Break-induced replication is activated to repair R-loop-associated double-strand breaks in SETX-deficient cells

Abstract

AbstractThe primary role of Break-induced replication (BIR) is thought to be repairing single-ended double-strand breaks (seDSBs) generated at broken replication forks and eroding telomeres. In this study, we demonstrated that when senataxin (SETX), an RNA/DNA helicase, is defective, hyperrecombination using the BIR mechanism is induced at R-loop-accumulated double-ended double-strand breaks (deDSBs), suggesting a potential role of BIR in repair of R-loop-associated deDSBs. Intriguingly, loss of SETX initiates a non-canonical hyper end resection pathway requiring RAD52 and XPF, which in turn causes accumulation of PCNA and PIF1, a key player for BIR, to R-loop-associated deDSBs to establish BIR. Strikingly, SETX-deficiency does not only induce hyper BIR, but also causes a drastic increase of template switching during BIR, which has a potential to induce complex chromosome rearrangements. Additionally, SETX is synthetic lethal with RAD52 and PIF1. Collectively, our work uncovers a pivotal new function of SETX in modulating BIR to safeguard genome integrity, sheds light on how R-loops influence the utilization and fidelity of DSB repair pathways and offers new strategies for targeted treatment of SETX-deficient tumors.