Variants of Cpf1 (Cas12a) with altered PAM specificity
Engineered CRISPR from Prevotella and Francisella 1 (Cpf1) nucleases with improved targeting range and enhanced on-target activity, and their use in genomic engineering, epigenomic engineering, base editing, genome targeting, genome editing, and in vitro diagnostics.
1. An isolated CRISPR from Prevotella and Francisella 1 (Cpf1) protein from Acidaminococcus sp. BV3L6 (AsCpf1), comprising an amino acid sequence having at least 95% sequence identity to the amino acid sequence of SEQ ID NO: 2, and further comprising an amino acid mutation, and the mutation is E174R.
2. The isolated Cpf1 protein of claim 1 , further comprising a mutation at one or more of the amino acids S170, K548, N551, T167, T539, N552, M604, K607, and/or S542.
3. The isolated protein of claim 2 , wherein the Cpf1 protein comprises a mutation at S542 and the mutation is S542Q, S542K, or S542R.
4. The isolated protein of claim 2 , comprising one or more of the following mutations: S170R, K548R, S170K, T167A, T539K, T539R, K548V, N551R, N552R, M604A, K607Q, K607R, K607S, and/or K607H.
5. The isolated protein of claim 2 , comprising the following mutations: S170R/E174R, E174R/K548R, E174R/S542R, E174R/S542R/K548R, E174R/N551R, E174R/S542R/K607R, E174R/S542R/K607H, E174R/S542R/K548R/N551R, E174R/S542R/K548V/N552R, or E174R/S542R/K607R of SEQ ID NO:2.
6. The isolated protein of claim 2 , further comprising one or more mutations that decrease nuclease activity at amino acids selected from the group consisting of D908, E993, R1226, D1235, and/or D1263.
7. The isolated protein of claim 5 , further comprising one or more mutations that decrease nuclease activity selected from the group consisting of mutations at D908, E993, R1226, D1235, and/or D1263.
8. A fusion protein comprising the isolated 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.
9. The fusion protein of claim 8 , wherein the heterologous functional domain is a transcriptional activation domain.
10. The fusion protein of claim 9 , wherein the transcriptional activation domain is VP16, VP64, Rta, NF-κB p65, or a VPR fusion.
11. The fusion protein of claim 8 , wherein the heterologous functional domain is a transcriptional silencer or transcriptional repression domain.
12. The fusion protein of claim 11 , wherein the transcriptional repression domain is a Krueppel-associated box (KRAB) domain, ERF repressor domain (ERD), or mSin3A interaction domain (SID).
13. The fusion protein of claim 11 , wherein the transcriptional silencer is Heterochromatin Protein 1 (HP1).
14. The fusion protein of claim 8 , wherein the heterologous functional domain is an enzyme that modifies the methylation state of DNA.
15. The fusion protein of claim 14 , wherein the enzyme that modifies the methylation state of DNA is a DNA methyltransferase (DNMT) or a TET protein.
16. The fusion protein of claim 15 , wherein the TET protein is TET1.
17. The fusion protein of claim 8 , wherein the heterologous functional domain is an enzyme that modifies a histone subunit.
18. The fusion protein of claim 17 , wherein the enzyme that modifies a histone subunit is a histone acetyltransferase (HAT), histone deacetylase (HDAC), histone methyltransferase (HMT), or histone demethylase.
19. The fusion protein of claim 18 , 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 8 , wherein the heterologous functional domain is FokI.
22. The fusion protein of claim 8 , wherein the heterologous functional domain is a deaminase.
23. The fusion protein of claim 22 , wherein the heterologous functional domain is a cytidine deaminase.
24. The fusion protein of claim 22 , wherein the heterologous functional domain is an adenosine deaminase.
25. The fusion protein of claim 8 , wherein the heterologous functional domain is an enzyme, domain, or peptide that inhibits or enhances endogenous DNA repair or base excision repair (BER) pathways.
26. The fusion protein of claim 25 , wherein the heterologous functional domain is uracil DNA glycosylase inhibitor (UGI) that inhibits uracil DNA glycosylase (UDG, also known as uracil N-glycosylase, or UNG); or Gam from the bacteriophage Mu.
27. An isolated nucleic acid encoding the protein of claim 1 .
28. A vector comprising the isolated nucleic acid of claim 27 .
29. The vector of claim 28 , wherein the encoded protein further comprises a mutation at one or more of the amino acids S170, K548, N551, T167, T539, N552, M604, K607, and/or S542.
30. An isolated host cell comprising the nucleic acid of claim 27 .
31. The isolated protein of claim 5 , comprising the mutations E174R/S542R/K548R.
32. The isolated protein of claim 6 , wherein the mutations are D908A, E993A, R1226A, D1235A, and/or D1263A.
33. The isolated protein of claim 7 , wherein the mutations are D908A, E993A, R1226A, D1235A, and/or D1263A.
34. The fusion protein of claim 23 , wherein the cytidine deaminase is selected from the group consisting of APOBEC1, APOBEC2, APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3D/E, APOBEC3F, APOBEC3G, APOBEC3H, APOBEC4, activation-induced cytidine deaminase (AID), cytosine deaminase 1 (CDA1), CDA2, and cytosine deaminase acting on tRNA (CDAT).
35. The fusion protein of claim 24 , wherein the adenosine deaminase 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).
36. The isolated host cell of claim 30 , wherein the host cell is a mammalian host cell.