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The primary role of break-induced replication (BIR) is to repair 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, hyper-recombination using the BIR mechanism is induced at R-loops/hybrids-accumulated double-ended DSBs (deDSBs), uncovering a role for BIR in repair of R-loops/hybrids-associated deDSBs. Intriguingly, the loss of SETX not only triggers non-canonical hyper-end resection requiring RAD52 and XPF, but also stalls Polα-primase-initiated end-fill DNA synthesis due to the accumulation of RNA/DNA hybrids on single-strand DNA (ssDNA) overhangs at deDSBs. This conflict between fill-in DNA synthesis and accumulated hybrids induces PCNA ubiquitination and PIF1 loading, thereby initiating the BIR mechanism at deDSBs. Hyper-resection further enhances PCNA ubiquitination and PIF1 loading, driving BIR-mediated hyper-recombination. Moreover, SETX is synthetic lethal with PIF1, RAD52, and XPF, offering new strategies for targeted treatment of SETX-deficient tumors.
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http://dx.doi.org/10.1101/2024.06.29.601361 | DOI Listing |
Nat Rev Mol Cell Biol
September 2025
Department of Biology and Rosenstiel Basic Medical Sciences Research Center Brandeis University, Waltham, MA, USA.
Methods Mol Biol
August 2025
Center for Education in Laboratory Animal Research, Chubu University, Kasugai, Aichi, Japan.
Complex chromosomal rearrangements (CCRs) present significant challenges and opportunities in cancer and congenital disease research. Reproducing these rearrangements experimentally in animal models has been challenging, limiting our insights into their mechanisms and impacts. Recql5 is a critical DNA helicase that participates in replication, transcription, and repair processes.
View Article and Find Full Text PDFNat Commun
August 2025
Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.
Mitotic DNA synthesis (MiDAS) serves to complete the replication of genomic loci that are not fully replicated in S phase in response to replication stress. Previous studies suggest that MiDAS might proceed via break-induced DNA replication, a sub-pathway of homologous recombination repair activated at broken or collapsed replication forks. We set out to define whether DNA double strand break end-resection factors play a role in MiDAS.
View Article and Find Full Text PDFNat Struct Mol Biol
August 2025
Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
DNA double-strand breaks (DSBs) are a severe threat to genome stability, as DSB-repair mechanisms with low fidelity contribute to loss of genome integrity. Break-induced replication (BIR) is a crucial DSB-repair pathway when classical homologous recombination mechanisms fail. BIR is often triggered by stalled or collapsed replication forks, following extensive end resection that generates a single-stranded DNA substrate, which can engage either canonical homology-driven BIR, or microhomology-mediated BIR (mmBIR), which requires shorter sequence homologies than does canonical BIR.
View Article and Find Full Text PDFChromosome Res
August 2025
Howard Hughes Medical Institute, Fred Hutch Cancer Center, 1100 Fairview Avenue N, Seattle, WA, 98109, USA.
The identification of CENPA, CENPB, and CENPC by Earnshaw and Rothfield 40 years ago has revealed the remarkable diversity and complexity of centromeres and confirmed most seed plants and animals have centromeres comprised of complex satellite arrays. The rapid evolution of centromeres and positive selection on CENPA and CENPC led to the centromere drive model, in which competition between tandem satellite arrays of differing size and centromere strength for inclusion in the egg of animals or megaspore of seed plants during female meiosis drives rapid evolution of centromeres and kinetochore proteins. Here we review recent work showing that non-B-form DNA structures in satellite centromeres make them sites of frequent replication fork stalling, and that repair of collapsed forks by break-induced replication rather than unequal sister chromatid exchange is likely the primary mode of satellite expansion and contraction, providing the variation in satellite copy number that is the raw material of centromere drive.
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