Translesion polymerase eta both facilitates DNA replication and promotes increased human genetic variation at common fragile sites

Significance Common fragile sites (CFSs) are normal loci that are genetically unstable under normal and oncogenic replication stress. Pol eta has been proposed to play a key role in CFS replication. Here, we show that in the absence of Pol eta, replication at five specific CFS loci is perturbed, with fork pausing observed at several sites. Sequence analysis showed that certain pause sites are associated with the presence of non-B DNA motifs, while others are not. Importantly, pause sites are located within regions of increased genetic variation in healthy human populations that could be attributed to Pol eta activity. Our data unveil a role for Pol eta in overcoming replication stress, reducing DNA breakage, and promoting genetic variation at CFSs.