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

The tumor suppressor BRCA1-associated protein 1 (BAP1) is frequently mutated in uveal melanoma, where its loss is associated with poor prognosis and metastatic progression. Although BAP1 is known to regulate homologous recombination (HR), its role in non-homologous end-joining (NHEJ) has remained unexplored. Here, we show that BAP1 functions as a central regulator of DNA double-strand break (DSB) repair, controlling both HR and NHEJ to preserve genomic integrity. BAP1 depletion in uveal melanoma cells impairs recruitment of RAD51 and 53BP1, thereby disrupting HR and NHEJ, respectively. Mechanistically, this dual defect is driven by aberrant accumulation of H2AK119ub at DSB sites, which inappropriately promotes DNA end resection. In G1-phase cells, this unscheduled resection inhibits NHEJ, the normally dominant repair mechanism in this phase. Pharmacological inhibition of H2AK119 ubiquitylation using PTC-209 restores 53BP1 localization and suppresses aberrant resection, establishing a causal link between BAP1-regulated chromatin dynamics and DSB repair pathway choice. Clinically, BAP1 loss correlates with pronounced genomic instability, providing a mechanistic explanation for its association with poor outcomes in uveal melanoma. Collectively, these findings identify BAP1 as a gatekeeper of DSB repair fidelity, safeguarding NHEJ in G1 and HR in S/G2, and highlight H2AK119ub modulation as a potential therapeutic strategy to target vulnerabilities in BAP1-deficient tumors. This work reveals a previously unrecognized role for BAP1 in safeguarding NHEJ activation. BAP1 loss derails repair pathway balance, fueling genome instability and driving uveal melanoma progression.