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Amrani N, Gao XD, Liu P, Edraki A, Mir A, Ibraheim R, Gupta A, Sasaki KE, Wu T, Donohoue PD, Settle AH, Lied AM, McGovern K, Fuller CK, Cameron P, Fazzio TG, Zhu LJ, Wolfe SA, Sontheimer EJ. NmeCas9 is an intrinsically high-fidelity genome-editing platform. Genome Biol 2018; 19:214. [PMID: 30518407 PMCID: PMC6282386 DOI: 10.1186/s13059-018-1591-1] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 11/17/2018] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The development of CRISPR genome editing has transformed biomedical research. Most applications reported thus far rely upon the Cas9 protein from Streptococcus pyogenes SF370 (SpyCas9). With many RNA guides, wildtype SpyCas9 can induce significant levels of unintended mutations at near-cognate sites, necessitating substantial efforts toward the development of strategies to minimize off-target activity. Although the genome-editing potential of thousands of other Cas9 orthologs remains largely untapped, it is not known how many will require similarly extensive engineering to achieve single-site accuracy within large genomes. In addition to its off-targeting propensity, SpyCas9 is encoded by a relatively large open reading frame, limiting its utility in applications that require size-restricted delivery strategies such as adeno-associated virus vectors. In contrast, some genome-editing-validated Cas9 orthologs are considerably smaller and therefore better suited for viral delivery. RESULTS Here we show that wildtype NmeCas9, when programmed with guide sequences of the natural length of 24 nucleotides, exhibits a nearly complete absence of unintended editing in human cells, even when targeting sites that are prone to off-target activity with wildtype SpyCas9. We also validate at least six variant protospacer adjacent motifs (PAMs), in addition to the preferred consensus PAM (5'-N4GATT-3'), for NmeCas9 genome editing in human cells. CONCLUSIONS Our results show that NmeCas9 is a naturally high-fidelity genome-editing enzyme and suggest that additional Cas9 orthologs may prove to exhibit similarly high accuracy, even without extensive engineering.
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Affiliation(s)
- Nadia Amrani
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Xin D Gao
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Pengpeng Liu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Alireza Edraki
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Aamir Mir
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Raed Ibraheim
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Ankit Gupta
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
- Present Address: Bluebird bio, Cambridge, MA, USA
| | - Kanae E Sasaki
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
- Present Address: Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
| | - Tong Wu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Paul D Donohoue
- Caribou Biosciences, Inc., 2929 7th Street, Suite 105, Berkeley, CA, 94710, USA
| | - Alexander H Settle
- Caribou Biosciences, Inc., 2929 7th Street, Suite 105, Berkeley, CA, 94710, USA
- Present Address: Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandra M Lied
- Caribou Biosciences, Inc., 2929 7th Street, Suite 105, Berkeley, CA, 94710, USA
| | - Kyle McGovern
- Caribou Biosciences, Inc., 2929 7th Street, Suite 105, Berkeley, CA, 94710, USA
- Present Address: Sangamo Therapeutics, Inc., Richmond, CA, USA
| | - Chris K Fuller
- Caribou Biosciences, Inc., 2929 7th Street, Suite 105, Berkeley, CA, 94710, USA
| | - Peter Cameron
- Caribou Biosciences, Inc., 2929 7th Street, Suite 105, Berkeley, CA, 94710, USA
| | - Thomas G Fazzio
- Program in Molecular Medicine, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Lihua Julie Zhu
- Program in Molecular Medicine, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA.
- Program in Molecular Medicine, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA.
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