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Genome-wide specificity of dCpf1 cytidine base editors

Cited 1 time in Web of Science Cited 1 time in Scopus
Authors
Kim, Daesik; Lim, Kayeong; Kim, Da-eun; Kim, Jin-Soo
Issue Date
2020-08
Citation
Nature Communications, Vol.11 No.1, p. 4072
Abstract
Cpf1-linked base editors broaden the targeting scope of programmable cytidine deaminases by recognizing thymidine-rich protospacer-adjacent motifs (PAM) without inducing DNA double-strand breaks (DSBs). Here we present an unbiased in vitro method for identifying genome-wide off-target sites of Cpf1 base editors via whole genome sequencing. First, we treat human genomic DNA with dLbCpf1-BE ribonucleoprotein (RNP) complexes, which convert C-to-U at on-target and off-target sites and, then, with a mixture of E. coli uracil DNA glycosylase (UDG) and DNA glycosylase-lyase Endonuclease VIII, which removes uracil and produces single-strand breaks (SSBs) in vitro. Whole-genome sequencing of the resulting digested genome (Digenome-seq) reveals that, on average, dLbCpf1-BE induces 12 SSBs in vitro per crRNA in the human genome. Off-target sites with an editing frequency as low as 0.1% are successfully identified by this modified Digenome-seq method, demonstrating its high sensitivity. dLbCpf1-BEs and LbCpf1 nucleases often recognize different off-target sites, calling for independent analysis of each tool.
ISSN
2041-1723
URI
https://hdl.handle.net/10371/171740
DOI
https://doi.org/10.1038/s41467-020-17889-9
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