Abstract

Base editors (BEs) enable the generation of targeted single-nucleotide mutations, but currently used rat APOBEC1-based BEs are relatively inefficient in editing cytosines in highly methylated regions or in GpC contexts. By screening a variety of APOBEC and AID deaminases, we show that human APOBEC3A-conjugated BEs and versions we engineered to have narrower editing windows can mediate efficient C-to-T base editing in regions with high methylation levels and GpC dinucleotide content.

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Acknowledgements

We are grateful to G.G. Carmichael and L.-L. Chen for critical reading of this paper, L. Lei and L. Wang for participating in the western blot and plasmid construction, and J. Liang for technical support. This work was supported by grants 31730111 (L.Y.), 91540115 (L.Y.), 31600654 (J.C.), 31600619 (B.Y.) and 31471241 (L.Y.) from the NSFC and grants 16PJ1407000 (J.C.) and 16PJ1407500 (B.Y.) from the Shanghai Pujiang Program.

Author information

Author notes

    • Xiao Wang
    • , Jianan Li
    • , Ying Wang
    • , Bei Yang
    •  & Jia Wei

    These authors contributed equally to this work.

Affiliations

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

    • Xiao Wang
    • , Jianan Li
    • , Jing Wu
    • , Ruixuan Wang
    • , Xingxu Huang
    •  & Jia Chen
  2. Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.

    • Xiao Wang
    •  & Jianan Li
  3. University of Chinese Academy of Sciences, Beijing, China.

    • Xiao Wang
    •  & Jianan Li
  4. Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, 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., L.Y. and X.H. conceived, designed and supervised the project. J.C. managed the project. X.W. and J.L. performed most experiments with the help of J. Wu and R.W. on cell culture and plasmid construction. J. Wei prepared libraries for deep sequencing and Y.W. performed bioinformatics analyses, supervised by L.Y. J.C., L.Y. and B.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 Jia Chen or Li Yang.

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    Life Sciences Reporting Summary

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    Supplementary Items

    Supplementary Tables 1 and 2 and Supplementary Note 1

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    Supplementary Table 3

    Calculation of indels

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    Supplementary Table 4

    Calculation of base substitutions

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DOI

https://doi.org/10.1038/nbt.4198