Human DNA polymerase eta is required for common fragile site stability during unperturbed DNA replication.

Human DNA polymerase eta (Pol eta) modulates susceptibility to skin cancer by promoting translesion DNA synthesis (TLS) past sunlight-induced cyclobutane pyrimidine dimers. Despite its well-established role in TLS synthesis, the role of Pol eta in maintaining genome stability in the absence of external DNA damage has not been well explored. We show here that short hairpin RNA-mediated depletion of Pol eta from undamaged human cells affects cell cycle progression and the rate of cell proliferation and results in increased spontaneous chromosome breaks and common fragile site expression with the activation of ATM-mediated DNA damage checkpoint signaling. These phenotypes were also observed in association with modified replication factory dynamics during S phase. In contrast to that seen in Pol eta-depleted cells, none of these cellular or karyotypic defects were observed in cells depleted for Pol iota, the closest relative of Pol eta. Our results identify a new role for Pol eta in maintaining genomic stability during unperturbed S phase and challenge the idea that the sole functional role of Pol eta in human cells is in TLS DNA damage tolerance and/or repair pathways following exogenous DNA damage.