PARP1 cooperates with ASXL1 to stimulate BAP1 deubiquitinase activity through its DNA-binding domain

Abstract

BAP1 is a tumor-suppressive deubiquitinase of the ubiquitin C-terminal hydrolase (UCH) family that regulates diverse cellular processes, including DNA repair, by removing ubiquitin from histone H2A and other substrates. Its activity is modulated by cofactors, most notably ASXL proteins: ASXL1, through its DEUBAD domain (ASXL1DEU), engages the UCH domain to form a ubiquitin-binding pocket and stimulate catalysis on nucleosomal substrates. PARP1 has recently been implicated as an additional regulator of BAP1, but the underlying mechanism has remained unclear. Here, we show that this regulation is mediated by the PARP1 DNA-binding domain (DBD). The DBD interacts with BAP1 primarily outside the UCH domain and, while inactive on its own, cooperates with, but cannot substitute for, the ASXL1DEU to stimulate BAP1 activity on nucleosomal substrates. This cooperative effect, absent with non-nucleosomal artificial substrates, is accompanied by reduced BAP1nucleosome association independent of ASXL1DEU, suggesting that the DBD limits nonproductive complexes and promotes more efficient substrate engagement. Importantly, the stimulatory role requires the integrity of the full DBD rather than its individual zinc fingers, underscoring the functional significance of the intact domain. Together, these findings identify the PARP1 DBD as an auxiliary regulatory module that cooperates with ASXL1 to enhance BAP1 activity, providing a mechanistic basis for its regulation in chromatin contexts and extending PARP1's functional scope to BAP1 catalysis.