More than just a passive brick in the wall: the nucleosome facilitates DNA polymerase β activity in linker DNA and its PARP-dependent regulation in the BER pathway choice

Abstract

DNA polymerase {beta} (Pol{beta}) is a central player of base excision repair (BER), performing gap-filling synthesis on damaged DNA. While nucleosome core particles (NCPs) are known to impede activity of BER enzymes, the regulation of this process in linker DNA adjacent to nucleosomes remains unclear. Here we demonstrate an unexpected stimulation of Pol{beta}-catalyzed gap-filling and strand-displacement synthesis in linker DNA by the adjacent NCP. Notably, the nucleosomal context reinforces the regulatory modulation of Pol{beta} activity by PARP1/PARP2 and FEN1. While linker histone H1 restricts strand-displacement synthesis at the nucleosome entry/exit site, PARP1 and PARP2 modulate Pol{beta} function through competitive binding to DNA gaps or nicks and via poly(ADP-ribosyl)ation (PARylation). At the same time, PARPs binding differentially regulates BER sub-pathway choice, and PARylation alleviates H1-mediated inhibition. These findings reveal a multi-layered regulatory system wherein the nucleosome acts as a dynamic platform coordinating Pol{beta} activity and its interplay with chromatin-associated factors, influencing the balance between short- and long-patch BER. The research advances understanding of chromatin-mediated control of BER DNA repair synthesis and the functional specialization of PARP1 and PARP2 in maintaining genome stability. HighlightsThe nucleosome core particle acts not only as a barrier but also as a stimulator of Pol{beta}-mediated DNA repair synthesis in adjacent linker DNA. The nucleosome acts as an allosteric platform that enhances the regulatory functions of chromatin-associated factors (PARP1, PARP2, H1) in the linker DNA repair synthesis. PARP1 suppresses overall Pol{beta} synthesis, while PARP2 specifically inhibits strand displacement, thereby gating the choice between short- and long-patch BER pathways.