BAP1 loss impairs Non-Homologous End Joining DNA repair promoting genomic instability

Abstract The tumor suppressor BRCA1-associated protein 1 (BAP1) is frequently mutated in uveal melanoma, where its loss is associated with poor prognosis. Although BAP1 has been implicated in homologous recombination (HR), its role in non-homologous end-joining (NHEJ) remains poorly defined. Here, we show that BAP1 functions as a central regulator of DNA double-strand break (DSB) repair by coordinating HR and NHEJ. BAP1 depletion disrupts recruitment and activity of the NHEJ machinery. Mechanistically, this defect is driven by aberrant accumulation of H2AK119-ub at DSB sites, promoting excessive DNA end resection and suppressing NHEJ activation. Importantly, inhibition of DNA end resection or suppression of H2AK119-ub restores NHEJ factor recruitment, establishing a causal link between BAP1-regulated histone modifications and repair pathway choice. Clinically, BAP1 loss correlates with genomic instability, providing a mechanistic basis for its association with poor outcomes in uveal melanoma. Collectively, these findings identify BAP1 as a gatekeeper of DSB repair fidelity, revealing a previously unrecognized role in safeguarding NHEJ and maintaining balanced DNA repair. Competing Interest Statement The authors have declared no competing interest. Footnotes This version of the manuscript includes new experimental data and expanded analyses that strengthen the main findings and establish clear causal relationships. Figures have been revised to incorporate the new data, and the manuscript has been reorganized to improve clarity and presentation of the results.