Molecular basis of nick ligation in the nucleosome by DNA Ligase IIIα

Genomic DNA is packaged into chromatin through a fundamental repeating unit known as the nucleosome core particle. Chromatinized genomic DNA is constantly exposed to endogenous and exogenous stresses that result in DNA damage, which must be repaired to maintain genome stability. Single-strand breaks (SSBs) are a prevalent form of DNA damage that arise via the oxidation-induced disintegration of the sugar-phosphate backbone or as repair intermediates during base excision repair. DNA ligase IIIα (LigIIIα) is one of the primary enzymes responsible for repairing ligatable SSBs during the terminal step of single-strand break repair (SSBR) and base excision repair (BER). To date, a mechanistic description of how LigIIIα processes nicks within chromatin remains elusive. Here, we use a combination of biochemical assays, molecular dynamics simulations, and cryogenic electron microscopy to define the molecular basis of nick ligation in the nucleosome by LigIIIα, providing foundational insight into the terminal step of chromatin-based SSBR/BER.