LAUSR

Significance The separation of DNA strands during replication and transcription creates torsional stress (supercoiling) that requires resolution by topoisomerases. Topoisomerase 1 (Top1) removes supercoils by transiently nicking one DNA strand, which allows its rotation around the intact, complementary strand. Stabilization of the covalent Top1–DNA cleavage intermediate results in potentially toxic DNA damage during replication, making this enzyme an attractive target of chemotherapeutic drugs. We find that genetic or chemical Top1 stabilization gives rise to large deletions that require the nonhomologous end-joining pathway and most likely reflect the joining of nonadjacent ends. Furthermore, the relevant Top1-mediated damage accumulates in nondividing cells, suggesting a potential mechanism for genetic change that occurs outside the context of replication. Topoisomerase I (Top1) resolves supercoils by nicking one DNA strand and facilitating religation after torsional stress has been relieved. During its reaction cycle, Top1 forms a covalent cleavage complex (Top1cc) with the nicked DNA, and this intermediate can be converted into a toxic double-strand break (DSB) during DNA replication. We previously reported that Top1cc trapping in yeast increases DSB-independent, short deletions at tandemly repeated sequences. In the current study, we report a type of DSB-dependent mutation associated with Top1cc stabilization: large deletions (median size, ∼100 bp) with little or no homology at deletion junctions. Genetic analyses demonstrated that Top1cc-dependent large deletions are products of the nonhomologous end-joining (NHEJ) pathway and require Top1cc removal from DNA ends. Furthermore, these events accumulated in quiescent cells, suggesting that the causative DSBs may arise outside the context of replication. We propose a model in which the ends of different, Top1-associated DSBs are joined via NHEJ, which results in deletion of the intervening sequence. These findings have important implications for understanding the mutagenic effects of chemotherapeutic drugs that stabilize the Top1cc.