Abstract

The targeting range of CRISPR–Cas9 base editors (BEs) is limited by their G/C-rich protospacer-adjacent motif (PAM) sequences. To overcome this limitation, we developed a CRISPR–Cpf1-based BE by fusing the rat cytosine deaminase APOBEC1 to a catalytically inactive version of Lachnospiraceae bacterium Cpf1. The base editor recognizes a T-rich PAM sequence and catalyzes C-to-T conversion in human cells, while inducing low levels of indels, non-C-to-T substitutions and off-target editing.

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Acknowledgements

This work was supported by grants 2014CB910600 (L.Y.) from MOST; grants 31600619 (B.Y.), 31600654 (J.C.), 31471241 (L.Y.), 31730111 (L.Y.) and 91540115 (L.Y.) from NSFC; and grants 16PJ1407000 (J.C.) and 16PJ1407500 (B.Y.) from the Shanghai Municipal Science and Technology Commission.

Author information

Author notes

    • Xiaosa Li
    • , Ying Wang
    • , Yajing Liu
    •  & Bei Yang

    These authors contributed equally to this work.

Affiliations

  1. School of Life Science and Technology, ShanghaiTech University, Shanghai, China.

    • Xiaosa Li
    • , Yajing Liu
    • , Xiao Wang
    • , Zongyang Lu
    • , Yuxi Zhang
    • , Jing Wu
    • , Xingxu Huang
    •  & Jia Chen
  2. Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.

    • Xiaosa Li
    • , Yajing Liu
    • , Xiao Wang
    •  & Zongyang Lu
  3. University of Chinese Academy of Sciences, Beijing, China.

    • Xiaosa Li
    • , Yajing Liu
    • , Xiao Wang
    •  & Zongyang Lu
  4. Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.

    • Ying Wang
    • , Jia Wei
    •  & Li Yang
  5. Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China.

    • Bei Yang

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Contributions

J.C., X.H. and L.Y. conceived, designed and supervised the project. J.C. managed the project. X.L. and Y.L. performed most experiments on plasmid construction and cell culture with the help of X.W., Z.L., Y.Z. and J. Wu. J. Wei. prepared libraries for deep sequencing, and Y.W. performed bioinformatics analyses, supervised by L.Y. J.C., B.Y. and L.Y. wrote the paper with input from all authors.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Xingxu Huang or Li Yang or Jia Chen.

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    Supplementary Text and Figures

    Supplementary Figures 1–11, Supplementary Tables 1 and 2, and Supplementary Notes 1 and 2

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    Life Sciences Reporting Summary

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    Supplementary Table 3

    Calculation of indels

  2. 2.

    Supplementary Table 4

    Calculation of base substitutions

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DOI

https://doi.org/10.1038/nbt.4102

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