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Genome-wide profiling of adenine base editor specificity by EndoV-seq

Author

Listed:
  • Puping Liang

    (Sun Yat-sen University
    Sun Yat-sen University)

  • Xiaowei Xie

    (Sun Yat-sen University
    Chinese Academy of Medical Sciences and Peking Union Medical College)

  • Shengyao Zhi

    (Sun Yat-sen University)

  • Hongwei Sun

    (Sun Yat-sen University)

  • Xiya Zhang

    (Sun Yat-sen University)

  • Yu Chen

    (Sun Yat-sen University)

  • Yuxi Chen

    (Sun Yat-sen University)

  • Yuanyan Xiong

    (Sun Yat-sen University)

  • Wenbin Ma

    (Sun Yat-sen University)

  • Dan Liu

    (Baylor College of Medicine)

  • Junjiu Huang

    (Sun Yat-sen University
    Sun Yat-sen University
    Sun Yat-sen University
    the Third Affiliated Hospital of Guangzhou Medical University)

  • Zhou Songyang

    (Sun Yat-sen University
    Sun Yat-sen University
    Baylor College of Medicine
    Sun Yat-sen University)

Abstract

The adenine base editor (ABE), capable of catalyzing A•T to G•C conversions, is an important gene editing toolbox. Here, we systematically evaluate genome-wide off-target deamination by ABEs using the EndoV-seq platform we developed. EndoV-seq utilizes Endonuclease V to nick the inosine-containing DNA strand of genomic DNA deaminated by ABE in vitro. The treated DNA is then whole-genome sequenced to identify off-target sites. Of the eight gRNAs we tested with ABE, 2–19 (with an average of 8.0) off-target sites are found, significantly fewer than those found for canonical Cas9 nuclease (7–320, 160.7 on average). In vivo off-target deamination is further validated through target site deep sequencing. Moreover, we demonstrated that six different ABE-gRNA complexes could be examined in a single EndoV-seq assay. Our study presents the first detection method to evaluate genome-wide off-target effects of ABE, and reveals possible similarities and differences between ABE and canonical Cas9 nuclease.

Suggested Citation

  • Puping Liang & Xiaowei Xie & Shengyao Zhi & Hongwei Sun & Xiya Zhang & Yu Chen & Yuxi Chen & Yuanyan Xiong & Wenbin Ma & Dan Liu & Junjiu Huang & Zhou Songyang, 2019. "Genome-wide profiling of adenine base editor specificity by EndoV-seq," Nature Communications, Nature, vol. 10(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-018-07988-z
    DOI: 10.1038/s41467-018-07988-z
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