Replication-associated formation and repair of human topoisomerase IIIα cleavage complexes

Abstract Topoisomerase IIIα (TOP3A) belongs to the conserved Type IA family of DNA topoisomerases. Here we report that TOP3A is associated with DNA replication as well as a TOP3A "self-trapping" mutant (TOP3A- R364W) that generates TOP3A DNA cleavage complexes (TOP3Accs) in human cells. We show that trapped TOP3Accs interfere with replication, induce DNA damage and genome instability. To elucidate the repair of TOP3Accs, we explored the role of Spartan (SPRTN), the metalloprotease associated with DNA replication, which digests proteins forming DNA protein crosslinks (DPCs). SPRTN-deficient cells show elevated TOP3Accs, whereas overexpression of SPRTN lowers cellular TOP3Accs. SPRTN is deubiquitinated and epistatic with TDP2 in response to TOP3Accs. In addition, we found that MRE11 can excise TOP3Accs and that cell cycle phases determine the preference for the SPRTN-TDP2 vs. the ATM- MRE11 pathways, in S vs. G2, respectively. Our study highlights the prevalence of TOP3Accs repair mechanisms to ensure normal DNA replication.