Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Programmable A-to-Y base editing by fusing an adenine base editor with an N-methylpurine DNA glycosylase


Here we developed an adenine transversion base editor, AYBE, for A-to-C and A-to-T transversion editing in mammalian cells by fusing an adenine base editor (ABE) with hypoxanthine excision protein N-methylpurine DNA glycosylase (MPG). We also engineered AYBE variants enabling targeted editing at genomic loci with higher transversion editing activity (up to 72% for A-to-C or A-to-T editing).

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Get just this article for as long as you need it


Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Engineering and optimization of AYBE.
Fig. 2: Characterization of editing profiles for AYBE via high-throughput target sequencing.

Data availability

Expression plasmids used in this study have been deposited at Addgene and will be available at (Addgene plasmid nos. 193966–193968). All data supporting the findings of this study are available in the paper (and in its Supplementary Information files). Targeted amplicon sequencing data have been deposited at the Sequence Read Archive and can be accessed at (ref. 21). All relevant original data are available from the corresponding authors upon reasonable request.

Code availability

Custom scripts for CRISPResso analyses supporting the findings of this study are available from the corresponding author upon reasonable request.


  1. Porto, E. M., Komor, A. C., Slaymaker, I. M. & Yeo, G. W. Base editing: advances and therapeutic opportunities. Nat. Rev. Drug Discov. 19, 839–859 (2020).

    Article  CAS  Google Scholar 

  2. Rees, H. A. & Liu, D. R. Base editing: precision chemistry on the genome and transcriptome of living cells. Nat. Rev. Genet. 19, 770–788 (2018).

    Article  CAS  Google Scholar 

  3. Gaudelli, N. M. et al. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature 551, 464–471 (2017).

    Article  CAS  Google Scholar 

  4. Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A. & Liu, D. R. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533, 420–424 (2016).

    Article  CAS  Google Scholar 

  5. Zhao, D. et al. Glycosylase base editors enable C-to-A and C-to-G base changes. Nat. Biotechnol. 39, 35–40 (2021).

    Article  CAS  Google Scholar 

  6. Kurt, I. C. et al. CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells. Nat. Biotechnol. 39, 41–46 (2021).

    Article  CAS  Google Scholar 

  7. Koblan, L. W. et al. Efficient C•G-to-G•C base editors developed using CRISPRi screens, target-library analysis, and machine learning. Nat. Biotechnol. 39, 1414–1425 (2021).

    Article  CAS  Google Scholar 

  8. Chen, L. et al. Programmable C:G to G:C genome editing with CRISPR–Cas9-directed base excision repair proteins. Nat. Commun. 12, 1384 (2021).

    Article  CAS  Google Scholar 

  9. Yuan, T. et al. Optimization of C-to-G base editors with sequence context preference predictable by machine learning methods. Nat. Commun. 12, 4902 (2021).

    Article  CAS  Google Scholar 

  10. Robertson, A. B., Klungland, A., Rognes, T. & Leiros, I. DNA repair in mammalian cells: base excision repair: the long and short of it. Cell. Mol. Life Sci. 66, 981–993 (2009).

    Article  CAS  Google Scholar 

  11. Hindi, N. N., Elsakrmy, N. & Ramotar, D. The base excision repair process: comparison between higher and lower eukaryotes. Cell. Mol. Life Sci. 78, 7943–7965 (2021).

    Article  CAS  Google Scholar 

  12. Saparbaev, M. & Laval, J. Excision of hypoxanthine from DNA containing dIMP residues by the Escherichia coli, yeast, rat, and human alkylpurine DNA glycosylases. Proc. Natl Acad. Sci. USA 91, 5873–5877 (1994).

    Article  CAS  Google Scholar 

  13. Lau, A. Y., Scharer, O. D., Samson, L., Verdine, G. L. & Ellenberger, T. Crystal structure of a human alkylbase-DNA repair enzyme complexed to DNA: mechanisms for nucleotide flipping and base excision. Cell 95, 249–258 (1998).

    Article  CAS  Google Scholar 

  14. Connor, E. E. & Wyatt, M. D. Active-site clashes prevent the human 3-methyladenine DNA glycosylase from improperly removing bases. Chem. Biol. 9, 1033–1041 (2002).

    Article  CAS  Google Scholar 

  15. Vallur, A. C., Maher, R. L. & Bloom, L. B. The efficiency of hypoxanthine excision by alkyladenine DNA glycosylase is altered by changes in nearest neighbor bases. DNA Repair (Amst). 4, 1088–1098 (2005).

    Article  CAS  Google Scholar 

  16. Tong, H. et al. High-fidelity Cas13 variants for targeted RNA degradation with minimal collateral effects. Nat. Biotechnol. (2022).

  17. Richter, M. F. et al. Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity. Nat. Biotechnol. 38, 883–891 (2020).

    Article  CAS  Google Scholar 

  18. Choi, J. Y., Lim, S., Kim, E. J., Jo, A. & Guengerich, F. P. Translesion synthesis across abasic lesions by human B-family and Y-family DNA polymerases α, δ, η, ι, κ, and REV1. J. Mol. Biol. 404, 34–44 (2010).

    Article  CAS  Google Scholar 

  19. Thompson, P. S. & Cortez, D. New insights into abasic site repair and tolerance. DNA Repair (Amst). 90, 102866 (2020).

    Article  CAS  Google Scholar 

  20. Clement, K. et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat. Biotechnol. 37, 224–226 (2019).

    Article  CAS  Google Scholar 

  21. Tong, H. et al. Sequence Read Archive. (2022).

Download references


We acknowledge technical support from the FACS facility of HuiGene Therapeutics Co., Ltd. This work was supported by HuiGene Therapeutics Co., Ltd. (H.T.).

Author information

Authors and Affiliations



H.Y. and H.T. jointly conceived the project. H.T. designed and conducted experiments. X.W. and N.L. performed experiments. Y.L. performed target sequencing data analysis. Y.L. and J.L assisted with cell experiments. Q.M., D.W. and J.L. participated in vector construction and FACS. H.Y., H.T. and C.X. supervised the whole project. H.Y., C.X. and H.T. wrote the manuscript draft, and all authors contributed to the editing of the manuscript.

Corresponding authors

Correspondence to Huawei Tong, Chunlong Xu or Hui Yang.

Ethics declarations

Competing interests

H.T. discloses a patent application related to the proteins described in this manuscript. H.T., N.L., Y.L., J.L, Q.M., D.W. and J.L. are employees of HuiGene Therapeutics Co., Ltd. H.Y. is a founder of HuiGene Therapeutics Co., Ltd. and HuiEdit Therapeutics Co., Ltd. The remaining authors declare no competing interests.

Peer review

Peer review information

Nature Biotechnology thanks the anonymous reviewers for their contribution to the peer review of this work.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary Figs. 1–16 and Supplementary Tables 1–4

Reporting Summary

Supplementary Table 5

gRNA spacers, barcoded primers and target sequences used in this study

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Tong, H., Wang, X., Liu, Y. et al. Programmable A-to-Y base editing by fusing an adenine base editor with an N-methylpurine DNA glycosylase. Nat Biotechnol (2023).

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI:


Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research