Engineered CRISPR-CAS9 nucleases with altered PAM specificity

1. An isolated variant Streptococcus pyogenes Cas9 (SpCas9) protein, comprising an amino acid sequence that has at least 90% sequence identity to SEQ ID NO: 1, with a mutation at D1135 and optionally at one or more of the following positions: G1104, 51109, L1111, 51136, G1218, N1317, R1335, T1337, wherein the isolated variant SpCas9 protein can interact with a guide RNA and a target DNA.

2. The isolated variant SpCas9 protein of claim 1 , wherein: the mutation at D1135 is selected from the group consisting of: D1135V; D1135E; D1135N; and D1135Y.

3. The isolated variant SpCas9 protein of claim 1 , wherein the mutations are:

(i) D1135E (D1135E variant);

(ii) D1135V/R1335Q/T1337R (VQR variant);

(iii) D1135V/G1218R/R1335Q/T1337R (VRQR variant);

(iv) D1135E/R1335Q/T1337R (EQR variant);

(v) D1135N/G1218R/R1335Q/T1337R (NRQR variant);

(vi) D1135Y/G1218R/R1335Q/T1337R (YRQR variant);

(vii) G1104K/D1135V/G1218R/R1335Q/T1337R (KVRQR variant);

(viii) S1109T/D1135V/G1218R/R1335Q/T1337R (TVRQR variant);

(ix) L1111H/D1135V/G1218R/R1335Q/T1337R (HVRQR variant);

(x) D1135V/S1136N/G1218R/R1335Q/T1337R (VNRQR variant);

(xi) D1135V/G1218R/N1317K/R1335Q/T1337R (VRKQR variant); or

(xii) D1135V/G1218R/R1335E/T1337R (VRER variant).

4. The isolated variant SpCas9 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.

5. The isolated variant SpCas9 protein of claim 4 , wherein the mutations are:

(i) D10A or D10N, and

(ii) H840A, H840N, or H840Y.

6. The isolated variant SpCas9 protein of claim 1 , comprising an amino acid sequence that has at least 95% sequence identity to the amino acid sequence of SEQ ID NO:1, with a mutation at D1135 and optionally at one or more of the following positions: G1104, 51109, L1111, S1136, G1218, N1317, R1335, T1337.

7. The isolated variant SpCas9 protein of claim 1 , comprising the amino acid sequence of SEQ ID NO:1, with a mutation at D1135, G1104, S1109, L1111, S1136, G1218, N1317, R1335 and T1337.

8. The isolated variant SpCas9 protein of claim 1 , wherein the isolated variant SpCas9 protein comprises one or more mutations at G1104, S1109, L1111, S1136, G1218, N1317, R1335 or T1337.

9. The isolated variant SpCas9 protein of claim 8 , wherein the isolated variant SpCas9 protein comprises one or more mutations selected from the group consisting of: G1104K; S1109T; L1111H; S1136N; G1218R; N1317K; R1335E; R1335Q and T1337R.

10. The isolated variant SpCas9 protein of claim 1 , wherein the mutations are D1135V, G1218R, R1335E and T1337R (VRER variant).

11. The isolated variant SpCas9 protein of claim 1 , wherein the mutations are D1135V, R1335Q and T1337R (VQR variant).

12. The isolated variant SpCas9 protein of claim 1 , wherein the mutations are D1135E, R1335Q and T1337R (EQR variant).

13. A fusion protein comprising the isolated variant SpCas9 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.

14. The fusion protein of claim 13 , wherein the heterologous functional domain is a transcriptional activation domain.

15. The fusion protein of claim 14 , wherein the transcriptional activation domain is from VP64 or NF-κB p65.

16. The fusion protein of claim 13 , wherein the heterologous functional domain is a transcriptional silencer or transcriptional repression domain.

17. The fusion protein of claim 16 , wherein the transcriptional repression domain is a Krueppel-associated box (KRAB) domain, ERF repressor domain (ERD), or mSin3A interaction domain (SID).

18. The fusion protein of claim 16 , wherein the transcriptional silencer is Heterochromatin Protein 1 (HP1).

19. The fusion protein of claim 13 , wherein the heterologous functional domain is an enzyme that modifies the methylation state of DNA.

20. The fusion protein of claim 19 , wherein the enzyme that modifies the methylation state of DNA is a DNA methyltransferase (DNMT) or a ten-eleven translocation (TET) protein.

21. The fusion protein of claim 20 , wherein the TET protein is ten-eleven translocation 1 (TET1).

22. The fusion protein of claim 13 , wherein the heterologous functional domain is an enzyme that modifies a histone subunit.

23. 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.

24. The fusion protein of claim 13 , wherein the heterologous functional domain is a biological tether.

25. The fusion protein of claim 24 , wherein the biological tether is MS2, Csy4 or lambda N protein.

26. The fusion protein of claim 13 , wherein the heterologous functional domain is FokI.

27. A host cell expressing the isolated variant SpCas9 protein of claim 1 .

28. A method of altering the genome of a cell, the method comprising expressing in the cell, or contacting the cell with, the isolated variant SpCas9 protein of claim 1 or the fusion protein of claim 13 , 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 isolated variant SpCas9 protein or fusion protein comprises one or more of a nuclear localization sequence, cell penetrating peptide sequence, and/or affinity tag.

30. The method of claim 28 , wherein the cell is a stem cell.

31. The method of claim 30 , wherein the cell is an embryonic stem cell, a mesenchymal stem cell, or an 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 isolated variant SpCas9 protein of claim 1 or the fusion protein of claim 13 , 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.