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Title: Systematic evaluation of CRISPR-Cas systems reveals design principles for genome editing in human cells
Authors: Wang, Yuanming
Liu, Ivy Kaiwen
Sutrisnoh, Norfala-Aliah
Srinivasan, Harini
Zhang, Junyi
Li, Jia
Zhang, Fan
Lalith, Charles Richard John
Xing, Heyun
Shanmugam, Raghuvaran
Foo, Jia Nee
Yeo, Hwee Ting
Ooi, Kean Hean
Bleckwehl, Tore
Par, Rachel Yi Yun
Lee, Shi Mun
Ismail, Nur Nadiah
Sanwari, Nur Aidah
Lee, Vanessa Si Ting
Lew, Jan
Tan, Meng How
Keywords: CRISPR
Genome Editing
Issue Date: 2018
Source: Wang, Y., Liu, I. K., Sutrisnoh, N.-A., Srinivasan, H., Zhang, J., Li, J., et al. (2018). Systematic evaluation of CRISPR-Cas systems reveals design principles for genome editing in human cells. Genome Biology, 19(1), 62-.
Series/Report no.: Genome Biology
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.
ISSN: 1474-760X
DOI: 10.1186/s13059-018-1445-x
Rights: © 2018 The Author(s). This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.
Fulltext Permission: open
Fulltext Availability: With Fulltext
Appears in Collections:SCBE Journal Articles

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