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Sequence-specific prediction of the efficiencies of adenine and cytosine base editors

Authors
 Myungjae Song  ;  Hui Kwon Kim  ;  Sungtae Lee  ;  Younggwang Kim  ;  Sang-Yeon Seo  ;  Jinman Park  ;  Jae Woo Choi  ;  Hyewon Jang  ;  Jeong Hong Shin  ;  Seonwoo Min  ;  Zhejiu Quan  ;  Ji Hun Kim  ;  Hoon Chul Kang  ;  Sungroh Yoon  ;  Hyongbum Henry Kim 
Citation
 NATURE BIOTECHNOLOGY, Vol.38(9) : 1037-1043, 2020-09 
Journal Title
 NATURE BIOTECHNOLOGY 
ISSN
 1087-0156 
Issue Date
2020-09
MeSH
Adenine* ; Aminohydrolases / metabolism ; CRISPR-Associated Protein 9 / metabolism ; CRISPR-Cas Systems ; Cytosine Deaminase / metabolism ; Cytosine* ; Gene Editing / methods* ; Genetic Engineering ; Genome, Human / genetics ; HEK293 Cells ; Humans ; Point Mutation ; RNA, Guide / genetics ; Targeted Gene Repair / methods*
Abstract
Base editors, including adenine base editors (ABEs)1 and cytosine base editors (CBEs)2,3, are widely used to induce point mutations. However, determining whether a specific nucleotide in its genomic context can be edited requires time-consuming experiments. Furthermore, when the editable window contains multiple target nucleotides, various genotypic products can be generated. To develop computational tools to predict base-editing efficiency and outcome product frequencies, we first evaluated the efficiencies of an ABE and a CBE and the outcome product frequencies at 13,504 and 14,157 target sequences, respectively, in human cells. We found that there were only modest asymmetric correlations between the activities of the base editors and Cas9 at the same targets. Using deep-learning-based computational modeling, we built tools to predict the efficiencies and outcome frequencies of ABE- and CBE-directed editing at any target sequence, with Pearson correlations ranging from 0.50 to 0.95. These tools and results will facilitate modeling and therapeutic correction of genetic diseases by base editing.
Full Text
https://www.nature.com/articles/s41587-020-0573-5
DOI
10.1038/s41587-020-0573-5
Appears in Collections:
1. College of Medicine (의과대학) > Dept. of Pediatrics (소아과학교실) > 1. Journal Papers
1. College of Medicine (의과대학) > Dept. of Pharmacology (약리학교실) > 1. Journal Papers
1. College of Medicine (의과대학) > Others (기타) > 1. Journal Papers
Yonsei Authors
Kang, Hoon Chul(강훈철) ORCID logo https://orcid.org/0000-0002-3659-8847
Kim, Younggwang(김영광) ORCID logo https://orcid.org/0000-0002-8033-4232
Kim, Hyongbum(김형범) ORCID logo https://orcid.org/0000-0002-4693-738X
Kim, Hui Kwon(김희권)
Song, Myungjae(송명재)
URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/179994
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