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Definitions

• DP1GM105378 awarded by the National Institutes of Health and W91 INF- 11-2-0056 awarded by the Defense Advanced Research Projects Agency (DARPA) of the Department of Defense. The Government has certain rights in the invention.
• This invention relates to methods and constructs for RNA-guided targeting of genetic and epigenomic regulatory proteins, e.g., transcriptional activators, histone modification enzymes, DNA methylation modifiers, to specific genomic loci.
• genetic and epigenomic regulatory proteins e.g., transcriptional activators, histone modification enzymes, DNA methylation modifiers
• CRISPR Clustered Regulatory Interspaced Short Palindromic Repeats
• cas CRISPR-associated genes
• CRISPR/Cas systems are used by various bacteria and archaea to mediate defense against viruses and other foreign nucleic acid. These systems use small RNAs to detect and silence foreign nucleic acids in a sequence- specific manner.
• CRISPR/Cas systems Three types have been described (Makarova et al, Nat. Rev. Microbiol. 9, 467 (2011); Makarova et al, Biol. Direct 1, 7 (2006); Makarova et al, Biol. Direct 6, 38 (2011)). Recent work has shown that Type II CRISPR/Cas systems can be engineered to direct targeted double-stranded DNA breaks in vitro to specific sequences by using a single "guide RNA" with complementarity to the DNA target site and a Cas9 nuclease (Jinek et al, Science 2012; 337:816-821). This targetable Cas9-based system also works in cultured human cells (Mali et al, Science.
• the present invention is based on the development of a fusion protein including a heterologous functional domain (e.g., a transcriptional activation domain) fused to a Cas9 nuclease that has had its nuclease activity inactivated by mutations (also known as "dCas9").
• a heterologous functional domain e.g., a transcriptional activation domain
• Cas9 nuclease that has had its nuclease activity inactivated by mutations
• the present disclosure provides the first demonstration that multiplex gRNAs can be used to bring multiple dCas9-VP64 fusions to a single promoter, thereby resulting in synergistic activation of transcription.
• the invention provides fusion proteins comprising a catalytically inactive CRISPR associated 9 (dCas9) protein linked to a heterologous functional domain (HFD) that modifies gene expression, histones, or DNA, e.g., transcriptional activation domain, transcriptional repressors (e.g., silencers such as
• Heterochromatin Protein 1 e.g., HPla or ⁇
• a transcriptional repression domain e.g., Krueppel-associated box (KRAB) domain, ERF repressor domain (ERD), or mSin3A interaction domain (SID)
• enzymes that modify the methylation state of DNA e.g., DNA methyltransferase (DNMT) or Ten-Eleven Translocation (TET) proteins, e.g., TETl, also known as Tet Methylcytosine Dioxygenase 1
• enzymes that modify histone subunit e.g., histone acetyltransferases (HAT), histone deacetylases (HDAC), or histone demethylases.
• the heterologous functional domain is a transcriptional repression domain, e.g., Krueppel-associated box (KRAB) domain, ERF repressor domain (ERD), or mSin3A interaction domain
• transcriptional activation domain e.g., a transcriptional activation domain from VP64 or NF-KB p65; an enzyme that catalyzes DNA demethylation, e.g., a TET; or histone modification (e.g., LSD1, histone methyltransferase, HDACs, or HATs) or a transcription silencing domain, e.g., from Heterochromatin Protein 1 (HP1), e.g., HPla or ⁇ ; or a biological tether, e.g., CRISPR/Cas Subtype Ypest protein 4 (Csy4), MS2,or lambda N protein.
• HP1 Heterochromatin Protein 1
• Csy4 CRISPR/Cas Subtype Ypest protein 4
• the catalytically inactive Cas9 protein is from S. pyogenes. In some embodiments, the catalytically inactive Cas9 protein comprises mutations at comprises mutations at D10, E762, H983, or D986; and at H840 or N863, e.g., at D10 and H840, e.g., Dl OA or DION and H840A or H840N or H840Y.
• the heterologous functional domain is linked to the N terminus or C terminus of the catalytically inactive Cas9 protein, with an optional intervening linker, wherein the linker does not interfere with activity of the fusion protein.
• the fusion protein includes one or both of a nuclear localization sequence and one or more epitope tags, e.g., c-myc, 6His, or FLAG tags, on the N-terminus, C-terminus, or in between the catalytically inactive CRISPR associated 9 (Cas9) protein and the heterologous functional domain, optionally with one or more intervening linkers.
• epitope tags e.g., c-myc, 6His, or FLAG tags
• the invention provides nucleic acids encoding the fusion proteins described herein, as well as expression vectors including the nucleic acids, and host cells expressing the fusion proteins.
• the invention provides methods for increasing expression of a target gene in a cell.
• the methods include expressing a Cas9-HFD fusion protein as described herein in the cell, e.g., by contacting the cell with an expression vector including a sequence encoding the fusion protein, and also expressing in the cell one or more guide RNAs with complementarity directed to the target gene, e.g., by contacting the cell with one or more expression vectors comprising nucleic acid sequences encoding one or more guide RNAs.
• the patent or application file contains at least one drawing executed in color.
• FIG. 1 A is a schematic illustration showing a single guide RNA (sgRNA) recruiting
• Cas9 nuclease to a specific DNA sequence and thereby introducing targeted alterations.
• the sequence of the guide RNA shown is
• FIG. IB is a schematic illustration showing a longer version of the sgRNA used to recruit Cas9 nuclease to a specific DNA sequence and to thereby introduce targeted alterations.
• the sequence of the guide RNA shown is
• FIG. 1C is a schematic illustration showing a Cas9 protein containing D10A and
• H840A mutations to render the nuclease portion of the protein catalytically inactive, fused to a transcriptional activation domain and recruited to a specific DNA sequence by a sgRNA.
• the sequence of the guide RNA shown is
• FIG. ID is a schematic depicting recruitment of dCas9-VP64 fusion protein to a specific genomic target sequence by a chimeric sgRNA.
• FIG. IE is a diagram illustrating the positions and orientations of 16 sgRNAs targeted to the endogenous human VEGFA gene promoter.
• Small horizontal arrows represent the first 20 nts of the gRNA complementary to the genomic DNA sequence with the arrow pointing 5 ' to 3 ' .
• Grey bars indicate DNasel hypersensitive sites previously defined in human 293 cells (Liu et al, J Biol Chem. 2001 Apr 6;276(14): 11323-34), numbered relative to the transcription start site (right-angle arrow).
• FIG. 2 A is a bar graph showing activation of VEGFA protein expression in 293 cells by various sgRNAs, each expressed with (grey bars) or without (black bars) dCas9-VP64. Fold-activation of VEGFA was calculated relative to the off-target sgRNA control as described in Methods. Each experiment was performed in triplicate and error bars represent standard errors of the mean. Asterisks indicate samples that are significantly elevated above the off-target control as determined by a paired, one-sided t-test (p ⁇ 0.05).
• FIG. 2B is a bar graph showing multiplex sgRNA expression induces synergistic activation of VEGFA protein expression by dCas9-VP64 protein.
• Fold-activation of VEGFA protein in 293 cells in which the indicated combinations of sgRNAs were co- expressed with dCas9-VP64 is shown. Note that in all of these experiments the amount of each individual sgRNA expression plasmid used for transfection was the same. Fold- activation values were calculated as described in 2A and shown as grey bars. The calculated sum of mean fold-activation values induced by individual sgRNAs is shown for each combination as black bars. Asterisks indicate all combinations that were found to be significantly greater than the expected sum as determined by an analysis of variance (ANOVA) (p ⁇ 0.05).
• ANOVA analysis of variance
• FIG. 3 A is a diagram illustrating the positions and orientations of six sgRNAs targeted to the endogenous human NTF3 gene promoter.
• Horizontal arrows represent the first 20 nts of the sgRNA complementary to the genomic DNA sequence with the arrow pointing 5' to 3'.
• Grey line indicates region of potential open chromatin identified from the ENCODE DNasel hypersensitivity track on the UCSC genome browser with the thicker part of the bar indicating the first transcribed exon. Numbering shown is relative to the transcription start site (+1, right-angle arrow).
• FIG. 3B is a bar graph showing activation of NTF3 gene expression by sgRNA- guided dCas9-VP64 in 293 cells. Relative expression of NTF3 mRNA, detected by quantitative RT-PCR and normalized to a GAPDH control (deltaCt x 10 4 ), is shown for 293 cells co-transfected with the indicated amounts of dCas9-VP64 and N7FJ-targeted sgRNA expression plasmids. All experiments were performed in triplicate with error bars representing standard errors of the mean. Asterisks indicate samples that are significantly greater than the off-target gRNA control as determined by a paired, one-sided T-test (P ⁇ 0.05).
• FIG. 3C is a bar graph showing multiplex gRNA expression induces synergistic activation of NTF3 mRNA expression by dCas9-VP64 protein. Relative expression of NTF3 mRNA, detected by quantitative RT-PCR and normalized to a GAPDH control
• deltaCt x 104 is shown for 293 cells co-transfected with dCas9-VP64 and the indicated combinations of NTF3 -targeted gRNA expression plasmids. Note that in all of these experiments the amount of each individual gRNA expression plasmid used for transfection was the same. All experiments were performed in triplicate with error bars representing standard errors of the mean. The calculated sum of mean fold-activation values induced by individual gR As is shown for each combination.
• FIG. 4 is an exemplary sequence of an sgR A expression vector.
• FIG. 5 is an exemplary sequence of CMV-T7-Cas9 D10A/H840A-3XFLAG-VP64 expression vector.
• FIG. 6 is an exemplary sequence of CMV-T7-Cas9 recoded D10A/H840A- 3XFLAG-VP64 expression vector.
• FIG. 7 is an exemplary sequence of a Cas9-HFD, i.e., a Cas9-activator.
• An optional 3xFLAG sequence is underlined; the nuclear localization signal PKKKRKVS (SEQ ID NO: 11) is in lower case; two linkers are in bold; and the VP64 transcriptional activator sequence,
• DALDDFDLDMLGSDALDDFDLDMLGSDALDDFDLDMLGSDALDDFDLDML (SEQ ID NO: 12), is boxed.
• FIG. 9 is an exemplary sequence of dCas9-TETl .
• FIG. 10 is a bar graph showing results obtained with various dCas9-VP64 fusion constructs.
• the optimized dCas9-VP64 architecture included an N-terminal NLS (NFN) and an additional NLS (N) or FLAG tag/NLS (NF) placed between dCas9 and VP64.
• NFN N-terminal NLS
• N additional NLS
• NF FLAG tag/NLS
• Expression plasmids encoding variants of dCas9-VP64 were co-transfected with a plasmid that expressed three gRNAs that targeted sites in a region upstream of the VEGFA start codon (in this experiment, the gRNAs were expressed from a single gRNA and processed out by the Csy4 endoribonuclease). VEGFA protein expression is measured by ELISA, and the mean of two replicates is shown with error bars indicating standard errors of the mean.
• FIGs. 11A-B are bar graphs showing the activities of dCas9-VP64 activators bearing alternative substitution mutations to catalytically inactivate Cas9 function.
• (1 IB) Plasmids expressing these dCas9-VP64 variants were also transfected into a HEK293 cell-line that stably expresses a single VEGFA-targeted gRNA. VEGFA protein levels were determined by ELISA with mean of two replicates and standard errors of the mean (error bars) shown.
• fusion proteins of a heterologous functional domain e.g., a transcriptional activation domain
• a catalytically inactivated version of the Cas9 protein for the purpose of enabling RNA-guided targeting of these functional domains to specific genomic locations in cells and living organisms.
• the CRISPR/Cas system has evolved in bacteria as a defense mechanism to protect against invading plasmids and viruses.
• Short protospacers derived from foreign nucleic acid, are incorporated into CRISPR loci and subsequently transcribed and processed into short CRISPR RNAs (crRNAs). These crRNAs, complexed with a second tracrRNA, then use their sequence complementarity to the invading nucleic acid to guide Cas9-mediated cleavage, and consequent destruction of the foreign nucleic acid.
• sgRNA single guide RNA
• sgRNA-mediated recruitment of a catalytically inactive mutant form of Cas9 could lead to repression of specific endogenous genes in E. coli as well as of an EGFP reporter gene in human cells (Qi et al, Cell 152, 1173-1183 (2013)).
• RNA-guided Cas9 did not test or demonstrate whether heterologous functional domains (e.g.— transcriptional activation domains) could be fused to dCas9 without disrupting its ability to be recruited to specific genomic sites by programmable sgRNAs or dual gRNAs (dgRNAs - i.e.- a customized crRNA and a tracrRNA).
• heterologous functional domains e.g.— transcriptional activation domains
• Cas9-HFD heterologous functional domains fused to Cas9
• Cas9-HFD single guide RNAs
• Cas9-activators Cas9- transcriptional activators
• the target sequence also includes a PAM sequence (a 2-5 nucleotide sequence specified by the Cas9 protein which is adjacent to the sequence specified by the RNA).
• the Cas9-HFD are created by fusing a heterologous functional domain (e.g., a transcriptional activation domain, e.g., from VP64 or NF- ⁇ p65), to the N-terminus or C- terminus of a catalytically inactive Cas9 protein.
• a heterologous functional domain e.g., a transcriptional activation domain, e.g., from VP64 or NF- ⁇ p65
• Cas9 protein variants A number of bacteria express Cas9 protein variants.
• the Cas9 from Streptococcus pyogenes is presently the most commonly used; some of the other Cas9 proteins have high levels of sequence identity with the S. pyogenes Cas9 and use the same guide RNAs.
• Cas9 molecules of a variety of species can be used in the methods and compositions described herein. While the S. pyogenes and S. thermophilus Cas9 molecules are the subject of much of the disclosure herein, Cas9 molecules of, derived from, or based on the Cas9 proteins of other species listed herein can be used as well. In other words, while the much of the description herein uses S. pyogenes and S. thermophilus Cas9 molecules, Cas9 molecules from the other species can replace them. Such species include those set forth in the following table, which was created based on supplementary figure 1 of Chylinski et al, 2013.
• the constructs and methods described herein can include the use of any of those Cas9 proteins, and their corresponding guide RNAs or other guide R As that are compatible.
• the Cas9 from Streptococcus thermophilus LMD-9 CRISPR1 system has been shown to function in human cells in Cong et al (Science 339, 819 (2013)). Additionally, Jinek et al. showed in vitro that Cas9 orthologs from S. thermophilus and L. innocua, (but not from N. meningitidis or C. jejuni, which likely use a different guide RNA), can be guided by a dual S. pyogenes gRNA to cleave target plasmid DNA, albeit with slightly decreased efficiency.
• the present system utilizes the Cas9 protein from
• S. pyogenes either as encoded in bacteria or codon-optimized for expression in mammalian cells, containing mutations at D10, E762, H983, or D986 and H840 or N863, e.g.,
• Dl 0A/D10N and H840A/H840N/H840Y to render the nuclease portion of the protein catalytically inactive; substitutions at these positions could be alanine (as they are in Nishimasu al, Cell 156, 935-949 (2014)) or they could be other residues, e.g., glutamine, asparagine, tyrosine, serine, or aspartate, e.g., E762Q, H983N, H983Y, D986N, N863D,
• N863S, or N863H Figure 1C.
• the sequence of the catalytically inactive S. pyogenes Cas9 that can be used in the methods and compositions described herein is as follows; the exemplary mutations of DIOA and H840A are in bold and underlined.
• PAAFKYFDTT IDRKRYTSTK EVLDATLIHQ SITGLYETRI DLSQLGGD (SEQ ID NO 1)
• the Cas9 nuclease used herein is at least about 50% identical to the sequence of S. pyogenes Cas9, i.e., at least 50%> identical to SEQ ID NO: 13.
• the nucleotide sequences are about 50%>, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% or 100% identical to SEQ ID NO: 13.
• the catalytically inactive Cas9 used herein is at least about 50%) identical to the sequence of the catalytically inactive S. pyogenes Cas9, i.e., at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% or 100% identical to SEQ ID NO : 13 , wherein the mutations at D 10 and H840, e.g. , D 10A/D 1 ON and
• any differences from SEQ ID NO: 13 are in non-conserved regions, as identified by sequence alignment of sequences set forth in Chylinski et al, RNA Biology 10:5, 1-12; 2013 (e.g., in supplementary figure 1 and supplementary table 1 thereof); Esvelt et al, Nat Methods. 2013 Nov; 10(11): 1116-21 and Fonfara et al, Nucl. Acids Res. (2014) 42 (4): 2577-2590. [Epub ahead of print 2013 Nov 22]
• the sequences are aligned for optimal comparison purposes (gaps are introduced in one or both of a first and a second amino acid or nucleic acid sequence as required for optimal alignment, and nonhomologous sequences can be disregarded for comparison purposes).
• the length of a reference sequence aligned for comparison purposes is at least 50% (in some embodiments, about 50%, 55%, 60%, 65%, 70%, 75%, 85%, 90%, 95%, or 100% of the length of the reference sequence) is aligned.
• the nucleotides or residues at corresponding positions are then compared. When a position in the first sequence is occupied by the same nucleotide or residue as the corresponding position in the second sequence, then the molecules are identical at that position.
• the percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences.
• the comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm.
• the percent identity between two amino acid sequences is determined using the Needleman and Wunsch ((1970) J. Mol. Biol. 48:444-453) algorithm which has been incorporated into the GAP program in the GCG software package, using a Blossum 62 scoring matrix with a gap penalty of 12, a gap extend penalty of 4, and a frameshift gap penalty of 5.
• transcriptional activation domains can be fused on the N or C terminus of the Cas9.
• other heterologous functional domains e.g., transcriptional repressors (e.g., KRAB, ERD, SID, and others, e.g., amino acids 473-530 of the ets2 repressor factor (ERF) repressor domain (ERD), amino acids 1-97 of the KRAB domain of KOXl, or amino acids 1-36 of the Mad mSF 3 interaction domain (SID); see Beerli et al, PNAS USA 95: 14628- 14633 (1998)) or silencers such as Heterochromatin Protein 1 (HP1, also known as swi6), e.g., HP la or ⁇ ; proteins or peptides that could recruit long non-coding RNAs
• RNA binding sequence such as those bound by the MS2 coat protein, endoribonuclease Csy4, or the lambda N protein
• enzymes that modify the methylation state of DNA e.g., DNA methyltransferase (DNMT) or TET proteins
• enzymes that modify histone subunits e.g., histone acetyltransferases (HAT), histone deacetylases (HDAC), histone methyltransferases (e.g., for methylation of lysine or arginine residues) or histone demethylases (e.g., for demethylation of lysine or arginine residues)
• histone subunits e.g., histone acetyltransferases (HAT), histone deacetylases (HDAC), histone methyltransferases (e.g., for methylation of lysine or arginine residues) or histone demethylases (e
• TET Ten-Eleven-Trans location
• Variant (1) represents the longer transcript and encodes the longer isoform (a).
• Variant (2) differs in the 5' UTR and in the 3' UTR and coding sequence compared to variant 1.
• the resulting isoform (b) is shorter and has a distinct C-terminus compared to isoform a.
• all or part of the full-length sequence of the catalytic domain can be included, e.g., a catalytic module comprising the cysteine-rich extension and the 20GFeDO domain encoded by 7 highly conserved exons, e.g., the Tetl catalytic domain comprising amino acids 1580-2052, Tet2 comprising amino acids 1290-1905 and Tet3 comprising amino acids 966-1678. See, e.g., Fig. 1 of Iyer et al, Cell Cycle. 2009 Jun 1 ;8(11): 1698-710.
• the sequence includes amino acids 1418-2136 of Tetl or the corresponding region in Tet2/3.
• heterologous functional domain is a biological tether, and comprises all or part of (e.g., DNA binding domain from) the MS2 coat protein, endoribonuclease Csy4, or the lambda N protein. These proteins can be used to recruit
• RNA molecules containing a specific stem-loop structure to a locale specified by the dCas9 gRNA targeting sequences For example, a dCas9 fused to MS2 coat protein,
• endoribonuclease Csy4, or lambda N can be used to recruit a long non-coding RNA
• the Csy4, MS2 or lambda N protein binding sequence can be linked to another protein, e.g., as described in Keryer-Bibens et al, supra, and the protein can be targeted to the dCas9 binding site using the methods and compositions described herein.
• the Csy4 is catalytically inactive.
• the fusion proteins include a linker between the dCas9 and the heterologous functional domains.
• Linkers that can be used in these fusion proteins (or between fusion proteins in a concatenated structure) can include any sequence that does not interfere with the function of the fusion proteins.
• the linkers are short, e.g., 2-20 amino acids, and are typically flexible (i.e., comprising amino acids with a high degree of freedom such as glycine, alanine, and serine).
• the linker comprises one or more units consisting of GGGS (SEQ ID NO: 14) or GGGGS (SEQ ID NO: 15), e.g., two, three, four, or more repeats of the GGGS (SEQ ID NO: 14) or GGGGS (SEQ ID NO: 15) unit.
• Other linker sequences can also be used.
• the described Cas9-HFD system is a useful and versatile tool for modifying the expression of endogenous genes.
• Current methods for achieving this require the generation of novel engineered DNA-binding proteins (such as engineered zinc finger or transcription activator-like effector DNA binding domains) for each site to be targeted. Because these methods demand expression of a large protein specifically engineered to bind each target site, they are limited in their capacity for multiplexing.
• Cas9-HFD require expression of only a single Cas9-HFD protein, which can be targeted to multiple sites in the genome by expression of multiple short gRNAs. This system could therefore easily be used to simultaneously induce expression of a large number of genes or to recruit multiple Cas9- HFDs to a single gene, promoter, or enhancer.
• This capability will have broad utility, e.g., for basic biological research, where it can be used to study gene function and to manipulate the expression of multiple genes in a single pathway, and in synthetic biology, where it will enable researchers to create circuits in cell that are responsive to multiple input signals.
• the relative ease with which this technology can be implemented and adapted to multiplexing will make it a broadly useful technology with many wide-ranging
• the methods described herein include contacting cells with a nucleic acid encoding the Cas9-HFD described herein, and nucleic acids encoding one or more guide RNAs directed to a selected gene, to thereby modulate expression of that gene.
• Guide RNAs gRNAs
• RNAs generally speaking come in two different systems: System 1, which uses separate crRNA and tracrRNAs that function together to guide cleavage by Cas9, and System 2, which uses a chimeric crRNA-tracrRNA hybrid that combines the two separate guide RNAs in a single system (referred to as a single guide RNA or sgRNA, see also Jinek et al., Science 2012; 337:816-821).
• the tracrRNA can be variably truncated and a range of lengths has been shown to function in both the separate system (system 1) and the chimeric gRNA system (system 2).
• tracrRNA may be truncated from its 3' end by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nts.
• the tracrRNA molecule may be truncated from its 5' end by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nts.
• the tracrRNA molecule may be truncated from both the 5' and 3' end, e.g., by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15 or 20 nts on the 5' end and at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nts on the 3' end.
• the gRNAs are complementary to a region that is within about 100-800 bp upstream of the transcription start site, e.g., is within about 500 bp upstream of the transcription start site, includes the transcription start site, or within about 100-800 bp, e.g., within about 500 bp, downstream of the transcription start site.
• vectors e.g., plasmids
• plasmids encoding more than one gRNA are used, e.g., plasmids encoding, 2, 3, 4, 5, or more gRNAs directed to different sites in the same region of the target gene.
• Cas9 nuclease can be guided to specific 17-20 nt genomic targets bearing an additional proximal protospacer adjacent motif (PAM), e.g., of sequence NGG, using a guide RNA, e.g., a single gRNA or a tracrRNA/crRNA, bearing 17-20 nts at its 5' end that are complementary to the complementary strand of the genomic DNA target site.
• PAM proximal protospacer adjacent motif
• the present methods can include the use of a single guide RNA comprising a crRNA fused to a normally trans-encoded tracrRNA, e.g., a single Cas9 guide RNA as described in Mali et al, Science 2013 Feb 15; 339(6121):823-6, with a sequence at the 5' end that is
• the single Cas9 guide RNA consists of the sequence:
• the guide RNAs can include X N which can be any sequence, wherein N (in the RNA) can be 0-200, e.g., 0-100, 0-50, or 0-20, that does not interfere with the binding of the ribonucleic acid to Cas9.
• the guide RNA includes one or more Adenine (A) or Uracil (U) nucleotides on the 3 ' end.
• the RNA includes one or more U, e.g., 1 to 8 or more Us (e.g., U, UU, UUU, UUUU, UUUUU, UUUUU, UUUUUU, UUUUUU, UUUUUU, UUUUUUU,
• gRNA e.g., the crRNA and tracrRNA found in naturally occurring systems.
• a single tracrRNA would be used in conjunction with multiple different crRNAs expressed using the present system, e.g., the following:
• the methods include contacting the cell with a tracrRNA comprising or consisting of the sequence
• the tracrRNA molecule may be truncated from its 3' end by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nts. In another embodiment, the tracrRNA molecule may be truncated from its 5' end by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nts.
• the tracrRNA molecule may be truncated from both the 5' and 3' end, e.g., by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15 or 20 nts on the 5' end and at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nts on the 3' end.
• Exemplary tracrRNA sequences in addition to SEQ ID NO: 8 include the following:
• tracrRNA is used as a crRNA, the following tracrRNA is used:
• tracrRNA when (Xi 7 _ 20 ) GUUUUAGAGCUAUGCU (SEQ ID NO: 104) is used as a crRNA, the following tracrRNA is used:
• the gR A is targeted to a site that is at least three or more mismatches different from any sequence in the rest of the genome in order to minimize off-target effects.
• RNA oligonucleotides such as locked nucleic acids (LNAs) have been demonstrated to increase the specificity of RNA-DNA hybridization by locking the modified oligonucleotides in a more favorable (stable) conformation.
• LNAs locked nucleic acids
• 2'-0- methyl RNA is a modified base where there is an additional covalent linkage between the 2' oxygen and 4' carbon which when incorporated into oligonucleotides can improve overall th rmal stability and selectivity (Formula I).
• the tru-gRNAs disclosed herein may comprise one or more modified RNA oligonucleotides.
• the truncated guide RNAs molecules described herein can have one, some or all of the region of the guideRNA complementary to the target sequence are modified, e.g., locked (2'-0-4'-C methylene bridge), 5'- methylcytidine, 2'-0-methyl-pseudouridine, or in which the ribose phosphate backbone has been replaced by a polyamide chain (peptide nucleic acid), e.g., a synthetic ribonucleic acid.
• a polyamide chain peptide nucleic acid
• one, some or all of the nucleotides of the tru-gRNA sequence may be modified, e.g., locked (2'-0-4'-C methylene bridge), 5'-methylcytidine, 2'-0- methyl-pseudouridine, or in which the ribose phosphate backbone has been replaced by a polyamide chain (peptide nucleic acid), e.g., a synthetic ribonucleic acid.
• a polyamide chain peptide nucleic acid
• the single guide RNAs and/or crRNAs and/or tracrRNAs can include one or more Adenine (A) or Uracil (U) nucleotides on the 3 ' end.
• A Adenine
• U Uracil
• RNA-DNA heteroduplexes can form a more promiscuous range of structures than their DNA-DNA counterparts.
• DNA- DNA duplexes are more sensitive to mismatches, suggesting that a DNA-guided nuclease may not bind as readily to off-target sequences, making them comparatively more specific than RNA-guided nucleases.
• the guide RNAs usable in the methods described herein can be hybrids, i.e., wherein one or more deoxyribonucleotides, e.g., a short DNA oligonucleotide, replaces all or part of the gRNA, e.g., all or part of the complementarity region of a gRNA.
• This DNA-based molecule could replace either all or part of the gRNA in a single gRNA system or alternatively might replace all of part of the crRNA and/or tracrRNA in a dual crRNA/tracrRNA system.
• Such a system that incorporates DNA into the complementarity region should more reliably target the intended genomic DNA sequences due to the general intolerance of DNA-DNA duplexes to mismatching compared to RNA-DNA duplexes.
• Methods for making such duplexes are known in the art, See, e.g., Barker et al., BMC Genomics. 2005 Apr 22;6:57; and Sugimoto et al., Biochemistry. 2000 Sep 19;39(37): 11270-81.
• one or both can be synthetic and include one or more modified (e.g., locked) nucleotides or
• complexes of Cas9 with these synthetic gRNAs could be used to improve the genome -wide specificity of the CRISPR/Cas9 nuclease system.
• the methods described can include expressing in a cell, or contacting the cell with, a Cas9 gRNA plus a fusion protein as described herein.
• a nucleic acid encoding a guide RNA or fusion protein can be cloned into an intermediate vector for transformation into prokaryotic or eukaryotic cells for replication and/or expression.
• Intermediate vectors are typically prokaryote vectors, e.g., plasmids, or shuttle vectors, or insect vectors, for storage or manipulation of the nucleic acid encoding the fusion protein or for production of the fusion protein.
• the nucleic acid encoding the guide RNA or fusion protein can also be cloned into an expression vector, for administration to a plant cell, animal cell, preferably a mammalian cell or a human cell, fungal cell, bacterial cell, or protozoan cell.
• a sequence encoding a guide RNA or fusion protein is typically subcloned into an expression vector that contains a promoter to direct
• Suitable bacterial and eukaryotic promoters are well known in the art and described, e.g., in Sambrook et al, Molecular Cloning, A Laboratory Manual (3d ed. 2001); Kriegler, Gene Transfer and Expression: A Laboratory Manual (1990); and Current Protocols in Molecular Biology (Ausubel et al, eds., 2010).
• Bacterial expression systems for expressing the engineered protein are available in, e.g., E. coli, Bacillus sp., and Salmonella (Palva et al, 1983, Gene 22:229-235). Kits for such expression systems are commercially available.
• Eukaryotic expression systems for mammalian cells, yeast, and insect cells are well known in the art and are also commercially available.
• the promoter used to direct expression of the nucleic acid depends on the particular application. For example, a strong constitutive promoter is typically used for expression and purification of fusion proteins. In contrast, when the fusion protein is to be
• a constitutive or an inducible promoter can be used, depending on the particular use of the fusion protein.
• a preferred promoter for administration of the fusion protein can be a weak promoter, such as HSV TK or a promoter having similar activity.
• the promoter can also include elements that are responsive to transactivation, e.g., hypoxia response elements, Gal4 response elements, lac repressor response element, and small molecule control systems such as tetracycline - regulated systems and the RU-486 system (see, e.g., Gossen & Bujard, 1992, Proc. Natl. Acad. Sci.
• the expression vector typically contains a transcription unit or expression cassette that contains all the additional elements required for the expression of the nucleic acid in host cells, either prokaryotic or eukaryotic.
• a typical expression cassette thus contains a promoter operably linked, e.g., to the nucleic acid sequence encoding the fusion protein, and any signals required, e.g., for efficient polyadenylation of the transcript, transcriptional termination, ribosome binding sites, or translation termination. Additional elements of the cassette may include, e.g., enhancers, and heterologous spliced intronic signals.
• the particular expression vector used to transport the genetic information into the cell is selected with regard to the intended use of the fusion protein, e.g., expression in plants, animals, bacteria, fungus, protozoa, etc.
• Standard bacterial expression vectors include plasmids such as pBR322 based plasmids, pSKF, pET23D, and commercially available tag-fusion expression systems such as GST and LacZ.
• a preferred tag-fusion protein is the maltose binding protein (MBP).
• MBP maltose binding protein
• Such tag-fusion proteins can be used for purification of the engineered TALE repeat protein.
• Epitope tags can also be added to recombinant proteins to provide convenient methods of isolation, for monitoring expression, and for monitoring cellular and subcellular localization, e.g., c-myc or FLAG.
• Expression vectors containing regulatory elements from eukaryotic viruses are often used in eukaryotic expression vectors, e.g., SV40 vectors, papilloma virus vectors, and vectors derived from Epstein-Barr virus.
• eukaryotic vectors include pMSG, pAV009/A+, pMTO10/A+, pMAMneo-5, baculovirus pDSVE, and any other vector allowing expression of proteins under the direction of the SV40 early promoter, SV40 late promoter, metallothionein promoter, murine mammary tumor virus promoter, Rous sarcoma virus promoter, polyhedrin promoter, or other promoters shown effective for expression in eukaryotic cells.
• the vectors for expressing the guide RNAs can include RNA Pol III promoters to drive expression of the guide RNAs, e.g., the HI, U6 or 7SK promoters. These human promoters allow for expression of gRNAs in mammalian cells following plasmid transfection. Alternatively, a T7 promoter may be used, e.g., for in vitro transcription, and the RNA can be transcribed in vitro and purified. Vectors suitable for the expression of short RNAs, e.g., siRNAs, shRNAs, or other small RNAs, can be used.
• Some expression systems have markers for selection of stably transfected cell lines such as thymidine kinase, hygromycin B phosphotransferase, and dihydrofolate reductase.
• High yield expression systems are also suitable, such as using a baculovirus vector in insect cells, with the fusion protein encoding sequence under the direction of the polyhedrin promoter or other strong baculovirus promoters.
• the elements that are typically included in expression vectors also include a replicon that functions in E. coli, a gene encoding antibiotic resistance to permit selection of bacteria that harbor recombinant plasmids, and unique restriction sites in nonessential regions of the plasmid to allow insertion of recombinant sequences.
• Standard transfection methods are used to produce bacterial, mammalian, yeast or insect cell lines that express large quantities of protein, which are then purified using standard techniques (see, e.g., Colley et al, 1989, J. Biol. Chem., 264: 17619-22; Guide to Protein Purification, in Methods in Enzymology, vol. 182 (Deutscher, ed., 1990)).
• Transformation of eukaryotic and prokaryotic cells are performed according to standard techniques (see, e.g., Morrison, 1977, J. Bacteriol. 132:349-351; Clark-Curtiss & Curtiss, Methods in Enzymology 101 :347-362 (Wu et al, eds, 1983).
• Any of the known procedures for introducing foreign nucleotide sequences into host cells may be used. These include the use of calcium phosphate transfection, polybrene, protoplast fusion, electroporation, nucleofection, liposomes, microinjection, naked DNA, plasmid vectors, viral vectors, both episomal and integrative, and any of the other well- known methods for introducing cloned genomic DNA, cDNA, synthetic DNA or other foreign genetic material into a host cell (see, e.g., Sambrook et al, supra). It is only necessary that the particular genetic engineering procedure used be capable of successfully introducing at least one gene into the host cell capable of expressing the protein of choice.
• the fusion protein includes a nuclear localization domain which provides for the protein to be translocated to the nucleus.
• nuclear localization sequences are known, and any suitable NLS can be used.
• many NLSs have a plurality of basic amino acids, referred to as a bipartite basic repeats (reviewed in Garcia-Bustos et al, 1991, Biochim. Biophys. Acta, 1071 :83-101).
• An NLS containing bipartite basic repeats can be placed in any portion of chimeric protein and results in the chimeric protein being localized inside the nucleus.
• a nuclear localization domain is incorporated into the final fusion protein, as the ultimate functions of the fusion proteins described herein will typically require the proteins to be localized in the nucleus. However, it may not be necessary to add a separate nuclear localization domain in cases where the DBD domain itself, or another functional domain within the final chimeric protein, has intrinsic nuclear translocation function.
• the present invention includes the vectors and cells comprising the vectors.
• RNA-guided transcriptional activators could be created by fusing the strong synthetic VP64 activation domain (Beerli et al., Proc Natl Acad Sci USA 95, 14628-14633 (1998)) to the carboxy-terminus of the catalytically inactivated dCas9 protein (Fig. ID).
• gRNAs guide RNAs
• a vector was engineered that would express the full length chimeric gRNA (a fusion of crRNA and tracrRNA originally described by Jinek et al. (Science 2012)) driven by a U6 promoter. Construction of the gRNA expression plasmids was performed as follows. Pairs of DNA oligonucleotides encoding the variable 20 nt gRNA targeting sequences were annealed together to generate short double-strand DNA fragments with 4bp overhangs (Table 1).
• V6 AAAACCCCACCCCCTTTCCAAAGCCG 65.
• a triple flag tag, nuclear localization signal and the VP64 activation domain were fused to the C-terminus of the inactive Cas9 (Fig. 6). Expression of this fusion protein was driven by the CMV promoter.
• dCas-VP64 expression plasmids were performed as follows. DNA encoding the Cas9 nuclease harboring inactivating D10A/H840A mutations (dCas9) was amplified by PCR from plasmid pMJ841 (Addgene plasmid #39318) using primers that add a T7 promoter site 5 ' to the start codon and a nuclear localization signal at the carboxy- terminal end of the Cas9 coding sequences and cloned into a plasmid containing a CMV promoter as previously described (Hwang et al, Nat Biotechnol 31, 227-229 (2013)) to yield plasmid pMLM3629.
• Oligonucleotides encoding a triple FLAG epitope were annealed and cloned into Xhol and Pstl sites in plasmid pMLM3629 to generate plasmid pMLM3647 expressing dCas9 with a C-terminal flag FLAG tag.
• DNA sequence encoding a Gly 4 Ser linker followed by the synthetic VP64 activation domain was introduced downstream of the FLAG-tagged dCas9 in plasmid pMLM3647 to yield plasmid pSL690.
• the D10A/H840A mutations were also introduced by QuikChange site-directed
• mutagenesis (Agilent) into plasmid pJDS247, which encodes a FLAG-tagged Cas9 sequence that has been codon optimized for expression in human cells, to yield plasmid pMLM3668.
• DNA sequence encoding the Gly 4 Ser linker and the VP64 activation domain were then cloned into pMLM3668 to yield a codon-optimized dCas9-VP64 expression vector named pMLM3705.
• sgRNAs 16 sgRNAs were constructed for target sequences within three DNase I hypersensitive sites (HSSs) located upstream, downstream or at the transcription start site of the human VEGF A gene in 293 cells (Fig. IE).
• HSSs DNase I hypersensitive sites
• each of these gRNAs was first assessed for its ability to direct Cas9 nuclease to its intended target site in human 293 cells.
• gRNA and Cas9 expression vectors were transfected in a 1 :3 ratio because previous optimization experiments demonstrated a high level of Cas9-induced DNA cleavage in U20S cells using this ratio of plasmids.
• GCACGTAACCTCACTTTCCT-3' (SEQ ID NO:84) and oFYF439 (5'- CTTGCTACCTCTTTCCTCTTTCT-3' (SEQ ID NO:85)).
• the +500 region was amplified using primers oFYF444 (5'- AGAGAAGTCGAGGAAGAGAGAG-3 ' (SEQ ID NO:86)) and oFYF445 (5'- CAGCAGAAAGTTCATGGTTTCG-3 ' (SEQ ID NO:87)).
• PCR products were purified using Ampure XP beads (Agencourt) and T7 Endonuclease I assays were performed and analyzed on a QIAXCEL capillary electrophoresis system as previously described (Reyon et al, Nat Biotech 30, 460-465 (2012)).
• All 16 gRNAs were able to mediate the efficient introduction of Cas9 nuclease- induced indel mutations at their respective target sites as assessed using a previously described T7E1 genotyping assay (Table 2). Thus all 16 gRNAs can complex with Cas9 nuclease and direct its activity to specific target genomic sites in human cells.
• Enzyme-Linked Immunoblot Assays of VEGFA protein were performed as follows. Culture medium of Flp-In T-Rex HEK293 cells transfected with plasmids encoding VEGFA-targeted sgRNA and dCas9-VP64 was harvested 40 hours post-transfection and VEGFA protein expression was measured by ELISA as previously described (Maeder et al, Nat Methods 10, 243-245 (2013)).
• VEGFA expression was calculated by dividing the concentration of VEGFA protein in media from cells in which both a sgRNA and dCas9-VP64 were expressed by the concentration of VEGFA protein in media from cells in which an off-target sgRNA
• dCas9-VP64 is stably expressed and can be directed by gRNAs to activate transcription of specific genomic loci in human cells.
• the greatest increase in VEGFA was observed in cells transfected with gRNA3, which induced protein expression by 18.7-fold.
• variable gRNAs to recruit a common dCas9-VP64 activator fusion
• expression of multiple guide RNAs in a single cell might enable multiplex or combinatorial activation of endogenous gene targets.
• 293 cells were transfected with dCas9- VP64 expression plasmid together with expression plasmids for four gRNAs (VI, V2, V3, and V4) that each individually induced expression from the VEGFA promoter.
• a Cas9-HFD e.g., a Cas9- activator protein (harboring the VP64 transcriptional activation domain) and a sgRNA with 20nt of sequence complementarity to sites in the human VEGF-A promoter in human HEK293 cells
• Increases in VEGF-A protein were measured by ELISA assay and it was found that individual gR As can function together with a Cas9-activator fusion protein to increase VEGF-A protein levels by up to ⁇ 18-fold (Fig. 2A).
• Fig. 2B it was possible to achieve even greater increases in activation through transcriptional synergy by introducing multiple gRNAs targeting various sites in the same promoter together with Cas9-activator fusion proteins
• RNA-guided activator platform could be used to induce the expression of the human NTF3 gene.
• six sgRNAs were designed to a predicted DNase I hypersensitive site (HSS) in the human NTF3 promoter and plasmids expressing each of these gRNAs were co-transfected with a plasmid encoding dCas9-VP64 protein that had been codon optimized for human cell expression (Fig. 3A).
• FIG. 3B shows that this multiplex gRNA expression induced synergistic activation of NTF3 mRNA expression by dCas9-VP64 protein.
• Fusion proteins are made in which an MS2 coat protein, Csy4 nuclease (preferably catalytically inactive Csy4, e.g., the H29A mutant described in Haurwitz et al. 329(5997): 1355-8 (2010)), or the lambda N are fused to the N- or C-terminus of the inactivated dCas9.
• MS2 and lambda N are bacteriophage proteins that bind to a specific RNA sequence, and thus can be used as adapters to tether to the dCas9 protein a heterologous RNA sequence tagged with the specific MS2 or lambda N RNA binding sequence.
• dCas9-MS2 fusions or dCas9-lambda N fusions are co-expressed with chimeric long non-coding RNAs (lncRNAs) fused to the MS2 or lambda N stem loop recognition sequence on either their 5 ' or 3 ' end.
• lncRNAs chimeric long non-coding RNAs
• Chimeric Xist or chimeric RepA lncRNAs will be specifically recruited by the dCas9 fusions and the ability of this strategy to induce targeted silencing will be assayed by measuring target gene expression.
• the system will be optimized by testing various alterations to the coat proteins and chimeric RNAs.
• the N55K and deltaFG mutations to the MS2 coat protein have been previously demonstrated to prevent protein aggregation and increase affinity for the stem-loop RNA. Additionally, we will test the high-affinity C-loop RNA mutant reported to increase affinity for the MS2 coat protein. Exemplary sequences for the MS2 and lambda N proteins are given below; the MS2 functions as a dimer, therefore the MS2 protein can include a fused single chain dimer sequence.
• Cys4 are given in Haurwitz et al. 329(5997): 1355-8 (2010), e.g., the inactivated form.
• the constructs are expressed in cells also expressing a regulatory RNA, e.g., a long non-coding RNA (lncRNA) such as HOTAIR, HOTTIP, XIST or XIST Rep A, that has been fused with the cognate stem-loop recognition sequence for the lambda N or MS2 on either its 5' or 3' end.
• a regulatory RNA e.g., a long non-coding RNA (lncRNA) such as HOTAIR, HOTTIP, XIST or XIST Rep A
• lncRNA long non-coding RNA
• AAACAUGAGGAUUACCCAUGUCG SEQ ID NO:96
• AAACAUGAGGAUCACCCAUGUCG (SEQ ID NO:97), respectively (see Keryer-Bibens et al, supra, FIG. 2); the nutL and nutR BoxB sequences to which lambda N binds are GCCCUGAAGAAGGGC (SEQ ID NO:98) and GCCCUGAAAAAGGGC (SEQ ID NO: 99), respectively.
• the sequence to which Csy4 binds is
• GTTCACTGCCGTATAGGCAG (truncated 20 nt) (SEQ ID NO: 100) or
• the binding of the dCas9/MS2 to a target site in a cell expressing an MS2-binding sequence tagged lncRNA recruits that lncRNA to the dCas9 binding site; where the lncRNA is a repressor, e.g., XIST, genes near the dCas9 binding site are repressed.
• a repressor e.g., XIST
• the dCas9 fusion proteins described herein can also be used to target silencing domains, e.g., Heterochromatin Protein 1 (HPl, also known as swi6), e.g., HPla or ⁇ . Truncated versions of HP 1 a or HP 1 ⁇ in which the chromodomain has been removed can be targeted to specific loci to induce heterochromatin formation and gene silencing.
• silencing domains e.g., Heterochromatin Protein 1 (HPl, also known as swi6)
• HPla or ⁇ e.g., HPla or ⁇ .
• Truncated versions of HP 1 a or HP 1 ⁇ in which the chromodomain has been removed can be targeted to specific loci to induce heterochromatin formation and gene silencing.
• Figs. 8A-8B Exemplary sequences of truncated HPl fused to dCas9 are shown in Figs. 8A-8B.
• the HPl sequences can be fused to the N- or C-terminus of the inactivated dCas9 as described above.
• Example 5 Engineering CRISPR/Cas-TET Fusion Systems -Sequence-Specific Demethylation
• the dCas9 fusion proteins described herein can also be used to target enzymes that modify the methylation state of DNA (e.g., DNA methyltransferase (DNMT) or TET proteins). Truncated versions of TET 1 can be targeted to specific loci to catalyze DNA demethylation. Exemplary sequences of truncated TET1 fused to dCas9 are shown in Fig. 9. The TET1 sequence can be fused to the N- or C-terminus of the inactivated dCas9 as described above.
• DNMT DNA methyltransferase
• dCas9-based transcription activators harboring the VP64 activation domain were optimized by varying the number and position of the nuclear localization signal(s) (NLS) and 3xFLAG-tags within these fusions ( Figure 10).
• dCas9-VP64 fusions that contain both an N-terminal NLS and an NLS that lies between the dCas9 and VP64 sequences consistently induce higher levels of target gene activation, perhaps resulting from enhanced nuclear localization of the activator ( Figure 10). Furthermore, even greater levels of activation were observed when a 3xFLAG tag was placed between the C-terminal end of dCas9 and the N-terminal end of VP64.
• the 3xFLAG tag may act as an artificial linker, providing necessary spacing between dCas9 and VP64 and perhaps allowing for better folding of the VP64 domain (that may not be possible when constrained near dCas9) or better recognition of VP64 by transcriptional mediator complexes that recruit RNA polymerase II.
• the negatively charged 3xFLAG tag might also function as a fortuitous transcriptional activation domain, enhancing the effects of the VP64 domain.
• Example 7 Optimized CatalyticallyCatlytically Inactive Cas9 Proteins (dCas9)

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