PARP1 regulates the genomic ribonucleotide processing activity of TOP1 to prevent the formation of toxic TOP1-DNA adducts and the associated mutations

Ribonucleotides are frequently incorporated into the genome during DNA replication and are normally removed by RNase H2. Alternatively, DNA topoisomerase 1 (TOP1) can process genomic ribonucleotides through two sequential cleavage events, generating a 2′,3′-cyclic phosphate-terminated nick and, subsequently, a TOP1 cleavage complex (TOP1cc). In addition, TOP1cc formation can lead to 2- to 5-bp slippage deletions, recently identified as the ID4 cancer signature. Here, we show that human TOP1 is intrinsically mutagenic, with a tendency to undergo secondary cleavage and form TOP1 cleavage complexes. We further demonstrate that PARP1, a central single-strand break repair factor, suppresses TOP1 secondary cleavage, TOP1cc formation, and the resulting slippage mutations. This regulation requires PARP1 to interact with both TOP1 and the 2′,3′-cyclic phosphate-terminated nick produced by the initial TOP1 cleavage. Notably, a PARP1 mutant defective in TOP1 interaction is partially impaired in restoring PARP inhibitor sensitivity in PARP1-knockout cells, suggesting that PARP inhibitor cytotoxicity may partly result from PARP1 trapping at 2′,3′-cyclic phosphate-terminated nicks and blocking their processing by TOP1 and other factors. Together, these findings reveal a novel role for PARP1 in regulating TOP1-dependent ribonucleotide processing, thereby suppressing cancer-signature mutations and contributing to the mechanism of PARP inhibitor cytotoxicity.