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Wang Y, Liu KI, Sutrisnoh NAB, Srinivasan H, Zhang J, Li J, Zhang F, Lalith CRJ, Xing H, Shanmugam R, Foo JN, Yeo HT, Ooi KH, Bleckwehl T, Par YYR, Lee SM, Ismail NNB, Sanwari NAB, Lee STV, Lew J, Tan MH. Systematic evaluation of CRISPR-Cas systems reveals design principles for genome editing in human cells. Genome Biol 2018; 19:62. [PMID: 29843790 PMCID: PMC5972437 DOI: 10.1186/s13059-018-1445-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [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: 06/17/2017] [Accepted: 05/07/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND While CRISPR-Cas systems hold tremendous potential for engineering the human genome, it is unclear how well each system performs against one another in both non-homologous end joining (NHEJ)-mediated and homology-directed repair (HDR)-mediated genome editing. RESULTS We systematically compare five different CRISPR-Cas systems in human cells by targeting 90 sites in genes with varying expression levels. For a fair comparison, we select sites that are either perfectly matched or have overlapping seed regions for Cas9 and Cpf1. Besides observing a trade-off between cleavage efficiency and target specificity for these natural endonucleases, we find that the editing activities of the smaller Cas9 enzymes from Staphylococcus aureus (SaCas9) and Neisseria meningitidis (NmCas9) are less affected by gene expression than the other larger Cas proteins. Notably, the Cpf1 nucleases from Acidaminococcus sp. BV3L6 and Lachnospiraceae bacterium ND2006 (AsCpf1 and LbCpf1, respectively) are able to perform precise gene targeting efficiently across multiple genomic loci using single-stranded oligodeoxynucleotide (ssODN) donor templates with homology arms as short as 17 nucleotides. Strikingly, the two Cpf1 nucleases exhibit a preference for ssODNs of the non-target strand sequence, while the popular Cas9 enzyme from Streptococcus pyogenes (SpCas9) exhibits a preference for ssODNs of the target strand sequence instead. Additionally, we find that the HDR efficiencies of Cpf1 and SpCas9 can be further improved by using asymmetric donors with longer arms 5' of the desired DNA changes. CONCLUSIONS Our work delineates design parameters for each CRISPR-Cas system and will serve as a useful reference for future genome engineering studies.
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Affiliation(s)
- Yuanming Wang
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, 637459, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, 138672, Singapore
| | - Kaiwen Ivy Liu
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, 138672, Singapore
| | - Norfala-Aliah Binte Sutrisnoh
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, 138672, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Harini Srinivasan
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, 637459, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, 138672, Singapore
| | - Junyi Zhang
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, 637459, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, 138672, Singapore
| | - Jia Li
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, 637459, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, 138672, Singapore
| | - Fan Zhang
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, 138672, Singapore
| | | | - Heyun Xing
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, 637459, Singapore
| | - Raghuvaran Shanmugam
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, 637459, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, 138672, Singapore
| | - Jia Nee Foo
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, 138672, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
| | - Hwee Ting Yeo
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, 138672, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Kean Hean Ooi
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, 637459, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Tore Bleckwehl
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, 637459, Singapore
| | - Yi Yun Rachel Par
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, 138672, Singapore
- School of Applied Science, Republic Polytechnic, Singapore, 738964, Singapore
| | - Shi Mun Lee
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, 637459, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, 138672, Singapore
| | - Nur Nadiah Binte Ismail
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, 138672, Singapore
- School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, Singapore, 599489, Singapore
| | - Nur Aidah Binti Sanwari
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, 138672, Singapore
- School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, Singapore, 599489, Singapore
| | - Si Ting Vanessa Lee
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, 138672, Singapore
- School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, Singapore, 599489, Singapore
| | - Jan Lew
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, 138672, Singapore
- School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, Singapore, 599489, Singapore
| | - Meng How Tan
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, 637459, Singapore.
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, 138672, Singapore.
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