R-loop editing by DNA cytosine deaminase APOBEC3B modulates the activity of oestrogen receptor enhancers
- Chi Zhang
- Yu-jing Lu
- Bingjie Chen
- Zhiyan Bai
- Qiaoxi Zeng
- Alexia Hervieu
- Marco P. Licciardello
- Konstantinos Mitsopoulos
- Bissan Al-Lazikani
- Marcello Tortorici
- Olivia W. Rossanese
- Paul Workman
- Paul A. Clarke
2026-02-17
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.