Patent ID: 12241096

Table 1: Selection results and activity in bacteria of variants on sites harboring NGTN PAMs

Table 2: Selection results and activity in bacteria of variants on sites harboring NGCN PAMs

Table 3: Selection results and activity in bacteria of variants on sites harboring NGAN PAMs

DETAILED DESCRIPTION

Recognition of a protospacer adjacent motif (PAM) byStreptococcus pyogenesCas9 (SpCas9) is the critical first step of target DNA recognition, enabling SpCas9 to bind and hydrolyze DNA. Although CRISPR-Cas9 nucleases are widely used for genome editing1-4, the range of sequences that Cas9 can cleave is constrained by the need for a specific PAM in the target site5, 6. For example, SpCas9, the most robust and widely used Cas9 to date, primarily recognizes NGG PAMs. As a result, it can often be difficult to target double-stranded breaks (DSBs) with the precision that is necessary for various genome editing applications. In addition, imperfect PAM recognition by Cas9 can lead to the creation of unwanted off-target mutations7, 8. Cas9 derivatives with purposefully altered and/or improved PAM specificities would address these limitations.

Crystal structures reveal that wild-type SpCas9 utilizes two arginine amino acid side chains (R1333 and R1335) to make base specific contacts to the guanines of the canonical NGG PAM sequence. However, to alter PAM recognition and improve the targeting range of SpCas9, we and others have shown that simply mutating either one or both of these arginines does not confer a switch in PAM preference (Anders et al,Nature2014; Kleinstiver et al,Nature2015; WO 2016141224). We previously undertook a selection approach to evolve variants of SpCas9 that could target NGA and NGCG PAM sequences (Kleinstiver et al,Nature2015; WO 2016141224); however, many alternative PAM sequences remain untargetable.

To further expand the utility of SpCas9 by enabling targeting of currently inaccessible PAM sequences, we conceived of an alternative strategy to select for SpCas9 variants capable of recognizing novel PAM sequences. Having established previously that certain positions within the SpCas9 coding sequence are important for PAM recognition (Kleinstiver et al.,Nature2015; WO 2016141224), we conducted a focused saturation mutagenesis approach where we randomized six amino acids within three separate regions of the PAM interacting domain to generate a library of SpCas9 variants with diverse codon usage at these positions: D1135/51136, G1218/E1219, and R1335/T1337. To do so, we sequentially cloned randomized oligonucleotide cassettes encoding NNS nucleotide triplets (where N is any nucleotide and S is G or C) at the codons of SpCas9 that contain encode these six amino acids (FIG.1A). The resulting library of SpCas9 variants was then subjected to selection using our bacterial positive selection assay as previously described (Kleinstiver et al.,Nature2015) to identify variants that can cleave target sites harboring various NGNN PAM sequences (FIG.1B). Briefly, bacteria can only survive selective conditions (plating on 10 mM arabinose, which induces transcription of the ccdB toxic gene) if an expressed SpCas9 variant can recognize the target site (PAM and spacer sequence) encoded in the positive selection plasmid. Strong PAM recognition will lead to hydrolysis of the selection plasmid, preventing induction of ccdB expression and thereby allowing bacterial growth. Thus, while screening SpCas9 libraries, colonies that grow on media containing 10 mM arabinose are expected to encode an SpCas9 PAM variant that can target a site bearing an alternate PAM of interest (FIG.1B).

Engineered Cas9 Variants with Altered PAM Specificities

The SpCas9 variants engineered in this study greatly increase the range of target sites accessible by wild-type SpCas9, further enhancing the opportunities to use the CRISPR-Cas9 platform to practice efficient HDR, to target NHEJ-mediated indels to small genetic elements, and to exploit the requirement for a PAM to distinguish between two different alleles in the same cell. The selection and rational design of variants that can now target formerly inaccessible NGTN and NGCH (where H is A, C, or T) PAM containing sites, and variants that can improve activity against NGAC, improve the prospects for accurate and high-resolution genome-editing. The altered PAM specificity SpCas9 variants can efficiently disrupt endogenous gene sites that are not currently targetable by SpCas9 in both bacterial and human cells, suggesting that they will work in a variety of different cell types and organisms.

All of the SpCas9 variants described herein can be rapidly incorporated into existing and widely used vectors, e.g., by simple site-directed mutagenesis, and because they require only a small number of mutations contained within the PAM-interacting domain, the variants should also work with other previously described improvements to the SpCas9 platform (e.g., truncated sgRNAs (Tsai et al.,Nat Biotechnol33, 187-197 (2015); Fu et al.,Nat Biotechnol32, 279-284 (2014)), nickase mutations (Mali et al.,Nat Biotechnol31, 833-838 (2013); Ran et al.,Cell154, 1380-1389 (2013)), dimeric FokI-dCas9 fusions (Guilinger et al.,Nat Biotechnol32, 577-582 (2014); Tsai et al.,Nat Biotechnol32, 569-576 (2014)); and high-fidelity variants (Kleinstiver et al.Nature2016).

SpCas9 Variants with Altered PAM Specificity

Thus, provided herein are SpCas9 variants. The SpCas9 wild type sequence is as follows:

(SEQ ID NO: 1)10         20         30         40MDKKYSIGLD IGTNSVGWAV ITDEYKVPSK KFKVLGNTDR50         60         70         80HSIKKNLIGA LLFDSGETAE ATRLKRTARR RYTRRKNRIC90        100        110        120YLQEIFSNEM AKVDDSFFHR LEESFLVEED KKHERHPIFG130        140        150        160NIVDEVAYHE KYPTIYHLRK KLVDSTDKAD LRLIYLALAH170        180        190        200MIKFRGHFLI EGDLNPDNSD VDKLFIQLVQ TYNQLFEENP210        220        230        240INASGVDAKA ILSARLSKSR RLENLIAQLP GEKKNGLFGN250        260        270        280LIALSLGLTP NFKSNFDLAE DAKLQLSKDT YDDDLDNLLA290        300        310        320QIGDQYADLF LAAKNLSDAI LLSDILRVNT EITKAPLSAS330        340        350        360MIKRYDEHHQ DLTLLKALVR QQLPEKYKEI FFDQSKNGYA370        380        390        400GYIDGGASQE EFYKFIKPIL EKMDGTEELL VKLNREDLLR410        420        430        440KQRTFDNGSI PHQIHLGELH AILRRQEDFY PFLKDNREKI450        460        470        480EKILTFRIPY YVGPLARGNS RFAWMTRKSE ETITPWNFEE490        500        510        520VVDKGASAQS FIERMTNFDK NLPNEKVLPK HSLLYEYFTV530        540        550        560YNELTKVKYV TEGMRKPAFL SGEQKKAIVD LLFKTNRKVT570        580        590        600VKQLKEDYFK KIECFDSVEI SGVEDRFNAS LGTYHDLLKI610        620        630        640IKDKDFLDNE ENEDILEDIV LTLTLFEDRE MIEERLKTYA650        660        670        680HLFDDKVMKQ LKRRRYTGWG RLSRKLINGI RDKQSGKTIL690        700        710        720DFLKSDGFAN RNFMQLIHDD SLTFKEDIQK AQVSGQGDSL730        740        750        760HEHIANLAGS PAIKKGILQT VKVVDELVKV MGRHKPENIV770        780        790        800IEMARENQTT QKGQKNSRER MKRIEEGIKE LGSQILKEHP810        820        830        840VENTQLQNEK LYLYYLQNGR DMYVDQELDI NRLSDYDVDH850        860        870        880IVPQSFLKDD SIDNKVLTRS DKNRGKSDNV PSEEVVKKMK890        900        910        920NYWRQLLNAK LITQRKFDNL TKAERGGLSE LDKAGFIKRQ930        940        950        960LVETRQITKH VAQILDSRMN TKYDENDKLI REVKVITLKS970        980        990       1000KLVSDFRKDF QFYKVREINN YHHAHDAYLN AVVGTALIKK1010       1020       1030       1040YPKLESEFVY GDYKVYDVRK MIAKSEQEIG KATAKYFFYS1050       1060       1070       1080NIMNFFKTEI TLANGEIRKR PLIETNGETG EIVWDKGRDF1090       1100       1110       1120ATVRKVLSMP QVNIVKKTEV QTGGFSKESI LPKRNSDKLI1130       1140       1150       1160ARKKDWDPKK YGGFDSPTVA YSVLVVAKVE KGKSKKLKSV1170       1180       1190       1200KELLGITIME RSSFEKNPID FLEAKGYKEV KKDLIIKLPK1210       1220       1230       1240YSLFELENGR KRMLASAGEL QKGNELALPS KYVNFLYLAS1250       1260       1270       1280HYEKLKGSPE DNEQKQLFVE QHKHYLDEII EQISEFSKRV1290       1300       1310       1320ILADANLDKV LSAYNKHRDK PIREQAENII HLFTLTNLGA1330       1340       1350       1360PAAFKYFDTT IDRKRYTSTK EVLDATLIHQ SITGLYETRIDLSQLGGD

The SpCas9 variants described herein can include mutations at one, two, three, four, five, or all six of the following positions: D1135, 51136, G1218, E1219, R1335, and/or T1337, e.g., D1135X/S1136X/G1218X/E1219X/R1335X/T1337X, where X is any amino acid (or at positions analogous thereto). In some embodiments, the SpCas9 variants are at least 80%, e.g., at least 85%, 90%, or 95% identical to the amino acid sequence of SEQ ID NO:1, e.g., have differences at up to 5%, 10%, 15%, or 20% of the residues of SEQ ID NO:1 replaced, e.g., with conservative mutations. In preferred embodiments, the variant retains desired activity of the parent, e.g., the nuclease activity (except where the parent is a nickase or a dead Cas9), and/or the ability to interact with a guide RNA and target DNA).

To determine the percent identity of two nucleic acid sequences, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes). The length of a reference sequence aligned for comparison purposes is at least 80% of the length of the reference sequence, and in some embodiments is at least 90% or 100%. The nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position (as used herein nucleic acid “identity” is equivalent to nucleic acid “homology”). 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. Percent identity between two polypeptides or nucleic acid sequences is determined in various ways that are within the skill in the art, for instance, using publicly available computer software such as Smith Waterman Alignment (Smith, T. F. and M. S. Waterman (1981)J Mol Biol147:195-7); “BestFit” (Smith and Waterman,Advances in Applied Mathematics,482-489 (1981)) as incorporated into GeneMatcher Plus™, Schwarz and Dayhof (1979)Atlas of Protein Sequence and Structure, Dayhof, M. O., Ed, pp 353-358; BLAST program (Basic Local Alignment Search Tool; (Altschul, S. F., W. Gish, et al. (1990)J Mol Biol215: 403-10), BLAST-2, BLAST-P, BLAST-N, BLAST-X, WU-BLAST-2, ALIGN, ALIGN-2, CLUSTAL, or Megalign (DNASTAR) software. In addition, those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the length of the sequences being compared. In general, for proteins or nucleic acids, the length of comparison can be any length, up to and including full length (e.g., 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, or 100%). For purposes of the present compositions and methods, at least 80% of the full length of the sequence is aligned using the BLAST algorithm and the default parameters.

For purposes of the present invention, the comparison of sequences and determination of percent identity between two sequences can be accomplished 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.

Conservative substitutions typically include substitutions within the following groups: glycine, alanine; valine, isoleucine, leucine; aspartic acid, glutamic acid, asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine.

In some embodiments, the SpCas9 variants include a set of mutations shown in Tables 1, 2, or 3, e.g., one of the following sets of mutations at D1135X/S1136X/G1218X/E1219X/R1335X/T1337X: SpCas9-LWKIQK, LWKIQK, IRAVQL, SWRVVV, SWKVLK, TAHFKV, MSGVKC, LRSVRS, SKTLRP, MWVHLN, TWSMRG, KRRCKV, VRAVQL, VSSVRS, VRSVRS, SRMHCK, GRKIQK, GWKLLR, GWKOQK, VAKLLR, VAKIQK, VAKILR, GRKILR, VRKLLR, LRSVQL, IRAVQL, VRKIQK, VRMHCK, LRKIQK, LRSVQK, or VRKIQK variant (e.g., for NGTN PAMs); WMQAYG, MQKSER, LWRSEY, SQSWRS, LKAWRS, LWGWQH, MCSFER, LWMREQ, LWRVVA, HSSWVR, MWSEPT, GSNYQS, FMQWVN, YCSWVG, MCAWCG, LWLETR, FMQWVR, SSKWPA, LSRWQR, ICCCER, VRKSER, or ICKSER (e.g., for NGCN PAMs); or LRLSAR, AWTEVTR, KWMMCG, VRGAKE, MRARKE, AWNFQV, LWTTLN, SRMHCK, CWCQCV, AEEQQR, GWEKVR, NRAVNG, SRQMRG, LRSYLH, VRGNNR, VQDAQR, GWRQSK, AWLCLS, KWARVV, MWAARP, SRMHCK, VKMAKG, QRKTRE, LCRQQR, CWSHQR, SRTHTQ, LWEVIR, VSSVRS, VRSVRS, LRSVRS, IRAVRS, SRSVRS, LWKIQK, VRMHCK, or SRMHCK (e.g., for NGAN PAMs). In some embodiments, the spCas9 variants include D1135L/S1136R/G1218S/E1219V/R1335X/T1337X, e.g., LRSVQL or LRSVRS. In some embodiments, the residue at D1135 is an L, G, I, V, M, or S. In some embodiments, the residue at S1136 is an R, Q, W, S, or C. In some embodiments, the residue at G1218 is an S, K, S, R, L, C, G, A, or Q. In some embodiments, the residue at E1219 is V, I, S, E, W, C, A, or R. In some embodiments, the residue at R1335 is an R, Q, E, V, T, or K. In some embodiments, the residue at T1337 is an S, K, L, R, A, E, T, or G. In some embodiments, the variants include one of the sets of mutations in Table A.

TABLE ANGTN PAMNGCN PAMNGAN PAMLRSVRSMQKSERVRGAKEGRKIQKLWRVVAMRARKELRSVQLLWLETRSRQMRGIRAVQLLSRWQRLRSVRSLRKIQKICCCERLRSVQKVRKSERVRKIQKICKSER

In some embodiments, the SpCas9 variants also include mutations at one of the following amino acid positions, which reduce or destroy the nuclease activity of the Cas9: D10, E762, D839, H983, or D986 and H840 or N863, e.g., D10A/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 other residues, e.g., glutamine, asparagine, tyrosine, serine, or aspartate, e.g., E762Q, H983N, H983Y, D986N, N863D, N863S, or N863H (see WO 2014/152432). In some embodiments, the variant includes mutations at D10A or H840A (which creates a single-strand nickase), or mutations at D10A and H840A (which abrogates nuclease activity; this mutant is known as dead Cas9 or dCas9).

In some embodiments, the SpCas9 variants also include mutations at one or more amino acid positions that increase the specificity of the protein (i.e., reduce off-target effects). In some embodiments, the SpCas9 variants include one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, or all thirteen mutations at the following residues: N497, K526, R661, R691, N692, M694, Q695, H698, K810, K848, Q926, K1003, and/or R0160. In some embodiments, the mutations are: N692A, Q695A, Q926A, H698A, N497A, K526A, R661A, R691A, M694A, K810A, K848A, K1003A, R0160A, Y450A/Q695A, L169A/Q695A, Q695A/Q926A, Q695A/D1135E, Q926A/D1135E, Y450A/D1135E, L169A/Y450A/Q695A, L169A/Q695A/Q926A, Y450A/Q695A/Q926A, R661A/Q695A/Q926A, N497A/Q695A/Q926A, Y450A/Q695A/D1135E, Y450A/Q926A/D1135E, Q695A/Q926A/D1135E, L169A/Y450A/Q695A/Q926A, L169A/R661A/Q695A/Q926A, Y450A/R661A/Q695A/Q926A, N497A/Q695A/Q926A/D1135E, R661A/Q695A/Q926A/D1135E, and Y450A/Q695A/Q926A/D1135E; N692A/M694A/Q695A/H698A, N692A/M694A/Q695A/H698A/Q926A; N692A/M694A/Q695A/Q926A; N692A/M694A/H698A/Q926A; N692A/Q695A/H698A/Q926A; M694A/Q695A/H698A/Q926A; N692A/Q695A/H698A; N692A/M694A/Q695A; N692A/H698A/Q926A; N692A/M694A/Q926A; N692A/M694A/H698A; M694A/Q695A/H698A; M694A/Q695A/Q926A; Q695A/H698A/Q926A; G582A/V583A/E584A/D585A/N588A/Q926A; G582A/V583A/E584A/D585A/N588A; T657A/G658A/W659A/R661A/Q926A; T657A/G658A/W659A/R661A; F491A/M495A/T496A/N497A/Q926A; F491A/M495A/T496A/N497A; K918A/V922A/R925A/Q926A; or 918A/V922A/R925A; K855A; K810A/K1003A/R1060A; or K848A/K1003A/R1060A. See, e.g., U.S. Pat. No. 9,512,446B1; Kleinstiver et al.,Nature.2016 Jan. 28; 529(7587):490-5; Slaymaker et al.,Science.2016 Jan. 1; 351(6268):84-8; Chen et al.,Nature.2017 Oct. 19; 550(7676):407-410; Tsai and Joung,Nature Reviews Genetics17:300-312 (2016); Vakulskas et al.,Nature Medicine24:1216-1224 (2018); Casini et al.,Nat Biotechnol.2018 March; 36(3):265-271. In some embodiments, the variants do not include mutations at K526 or R691.

In some embodiments, the SpCas9 variants include mutations at one, two, three, four, five, six or all seven of the following positions: L169A, Y450, N497, R661, Q695, Q926, and/or D1135E, e.g., in some embodiments, the variant SpCas9 proteins comprise mutations at one, two, three, or all four of the following: N497, R661, Q695, and Q926, e.g., one, two, three, or all four of the following mutations: N497A, R661A, Q695A, and Q926A. In some embodiments, the variant SpCas9 proteins comprise mutations at Q695 and/or Q926, and optionally one, two, three, four or all five of L169, Y450, N497, R661 and D1135E, e.g., including but not limited to Y450A/Q695A, L169A/Q695A, Q695A/Q926A, Q695A/D1135E, Q926A/D1135E, Y450A/D1135E, L169A/Y450A/Q695A, L169A/Q695A/Q926A, Y450A/Q695A/Q926A, R661A/Q695A/Q926A, N497A/Q695A/Q926A, Y450A/Q695A/D1135E, Y450A/Q926A/D1135E, Q695A/Q926A/D1135E, L169A/Y450A/Q695A/Q926A, L169A/R661A/Q695A/Q926A, Y450A/R661A/Q695A/Q926A, N497A/Q695A/Q926A/D1135E, R661A/Q695A/Q926A/D1135E, and Y450A/Q695A/Q926A/D1135E. See, e.g., Kleinstiver et al.,Nature529:490-495 (2016); WO 2017/040348; U.S. Pat. No. 9,512,446).

In some embodiments, the SpCas9 variants also include mutations at one, two, three, four, five, six, seven, or more of the following positions: F491, M495, T496, N497, G582, V583, E584, D585, N588, T657, G658, W659, R661, N692, M694, Q695, H698, K918, V922, and/or R925, and optionally at Q926, preferably comprising a sequence that is at least 80% identical to the amino acid sequence of SEQ ID NO:1 with mutations at one, two, three, four, five, six, seven, or more of the following positions: F491, M495, T496, N497, G582, V583, E584, D585, N588, T657, G658, W659, R661, N692, M694, Q695, H698, K918, V922, and/or R925, and optionally at Q926, and optionally one or more of a nuclear localization sequence, cell penetrating peptide sequence, and/or affinity tag.

In some embodiments, the proteins comprise mutations at one, two, three, or all four of the following: N692, M694, Q695, and H698; G582, V583, E584, D585, and N588; T657, G658, W659, and R661; F491, M495, T496, and N497; or K918, V922, R925, and Q926.

In some embodiments, the proteins comprise one, two, three, four, or all of the following mutations: N692A, M694A, Q695A, and H698A; G582A, V583A, E584A, D585A, and N588A; T657A, G658A, W659A, and R661A; F491A, M495A, T496A, and N497A; or K918A, V922A, R925A, and Q926A.

In some embodiments, the proteins comprise mutations: N692A/M694A/Q695A/H698A.

In some embodiments, the proteins comprise mutations: N692A/M694A/Q695A/H698A/Q926A; N692A/M694A/Q695A/Q926A; N692A/M694A/H698A/Q926A; N692A/Q695A/H698A/Q926A; M694A/Q695A/H698A/Q926A; N692A/Q695A/H698A; N692A/M694A/Q695A; N692A/H698A/Q926A; N692A/M694A/Q926A; N692A/M694A/H698A; M694A/Q695A/H698A; M694A/Q695A/Q926A; Q695A/H698A/Q926A; G582A/V583A/E584A/D585A/N588A/Q926A; G582A/V583A/E584A/D585A/N588A; T657A/G658A/W659A/R661A/Q926A; T657A/G658A/W659A/R661A; F491A/M495A/T496A/N497A/Q926A; F491A/M495A/T496A/N497A; K918A/V922A/R925A/Q926A; or 918A/V922A/R925A. See, e.g., Chen et al., “Enhanced proofreading governs CRISPR-Cas9 targeting accuracy,” bioRxiv, doi.org/10.1101/160036 (Aug. 12, 2017).

In some embodiments, the variant proteins include mutations at one or more of R780, K810, R832, K848, K855, K968, R976, H982, K1003, K1014, K1047, and/or R1060, e.g., R780A, K810A, R832A, K848A, K855A, K968A, R976A, H982A, K1003A, K1014A, K1047A, and/or R1060A, e.g., K855A; K810A/K1003A/R1060A; (also referred to as eSpCas9 1.0); or K848A/K1003A/R1060A (also referred to as eSpCas9 1.1) (see Slaymaker et al.,Science.2016 Jan. 1; 351(6268):84-8).

Also provided herein are isolated nucleic acids encoding the SpCas9 variants, vectors comprising the isolated nucleic acids, optionally operably linked to one or more regulatory domains for expressing the variant proteins, and host cells, e.g., mammalian host cells, comprising the nucleic acids, and optionally expressing the variant proteins.

The variants described herein can be used for altering the genome of a cell; the methods generally include expressing the variant proteins in the cells, along with a guide RNA having a region complementary to a selected portion of the genome of the cell. Methods for selectively altering the genome of a cell are known in the art, see, e.g., U.S. Pat. No. 8,697,359; US2010/0076057; US2011/0189776; US2011/0223638; US2013/0130248; WO/2008/108989; WO/2010/054108; WO/2012/164565; WO/2013/098244; WO/2013/176772; US20150050699; US20150045546; US20150031134; US20150024500; US20140377868; US20140357530; US20140349400; US20140335620; US20140335063; US20140315985; US20140310830; US20140310828; US20140309487; US20140304853; US20140298547; US20140295556; US20140294773; US20140287938; US20140273234; US20140273232; US20140273231; US20140273230; US20140271987; US20140256046; US20140248702; US20140242702; US20140242700; US20140242699; US20140242664; US20140234972; US20140227787; US20140212869; US20140201857; US20140199767; US20140189896; US20140186958; US20140186919; US20140186843; US20140179770; US20140179006; US20140170753; Makarova et al., “Evolution and classification of the CRISPR-Cas systems” 9(6)Nature Reviews Microbiology467-477 (1-23) (June 2011); Wiedenheft et al., “RNA-guided genetic silencing systems in bacteria and archaea” 482Nature331-338 (Feb. 16, 2012); Gasiunas et al., “Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria” 109(39) Proceedings of the National Academy of Sciences USA E2579-E2586 (Sep. 4, 2012); Jinek et al., “A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity” 337Science816-821 (Aug. 17, 2012); Carroll, “A CRISPR Approach to Gene Targeting” 20(9)Molecular Therapy1658-1660 (September 2012); U.S. Appl. No. 61/652,086, filed May 25, 2012; Al-Attar et al., Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs): The Hallmark of an Ingenious Antiviral Defense Mechanism in Prokaryotes,Biol Chem. (2011) vol. 392, Issue 4, pp. 277-289; Hale et al., Essential Features and Rational Design of CRISPR RNAs That Function With the Cas RAMP Module Complex to Cleave RNAs,Molecular Cell, (2012) vol. 45, Issue 3, 292-302.

The variant proteins described herein can be used in place of the SpCas9 proteins described in the foregoing references with guide RNAs that target sequences that have PAM sequences according to Tables 1, 2, or 3.

In addition, the variants described herein can be used in fusion proteins in place of the wild-type Cas9 or other Cas9 mutations (such as the dCas9 or Cas9 nickase described above) as known in the art, e.g., a fusion protein with a heterologous functional domains as described in WO 2014/124284. For example, the variants, preferably comprising one or more nuclease-reducing or killing mutation, can be fused on the N or C terminus of the Cas9 to a transcriptional activation domain or 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 KOX1, or amino acids 1-36 of the Mad mSIN3 interaction domain (SID); see Beerli et al.,PNAS USA95:14628-14633 (1998)) or silencers such as Heterochromatin Protein 1 (HP1, also known as swi6), e.g., HP1α or HP1β; proteins or peptides that could recruit long non-coding RNAs (lncRNAs) fused to a fixed 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)).

In some embodiments, the heterologous functional domain is a base editor, e.g., a deaminase that modifies cytosine DNA bases, e.g., a cytidine deaminase from the apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like (APOBEC) family of deaminases, including APOBEC1, APOBEC2, APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3D/E, APOBEC3F, APOBEC3G, APOBEC3H, and APOBEC4 (see, e.g., Yang et al.,J Genet Genomics.2017 Sep. 20; 44(9):423-437); activation-induced cytidine deaminase (AID), e.g., activation induced cytidine deaminase (AICDA); cytosine deaminase 1 (CDA1) and CDA2; and cytosine deaminase acting on tRNA (CDAT). The following table provides exemplary sequences; other sequences can also be used.

GenBank Accession Nos.DeaminaseNucleic AcidAmino AcidhAID/AICDANM_020661.3 isoform 1NP_065712.1 variant 1NM_020661.3 isoform 2NP_065712.1 variant 2APOBEC1NM_ 001644.4 isoform aNP_001635.2 variant 1NM_005889.3 isoform bNP_005880.2 variant 3APOBEC2NM_006789.3NP_006780.1APOBEC3ANM_145699.3 isoform aNP_663745.1 variant 1NM_001270406.1 isoform bNP_001257335.1 variant 2APOBEC3BNM_004900.4 isoform aNP_004891.4 variant 1NM_001270411.1 isoform bNP_001257340.1 variant 2APOBEC3CNM_014508.2NP_055323.2APOBEC3D/ENM_152426.3NP_689639.2APOBEC3FNM_145298.5 isoform aNP_660341.2 variant 1NM_001006666.1 isoform bNP_001006667.1 variant 2APOBEC3GNM_021822.3 (isoform a)NP_068594.1 (variant 1)APOBEC3HNM_001166003.2NP_001159475.2(variant SV-200)APOBEC4NM_203454.2NP_982279.1CDA1*NM_127515.4NP_179547.1*fromSaccharomyces cerevisiaeS288C

In some embodiments, the heterologous functional domain is a deaminase that modifies adenosine DNA bases, e.g., the deaminase is an adenosine deaminase 1 (ADA1), ADA2; adenosine deaminase acting on RNA 1 (ADAR1), ADAR2, ADAR3 (see, e.g., Savva et al.,Genome Biol.2012 Dec. 28; 13(12):252); adenosine deaminase acting on tRNA 1 (ADAT1), ADAT2, ADAT3 (see Keegan et al., RNA. 2017 September; 23(9):1317-1328 and Schaub and Keller, Biochimie. 2002 August; 84(8):791-803); and naturally occurring or engineered tRNA-specific adenosine deaminase (TadA) (see, e.g., Gaudelli et al.,Nature.2017 Nov. 23; 551(7681):464-471) (NP 417054.2 (Escherichia colistr. K-12 substr. MG1655); See, e.g., Wolf et al.,EMBO J.2002 Jul. 15; 21(14):3841-51). The following table provides exemplary sequences; other sequences can also be used.

GenBank Accession Nos.DeaminaseNucleic AcidAmino AcidADA (ADA1)NM_000022.3 variant 1NP_000013.2 isoform 1ADA2NM_001282225.1NP_001269154.1ADARNM_001111.4NP_001102.2ADAR2NM_001112.3 variant 1NP_001103.1 isoform 1(ADARB1)ADAR3NM_018702.3NP_061172.1(ADARB2)ADAT1NM_012091.4 variant 1NP_036223.2 isoform 1ADAT2NM_182503.2 variant 1NP_872309.2 isoform 1ADAT3NM_138422.3 variant 1NP_612431.2 isoform 1

In some embodiments, the heterologous functional domain is an enzyme, domain, or peptide that inhibits or enhances endogenous DNA repair or base excision repair (BER) pathways, e.g., thymine DNA glycosylase (TDG; GenBank Acc Nos. NM_003211.4 (nucleic acid) and NP_003202.3 (protein)) or uracil DNA glycosylase (UDG, also known as uracil N-glycosylase, or UNG; GenBank Acc Nos. NM_003362.3 (nucleic acid) and NP_003353.1 (protein)) or uracil DNA glycosylase inhibitor (UGI) that inhibits UNG mediated excision of uracil to initiate BER (see, e.g., Mol et al.,Cell82, 701-708 (1995); Komor et al.,Nature.2016 May 19; 533(7603)); or DNA end-binding proteins such as Gam, which is a protein from the bacteriophage Mu that binds free DNA ends, inhibiting DNA repair enzymes and leading to more precise editing (less unintended base edits). See, e.g., Komor et al.,Sci Adv.2017 Aug. 30; 3(8):eaao4774.

See, e.g., Komor et al.,Nature.2016 May 19; 533(7603):420-4; Nishida et al.,Science.2016 Sep. 16; 353(6305). pii: aaf8729; Rees et al.,Nat Commun.2017 Jun. 6; 8:15790; or Kim et al.,Nat Biotechnol.2017 April; 35(4):371-376) as are known in the art can also be used.

A number of sequences for domains that catalyze hydroxylation of methylated cytosines in DNA. Exemplary proteins include the Ten-Eleven-Translocation (TET) 1-3 family, enzymes that converts 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC) in DNA.

Sequences for human TET1-3 are known in the art and are shown in the following table:

GenBank Accession Nos.GeneAmino AcidNucleic AcidTET1NP_085128.2NM_030625.2TET2*NP_001120680.1 (var 1)NM_001127208.2NP_060098.3 (var 2)NM_017628.4TET3NP_659430.1NM_144993.1*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 sequencecompared to variant 1. The resulting isoform (b) is shorter and has a distinct C-terminus compared to isoform a.

In some embodiments, 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 2OGFeDO domain encoded by 7 highly conserved exons, e.g., the Tet1 catalytic domain comprising amino acids 1580-2052, Tet2 comprising amino acids 1290-1905 and Tet3 comprising amino acids 966-1678. See, e.g.,FIG.1of Iyer et al.,Cell Cycle.2009 Jun. 1; 8(11):1698-710. Epub 2009 Jun. 27, for an alignment illustrating the key catalytic residues in all three Tet proteins, and the supplementary materials thereof for full length sequences (see, e.g., seq 2c); in some embodiments, the sequence includes amino acids 1418-2136 of Tet1 or the corresponding region in Tet2/3.

Other catalytic modules can be from the proteins identified in Iyer et al., 2009.

In some embodiments, the 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 variant fused to MS2 coat protein, endoribonuclease Csy4, or lambda N can be used to recruit a long non-coding RNA (lncRNA) such as XIST or HOTAIR; see, e.g., Keryer-Bibens et al.,Biol. Cell100:125-138 (2008), that is linked to the Csy4, MS2 or lambda N binding sequence. Alternatively, 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 variant binding site using the methods and compositions described herein. In some embodiments, the Csy4 is catalytically inactive. In some embodiments, the Cas9 variant, preferably a dCas9 variant, is fused to FokI as described in WO 2014/204578.

In some embodiments, the fusion proteins include a linker between the dCas9 variant 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. In preferred embodiments, 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). In some embodiments, the linker comprises one or more units consisting of GGGS (SEQ ID NO:2) or GGGGS (SEQ ID NO:3), e.g., two, three, four, or more repeats of the GGGS (SEQ ID NO:2) or GGGGS (SEQ ID NO:3) unit. Other linker sequences can also be used.

Delivery and Expression Systems

To use the Cas9 variants described herein, it may be desirable to express them from a nucleic acid that encodes them. This can be performed in a variety of ways. For example, the nucleic acid encoding the Cas9 variant 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 Cas9 variant for production of the Cas9 variant. The nucleic acid encoding the Cas9 variant 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.

To obtain expression, a sequence encoding a Cas9 variant is typically subcloned into an expression vector that contains a promoter to direct transcription. 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, GeneTransfer and Expression: A Laboratory Manual(1990); andCurrent Protocols in Molecular Biology(Ausubel et al., eds., 2010). Bacterial expression systems for expressing the engineered protein are available in, e.g.,E. coli, Bacillussp., andSalmonella(Palva et al., 1983, Gene22:229-235). 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 a 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 Cas9 variant is to be administered in vivo for gene regulation, either a constitutive or an inducible promoter can be used, depending on the particular use of the Cas9 variant. In addition, a preferred promoter for administration of the Cas9 variant 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. USA,89:5547; Oligino et al., 1998, Gene Ther.,5:491-496; Wang et al., 1997, Gene Ther.,4:432-441; Neering et al., 1996, Blood,88:1147-55; and Rendahl et al., 1998, Nat. Biotechnol.,16:757-761).

In addition to the promoter, 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 Cas9 variant, 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 Cas9 variant, 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.

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. Other exemplary eukaryotic vectors include pMSG, pAV009/A+, pMT010/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 Cas9 variants can include RNA Pol III promoters to drive expression of the guide RNAs, e.g., the H1, U6 or 7SK promoters. These human promoters allow for expression of Cas9 variants in mammalian cells following plasmid transfection.

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 gRNA 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 inE. 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, inMethods 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 Enzymology101:347-362 (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 Cas9 variant.

Alternatively, the methods can include delivering the Cas9 variant protein and guide RNA together, e.g., as a complex. For example, the Cas9 variant and gRNA can be can be overexpressed in a host cell and purified, then complexed with the guide RNA (e.g., in a test tube) to form a ribonucleoprotein (RNP), and delivered to cells. In some embodiments, the variant Cas9 can be expressed in and purified from bacteria through the use of bacterial Cas9 expression plasmids. For example, His-tagged variant Cas9 proteins can be expressed in bacterial cells and then purified using nickel affinity chromatography. The use of RNPs circumvents the necessity of delivering plasmid DNAs encoding the nuclease or the guide, or encoding the nuclease as an mRNA. RNP delivery may also improve specificity, presumably because the half-life of the RNP is shorter and there's no persistent expression of the nuclease and guide (as you′d get from a plasmid). The RNPs can be delivered to the cells in vivo or in vitro, e.g., using lipid-mediated transfection or electroporation. See, e.g., Liang et al. “Rapid and highly efficient mammalian cell engineering via Cas9 protein transfection.”Journal of biotechnology208 (2015): 44-53; Zuris, John A., et al. “Cationic lipid-mediated delivery of proteins enables efficient protein-based genome editing in vitro and in vivo.”Nature biotechnology33.1 (2015): 73-80; Kim et al. “Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins.”Genome research24.6 (2014): 1012-1019.

The present invention includes the vectors and cells comprising the vectors.

EXAMPLES

The invention is further described in the following examples, which do not limit the scope of the invention described in the claims.

Methods

The following materials and methods were used in Example 1.

Plasmids and Oligonucleotides

Sequences of oligonucleotides used to amplify endogenous human gene target sites for T7E1 assays are found in Table 4.

TABLE 4SEQPrimers used for T7E1 experimentsIDsequencedescriptionNO:GGAGCAGCTGforward primer targeted to4GTCAGAGGGGEMX1 in U2OS human cellsCCATAGGGAAreverse primer targeted to5GGGGGACACTEMX1 in U2OS human cellsGGGGGCCGGGAAforward primer targeted to6AGAGTTGCTGFANCF in U2OS human cellsGCCCTACATCreverse primer targeted to7TGCTCTCCCTFANCF in U2OS human cellsCCCCAGCACAACforward primer targeted to8TTACTCGCACRUNX1 in U2OS human cellsTTGACCATCACCAACreverse primer targeted to9CCACAGCCAARUNX1 in U2OS human cellsGGGATGAGGGCTforward primer targeted to10CCAGATGGCAVEGFA in U2OS human cellsCGAGGAGGGAGreverse primer targeted to11CAGGAAAGTGVEGFA in U2OS human cellsAGG

Bacterial Cas9/sgRNA expression plasmids were constructed as previously described (Kleinstiver et al.,Nature2015) with two T7 promoters to separately express Cas9 and the sgRNA. Bacterial expression plasmids containing variable amino acids at positions D1135, 51136, G1218, E1219, R1335, and T1337 were generated by cloning oligonucleotides encoding randomized codons at these positions into the parental SpCas9 bacterial expression vectors (FIG.1).

For expression in human cells, point mutations in SpCas9 were generated by isothermal assembly into a pCMV-T7-hSpCas9-NLS-3xFLAG vector (JDS246; sequences found here at addgene.org/43861/sequences/).

Plasmids for U6 expression of sgRNAs (into which desired spacer oligos can be cloned) were generated by cloning appropriate annealed oligos into BsmBI digested BPK1520.

Bacterial-Based Positive Selection Assay for Evolving SpCas9 Variants

CompetentE. coliBW25141(λDE3)23containing a positive selection plasmid (with embedded target site) were transformed with Cas9/sgRNA-encoding plasmids. Following a 60 minute recovery in SOB media, transformations were plated on LB plates containing either chloramphenicol (non-selective) or chloramphenicol+10 mM arabinose (selective).

To select for SpCas9 variants that can cleave novel PAMs, plasmids encoding randomized D1135X/S1136X/G1218X/E1219X/R1335X/T1337X SpCas9 libraries were electroporated intoE. coliBW25141(λDE3) cells that already harbored a positive selection plasmid that encodes a target site with a PAM of interest. Surviving colonies were grown overnight, miniprepped to extract the SpCas9-expression plasmid, and retransformed individually intoE. coliBW25141(λDE3) cells containing a positive selection with the previously described PAM sequence to re-test linkage of the survival phenotype to those plasmids and thereby eliminate false positive clones. Generally ˜300 clones were re-screened in follow-up experiments. The SpCas9 expression plasmids of bona fide surviving colonies in the secondary screen were sequenced to identify the amino acids at positions D1135, 51136, G1218, E1219, R1335, and/or T1337 that led to the alteration in specificity (see Tables 1-3). Mutations observed in the sequenced clones were chosen for further assessment based on their frequency in surviving clones, and (in some cases) activities in a human cell-based EGFP disruption assay.

Human Cell Culture and Transfection

U2OS cells and U2OS.EGFP cells harboring a single integrated copy of an EGFP-PEST reporter gene (Reyon, D. et al. FLASH assembly of TALENs for high-throughput genome editing.Nat Biotechnol30, 460-465 (2012)) were cultured in Advanced DMEM medium (Life Technologies) with 10% FBS, penicillin/streptomycin, and 2 mM GlutaMAX (Life Technologies) at 37° C. with 5% CO2. Cell line identities were validated by STR profiling (ATCC) and deep sequencing, and cells were tested bi-weekly formycoplasmacontamination. U2OS.EGFP culture medium was additionally supplemented with 400 μg/mL G418. Cells were co-transfected with 750 ng Cas9 plasmid and 250 ng sgRNA plasmid using the DN-100 program of a Lonza 4D-nucleofector following the manufacturer's instructions. Cas9 plasmid transfected together with an empty U6 promoter plasmid was used as a negative control for all human cell experiments.

Human Cell EGFP Disruption Assay

EGFP disruption experiments were performed as previously described (Fu, Y. et al. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells.Nat Biotechnol31, 822-826 (2013); Reyon, D. et al. FLASH assembly of TALENs for high-throughput genome editing.Nat Biotechnol30, 460-465 (2012)). Approximately 52 hours post-transfection, a Fortessa flow cytometer (BD Biosciences) was used to measure EGFP fluorescence in transfected U2OS.EGFP cells. Negative control transfections of Cas9 and empty U6 promoter plasmids were used to establish background EGFP loss at ˜2.5% for all experiments.

T7E1 Assay

T7E1 assays were performed as previously described15. For U2OS human cells, genomic DNA was extracted from transfected cells ˜72 hours post-transfection using the Agencourt DNAdvance Genomic DNA Isolation Kit (Beckman Coulter Genomics). Target loci from human cell genomic DNA were amplified using the primers listed in Table 4. Roughly 200 ng of purified PCR product was denatured, annealed, and digested with T7E1 (New England BioLabs). Mutagenesis frequencies were quantified using a Qiaxcel capillary electrophoresis instrument (Qlagen), as previously described15.

Example 1

To further expand the utility of SpCas9 by enabling targeting of currently inaccessible PAM sequences, we conceived of an alternate strategy to select for SpCas9 variants capable of recognizing novel PAM sequences. Having established previously that certain positions within the SpCas9 coding sequence are important for PAM recognition (Kleinstiver et al.,Nature2015), we conducted a focused mutagenesis approach where we randomized the amino acids at six positions to generate a library of SpCas9 variants with diverse codon usage within three separate regions of the PAM interacting domain: D1135/S1136, G1218/E1219, and R1335/T1337. To do so, we sequentially cloned in randomized oligonucleotide cassettes encoding NNS nucleotide triplets (where N is any nucleotide and S is G or C) at the codons of SpCas9 that contain encode these six amino acids (FIG.1A). The resulting library of SpCas9 variants was then screened in our bacterial positive selection assay as previously described (Kleinstiver et al.,Nature2015), against target sites that encode various NGNN PAM sequences (FIG.1B). Briefly, bacteria can only survive selective conditions (plating on 10 mM arabinose, which induces transcription of the ccdB toxic gene) if SpCas9 can recognize the target site (PAM and spacer sequence) encoded in the positive selection plasmid. Strong PAM recognition will lead to hydrolysis of the selection plasmid, preventing induction of ccdB expression and allowing bacterial growth. Thus, while screening SpCas9 libraries, colonies that grow on media containing 10 mM arabinose are expected to encode an SpCas9 PAM variant that can target alternate PAMs (FIG.1B).

We first screened the randomized D1135X/S1136X/G1218X/E1219X/R1335X/T1337X SpCas9 library (SpCas9-XXXXXX, where X is any amino acid) on positive selection plasmids that encode target sites with NGTG, NGTT, NGTC, and NGTA PAMs. For each different PAM selection, 48 surviving colonies from the arabinose selection were picked and grown overnight in chloramphenicol containing media to recover the nuclease encoding plasmid. To reduce false positive rate in the primary screen, all putative PAM variant plasmids were subsequently re-screened against positive selection plasmids encoding the target site and PAM against which they were originally screened (data not shown). A subset of bona fide variants with at least 50% survival in this re-screening assay were sequenced to identify the amino acids at residues 1135, 1136, 1218, 1219, 1335, 1337 (Table 1), and then these variants were screened more broadly against NGTG, NGTT, NGTC, and NGTA PAMs to assess activity against NGTN sites (FIGS.2a-band Table 1). Note: subsequent to this point, in bacterial assays SpCas9 variants will be described by their variant number (vNGTN- #) or in human assays by their ‘amino acid name’, where the amino acid name will be in the form SpCas9-XXXXXX with the six Xs representing the amino acids identities at positions 1135, 1136, 1218, 1219, 1335, and 1337 (found in Tables 1-3). Re-screening identified a few trends, where in some cases the variant had the highest activity on the NGTN PAM against which it was originally selected (ex. vNGTN-1, -3, -12, -27, -28, etc.), that some variants could target a combination of NGTN PAMs (ex. vNGTN-15, -31, -35, etc., that can target NGTC and NGTA), and some variants can target all NGTN PAMs (ex. vNGTN-9, -10, -30, etc.) (FIGS.2A-Band Table 1). Based on these results, novel variants were rationally designed based on frequently occurring amino acids at positions 1135, 1136, 1218, 1219, 1335, and 1337 in the clones that performed well in the initial screens. These rationally designed NGTN variants were assessed in the bacterial screen against NGTG, NGTT, NGTC, and NGTA PAMs (FIGS.2C-F), and in some cases also screened against NGAN PAMs (NGAG, NGAT, NGAC, NGAA;FIGS.2C,2E-F). Again a number of interesting variants were identified with properties consistent with the preferences above, but notably some additional variants were identified that could impart a preference on the 4thposition of the PAM (ex., vNGTG-37 that could target NGTGor NGAGPAMs or vNGTG-18 and -41 on NGTCand NGACPAMs, etc.), additional variants that can target all NGTNPAMs (ex. vNGTN-40, -46, -48, etc.), and variants that can target all or nearly all NGTNor NGANPAMs (ex. vNGTN-7, -44, -59, etc.;FIGS.2C-Fand Table 1).

Having identified several variants that can target NGTN PAM sites in bacteria, we sought to determine whether these preferences would translate to bona fide activity in human cells. In in initial screen of twelve different NGTN PAM variants in our human U2OS EGFP-disruption assay, we identified variants that could robustly target NGTTand NGTGPAMs (ex. SpCas9-GRKIQK, -VAKLLR, -VRKLLR, etc.), and some that could modify all NGTNPAM sites (ex. SpCas9-LRSVQL, -IRAVQL, etc.) (FIG.3A). Further screening of a subset of these variants and additional rationally designed variants in the human cell EGFP-disruption assay identified SpCas9-LRSVQL, -LRKIQK, -LRSVQK, and others as promising variants that can target NGTNPAM sequences (FIG.3B). To more stringently characterize the activity of SpCas9-LRSVQL on NGTN PAM sequences in human cells, we examined the activity of this nuclease variant across 32 different endogenous sites across the EMX1, FANCF, and RUNX1 genes in human U2OS cells. This analysis revealed robust activity of SpCas9-LRSVQL on various endogenous sites bearing NGTG, NGTA, NGTC, and NGTT PAMs (FIG.3C, demonstrating that our selected and rationally designed PAM variants can function efficiently across numerous loci not previously targetable with published SpCas9 variants.

We have previously described an SpCas9 variant that can effectively target NGCG PAM sites (Kleinstiver et al.,Nature,2015), called SpCas9-VRER (that encodes D1135V/G1218R/R1335E/T1337R substitutions). While this variant enables targeting of previously inaccessible sites, it is restricted to activity on sites with an extended NGCG PAM. To expand the utility of SpCas9 PAM variants by potentially targeting all NGCNPAMs to now include NGCT, NGCC, and NGCAwe performed similar selections to those described above, but screened the SpCas9-XXXXXX library against positive selection plasmids harboring a target site with either an NGCG, NGCT, NGCC, or NGCA PAM (FIGS.4A-Band Table 2). Much like we observed with the NGTN selections, re-screening of NGCNvariants identified cases where the variant had the highest activity on the NGCN PAM against which it was originally selected (ex. vNGCN-3, -8, -9, -17, etc.), that some variants could target a combination of NGCNPAMs (ex. vNGCN-10, etc., that can target NGCT, NGCC and NGCA), and some variants can target all NGCNPAMs (ex. vNGCN-1, -2, -5, -18, -26 etc.) (FIGS.4A-Band Table 2). Various rationally generated NGCN variants were cloned based on observations of amino acid enrichment in SpCas9-XXXXXX selected clones, and tested in bacteria for activity against NGCN PAMs (FIGS.4A-B, Table 2, and data not shown).

Next, we examined the activities of various NGCN selected SpCas9 PAM variants in our U2OS EGFP-disruption assay to determine whether their re-targeted PAM preferences and nuclease activities could be recapitulated in human cells (FIGS.5A-D). We observed activity of numerous variants against NGCA PAMs (SpCas9-MQKSER, -LWRVVA, -LWLETR, etc.;FIG.5A), NGCC PAMs (SpCas9-MQKSER, -LSRWQR, -ICCCER, etc.;FIG.5A), NGCT PAMs (SpCas9-MQKSER;FIG.5C), or NGCC and NGCT PAMs (SpCas9-MQKSER, -VRKSER, -ICKSER, etc.;FIG.5C). Further testing of the SpCas9-MQKSER, -VRKSER, -ICKSER variants against 15 total NGCA, NGCC, NGCT, and NGCG sites revealed robust activity of each variant against all classes of NGCNPAMs (FIG.5E). In some cases, these variants can outperform the published SpCas9-VRER (e.g., as shown inFIGS.5B-C), though this was generally on PAMs that were previously shown to be ineffectively targeted by SpCas9-VRER. Collectively, these new variants expand SpCas9 targeting to NGCT, NGCC, and NGCA instead of the formerly accessible NGCG, with SpCas9-MQKSER and other variants having robust activity on all NGCNPAMs.

Additionally, we have also previously described SpCas9 variant that can effectively target NGANPAM sites, called SpCas9-VQR (D1135V/R1335Q/T1337R; Kleinstiver et al.,Nature,2015), and SpCas9-VRQR (D1135V/G1218R/R1335Q/T1337R; Kleinstiver and Pattanayak et al.,Nature,2016). However, these variants have a preference for subclasses of NGANPAMs in the order of NGAG>NGAA=NGAT>NGAC, i.e., they have suboptimal activity against NGACPAM sites. To potentially improve SpCas9 targeting of NGAN PAMs, we performed selections with the SpCas9-XXXXXX library as described above on positive selection plasmids encoding NGAG, NGAT, NGAC, and NGAA PAMs (FIGS.6A-Band Table 3). Re-screening of NGANvariants revealed clones that had the highest activity on the NGANPAM against which it was originally selected (ex. vNGAN-1, -2, -17, -26 through -30, etc. on NGAG, vNGAN-32 on NGAT, vNGAN-4, -5, -40, -41, etc. on NGAC, etc.), that some variants could target a combination of NGANPAMs (ex. vNGAN-20, -21, etc., that can target NGATand NGAC, or vNGAN-22 that can target NGAGand NGAC), and some variants can target all NGANPAMs (ex. vNGAN-3, -13, -25, -31 etc.) (FIGS.6A-Band Table 3).

Because numerous SpCas9-XXXXXX variants revealed strong NGAC PAM targeting in the bacterial screen, many variants were sub-cloned into our human expression vector to examine activity in our human cell U2OS EGFP-disruption assay. An initial screen of a subset of variants against single NGAA, NGAC, NGAT and NGAG PAM sites in EGFP revealed that certain variants could potentially outperform SpCas9-VQR at sites harboring NGAC PAMs (FIG.7A). More extensive testing of variants fromFIG.7Aand additional selected variants revealed that multiple SpCas9 variants had improved activity relative to SpCas9-VRQR on some or all four of the NGAC PAM sites examined in the EGFP disruption assay (FIG.7B), including SpCas9-LRSVRS, -MRARKE, -SRQMRG, and others.

We then compared the activity of our SpCas9 variants to a recently described SpCas9 PAM variant called xCas9 that has a reported relaxed NG PAM preference (Hu et al.,Naturevolume 556, pages 57-63 (5 Apr. 2018)). Consistent with our previous results, we observed robust nuclease targeting (between 15-50% as assessed by T7E1 assay) of sites with NGA PAMs with the VRQR variant (also known as VSREQR), of sites with NGCG PAMs with the VRER (also known as VSREER) and MQKSER variants, and of sites with NGT PAMs with the LRSVQL variant (FIG.8). However, with the xCas9 variant, no targeting of sites with NGA, NGCG, or NGT PAMs was observed at greater than 10% efficiency; furthermore, we observed that xCas9 was on average about 2-fold less effective at targeting sites with NGG PAMs as compared to wild-type SpCas9 (FIG.8). These results demonstrate that our SpCas9 PAM variants are more effective nucleases against a variety of PAMs when compared to xCas9.

Example 2

The ability to perform precise single base editing events has recently been demonstrated using engineered SpCas9 base editor (BE) constructs (see, e.g., Komor et al.,Nature.2016 May 19; 533(7603):420-4; Nishida et al.,Science.2016 Sep. 16; 353(6305); Kim et al.,Nat Biotechnol.2017 April; 35(4):371-376; Komor et al.,Sci Adv.2017 August 30; 3(8):eaao4774; and Gaudelli et al.,Nature.2017 November 23; 551(7681):464-471), which exploit the formation of SpCas9-gRNA formed R-loops that cause ssDNA accessibility of the non-target DNA strand. The fusion of heterologous cytidine or adenine deaminase enzymatic domains to SpCas9 can therefore act on the exposed ssDNA strand, leading to the efficient introduction of C to T changes (so-called cytosine base editors, or CBEs), or A to G (so-called adenosine base editors, or ABEs), respectively. Because cellular base-excision repair (BER) employs uracil DNA glycosylase (UDG; also known as uracil N-glycosylase, or UNG) to excise uracil bases, this endogenous process can effectively reverse edits generated by cytidine BEs because the deamination of cytidine leads to a uracil intermediate. Therefore, to improve the efficiency of cytidine BEs, heterologous effector domains such as uracil glycosylase inhibitor (UGI) can also be fused to SpCas9 to inhibit UDG, subverting the initiation of BER and increasing the effectiveness of cytidine BEs.

We therefore sought to determine whether the expanded targeting range of our SpCas9 PAM variants could improve the utility of base editors by enabling editing of previously inaccessible sites. To do so, we constructed BE3 (Komor et al.,Nature.2016 May 19; 533(7603):420-4) PAM variants to generate CBEs capable of recognizing sites with NGA and NGT PAMs. We found that on sites with NGA PAMs the CBE-VRQR variant exhibited between 7.5% to 64.2% conversion of Cs to Ts in the editing window, whereas xCas9 exhibited 0%-19.9% C-to-T editing on the same sites (FIG.9A). Similarly, on sites with NGT PAMs the CBE-LRSVQL variant exhibited between 10.8% to 50.3% conversion of Cs to Ts, whereas CBE-xCas9 exhibited 0%-28.5% C-to-T editing on the same sites (FIG.9A). We also observed a marked decrease in C-to-T editing activity with CBE-xCas9 (26.7%-37.2%) compared to wild-type SpCas9 (52.5%-62.4%) on sites with NGG PAMs (FIG.9A). These results demonstrate that the BE3 versions of VRQR and LRSVQL are effective CBEs on sites with NGA and NGT PAMs, respectively, at rates ˜2-fold greater than with xCas9.

Next, we constructed ABE(7.10) (Gaudelli et al.,Nature.2017 Nov. 23; 551(7681):464-471) versions of our PAM variants to determine their effectiveness as ABEs that mediate A-to-G conversion in human cells. We observed strong A-to-G editing activity with ABE-VRQR (8.0%-77.3%) on sites with NGA PAMs, compared to 0%-12.5% editing observed with ABE-xCas9 (FIG.9B). Similarly, on sites with NGCG PAMs, the ABE-VRER (0%-75.9%) and ABE-MQKSER (5.4%-90.4%) variants once again outperformed ABE-xCas9 (0%-62.3%) for A-to-G editing (FIG.9B). We also observed decreased A-to-G editing with ABE-xCas9 (0%-16.9%) compared to wild-type SpCas9 (13.9%-50.4%) on sites with NGG PAMs (FIG.9B). Our results reveal that the ABE(7.10) version of VRQR is effective at mediating A-to-G editing on sites with NGA PAMs, and that the ABE(7.10) versions of VRER and MQKSER are effective on sites with NGCG PAMs.

REFERENCES

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Other Embodiments

It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.

TABLE 1Selection results and activity in bacteria of variants against NGTN PAMsOriginallyselectedApproximate survival inAmino acid substitutionsagainstbacterial assay against:in variant:Sample #(NGTN)NGTGNGTTNGTCNGTAVariant nameD1135S1136G1218E1219R1335T1337vNGTN-1G30%0%3%3%SpCas9-DKVHVRDKVHVRVNGTN-2G15%40%40%40%SpCas9-NRMMRTNRMMRTVNGTN-3G100%40%40%10%SpCas9-ASQLMRASQLMRVNGTN-4G100%40%10%40%SpCas9-LRQYTRLRQYTRvNGTN-5G100%15%10%20%SpCas9-GCACMRGCACMRVNGTN-6G100%50%30%20%SpCas9-SRSCMVSRSCMVVNGTN-7T100%n/an/an/aSpCas9-LWKIQKLWKIQKVNGTN-8T50%50%20%30%SpCas9-YSAFCCYSAFCCVNGTN-9T100%100%70%80%SpCas9-IRAVQLIRAVQLVNGTN-10T100%80%70%60%SpCas9-SWRVVVSWRVVVVNGTN-11T100%80%70%60%SpCas9-SWKVLKSWKVLKVNGTN-12T3%80%3%3%SpCas9-LWSVGGLWSVGGVNGTN-13C——10%20%SpCas9-SRAAKWSRAAKWVNGTN-14C——10%10%SpCas9-RNGWRIRNGWRIVNGTN-15C0%3%90%90%SpCas9-TAHFKVTAHFKVVNGTN-16c——80%80%SpCas9-MSGVKCMSGVKCVNGTN-17——50%50%SpCas9-VMRCKLVMRCKLVNGTN-18C——75%75%SpCas9-LRSVRSLRSVRSVNGTN-19A——n/a30%SpCas9-RWNLRRRWNLRRVNGTN-20A3%3%0%0%SpCas9-VRCVRCVRCVRCVNGTN-21A——20%20%SpCas9-GRTSRCGRTSRCVNGTN-22A——65%65%SpCas9-LKLCKRLKLCKRVNGTN-23A——70%65%SpCas9-AKLCRTAKLCRTVNGTN-24A——75%100%SpCas9-SKTLRPSKTLRPVNGTN-25G50%20%40%40%SpCas9-SRRSQRSRRSQRVNGTN-26G50%20%40%50%SpCas9-DKVHVRDKVHVRVNGTN-27G50%———SpCas9-GAKLLRGAKLLRVNGTN-28T20%100%40%40%SpCas9-MWAFGCMWAFGCVNGTN-29T—35%——SpCas9-GWRVTWGWRVTWVNGTN-30T85%100%100%80%SpCas9-MWVHLNMWVHLNVNGTN-31C——100%85%SpCas9-TWSMRGTWSMRGVNGTN-32C——80%35%SpCas9-ISGTKNISGTKNVNGTN-33C——50%45%SpCas9-SRAAKWSRAAKWvNGTN-34A75%75%50%40%SpCas9-KCAFCCKCAFCCVNGTN-35A——100%100%SpCas9-KRRCKVKRRCKVVNGTN-36A——90%100%SpCas9-MWGGRCMWGGRCVNGTN-37created80%—5%3%SpCas9-VSKLLRVSKLLRvariantVNGTN-38created90%20%10%10%SpCas9-VRKLLRVRKLLRvariantvNGTN-27*G75%———SpCas9-GAKLLRGAKLLRvNGTN-39created50%95%5%2%SpCas9-VSAVQLVSAVQLvariantVNGTN-40created90%95%95%50%SpCas9-VRAVQLVRAVQLvariantvNGTN-9*T90%95%95%90%SpCas9-IRAVQLIRAVQLVNGTN-41created——95%90%SpCas9-VSSVRSVSSVRSvariantVNGTN-42created——95%90%SpCas9-VRSVRSVRSVRSvariantvNGTN-18*C——100%95%SpCas9-LRSVRSLRSVRSVNGTN-43N/A————SpCas9-SRGERTSRGERTVNGTN-44N/A80%35%100%90%SpCas9-SRMHCKSRMHCKVNGTN-45createdSpCas9-GRKIQKGRKIQKvariantVNGTN-46createdSpCas9-GWKLLRGWKLLRvariantVNGTN-47createdSpCas9-GWKOQKGWKQQKvariantVNGTN-48createdSpCas9-VAKLLRVAKLLRvariantVNGTN-49createdSpCas9-VAKIQKVAKIQKvariantvNGTN-50createdSpCas9-VAKILRVAKILRvariantVNGTN-51createdSpCas9-GRKILRGRKILRvariantVNGTN-52created——100%90%SpCas9-VRKLRSVRKLRSvariantVNGTN-38created100%85%60%50%SpCas9-VRKLLRVRKLLRvariantVNGTN-53created100%100%100%100%SpCas9-LRSVQLLRSVQLvariantvNGTN-18C—1%100%100%SpCas9-LRSVRSLRSVRSVNGTN-54created—5%100%100%SpCas9-IRAVRSIRAVRSvariantVNGTN-55T100%100%95%95%SpCas9-IRAVQLIRAVQLVNGTN-56created——50%50%SpCas9-VRKLKRVRKLKRvariantvNGTN-38created100%50%25%25%SpCas9-VRKLLRVRKLLRvariantVNGTN-57created——100%100%SpCas9-SRSVRSSRSVRSvariantvNGTN-18C—95%90%—SpCas9-LRSVRSLRSVRSVNGTN-58created100%85%100%100%SpCas9-VRKIQKVRKIQKvariantvNGTN-7*T100%85%100%100%SpCas9-LWKIQKIWKIQKVNGTN-59created100%85%100%100%SpCas9-VRMHCKVRMHCKvariantvNGTN-44*N/A100%60%100%95%SpCas9-SRMHCKSRMHCKVNGTN-61createdn/an/an/an/aSpCas9-GRKLLRGRKLLRvariantvNGTN-62createdn/an/an/an/aSpCas9-LRKIQKLRKIQKvariantvNGTN-63createdn/an/an/an/aSpCas9-LRSVQKLRSVQKvariantvNGTN-64createdn/an/an/an/aSpCas9-VRKIQKVRKIQKvariantVNGTN-65createdn/an/an/an/aSpCas9-GRSVQLGRSVQLvariantVNGTN-66createdn/an/an/an/aSpCas9-GRKIQLGRKIQLvariant*= that the variant has already been screened in other experimentsn/a = survival was not assessed in that experiment on that PAM

TABLE 2Selection results and activity in bacteria of variants against NGCN PAMsOriginallyselectedApproximate survival inAmino acid substitutionsagainstbacterial assay against:in variant:Sample #(NGCN)NGCGNGCTNGCCNGCAVariant nameD1135S1136G1218E1219R1335T1337VNGCN-1G100%100%100%100%SpCas9-WMQAYGWMQAYGVNGCN-2G100%100%100%n/aSpCas9-MQKSERMQKSERVNGCN-3G100%——40%SpCas9-YSVCERYSVCERVNGCN-4T90%85%90%95%SpCas9-CWNWNSCWNWNSVNGCN-5T100%100%100%100%SpCas9-LWRSEYLWRSEYVNGCN-6T—95%95%100%SpCas9-QSTWNKQSTWNKVNGCN-7Cn/an/an/an/aSpCas9-LFEWRALFEWRAVNGCN-8C——100%—SpCas9-SQSWRSSQSWRSVNGCN-9C——100%—SpCas9-LKAWRSLKAWRSVNGCN-10A—100%100%100%SpCas9-LWGWQHLWGWQHVNGCN-11A—15%15%95%SpCas9-LSYWAKLSYWAKVNGCN-12A50%10%20%95%SpCas9-RQMYQGRQMYQGvNGCN-13created————SpCas9-LWREERLWREERvariantVNGCN-14created100%5%10%20%SpCas9-VSSWERVSSWERvariantVNGCN-15created100%3%5%15%SpCas9-VSAWERVSAWERvariantVNGCN-16created————SpCas9-DWREERDWREERvariantVNGCN-17created100%———SpCas9-VSGWERVSGWERvariantVNGCN-18G100%100%100%100%SpCas9-MCSFERMCSFERVNGCN-19G100%——25%SpCas9-VLMYERVLMYERVNGCN-20G100%n/an/an/aSpCas9-QGANERQGANERVNGCN-21G100%50%15%50%SpCas9-GCACERGCACERVNGCN-22G100%——5%SpCas9-SRIAERSRIAERVNGCN-23G100%——25%SpCas9-SRRNERSRRNERvNGCN-10*T—100%90%100%SpCas9-LWGWQHLWGWQHVNGCN-24T—5%——SpCas9-WMQAVVWMQAVVvNGCN-25T—100%—75%SpCas9-AYRWSKAYRWSKVNGCN-26T100%100%30%65%SpCas9-LWMREQLWMREQvNGCN-27T—100%5%50%SpCas9-LWRVVALWRVVAvNGCN-28T100%100%n/a75%SpCas9-HSSWVRHSSWVRVNGCN-29C100%100%100%85%SpCas9-MWSEPTMWSEPTVNGCN-30C100%100%50%80%SpCas9-GWSMQRGWSMQRVNGCN-31C—n/a75%—SpCas9-NKAWRVNKAWRVVNGCN-3275%—95%50%SpCas9-LCTYEYLCTYEYvNGCN-3380%5%50%50%SpCas9-GSNWCKGSNWCKvNGCN-34C85%50%90%100%SpCas9-GSNYQSGSNYQSVNGCN-35An/a50%25%90%SpCas9-FMQWVNFMQWVNvNGCN-36A40%50%75%100%SpCas9-YCSWVGYCSWVGvNGCN-37A50%—25%85%SpCas9-LWKFEGLWKFEGVNGCN-38A25%35%5%100%SpCas9-MCAWCGMCAWCGvNGCN-39A50%—50%50%SpCas9-GKNWNRGKNWNRvNGCN-2*A100%25%25%75%SpCas9-MQKSERMQKSERVNGCN-40createdn/an/an/an/aSpCas9-VRREERVRREERvariantVNGCN-41An/an/an/an/aSpCas9-AARWCQAARWCQvNGCN-42An/an/an/an/aSpCas9-LWLETRLWLETRvNGCN-43An/an/an/a85%SpCas9-FMQWVRFMQWVRVNGCN-44An/an/an/a75%SpCas9-SSKWPASSKWPAvNGCN-45Cn/an/a50%n/aSpCas9-MWASEGMWASEGvNGCN-46An/an/an/a100%SpCas9-LSRWQRLSRWQRvNGCN-47G90%n/an/an/aSpCas9-YAIYERYAIYERvNGCN-48G75%n/an/an/aSpCas9-ICCCERCCCERvNGCN-49G95%n/an/an/aSpCas9-DWFYERDWFYERvNGCN-50G80%n/an/an/aSpCas9-REATERREATERVNGCN-51G75%n/an/an/aSpCas9-GWAYERGWAYERvNGCN-52G75%n/an/an/aSpCas9-YAIYERYAIYERvNGCN-53G85%n/an/an/aSpCas9-LSVSERLSVSERVNGCN-54An/an/an/a75%SpCas9-VRAWCRVRAWCRVNGCN-55G75%n/an/an/aSpCas9-KWREQRKWREQRVNGCN-56G75%n/an/an/aSpCas9-ARGAERARGAERVNGCN-57Cn/an/a75%n/aSpCas9-HASWCKHASWCKvNGCN-58G100%n/an/an/aSpCas9-YVRSERYVRSERvNGCN-59G80%n/an/an/aSpCas9-QRLAERQRLAERVNGCN-60An/an/an/an/aSpCas9-AARWERAARWERvNGCN-61G75%n/an/an/aSpCas9-LILSERLILSERvNGCN-62An/an/an/an/aSpCas9-LWPSRGLWPSRGVNGCN-63An/an/an/an/aSpCas9-LWTWIKLWTW-KVNGCN-64createdn/an/an/an/aSpCas9-VRKSERVRKSERvariantVNGCN-65createdn/an/an/an/aSpCas9-ICKSERCKSERvariantvNGCN-66C/Tn/an/an/an/aSpCas9-MQSVQLMQSVQLVNGCN-67createdn/an/an/an/aSpCas9-LRSVERLRSVERvariantvNGCN-68createdn/an/an/an/aSpCas9-LSRWERLSRWERvariant*= that the variant has already been screened in other experimentsn/a = survival was not assessed in that experiment on that PAM

TABLE 3Selection results and activity in bacteria of variants against NGAN PAMsOriginallyselectedApproximate survival inAmino acid substitutionsagainstbacterial assay against:in variant:Sample #(NGAN)NGAGNGATNGACNGAAVariant nameD1135S1136G1218E1219R1335T1337vNGAN-1G100%10%5%1%SpCas9-LRLSARLRLSARVNGAN-2G100%—1%—SpCas9-ASEVTRASEVTRVNGAN-3T100%100%95%90%SpCas9-KWMMCGKWMMCGVNGAN-4C——100%—SpCas9-VRGAKEVRGAKEVNGAN-5C——100%-SpCas9-MRARKEMRARKEVNGAN-6G75%———SpCas9-AEEQQRAEEQQRVNGAN-7A95%5%—80%SpCas9-TRGSFRTRGSFRVNGAN-8A95%10%90%90%SpCas9-VRNYTKVRNYTKVNGAN-9T100%100%95%95%SpCas9-AWNFQVAWNFQVvNGAN-10A100%35%—20%SpCas9-WMRKVAWMRKVAvNGAN-11A40%100%—75%SpCas9-CWTCLQCWTCLQvNGAN-12A100%100%5%75%SpCas9-LWTTLNLWTTLNVNGAN-13G100%95%95%95%SpCas9-SRMHCKSRMHCKvNGAN-14T100%100%95%95%SpCas9-CWCQCVCWCQCVVNGAN-15T100%5%—10%SpCas9-GCLCVRGCLCVRvNGAN-16C100%50%——SpCas9-GGCQLRGGCQLRvNGAN-17G100%———SpCas9-AEEQQRAEEQQRvNGAN-18G90%100%10%25%SpCas9-QNNQVFQNNQVFvNGAN-19T100%100%100%SpCas9-GWEKVRGWEKVRVNGAN-20T1%100%50%—SpCas9-NRAVNGNRAVNGVNGAN-21?1%100%50%—SpCas9-NRAVNGNRAVNGvNGAN-22C100%1%100%—SpCas9-SRQMRGSRQMRGVNGAN-23C————SpCas9-RAQPNLRAQPNLVNGAN-24A50%5%—100%SpCas9-LRSYLHLRSYLHvNGAN-25G100%95%100%90%SpCas9-SRMHCKSRMHCKvNGAN-26G100%———SpCas9-ACTSVRACTSVRVNGAN-27G100%———SpCas9-MVVHIRMVVHIRVNGAN-28G100%———SpCas9-VRGNNRVRGNNRVNGAN-29G100%———SpCas9-RGFCLRRGFCLRvNGAN-30G100%———SpCas9-VQDAQRVQDAQRvNGAN-31T100%100%95%95%SpCas9-GWRQSKGWRQSKVNGAN-32T5%100%——SpCas9-AWLCLSAWLCLSvNGAN-33T100%100%—100%SpCas9-KWARVVKWARVVVNGAN-34T80%100%20%15%SpCas9-LAAQTPLAAQTPVNGAN-35T95%100%10%90%SpCas9-GWNHLQGWNHLQvNGAN-36T100%100%100%5%SpCas9-MWAARPMWAARPvNGAN-37C95%100%50%30%SpCas9-KWRCTGKWRCTGvNGAN-38C50%—100%—SpCas9-LAKARPLAKARPVNGAN-39C100%100%100%30%SpCas9-SRMHCKSRMHCKvNGAN-40C——100%—SpCas9-VKMAKGVKMAKGvNGAN-41C——100%—SpCas9-QRKTREQRKTREvNGAN-42C——50%—SpCas9-NTAVKQNTAVKQvNGAN-43A100%100%50%100%SpCas9-LCRQQRLCRQQRVNGAN-44A100%90%100%100%SpCas9-CWSHQRCWSHQRvNGAN-45A30%90%25%100%SpCas9-MWVHLNMWVHLNvNGAN-46A100%100%25%100%SpCas9-SRTHTQSRTHTQvNGAN-47A100%50%—100%SpCas9-LQKSMRLQKSMRvNGAN-48A100%100%—90%SpCas9-LWEVIRLWEVIRVNGTN-37created20%———SpCas9-VSKLLRVSKLLRvariantVNGTN-38created50%———SpCas9-VRKLLRVRKLLRvariantvNGTN-27*NGTG10%———SpCas9-GAKLLRGAKLLRVNGTN-39created————SpCas9-VSAVQLVSAVQLvariantVNGTN-40created1%———SpCas9-VRAVQLVRAVQLvariantvNGTN-9*NGTT5%—1%—SpCas9-IRAVQLIRAVQLvNGTN-41created1%—100%—SpCas9-VSSVRSVSSVRSvariantvNGTN-42created25%—100%—SpCas9-VRSVRSVRSVRSvariantvNGTN-18*NGTC25%—100%—SpCas9-LRSVRSLRSVRSVNGTN-43N/A50%—1%SpCas9-SRGERTSRGERTVNGTN-44N/A90%80%n/a50%SpCas9-SRMHCKSRMHCKVNGTN-52created60%-75%-SpCas9-VRKLRSVRKLRSvariantvNGTN-38*created60%--SpCas9-VRKLLRVRKLLRvariantVNGTN-53created15%5%10%1%SpCas9-LRSVQLLRSVQLvariantvNGTN-18*NGTC50%5%100%—SpCas9-LRSVRSLRSVRSvariantVNGTN-54created50%5%100%—SpCas9-IRAVRSIRAVRSvariantVNGTN-55NGTT5%1%1%—SpCas9-IRAVQLIRAVQLVNGTN-56created5%—35%—SpCas9-VRKLKRVRKLKRvariantvNGTN-38*created35%———SpCas9-VRKLLRVRKLLRvariantVNGTN-57created20%—100%—SpCas9-SRSVRSSRSVRSvariantvNGTN-18*NGTC25%—100%—SpCas9-LRSVRSLRSVRSVNGTN-58created85%5%95%25%SpCas9-VRKIQKVRKIQKvariantVNGTN-7*NGTT85%100%100%95%SpCas9-LWKIQKLWKIQKVNGTN-59created95%100%100%90%SpCas9-VRMHCKVRMHCKvariantvNGTN-44*N/A85%90%100%75%SpCas9-SRMHCKSRMHCK*= that the variant has already been screened in other experimentsn/a = survival was not assessed in that experiment on that PAM