Engineered CRISPR-Cas9 nucleases with altered PAM specificity
Engineered CRISPR-Cas9 nucleases with altered and improved PAM specificities and their use in genomic engineering, epigenomic engineering, and genome targeting.
1. An Streptococcus pyogenes Cas9 (SpCas9) protein, comprising an amino acid sequence that has at least 80% sequence identity to the amino acid sequence of SEO ID NO: 1, with mutations at all six of the following positions: D1135, S1136, G1218, E1219, R1335, and T1337, wherein the mutations are LRSVQL, LRKIQK, LRSVQK, LWKIQK, VRKIQK, IRAVQL, GRKIQK, SWRVW, SWKVLK, TAHFKV, MWVHLN, KRRCKV, VRAVQL, SRMHCK, GWKLLR, GWKOQK, VAKLLR, VAKIQK, VAKILR, GRKILR, VRKLLR, IRAVQL, MQKSER, VRKSER, ICKSER, LRSVER, MQSVQL, ICCCER, LWRWA, WMQAYG, LWRSEY, MCSFER, LWMREQ, FMQWVN, YCSWVG, MCAWCG, FMQWVR, MRARKE, LRLSAR, KWMMCG, AWNFQV, LWTTLN, CWCQCV, AEEQQR, GWEKVR, NRAVNG, LRSYLH, VQDAQR, GWRQSK, AWLCLS, KWARW, VKMAKG, QRKTRE, LCRQQR, CWSHQR, SRTHTQ, or LWEVIR.
2. The protein of claim 1 , further comprising one or more mutations that decrease nuclease activity selected from the group consisting of mutations at D10, E762, D839, H983, or D986; and at H840 or N863.
3. The protein of claim 2 , wherein the mutations are:
(i) D10A or D10N, and
(ii) H840A, H840N, or H840Y.
4. A fusion protein comprising the protein of claim 1 , fused to a heterologous functional domain, with an optional intervening linker, wherein the linker does not interfere with activity of the fusion protein.
5. The fusion protein of claim 4 , wherein the heterologous functional domain is a transcriptional activation domain.
6. The fusion protein of claim 4 , wherein the transcriptional activation domain is from VP16, VP64, rTA, NF-κB p65, or the composite VPR (VP64-p65-rTA).
7. The fusion protein of claim 4 , wherein the heterologous functional domain is a transcriptional silencer or transcriptional repression domain.
8. The fusion protein of claim 7 , wherein the transcriptional repression domain is a Krueppel-associated box (KRAB) domain, ERF repressor domain (ERD), or mSin3A interaction domain (SID).
9. The fusion protein of claim 7 , wherein the transcriptional silencer is Heterochromatin Protein 1 (HP1).
10. The fusion protein of claim 7 , wherein the heterologous functional domain is an enzyme that modifies the methylation state of DNA.
11. The fusion protein of claim 10 , wherein the enzyme that modifies the methylation state of DNA is a DNA methyltransferase (DNMT) or a TET protein.
12. The fusion protein of claim 11 , wherein the TET protein is TET1.
13. The fusion protein of claim 4 , wherein the heterologous functional domain is an enzyme that modifies a histone subunit.
14. The fusion protein of claim 13 , wherein the enzyme that modifies a histone subunit is a histone acetyltransferase (HAT), histone deacetylase (HDAC), histone methyltransferase (HMT), or histone demethylase.
15. The fusion protein of claim 4 , wherein the heterologous functional domain is a base editor.
16. The fusion protein of claim 15 , wherein the base editor is (i) a cytidine deaminase domain, or (ii) an adenosine deaminase.
17. The fusion protein of claim 16 , wherein the base editor is a cytidine deaminase domain and is selected from the group consisting of apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like (APOBEC) family of deaminases; activation-induced cytidine deaminase (AID); and cytosine deaminase acting on tRNA (CDAT).
18. The fusion protein of claim 16 , wherein the base editor is an adenosine deaminase and is selected from the group consisting of adenosine deaminase 1 (ADA1), ADA2; adenosine deaminase acting on RNA 1 (ADAR1), ADAR2, ADAR3; adenosine deaminase acting on tRNA 1 (ADAT1), ADAT2, ADAT3; and naturally occurring or engineered tRNA-specific adenosine deaminase (TadA).
19. The fusion protein of claim 4 , wherein the heterologous functional domain is a biological tether.
20. The fusion protein of claim 19 , wherein the biological tether is MS2, Csy4 or lambda N protein.
21. The fusion protein of claim 4 , wherein the heterologous functional domain is FokI.
22. The fusion protein of claim 4 , wherein the fusion protein comprises one or more of a nuclear localization sequence, cell penetrating peptide sequence, and/or affinity tag.
23. A nucleic acid encoding a Streptococcus pyogenes Cas9 (SpCas9) protein, comprising an amino acid sequence that has at least 80% sequence identity to the amino acid sequence of SEO ID NO: 1, with mutations at all six of the following positions: D1135, S1136, G1218, E1219, R1335, and T1337, wherein the mutations are LRSVQL, LRKIQK, LRSVQK, LWKIQK, VRKIQK, IRAVQL, GRKIQK, SWRVW, SWKVLK, TAHFKV, MWVHLN, KRRCKV, VRAVQL, SRMHCK, GWKLLR, GWKOQK, VAKLLR, VAKIQK, VAKILR, GRKILR, VRKLLR, IRAVQL, MQKSER, VRKSER, ICKSER, LRSVER, MQSVQL, ICCCER, LWRVVA, WMQAYG, LWRSEY, MCSFER, LWMREQ, FMQWVN, YCSWVG, MCAWCG, FMQWVR, MRARKE, LRLSAR, KWMMCG, AWNFQV, LWTTLN, CWCQCV, AEEQQR, GWEKVR, NRAVNG, LRSYLH, VQDAQR, GWRQSK, AWLCLS, KWARW, VKMAKG, QRKTRE, LCRQQR, CWSHQR, SRTHTQ, or LWEVIR.
24. A vector comprising the nucleic acid of claim 23 .
25. A vector comprising the nucleic acid of claim 23 , which is operably linked to one or more regulatory domains for expressing the Streptococcus pyogenes Cas9 (SpCas9) protein.
26. A host cell, comprising the nucleic acid of claim 23 .
27. The host cell of claim 26 , wherein the host cell is a mammalian cell.
28. A method of altering the genome of a cell, the method comprising expressing in the cell, or contacting the cell with, the protein of claim 1 , and a guide RNA having a region complementary to a selected portion of the genome of the cell.
29. The method of claim 28 , wherein the protein comprises one or more of a nuclear localization sequence, cell penetrating peptide sequence, and/or affinity tag.
30. The method of claim 29 , wherein the cell is a stem cell.
31. The method of claim 30 , wherein the cell is an embryonic stem cell, mesenchymal stem cell, or induced pluripotent stem cell; is in a living animal; or is in an embryo.
32. A method of altering a double stranded DNA (dsDNA) molecule, the method comprising contacting the dsDNA molecule with the protein of claim 1 , and a guide RNA having a region complementary to a selected portion of the dsDNA molecule.
33. The method of claim 32 , wherein the dsDNA molecule is in vitro.
34. The method of claim 32 , wherein the protein and RNA are in a ribonucleoprotein complex.
35. The protein of claim 1 , wherein the protein comprises one or more of a nuclear localization sequence, cell penetrating peptide sequence, and/or affinity tag.