein the CRISPR/Cas effector polypeptide is a type II CRISPR/Cas effector polypeptide, a type V CRISPR/Cas effector polypeptide, or a type VI CRISPR/Cas effector polypeptide.
[00199] Aspect 16. The fusion polypeptide of any one of aspects 1-14, wherein the CRISPR/Cas effector polypeptide is a type II CRISPR/Cas effector polypeptide.
[00200] Aspect 17. The fusion polypeptide of aspect 16, wherein the type II CRISPR/Cas effector polypeptide is a Cas9 polypeptide.
[00201] Aspect 18. The fusion polypeptide of any one of aspects 1-14, wherein the CRISPR/Cas effector polypeptide is a type V CRISPR/Cas effector polypeptide.
[00202] Aspect 19. The fusion polypeptide of aspect 18, wherein the type V CRISPR/Cas effector polypeptide is a Casl2a, a Casl2b, a Casl2c, a Casl2d, or a Casl2e polypeptide.
[00203] Aspect 20. The fusion polypeptide of any one of aspects 1-14, wherein the CRISPR/Cas effector polypeptide is a type VI CRISPR/Cas effector polypeptide.
[00204] Aspect 21. The fusion polypeptide of aspect 20, wherein the type VI CRISPR/Cas effector polypeptide is a Casl3a, a Casl3b, a Casl3c, or a Casl3d polypeptide.
[00205] Aspect 22. The fusion polypeptide of any one of aspects 1-14, wherein the CRISPR/Cas effector polypeptide is a Casl4a, a Casl4b, or a Casl4c polypeptide.
[00206] Aspect 23. The fusion polypeptide of any one of aspects 1-22, wherein the CRISPR/Cas effector polypeptide is enzymatically active.
[00207] Aspect 24. The fusion polypeptide of any one of aspects 1-22, wherein the CRISPR/Cas effector polypeptide exhibits reduced enzymatic activity.
[00208] Aspect 25. The fusion polypeptide of any one of aspects 1-22, wherein the CRISPR/Cas effector polypeptide exhibits nickase activity.
[00209] Aspect 26. The fusion polypeptide of aspect 25, wherein the CRISPR/Cas effector polypeptide comprises a D10A substitution or an H840A substitution, based on the amino acid numbering of Streptococcus pyogenes Cas9, or a corresponding amino acid in another Cas9 polypeptide. [00210] Aspect 27. The fusion polypeptide of any one of aspects 1-22, wherein the CRISPR/Cas effector polypeptide is enzymatically inactive.
[00211] Aspect 28. The fusion polypeptide of aspect 27, wherein the CRISPR/Cas effector polypeptide comprises a D10A substitution and an H840A substitution, based on the amino acid numbering of Streptococcus pyogenes Cas9, or the corresponding amino acids in another Cas9 polypeptide. [00212] Aspect 29. The fusion polypeptide of any one of aspects 1-28, wherein the fusion polypeptide comprises, in order from N-terminus to C-terminus: a) the CRISPR/Cas effector polypeptide; and b) the chromatin modifying polypeptide.
[00213] Aspect 30. The fusion polypeptide of any one of aspects 1-28, wherein the fusion polypeptide comprises, in order from N-terminus to C-terminus: a) the chromatin modifying polypeptide; and b) the CRISPR/Cas effector polypeptide.
[00214] Aspect 31. The fusion polypeptide of any one of aspects 1-28, wherein the fusion polypeptide comprises, in order from N-terminus to C-terminus: a) an N-terminal portion of the CRISPR/Cas effector polypeptide; b) the chromatin modifying polypeptide; and c) a C-terminal portion of the CRISPR/Cas effector polypeptide.
[00215] Aspect 32. The fusion polypeptide of any one of aspects 1-28, wherein the fusion polypeptide comprises, in order from N-terminus to C-terminus: a) a C-terminal portion of the CRISPR/Cas effector polypeptide; b) the chromatin modifying polypeptide; and c) an N-terminal portion of the CRISPR/Cas effector polypeptide.
[00216] Aspect 33. The fusion polypeptide of any one of aspects 1-32, further comprising one or more nuclear localization signals.
[00217] Aspect 34. A nucleic acid comprising a nucleotide sequence encoding the fusion polypeptide of any one of aspects 1-33.
[00218] Aspect 35. The nucleic acid of aspect 34, wherein the nucleotide sequence is operably linked to a promoter that is functional in a eukaryotic cell.
[00219] Aspect 36. The nucleic acid of aspect 35, wherein the promoter is functional in one or more of: a plant cell, a fungal cell, an animal cell, cell of an invertebrate, a fly cell, a cell of a vertebrate, a mammalian cell, a primate cell, a non-human primate cell, and a human cell.
[00220] Aspect 37. The nucleic acid of aspect 35 or 36, wherein the promoter is a constitutive promoter, an inducible promoter, a cell type-specific promoter, or a tissue-specific promoter.
[00221] Aspect 38. A recombinant expression vector comprising the nucleic acid of any one of aspects 34-37.
[00222] Aspect 39. The recombinant expression vector of aspect 38, wherein the recombinant expression vector is a recombinant adenoassociated viral vector, a recombinant retroviral vector, or a recombinant lentiviral vector.
[00223] Aspect 40. A eukaryotic cell comprising the fusion polypeptide of any one of aspects 1-
33, or a nucleic acid comprising a nucleotide sequence encoding the fusion polypeptide of any one of aspects 1-33. [00224] Aspect 41. The eukaryotic cell of aspect 40, further comprising a CRISPR/Cas guide nucleic acid, or a nucleic acid comprising a nucleotide sequence encoding a CRISPR/Cas guide nucleic acid.
[00225] Aspect 42. The eukaryotic cell of aspect 40 or aspect 41, further comprising a donor
DNA template.
[00226] Aspect 43. The eukaryotic cell of any one of aspects 40-42, wherein the eukaryotic cell is a plant cell, a mammalian cell, an insect cell, an arachnid cell, a yeast cell, a fungal cell, a bird cell, a reptile cell, an amphibian cell, an invertebrate cell, a mouse cell, a rat cell, a primate cell, a non-human primate cell, or a human cell.
[00227] Aspect 44. A composition comprising: a) the fusion polypeptide of any one of aspects 1-
33; and b) a buffer.
[00228] Aspect 45. A composition comprising: a) the fusion polypeptide of any one of aspects 1-
33; and b) a CRISPR/Cas guide nucleic acid, or one or more DNA molecules comprising a nucleotide sequence(s) encoding the CRISPR/Cas guide nucleic acid.
[00229] Aspect 46. The composition of aspect 45, wherein the CRISPR/Cas guide nucleic acid is an RNA, a DNA, or an RNA/DNA hybrid.
[00230] Aspect 47. The composition of aspect 44 or aspect 45, wherein the composition comprises a lipid.
[00231] Aspect 48. The composition of aspect 44 or aspect 45, wherein a) and b) are within a liposome.
[00232] Aspect 49. The composition of any one of aspects 44-47, wherein a) and b) are within a particle.
[00233] Aspect 50. The composition of any one of aspects 44-49, comprising one or more of: a buffer, a nuclease inhibitor, and a protease inhibitor.
[00234] Aspect 51. The composition of any one of aspects 44-50, further comprising a DNA donor template.
[00235] Aspect 52. A system comprising one of: a) a fusion polypeptide of any one of aspects 1-33; and a CRISPR/Cas guide nucleic acid; b) a fusion polypeptide of any one of aspects 1-33; a CRISPR/Cas guide nucleic acid, and a DNA donor template; c) a fusion polypeptide of any one of aspects 1-33; and a CRISPR/Cas guide RNA; d) a fusion polypeptide of any one of aspects 1-33; a CRISPR/Cas guide RNA, and a DNA donor template; e) an mRNA encoding a fusion polypeptide of any one of aspects 1-33; and a CRISPR/Cas guide nucleic acid; f) an mRNA encoding a fusion polypeptide of any one of aspects 1-33; a CRISPR/Cas guide nucleic acid, and a DNA donor template; g) an mRNA encoding a fusion polypeptide of any one of aspects 1-33; and a CRISPR/Cas guide RNA; h) an mRNA encoding a fusion polypeptide of any one of aspects 1-33; a CRISPR/Cas guide RNA, and a DNA donor template; i) one or more recombinant expression vectors comprising: i) a nucleotide sequence encoding a fusion polypeptide of any one of aspects 1-33; and ii) a nucleotide sequence encoding a CRISPR/Cas guide nucleic acid; j) one or more recombinant expression vectors comprising: i) a nucleotide sequence encoding a fusion polypeptide of any one of aspects 1-33; ii) a nucleotide sequence encoding a CRISPR/Cas guide nucleic acid; and iii) a DNA donor template; k) one or more recombinant expression vectors comprising: i) a nucleotide sequence encoding a fusion polypeptide of any one of aspects 1-33; and ii) a nucleotide sequence encoding a CRISPR/Cas guide RNA; and l) one or more recombinant expression vectors comprising: i) a nucleotide sequence encoding a fusion polypeptide of any one of aspects 1-33; ii) a nucleotide sequence encoding a CRISPR/Cas guide RNA; and a DNA donor template.
[00236] Aspect 53. The system of aspect 52, wherein the donor template nucleic acid has a length of from 8 nucleotides to 10,000 nucleotides.
[00237] Aspect 54. The system of aspect 52, wherein the donor template nucleic acid has a length of from 25 nucleotides to 5,000 nucleotides.
[00238] Aspect 55. A kit comprising the system of any one of aspects 52-54.
[00239] Aspect 56. The kit of aspect 55, wherein the components of the kit are in the same container.
[00240] Aspect 57. The kit of aspect 55, wherein the components of the kit are in separate containers.
[00241] Aspect 58. A sterile container comprising the system of any one of aspects 52-54.
[00242] Aspect 59. The sterile container of aspect 58, wherein the sterile container is a syringe.
[00243] Aspect 60. An implantable device comprising the system of any one of aspects 52-54.
[00244] Aspect 61. The device of aspect 60, wherein the system is within a matrix.
[00245] Aspect 62. The device of aspect 60, wherein the system is in a reservoir. [00246] Aspect 63. The device of any one of aspects 60-62, wherein the device comprises a catheter.
[00247] Aspect 64. The device of any one of aspects 60-63, wherein the device provides for controlled release of the system.
[00248] Aspect 65. A method of modifying a target nucleic acid, the method comprising contacting the target nucleic acid with: a) the fusion polypeptide of any one of aspects 1-33; and b) a guide nucleic acid that comprises: i) a guide sequence that hybridizes to a target sequence of the target nucleic acid; and ii) an activator sequence that binds to the CRISPR/Cas effector polypeptide, wherein said contacting results in modification of the target nucleic acid by the CRISPR/Cas effector polypeptide. [00249] Aspect 66. The method of aspect 65, wherein said modification comprises cleavage of the target nucleic acid.
[00250] Aspect 67. The method of aspect 65 or aspect 66, wherein said modification comprises homology-directed repair of the target nucleic acid.
[00251] Aspect 68. The method of any one of aspects 65-67, wherein the target nucleic acid is present in chromatin.
[00252] Aspect 69. The method of any one of aspects 65-68, wherein said contacting takes place in vitro outside of a cell.
[00253] Aspect 70. The method of any one of aspects 65-68, wherein said contacting takes place inside of a cell in in vitro culture.
[00254] Aspect 71. The method of any one of aspects 65-68, wherein said contacting takes place inside of a eukaryotic cell in vivo.
[00255] Aspect 72. The method of aspect 70 or aspect 71, wherein the cell is selected from: a plant cell, a fungal cell, a mammalian cell, a reptile cell, an insect cell, an avian cell, a fish cell, a parasite cell, an arthropod cell, a cell of an invertebrate, a cell of a vertebrate, a rodent cell, a mouse cell, a rat cell, a primate cell, a non-human primate cell, and a human cell.
[00256] Aspect 73. The method of aspect any one of aspects 65-72, wherein said contacting comprises: introducing into a cell: (a) the fusion polypeptide, or a nucleic acid comprising a nucleotide sequence encoding the fusion polypeptide, and (b) the guide nucleic acid, or a nucleic acid comprising a nucleotide sequence encoding the guide nucleic acid.
[00257] Aspect 74. The method of any one of aspects 65-73, wherein said contacting further comprises: introducing a DNA donor template into the cell.
[00258] Aspect 75. A method of modifying a target nucleic acid present in chromatin in a eukaryotic cell, the method comprising: a) contacting the chromatin with a first fusion polypeptide comprising: i) an enzymatically inactive CRISPR/Cas effector polypeptide; and ii) a chromatin marker polypeptide that modifies a histone polypeptide present in chromatin, wherein the modification marks the chromatin as a site for recombination; and b) contacting the marked chromatin with: i) a complex comprising an enzymatically active CRISPR/Cas effector polypeptide and a guide nucleic acid; and ii) a donor template DNA.
[00259] Aspect 76. A method of modifying chromatin in a eukaryotic cell, the method comprising contacting the chromatin with the fusion polypeptide of any one of aspects 1-33.
[00260] Aspect 77. A method of modifying chromatin in a gamete, the method comprising contacting the chromatin in the gamete with: a) the fusion polypeptide of any one of aspects 1-33; and b) a guide nucleic acid comprising a nucleotide sequence that hybridizes to a target nucleic acid in the chromatin, thereby a gamete comprising chromatin comprising a modification.
[00261] Aspect 78. The method of aspect 77, wherein the gamete is a sperm.
[00262] Aspect 79. The method of aspect 77, wherein the game is an oocyte.
[00263] Aspect 80. The method of any one of aspects 77-79, wherein the modification generates a recombination hotspot.
EXAMPLES
[00264] The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the present invention, and are not intended to limit the scope of what the inventors regard as their invention nor are they intended to represent that the experiments below are all or the only experiments performed. Efforts have been made to ensure accuracy with respect to numbers used (e.g. amounts, temperature, etc.) but some experimental errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, molecular weight is weight average molecular weight, temperature is in degrees Celsius, and pressure is at or near atmospheric. Standard abbreviations may be used, e.g., bp, base pair(s); kb, kilobase(s); pi, picoliter(s); s or sec, second(s); min, minute(s); h or hr, hour(s); aa, amino acid(s); kb, kilobase(s); bp, base pair(s); nt, nucleotide(s); i.m., intramuscular(ly); i.p., intraperitoneal(ly); s.c., subcutaneous(ly); and the like.
Example 1
METHODS
Target site selection
[00265] Target sites were selected based on narrow-peak calls for H3K4me3 and H3K36me3 in
HEK293 cells. Call sets were obtained from the ENCODE portal with the following identifier: ENCSR372WXC. https:(//)www(dot)encodeproject(dot)org/reference-epigenomes/ENCSR372WXC/. Plasmid construction
[00266] The Cas9 expression plasmid pCAGGS was used. Cas9 was amplified from the expression plasmid using CloneAmp HiFi polymerase chain reaction (PCR) Premix (Takara Bio) for 35 cycles (98°C for 10 s, 55°C for 15 s, and 72°C for 10 s; then 72°C for 1 min). PRDM9 and PRDM9dC was amplified from human cDNA purchased from GenScript (ORF Clone ID OFiu03253). SETD2 was amplified from SETD2-GFP (Addgene plasmid # 80653; http://n2t.net/addgene:80653), and SETMAR was amplified from SETMAR (3B05) (Addgene plasmid # 25250; http://n2t.net/addgene:25250). In- Fusion Cloning (Takara Bio) was used to clone PRDM9-Cas9, PRDM9dC-Cas9, SETD2-Cas9, and SETMAR-Cas9 into the pCAGGS expression vector. All Cas9 variants were confirmed by Sanger sequencing.
Mammalian cell line culture and lipofection
[00267] All cell lines (FIEK293T, FieLa, U20S, IMR90) were cultured in Dulbecco's Modified
Eagle Medium (DMEM; Thermo Fisher) supplemented with 10% fetal bovine serum (FBS, VWR), and 1% Penicillin/Streptomycin (P/S, Gibco). All cells were cultured at 37°C in a 5% C02 air incubator. Lipofection was performed using Lipofectamine 3000 (Thermo Fisher Scientific) according to the manufacturer’s instructions. 50,000 cells per well were seeded in 24-weII plates 24 hours prior to lipofection. Cells were transfected with 500 ng Cas nuclease expression plasmid, 150 ng sgRNA expression plasmid, and 1.5 pmol single-stranded oligodeoxynucleotide (ssODN) template (IDT) per well.
HEK293T BFP to EGFP Reporter
[00268] A HEK293T blue fluorescent protein-green fluorescent protein (BFP-GFP) reporter cell line (Richardson et al. (2016) Nature Biotechnology, 34(3), 339-344) was used. The cell line expresses blue fluorescent protein (BFP) constitutively. The cells can be edited using CRISPR-Cas9 and an asymmetric single stranded DNA template donor, as described in (Richardson et al., 2016, supra). If the double stranded break (DSB) is repaired via homology directed repair (HDR), the cells start expressing Enhanced Green Fluorescent Protein (EGFP) and no longer express BFP. The cells lose all fluorescence, if the DSBs caused by CRISPR-Cas9 introduce insertions and deletions (indels), typical when repair happens through non homologous end joining (NHEJ).
Transfections
[00269] 20,000 HEK293T BFP to EGFP cells were seeded in 24-weII plates. The next day, cells were transfected with 1.5m1 of Lipofectamine 3000, Imΐ of p300 enhancer, 500ng of nuclease (Cas9 or Cas9-PRDM9 \C), 150ng of sgRNA and 1.5 pmol of DNA template ordered from IDT. The sequence of the ssDNA template was: [00270] GCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGC CCGTGCCCTGGCCCACCCTCGTGACCACCCTGACGTACGGCGTGCAGTGCTTCAGCCGCTAC
CCCGACCACATGA (SEQ ID NO: 100)
[00271] Transfected cells were incubated for 72 hours prior to collection.
[00272] The protospacer targeted with the sgRNA was: GCTGAAGCACTGCACGCCAT (SEQ
ID NO:101)
Western blotting
[00273] Cells were resuspended in lysis buffer (20mM Tris pH 7.5, ImM MgC12, ImM CaC12,
137mM NaCl, 10% Glycerol, 1% NP-40) containing Benzonase (12.5 u/mL) and Protease Inhibitor Cocktail (Roche) and incubated at 4°C for 1 h with rotation. Proteins from whole cell lysates were separated by 4-20% TGX gel (Bio-Rad) and transferred to a nitrocellulose membrane (0.2pm pore size) (Invitrogen). Membranes were blocked and incubated with primary antibodies at 4°C overnight followed by secondary antibodies at room temperature for 1 h. Primary antibodies used for Western blot analysis were FLAG (Sigma) and GAPDH (Cell Signaling Technology). Secondary Alexa Fluor antibodies were purchased from Thermo Fisher.
[00274] Imaging was performed using the Odyssey imaging system (LI-COR). Double bands were caused by incomplete cleavage at the self-cleaving P2A peptide, leading to an uncleaved byproduct (Kim et al., (2011) PLOS ONE, 6(4), el8556. https://doi.org/10.1371/journal.pone.0018556 Chromatin immunoprecipitation
[00275] Chromatin immunoprecipitation (ChIP) was performed. Briefly, cells were cross! inked for 5 min in 1% formaldehyde, and the reaction was quenched by the addition of glycine to 125 mM and incubation for 5 min. Cells were washed twice with lysis buffer 1 and 2, respectively. Then, cells were resuspended in lysis buffer 3 and sheared by sonication (30s on/30s off) using a Covaris S2 (UC Berkeley Functional Genomics Laboratory). 500 pg lysate was incubated at 4°C overnight with 2 pg of appropriate antibodies (H3K4me3 (Abeam), H3K36me3 (Abeam), H3K36me2 (Diagonde), and IgG (Abeam)) pre-bound to 30 pL of Protein G Magnetic Beads (Thermo Fisher). The IP/bead mixture was washed 5 times with RIPA wash buffer and eluted from the beads for 30 min at 65 °C. Both input and immunoprecipitation (IP) samples were reverse crosslinked by incubating at 65°C overnight with shaking. Then, samples were incubated at 37°C for 2 h with RNase A (0.2 mg/mL) and at 55°C for 2 h with Proteinase K (0.2 mg/mL). DNA samples were purified using 400 uL UltraPure™ Phenol:Chloroform:Isoamyl Alcohol (25:24:1) (Thermo Fisher).
Collections and flow cytometry
[00276] After 72 hours, media was aspirated from cells and cells were washed with phosphate buffered saline (PBS). Cells were then dissociated with trypsin, quenched with media and washed with PBS to remove all media. Cells were then resuspended in PBS + 1% BSA and ImM EDTA. 20000 cells per condition were then sorted in an Attune NxT acoustic focusing cytometer based on green and blue fluorescence. Data were then processed and plotted using FLOWJO.
Transfections
[00277] 200,000 HEK293T BFP to GFP cells were seeded in 10cm plates. The next day, cells were transfected with 15m1 Lipofectamine 3000, 10m1 of p300 enhancer, 5ug of nuclease (dCas9 or dCas9-PRDM9 \C), 1.5pg of sgRNA and 15 pmol of DNA template ordered from Integrated DNA Technologies (IDT). The target site was: chr20:32761950 -32761969.
[00278] The protospacer targeted with sgRNA was: GGCACTGCGGCTGGAGGTGG (SEQ ID
NO: 102).
[00279] The ssDNA template was:
GGATGACAGGCAGGGGCACCGCGGCGCCCCGGTGGCACTGCGGCTGGAGTTGGGAATTAA AGCGGAGACTCTGGTGCTGTGTGACTACAGTGGGGGCCCT (SEQ ID NO: 103)
Crosslinking and quantitative polymerase chain reaction (qPCR)
[00280] The cells were cross-linked with a final concentration of 1 % formaldehyde by shaking at
100 rpm for 5 min at room temperature. The cross-linking reaction was quenched by the addition of 2.5 M glycine to a final concentration of 125 mM, followed by shaking at 100 rpm for an additional 5 min followed by two washes in cold PBS. Nuclei were then isolated from 20 million cells as described in Shah et al. ((2013) Genes & Development, 27(16), 1787-1799) and chromatin was sheared to 250-bp average size using a Covaris S220. Immunoprecipitations were performed using 500 mg of sheared chromatin lysate and 2 pg of antibodies preconjugated to protein G beads (Invitrogen): H3K4me3 (ab8580, Abeam), H3K36me3 (61101, Active Motif) and rabbit anti-mouse IgG control (ab46540, Abeam). ChIP reactions were incubated for 16 hours at 4°C with rotation and then washed four times in wash buffer [50 mM Hepes-HCl (pH 8), 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, and 0.5% A-laurylsarcosine] , followed by one wash in ChIP final wash buffer (lx tris- EDTA (TE) Buffer and 50 mM NaCl). Immunoprecipitated DNA was eluted from washed beads and reverse cross-linked overnight. DNA was then purified by phenohchloroform extraction and ethanol precipitation and resuspended in lx TE buffer. qPCR was carried out with Power SYBR (Applied Biosystems) using primers for the target site on chromosome 20 or an upstream control.
[00281] qPCR primers on target:
[00282] fwd: TGGTTCAATGGTCATCCCAGG (SEQ ID NO: 104), rev:
GCATGGACTGACTGAGGGAG (SEQ ID NO: 105)
[00283] Upstream control: [00284] fwd: AGTAGAAACGGGGTGTCTCCA (SEQ ID NO: 106) rev: TTGGGAGGCTGAGGTGGG (SEQ ID NO: 107).
[00285] Primers for target site 7 :
[00286] qPCR-F: CGCCTGTGATGGGCTAATTG (SEQ ID NO: 108)
[00287] qPCR-R: GGCCTCTCCAGCCTCATTTG (SEQ ID NO: 109)
[00288] Primers for downstream control site:
[00289] qPCR-F: CCACATTGGCTCCACCCATC (SEQ ID NO: 110)
[00290] qPCR-R: CTTGGTTGTGTCACGTGGTT (SEQ ID NO: 111)
Illumina deep sequencing analysis
[00291] DNA was extracted 72 hours post-transfection using QuickExtract DNA Extraction
Solution (Lucigen) and heated at 65°C for 20 min followed by 95°C for 20 min. DNA samples were then amplified with PrimeSTAR GXL DNA Polymerase (Takara Bio) with PCR forward/reverse primers containing Illumina adapter sequences for 30 cycles (98°C for 10 s, 55°C for 15 s, and 68°C for 1 min). [00292] The resulting amplicons were cleaned by adding 25 pF of amplicon to 45 pF of magnetic beads (UC Berkeley Sequencing Core). The samples were placed on a 96-well magnetic plate for 5 min, and the supernatant was removed. The samples were washed twice with 200 pL of 70% ethanol and eluted in 40 pL of Tris-EDTA Buffer (Corning).
[00293] The purified samples were sequenced on an Illumina iSeq by QB3 Genomics at UC
Berkeley. NGS sequencing reads were analyzed for HDR-mediated modifications and indels using CRISPResso2 (https:(//)crispresso(dot)pinellolab(dot)partners(dot)org) in batch mode using default parameters.
RESULTS
[00294] The data are shown in FIG. 14-FIG. 16. FIG. 1A provides a schematic model of how a
PRDM9AC/Cas9 fusion protein decorates adjacent nucleosomes with H3K4me3 (yellow) and H3K36me3 (orange) during donor template-mediated HDR, to improve HDR rates. FIG. IB. HEK293T BFP-EGFP reporter cell line expresses EGFP upon HDR and loses fluorescence if DNA repair proceeds through NHEJ. Flow cytometry of 20,000 cells precondition shows Cas9-PRDM9AC (with guide RNA + donor DNA template) provides for increased HDR and decreased NHEJ, compared to Cas9 (not fused to PRDM9AC) and control. FIG. 1C. Cas9-PRDM9AC (with guide RNA + donor DNA template) shows a 2-fold increase (p<0.05) in HDRdndel ratio compared to Cas9 alone (not fused to PRDM9AC) (with guide RNA + donor DNA template) (n = 3). FIG. ID. ChIP-qPCR experiments show dCas9-PRDM9AC selectively decorates target sites with H3K4me3 and H3K36me3. Endogenous chromatin architecture mediates DNA repair pathway choice
[00295] To assess whether endogenous chromatin architecture affects Cas9 activity and DNA repair pathway choice, endogenous loci with varying chromatin modifications were identified based on publicly available ENCODE-ChIP-seq data from human embryonic kidney 293 cells (HEK293T). Nine target sites with varying levels of H3K4me3 and H3K36me3 enrichment were selected (FIG. 14A), including disease-relevant sites (HBB and LDLR) as CRISPR-Cas9 precise editing at these sites can be a powerful strategy to introduce desired sequence alterations for clinical applications. HDR frequencies at the selected sites were examined by transfecting HEK293T cells with Cas9 and single guide RNA (sgRNA) expression plasmids along with an ssODN donor template encoding a point mutation upstream of the PAM. Notably, while absolute HDR frequencies did not correlate with endogenous histone modifications, the HDRdndel ratios were significantly higher at sites highly enriched with both H3K4me3 and H3K36me3 marks compared to unenriched sites (FIG. 14B). Of note, the HDRdndel ratio (0.77 ± 0.04) at site 5, which is heavily decorated with histone marks, is 4-fold higher compared to sites without H3K4me3 and H3K36me3 enrichment. These results suggest that endogenous H3K4me3 and H3K36me3 marks influence the choice of DNA repair pathway following Cas9-induced DSBs, specifically favoring HDR over NHEJ compared to sites devoid of these marks.
Engineered CRISPR-Cas9 epigenetic fusions deposit histone modifications in a site-specific manner [00296] Epigenetic fusion nucleases were engineered, and it was tested whether newly deposited histone modifications could increase HDR frequency and HDRdndel ratio (FIG. 14C). Four fusion constructs were constructed by fusing histone methyltransferases at the N-terminus of Cas9 in the pCAGGS expression vector (FIG. 14C). The PRDM9-Cas9 fusion comprises the KRAB domain which recruits additional proteins to facilitate recombination, the PR/SET domain which catalyzes methyltransf erase activity, and a post-SET single zinc finger (ZnF) (Thibault-Sennett et al., (2018) Genetics, 209(2), 475-487. https://doi.org/10.1534/genetics.118.300565). Additionally, the N-terminal domains of PRDM9 may be important for mediating interactions with HEEES and forming a pioneer complex to open chromatin. The C-terminal ZnF array of PRDM9 was excluded to remove endogenous DNA binding activity (Striedner et al., (2017) Chromosome Research, 25(2), 155-172. https://doi.org/10.1007/sl0577-017-9552-l). PRDM9dC-Cas9 is a truncated version lacking the post- SET ZnF involved in negative autoregulation of methyltransferase activity and is thus predicted to show higher methylation activity. SETD2-Cas9 includes a SET domain which deposits H3K36me3 marks. Additionally, a SETMAR-Cas9 fusion was generated, which consists of a SET domain which deposits H3K36me2 marks shown to be important for NHEJ repair.
[00297] Western blot analysis was performed to determine the level of expression of each fusion compared to unmodified Cas9 in HEK293T cells. When equal amounts (500ng) of plasmids expressing either Cas9 or the fusion proteins were delivered, slightly lower expression of each fusion compared to Cas9 was observed. Scaling the amounts of plasmids expressing the fusion proteins based on the size of each fusion compared to unmodified Cas9 did not lead to increased expression.
[00298] It was then investigated whether the newly developed Cas9 epigenetic fusions deposit histone modifications in a site-specific manner. Sites 7 (intergenic) and 9 (within LDLR) were selected. H3K4me3 and H3K36me3 enrichment was determined by chromatin immunoprecipitation followed by quantitative PCR (ChIP-qPCR). To eliminate the potential effects of DSB remodeling on chromatin modifications, nuclease-dead Cas9 (dCas9) fusions to each histone methyltransferase described above were engineered. ChIP was performed using HEK293T cells transfected with either dCas9 or one of the dCas9 fusions and sgRNAs for site 7 or 9. By qPCR with primers flanking each target site or respective control genomic sites ~20 kilobases downstream, the presence of H3K4me3 and H3K36me3 was determined on day 3 post-transfection. Strikingly, both PRDM9-dCas9 and PRDM9dC-dCas9 resulted in a 2-log increase in H3K4me3 and H3K36me3 at site 7 compared to dCas9 without modifying the downstream site, indicating that the fusions specifically deposited histone marks at the target site (FIG. 14D). The PRDM9 fusions also effectively deposited H3K4me3 marks at site 9 (100-fold enrichment by PRDM9-Cas9 and 30-fold enrichment by PRDM9dC-Cas9), although they only increased H3K36me3 by up to 4.6-fold. SETD2-dCas9 increased H3K36me3 by 42-fold at site 7 and 15-fold at site 9 (FIG. 14D). SETMAR-dCas9 only achieved a 1.7-fold increase in H3K36me2 at site 7 and a 1.3-fold increase at site 9 compared to dCas9 (FIG. 14D).
PRDM9-Cas9 fusions display higher HDR and HDRdndel ratios
[00299] The editing outcomes of the fusion constructs via a BFP-to-GFP conversion assay in
HEK293T cells stably expressing a BFP reporter was evaluated (Richardson et al., (2016) supra). Cells were transfected with a sgRNA targeting the BFP gene and an ssODN template encoding a three- nucleotide change. Cells express GFP if the Cas9-induced DSB is repaired via HDR; on the other hand, cells lose BFP expression if the cut is repaired via NHEJ (FIG. 15A). BFP-/GFP+ (HDR) and BFP- /GFP- (NHEJ) cells were gated relative to cells transfected with a non-targeting control sgRNA (FIG. 15B). Using flow cytometry 7 days post-transfection, it was observed that in the absence of HDR templates, the epigenetic fusions exhibited modestly lower nuclease activity than unmodified Cas9, except for PRDM9dC-Cas9 which displayed a 50% decrease in editing efficiency (FIG. 15C). When HDR templates were co-introduced, PRDM9 and SETD2 fusions greatly increased HDR frequency and HDRdndel ratios (FIG. 15D-15E). Strikingly, PRDM9-Cas9 achieved a 15.62 ± 0.79% HDR knock-in efficiency compared to 9.57 ± 0.47% with unmodified Cas9. Additionally, PRDM9-Cas9 displayed a 2- fold higher HDRdndel ratio (0.28 ± 0.02) compared to Cas9 (0.14 ± 0.01). Together, these data provide evidence that the Cas9 epigenetic fusions improve HDR while decreasing indel formation. PRDM9-Cas9 fusions display increased HDRdndel ratios across multiple endogenous sites and different cell types
[00300] The ability of the epigenetic fusions to drive HDR at endogenous intergenic (site 7) and exonic disease-relevant (site 9, LDLR) sites was examined. To this end, HEK293T cells were transfected with the previously described sgRNAs and ssODN templates (FIG. 14A) and measured the extent of genome modification by next-generation sequencing. PRDM9-Cas9, PRDM9dC-Cas9, and SETD2-Cas9 all achieved higher HDR efficiency than unmodified Cas9 at both sites (FIG. 16A-16B). In particular, PRDM9-Cas9 displayed HDR frequencies of 10.99 ± 0.18% and 9.17 ± 0.57% at sites 7 and 9, compared to 5.82 ± 0.50% and 5.56 ± 0.23% with Cas9 at the respective sites. Moreover, PRDM9-Cas9 and SETD2-Cas9 improved HDRdndel ratios by 3-fold or more compared to unmodified Cas9.
[00301] Since PRDM9-Cas9 offered the highest HDR frequency at both sites, we sought to test this fusion at additional endogenous sites. The results showed that the HDR frequencies of PRDM9-Cas9 were up to 2-fold higher than Cas9 at sites 6-9, which lacked endogenous histone modifications (FIG. 16C). However, the fusion did not display enhanced HDR efficiencies at 2 additional highly characterized sites 10 (HEK2) and 11 (exon in SERPINA). Endogenous H3K4me3 or H3K36me3 enrichment was not detected at these two sites based on the analysis of ENCODE data, which suggests that other factors beyond chromatin architecture are also important in DNA repair pathway choice. PRDM9-Cas9 also showed higher HDRdndel ratios compared to Cas9 at sites 6-9, but only achieved modest improvements in HDRdndel ratios at sites 10 and 11. Given that the fusions can modify adjacent chromatin, it was then examined whether this can lead to higher off-target editing by evaluating their editing activity at 6 potential off-target sites predicted from 2 sgRNAs. The results showed that PRDM9- Cas9 does not lead to higher off-target effects compared to Cas9 (FIG. 16D). Together, these data highlight the ability of PRDM9-Cas9 to significantly improve Cas9-mediated HDR efficiency and HDRdndel ratio via de novo modifications of chromatin architecture in response to a targeted DSB. [00302] The HDR efficiency of PRDM9-Cas9 was compared to that of Cas9 in combination with ssODN templates either with or without a mutation at the PAM site. Previous reports have shown that ssODNs with a blocking mutation at PAM significantly increases HDR efficiency by preventing the retargeting of the edited site ((Okamoto et al., (2019) Scientific Reports, 9(1), 4811. https://doi.org/10.1038/s41598-019-41121-4). Single-stranded ODN templates were designed that either disrupt or retain PAM at sites 7, 9, and 10. Consistent with previous reports, unmodified Cas9 showed 2- fold higher HDR efficiency at sites 7 and 9 using ssODNs with PAM mutations (10.6% ± 0.3% and 12.3% ± 0.5%) compared to ssODNs without PAM mutations (5.8% ± 0.5% and 5.6% ± 0.2%) although no significant difference was observed at site 10 (FIG. 17A) (Okamoto et al., (2019) supra). Importantly, this PRDM9-Cas9 fusion approach alone achieved similar improvements in HDR efficiency compared to unmodified Cas9 using ssODN templates with PAM mutations (FIG. 17A). Furthermore, PRDM9-Cas9 increased HDRtindel ratio more significantly than the PAM mutation strategy (FIG. 17B). Taken together, these findings suggest that PRDM9-Cas9 can be utilized to improve HDR efficiency effectively without the need to introduce PAM mutations.
[00303] It has been previously reported that the identity of the position 4 nucleotide before the
PAM influences the pattern of indels following Cas9-mediated DSBs (Shen et al., (2018) Nature, 567(7733), 646-651. https://doi.org/10.1038/s41586-018-0686-x; Taheri-Ghahfarokhi et al., (2018) Nucleic Acids Research, 46(16), 8417-8434. https://doi.org/10.1093/nar/gky653; Tatiossian et al., (2021) Molecular Therapy: The Journal of the American Society of Gene Therapy, 29(3), 1057-1069. https://doi.org/10.1016/j-ymthe.2020.10.006). A guanine at position 4 shows the lowest frequency of single nucleotide indels and promotes the formation of primarily deletions (Taheri-Ghahfarokhi et al., (2018) supra). It was investigated whether position 4 nucleotide identity predicts indel patterns using either Cas9 or PRDM9-Cas9 without a donor template at sites 6-11. The frequencies of NHEJ were quantified as deletions of less than 3bp and insertions, and MMEJ as deletions of more than 3bp (Tatiossian et al., (2021) supra). The results did not show a significant correlation between the nucleotide identity at position 4 and the relative frequency of NHEJ and MMEJ. Importantly, Cas9 and PRDM9- Cas9 showed the same indel patterns at each target site.
[00304] To investigate whether PRDM9-Cas9 can improve HDR efficiency in other cell types, the fusion construct at sites 7, 8 (HBB), and 9 (LDLR) were tested in HeLa and U20S cells. A consistent increase in HDR frequency by PRDM9-Cas9 was not observed in these cell types, which may be due to differences in histone modifications and DNA repair processes that are cell type-specific (FIG. 17C- 17D). Nonetheless, PRDM9-Cas9 enhanced HDRtindel ratios by up to 2-fold across all three target sites in both cell types. Overall, PRDM9-Cas9 improves the relative frequency of HDR to indel at multiple endogenous sites across different mammalian cell lines.
[00305] FIG. 14A-14D. Endogenous histone modifications mediate DNA repair pathway choice.
FIG. 14A. Endogenous trimethylation of H3K4 and H3K36 at target sites based on reanalyzed ENCODE ChIP-seq data in HEK293T cells. FIG. 14B. HDR frequency and HDRtindel ratio measured by NGS at target sites in HEK293T cells transfected with Cas9 and sgRNA with ssODN template. Data represents mean ± standard error (n = 3). FIG. 14C. Schematic of a novel strategy to decorate chromatin to increase HDR efficiency using 4 distinct epigenetic writer fusions. FIG. 14D. H3K4me3, H3K36me3, and H3K36me2 enrichment measured by ChIP-qPCR at site 7. Data represents mean ± standard error (n = 2).
[00306] FIG. 15A-15E. Engineered CRISPR-Cas9 epigenetic fusions display higher HDR and
HDRtindel ratios. FIG. 15 A. Schematic of BFP-to-GFP reporter assay. In brief, BFP+/GFP- cells can be converted to BFP-/GFP+ cells via HDR or to BFP-/GFP- via NHEJ. FIG. 15B. Frequency of HDR (lower right quadrant) and NHEJ (upper left quadrant) measured by flow cytometry in BFP-to-GFP reporter cells transfected with the fusions and sgRNA with ssODN template. FIG. 15C. Editing activity of epigenetic fusions in the absence of ssODN template measured by flow cytometry in BFP-to-GFP reporter cells. FIG. 15D. FiDR frequency measured by flow cytometry in BFP-to-GFP reporter cells transfected with the fusions and sgRNA with ssODN template. FIG. 15E. HDR:indel ratio measured by flow cytometry in BFP-to-GFP reporter cells transfected with the fusions and sgRNA with ssODN template. For C-E, data represents mean ± standard error (n = 3).
[00307] FIG. 16A-16D. Epigenetic fusions display increased FiDR efficiency and HDR:indel ratios across multiple endogenous sites. FIG. 16A. FiDR frequency and HDR:indel ratio measured by NGS at an intergenic genomic locus (site 7) in FIEK293T cells transfected with the fusions and sgRNA with ssODN template. FIG. 16B. FiDR frequency and HDR:indel ratio measured by NGS at an exonic disease-relevant genomic locus (site 9) in FIEK293T cells transfected with the fusions and sgRNA with ssODN template. FIG. 16C. FiDR frequency and HDR:indel ratio measured by NGS at multiple genomic loci (sites 6-11) in FIEK293T cells transfected with PRDM9-Cas9 and sgRNA with ssODN template. FIG. 16D. Off-target activity of PRDM9-Cas9 measured by NGS at 6 off-target sites predicted from 2 sgRNAs. For A-D, data represents mean ± standard error (n = 3).
[00308] FIG. 17A-17D. PRDM9-Cas9 fusion displays increased HDR:indel ratios across different cell types. FIG. 17A. FiDR frequency measured by NGS at multiple genomic loci (sites 7, 9, 10) in FIEK293T cells transfected with PRDM9-Cas9 and sgRNA with ssODN templates either with or without a mutation at the PAM site. FIG. 17B. HDR:indel ratio measured by NGS at multiple genomic loci (sites 7, 9, 10) in FIEK293T cells transfected with PRDM9-Cas9 and sgRNA with ssODN templates either with or without a mutation at the PAM site. FIG. 17C. FiDR frequency and HDR:indel ratio measured by NGS at multiple genomic loci (sites 7-9) in FieLa cells transfected with PRDM9-Cas9 and sgRNA with ssODN template. FIG. 17D. FiDR frequency and HDR:indel ratio measured by NGS at multiple genomic loci (sites 7-9) in U20S cells transfected with PRDM9-Cas9 and sgRNA with ssODN template. For A-D, data represents mean ± standard error (n = 3).
Example 2
[00309] Decorating chromatin for precise genome editing was carried out as described in
Example 1, but with different constructs. FIG. 1A provides a schematic showing CRISPR-Cas9 fused with a lysine methyl transferase (KMT) deposits methyl marks to increase homology directed repair.
FIG. 18 provides a schematic depiction of CRISPR-Cas9 fusions that were generated and tested. The CRISPR-Cas9 fusions were as follows: PRDM9 (416aa; amino acids 1-416)-Cas9; ii) PRDM9dC (371aa; amino acids 1-371)-Cas9; iii) SETD2 (196 aa; amino acids 1494-1690)-Cas9; and iv) SETMAR (263 aa; amino acids 14-277)-Cas9. The CRISPR-Cas fusions were tested, as described in Example 1, using a BFP-to-GFP conversion assay. The data are shown in FIG. 19A-19E and in FIG. 20A-20B. [00310] FIG. 19A-19E: PRDM9 fusions show increased HDR and increased HDRdndel ratios compared to Cas9 alone. A) A BFP to GFP conversion assay. B) Flow Cytometry panels showing increased HDR and decreased NHEJ for PRDM9 fusions. C) Cas9-KMT fusions display similar NHEJ % when no template is provided, except for PRDM9dC which shows a 50% reduction in NHEJ events. D) PRDM9 fusions show up to 50% more HDR compared to Cas9 alone. E) PRDM9 fusions show up to 3 fold HDRdndel ratios compared to Cas9 alone.
[00311] FIG. 20A-20B. PRDM9-Cas9 fusion showed up to 2-fold increased HDR and 3-fold increased HDRdndel ratio across 6 endogenous sites tested, including 2 disease specific mutations on genes (HBB and LDLR).
[00312] While the present invention has been described with reference to the specific embodiments thereof, it should be understood by those skilled in the art that various changes may be made and equivalents may be substituted without departing from the true spirit and scope of the invention. In addition, many modifications may be made to adapt a particular situation, material, composition of matter, process, process step or steps, to the objective, spirit and scope of the present invention. All such modifications are intended to be within the scope of the claims appended hereto.

Claims

CLAIMS What is claimed is:
1. A fusion polypeptide comprising: a) a CRISPR/Cas effector polypeptide; and b) a chromatin marker polypeptide that provides for modification of a histone polypeptide present in chromatin, wherein the modification marks the chromatin as a site for recombination.
2. The fusion polypeptide of claim 1, wherein the chromatin marker polypeptide is a histone methyltransf erase (HMT).
3. The fusion polypeptide of claim 2, wherein the HMT methylates Lys4 or Lys36 of histone H3.
4. The fusion polypeptide of claim 3, wherein the HMT is a PRDM9 polypeptide, a SETD2 polypeptide, or a SETMAR polypeptide.
5. The fusion polypeptide of claim 1, wherein the chromatin marker polypeptide is a histone acetyltransferase.
6. The fusion polypeptide of claim 5, wherein the histone acetyltransferase acetylates Lysl6 of histone H4.
7. The fusion polypeptide of claim 6, wherein the histone acetyltransferase is a MOF polypeptide.
8. The fusion polypeptide of claim 4, wherein the PRDM9 polypeptide comprises a KRAB domain, an SSXRD domain, and a PR/SET domain, and does not include a zinc finger DNA-binding domain.
9. The fusion polypeptide of claim 8, wherein the PRDM9 polypeptide has a length of from about 350 amino acids to about 390 amino acids, and wherein the PRDM9 polypeptide comprises an amino acid sequence having at least 85% amino acid sequence identity to amino acids 1-370 of the amino acid sequence of the PRDM9 polypeptide depicted in FIG. 2A (SEQ ID NO:l) or at least 85% amino acid sequence identity to amino acids 1-371 of the amino acid sequence of the PRDM9 polypeptide depicted in FIG. 2B (SEQ ID NO:2).
10. The fusion polypeptide of claim 1, wherein the fusion polypeptide comprises an amino acid sequence having at least 85% amino acid sequence identity to the amino acid sequence depicted in FIG. 3A (SEQ ID NOG) or FIG. 3B (SEQ ID NO:4).
11. The fusion polypeptide of claim 1, wherein the chromatin marker polypeptide binds H3K4me3 and/or H3K36me3.
12. The fusion polypeptide of claim 11, wherein the chromatin marker polypeptide is a ZMYND8 polypeptide or a ZCWPWI polypeptide.
13. The fusion polypeptide of claim 1, wherein the chromatin marker polypeptide is a PRDM9- binding polypeptide.
14. The fusion polypeptide of claim 13, wherein the PRDM9-binding polypeptide is EWSR1 or PREC8.
15. The fusion polypeptide of any one of claims 1-14, wherein the CRISPR/Cas effector polypeptide is a type II CRISPR/Cas effector polypeptide, a type V CRISPR/Cas effector polypeptide, or a type VI CRISPR/Cas effector polypeptide.
16. The fusion polypeptide of any one of claims 1-14, wherein the CRISPR/Cas effector polypeptide is a type II CRISPR/Cas effector polypeptide.
17. The fusion polypeptide of claim 16, wherein the type II CRISPR/Cas effector polypeptide is a Cas9 polypeptide.
18. The fusion polypeptide of any one of claims 1-14, wherein the CRISPR/Cas effector polypeptide is a type V CRISPR/Cas effector polypeptide.
19. The fusion polypeptide of claim 18, wherein the type V CRISPR/Cas effector polypeptide is a Casl2a, a Casl2b, a Casl2c, a Casl2d, or a Casl2e polypeptide.
20. The fusion polypeptide of any one of claims 1-14, wherein the CRISPR/Cas effector polypeptide is a type VI CRISPR/Cas effector polypeptide.
21. The fusion polypeptide of claim 20, wherein the type VI CRISPR/Cas effector polypeptide is a Casl3a, a Casl3b, a Casl3c, or a Casl3d polypeptide.
22. The fusion polypeptide of any one of claims 1-14, wherein the CRISPR/Cas effector polypeptide is a Casl4a, a Casl4b, or a Casl4c polypeptide.
23. The fusion polypeptide of any one of claims 1-22, wherein the CRISPR/Cas effector polypeptide is enzymatically active.
24. The fusion polypeptide of any one of claims 1-22, wherein the CRISPR/Cas effector polypeptide exhibits reduced enzymatic activity.
25. The fusion polypeptide of any one of claims 1-22, wherein the CRISPR/Cas effector polypeptide exhibits nickase activity.
26. The fusion polypeptide of claim 25, wherein the CRISPR/Cas effector polypeptide comprises a D10A substitution or an H840A substitution, based on the amino acid numbering of Streptococcus pyogenes Cas9, or a corresponding amino acid in another Cas9 polypeptide.
27. The fusion polypeptide of any one of claims 1-22, wherein the CRISPR/Cas effector polypeptide is enzymatically inactive.
28. The fusion polypeptide of claim 27, wherein the CRISPR/Cas effector polypeptide comprises a D10A substitution and an H840A substitution, based on the amino acid numbering of Streptococcus pyogenes Cas9, or the corresponding amino acids in another Cas9 polypeptide.
29. The fusion polypeptide of any one of claims 1-28, wherein the fusion polypeptide comprises, in order from N-terminus to C-terminus: a) the CRISPR/Cas effector polypeptide; and b) the chromatin modifying polypeptide.
30. The fusion polypeptide of any one of claims 1-28, wherein the fusion polypeptide comprises, in order from N-terminus to C-terminus: a) the chromatin modifying polypeptide; and b) the CRISPR/Cas effector polypeptide.
31. The fusion polypeptide of any one of claims 1-28, wherein the fusion polypeptide comprises, in order from N-terminus to C-terminus: a) an N-terminal portion of the CRISPR/Cas effector polypeptide; b) the chromatin modifying polypeptide; and c) a C-terminal portion of the CRISPR/Cas effector polypeptide.
32. The fusion polypeptide of any one of claims 1-28, wherein the fusion polypeptide comprises, in order from N-terminus to C-terminus: a) a C-terminal portion of the CRISPR/Cas effector polypeptide; b) the chromatin modifying polypeptide; and c) an N-terminal portion of the CRISPR/Cas effector polypeptide.
33. The fusion polypeptide of any one of claims 1-32, further comprising one or more nuclear localization signals.
34. A nucleic acid comprising a nucleotide sequence encoding the fusion polypeptide of any one of claims 1-33.
35. The nucleic acid of claim 34, wherein the nucleotide sequence is operably linked to a promoter that is functional in a eukaryotic cell.
36. The nucleic acid of claim 35, wherein the promoter is functional in one or more of: a plant cell, a fungal cell, an animal cell, cell of an invertebrate, a fly cell, a cell of a vertebrate, a mammalian cell, a primate cell, a non-human primate cell, and a human cell.
37. The nucleic acid of claim 35 or 36, wherein the promoter is a constitutive promoter, an inducible promoter, a cell type-specific promoter, or a tissue-specific promoter.
38. A recombinant expression vector comprising the nucleic acid of any one of claims 34-37.
39. The recombinant expression vector of claim 38, wherein the recombinant expression vector is a recombinant adenoassociated viral vector, a recombinant retroviral vector, or a recombinant lentiviral vector.
40. A eukaryotic cell comprising the fusion polypeptide of any one of claims 1-33, or a nucleic acid comprising a nucleotide sequence encoding the fusion polypeptide of any one of claims 1-33.
41. The eukaryotic cell of claim 40, further comprising a CRISPR/Cas guide nucleic acid, or a nucleic acid comprising a nucleotide sequence encoding a CRISPR/Cas guide nucleic acid.
42. The eukaryotic cell of claim 40 or claim 41, further comprising a donor DNA template.
43. The eukaryotic cell of any one of claims 40-42, wherein the eukaryotic cell is a plant cell, a mammalian cell, an insect cell, an arachnid cell, a yeast cell, a fungal cell, a bird cell, a reptile cell, an amphibian cell, an invertebrate cell, a mouse cell, a rat cell, a primate cell, a non-human primate cell, or a human cell.
44. A composition comprising: a) the fusion polypeptide of any one of claims 1-33; and b) a buffer.
45. A composition comprising: a) the fusion polypeptide of any one of claims 1-33; and b) a CRISPR/Cas guide nucleic acid, or one or more DNA molecules comprising a nucleotide sequence(s) encoding the CRISPR/Cas guide nucleic acid.
46. The composition of claim 44, wherein the CRISPR/Cas guide nucleic acid is an RNA, a DNA, or an RNA/DNA hybrid.
47. The composition of claim 44 or claim 45, wherein the composition comprises a lipid.
48. The composition of claim 44 or claim 45, wherein a) and b) are within a liposome.
49. The composition of any one of claims 44-47, wherein a) and b) are within a particle.
50. The composition of any one of claims 44-49, comprising one or more of: a buffer, a nuclease inhibitor, and a protease inhibitor.
51. The composition of any one of claims 44-50, further comprising a DNA donor template.
52. A system comprising one of: a) a fusion polypeptide of any one of claims 1-33; and a CRISPR/Cas guide nucleic acid; b) a fusion polypeptide of any one of claims 1-33; a CRISPR/Cas guide nucleic acid, and a DNA donor template; c) a fusion polypeptide of any one of claims 1-33; and a CRISPR/Cas guide RNA; d) a fusion polypeptide of any one of claims 1-33; a CRISPR/Cas guide RNA, and a DNA donor template; e) an mRNA encoding a fusion polypeptide of any one of claims 1-33; and a CRISPR/Cas guide nucleic acid; f) an mRNA encoding a fusion polypeptide of any one of claims 1-33; a CRISPR/Cas guide nucleic acid, and a DNA donor template; g) an mRNA encoding a fusion polypeptide of any one of claims 1-33; and a CRISPR/Cas guide RNA; h) an mRNA encoding a fusion polypeptide of any one of claims 1-33; a CRISPR/Cas guide RNA, and a DNA donor template; i) one or more recombinant expression vectors comprising: i) a nucleotide sequence encoding a fusion polypeptide of any one of claims 1-33; and ii) a nucleotide sequence encoding a CRISPR/Cas guide nucleic acid; j) one or more recombinant expression vectors comprising: i) a nucleotide sequence encoding a fusion polypeptide of any one of claims 1-33; ii) a nucleotide sequence encoding a CRISPR/Cas guide nucleic acid; and iii) a DNA donor template; k) one or more recombinant expression vectors comprising: i) a nucleotide sequence encoding a fusion polypeptide of any one of claims 1-33; and ii) a nucleotide sequence encoding a CRISPR/Cas guide RNA; and l) one or more recombinant expression vectors comprising: i) a nucleotide sequence encoding a fusion polypeptide of any one of claims 1-33; ii) a nucleotide sequence encoding a CRISPR/Cas guide RNA; and a DNA donor template.
53. The system of claim 52, wherein the donor template nucleic acid has a length of from 8 nucleotides to 10,000 nucleotides.
54. The system of claim 52, wherein the donor template nucleic acid has a length of from 25 nucleotides to 5,000 nucleotides.
55. A kit comprising the system of any one of claims 52-54.
56. The kit of claim 55, wherein the components of the kit are in the same container.
57. The kit of claim 55, wherein the components of the kit are in separate containers.
58. A sterile container comprising the system of any one of claims 52-54.
59. The sterile container of claim 58, wherein the sterile container is a syringe.
60. An implantable device comprising the system of any one of claims 52-54.
61. The device of claim 60, wherein the system is within a matrix.
62. The device of claim 60, wherein the system is in a reservoir.
63. The device of any one of claims 60-62, wherein the device comprises a catheter.
64. The device of any one of claims 60-63, wherein the device provides for controlled release of the system.
65. A method of modifying a target nucleic acid, the method comprising contacting the target nucleic acid with: a) the fusion polypeptide of any one of claims 1-33; and b) a guide nucleic acid that comprises: i) a guide sequence that hybridizes to a target sequence of the target nucleic acid; and ii) an activator sequence that binds to the CRISPR/Cas effector polypeptide, wherein said contacting results in modification of the target nucleic acid by the CRISPR/Cas effector polypeptide.
66. The method of claim 65, wherein said modification comprises cleavage of the target nucleic acid.
67. The method of claim 65 or claim 66, wherein said modification comprises homology-directed repair of the target nucleic acid.
68. The method of any one of claims 65-67, wherein the target nucleic acid is present in chromatin.
69. The method of any one of claims 65-68, wherein said contacting takes place in vitro outside of a cell.
70. The method of any one of claims 65-68, wherein said contacting takes place inside of a cell in in vitro culture.
71. The method of any one of claims 65-68, wherein said contacting takes place inside of a eukaryotic cell in vivo.
72. The method of claim 70 or claim 71, wherein the cell is selected from: a plant cell, a fungal cell, a mammalian cell, a reptile cell, an insect cell, an avian cell, a fish cell, a parasite cell, an arthropod cell, a cell of an invertebrate, a cell of a vertebrate, a rodent cell, a mouse cell, a rat cell, a primate cell, a nonhuman primate cell, and a human cell.
73. The method of claim any one of claims 65-72, wherein said contacting comprises: introducing into a cell: (a) the fusion polypeptide, or a nucleic acid comprising a nucleotide sequence encoding the fusion polypeptide, and (b) the guide nucleic acid, or a nucleic acid comprising a nucleotide sequence encoding the guide nucleic acid.
74. The method of any one of claims 65-73, wherein said contacting further comprises: introducing a DNA donor template into the cell.
75. A method of modifying a target nucleic acid present in chromatin in a eukaryotic cell, the method comprising: a) contacting the chromatin with a first fusion polypeptide comprising: i) an enzymatically inactive CRISPR/Cas effector polypeptide; and ii) a chromatin marker polypeptide that modifies a histone polypeptide present in chromatin, wherein the modification marks the chromatin as a site for recombination; and b) contacting the marked chromatin with: i) a complex comprising an enzymatically active CRISPR/Cas effector polypeptide and a guide nucleic acid; and ii) a donor template DNA.
76. A method of modifying chromatin in a eukaryotic cell, the method comprising contacting the chromatin with the fusion polypeptide of any one of claims 1-33, thereby modifying the chromatin in the cell.
77. A method of modifying chromatin in a gamete, the method comprising contacting the chromatin in the gamete with: a) the fusion polypeptide of any one of claims 1-33; and b) a guide nucleic acid comprising a nucleotide sequence that hybridizes to a target nucleic acid in the chromatin, thereby a gamete comprising chromatin comprising a modification.
78. The method of claim 77, wherein the gamete is a sperm.
79. The method of claim 77, wherein the game is an oocyte.
80. The method of any one of claims 77-79, wherein the modification generates a recombination hotspot.
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Title
DATABASE Protein [Https://www.ncbi.nlm.nih.gov/protein/872725204] 2 March 2021 (2021-03-02), WELLS, D ET AL.: "histone-lysine N-methyltransferase PRDM9 isoform PRDM9 A [Homo sapiens]", XP055972552, retrieved from NCBI *
DATABASE Protein [Https://www.ncbi.nlm.nih.gov/protein/ANZ03364.1] 17 June 2022 (2022-06-17), "Cas9 [Cloning vector Cas9/gRNA", XP055494798, retrieved from NCBI Database accession no. ANZ03364.1 *
IMAI, Y ET AL.: "The PRDM9 KRAB domain is required for meiosis and involved in protein interactions", CHROMOSOMA, vol. 126, no. 6, 19 May 2017 (2017-05-19), pages 681 - 695, XP036364491, DOI: 10.1007/s00412-017-0631-z *

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