Abstract
Oestrogen receptor (ER) activation leads to the formation of DNA double strand breaks (DSB), promoting genomic instability and tumour heterogeneity. The single-stranded DNA cytosine deaminase APOBEC3B (A3B) serves as a co-activator of ER and is implicated in inducing DSBs at transcriptional enhancers regulated by ER. Using whole-genome sequencing in an engineered cell model lacking base excision repair (BER) function, we demonstrate that A3B preferentially targets transcriptionally active regulatory regions in an R-loop-dependent manner. Strand-specific DNA:RNA immunoprecipitation sequencing (ssDRIP-seq) and ssDNA-associated protein immunoprecipitation sequencing (SPI-seq) confirm that A3B binds to and deaminates ssDNA within R-loops, a process facilitated by ER transactivation. Furthermore, BER-mediated processing of A3B-induced uracil bases contributes to the formation of R-loop-associated DSBs, which are essential for ER-regulated gene activation. These findings establish a role for A3B in R-loop homeostasis and transcriptional regulation, with implications for understanding ER-driven genomic instability and potential therapeutic targeting of A3B.
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Data availability
The WGS, ChIP-seq, SPI-seq, ssDRIP-seq, DSBCapture-seq, and RNA-seq data generated in this study have been deposited in NCBI’s Gene Expression Omnibus (GEO) database under the GEO series accession code GSE193234. The processed RNA-seq data generated in this study are provided in Supplementary Data 1 Source data are provided in this paper.
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Acknowledgements
This work is financially supported by Cancer Research UK (C309/A11566 and C2739/A22897) and ICR (London, United Kingdom). C.Z. was sponsored by the Science and Technology Commission of Shanghai Municipality (23S11901100). P.W. and C.Z. acknowledge additional grant support from the Wellcome Trust (212969/Z/18/Z and 094885/Z/10/Z), Cancer Research UK (C35696/A23187). P.W. is a CRUK Life Fellow and acknowledges support from CRUK Strategic Award C35696/A23187 and Infrastructure Award C309/A27413, and funding for the CRUK Children’s Brain Tumour Centre of Excellence (C9685/A26398/RG93685); Wellcome Trust (Biomedical Resource and Technology Development Grant 212969/Z/18/Z to support the Chemical Probes Portal), Chordoma Foundation, Marcus Foundation, Mark Foundation, Bone Cancer Research Trust, CRIS Cancer, and The Institute of Cancer Research. Z.B. was supported by the Science, Technology, and Innovation Commission of Shenzhen Municipality (ZDSYS20200811142605017). We thank Prof. Ping Yuan from Sun Yat-sen University, Dr. Mike Walton and Dr. Alexandra Vasile from ICR for helpful discussions.
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C.Z., O.W.R., P.A.C. and P.W. conceived and designed this study. C.Z., Y.L., Q.Z. and M.T. conducted the experiments and analysis unless otherwise noted. B.C., Z.B., K.M. and B.A.-L. conducted analysis of sequencing data and provided guidance on data analysis using sequencing data. C.Z., A.H., M.P.L., O.W.R., P.W. and P.A.C. prepared the manuscript.
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C.Z., A.H., M.P.L., O.W.R., P.A.C., K.M., M.T., and P.W. are current or past employees of The Institute of Cancer Research, which has a commercial interest in a range of drug targets and operates a Rewards to Discoverers scheme, including A3B inhibitors, through which employees may receive financial benefits following the commercial licensing of a project. P.W. is an independent director at Storm Therapeutics, is a consultant/advisory board member at Astex Pharmaceuticals, CV6 Therapeutics, Black Diamond Therapeutics, Vividion Therapeutics and Nextechinvest; reports receiving a commercial research grant from Sixth Element Capital, Astex Pharmaceuticals, and Merck; has ownership interest in Storm Therapeutics, Chroma Therapeutics, and Nextechinvest; and has an unpaid consultant/advisory board relationship with the Chemical Probes Portal. The remaining authors declare no competing interests.
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Zhang, C., Lu, Yj., Chen, B. et al. R-loop editing by DNA cytosine deaminase APOBEC3B modulates the activity of oestrogen receptor enhancers. Nat Commun (2026). https://doi.org/10.1038/s41467-026-69679-4
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DOI: https://doi.org/10.1038/s41467-026-69679-4
