Strand- and replication timing-dependent functions of DNA polymerase η in human DNA replication and mutagenesis.

Efficient eukaryotic DNA replication relies on the coordinated actions of replicative and error-prone polymerases, with the latter providing flexibility at the cost of mutagenesis. DNA polymerase η (Pol η) is most recognised for tolerating UV-induced DNA damage via translesion synthesis (TLS). However, emerging evidence suggests a broader contribution of error-prone polymerases to DNA synthesis. To elucidate the roles of Pol η during unperturbed replication, we applied polymerase usage sequencing (Pu-seq) to map its activity genome-wide. Our findings demonstrate that Pol η preferentially participates in lagging-strand replication, consistent with observations in budding yeast. Furthermore, Pol η usage varied throughout S phase, with a pronounced enrichment in late-replicating domains, dependent on PCNA ubiquitylation. Under moderate doses of UV, Pol η usage retained its replicative strand bias, which contrasted with the prominent strand bias observed in transcribed regions resulting from asymmetric repair processes. These results reveal that Pol η′s flexibility and intrinsic coupling with replication forks extend beyond TLS in human cells. In cancer genomes, characteristic Pol η mutations are enriched in late-replicating regions and correlate with RAD18 expression, implicating PCNA-mediated Pol η activation in mutagenesis. Together, these findings reveal an unexpected bias in Pol η usage during unperturbed replication which may represent a key contribution to the mutational burden in the human genome.