Spontaneous mutagenesis in human cells is controlled by REV1-Polymerase ζ and PRIMPOL.

Translesion DNA synthesis (TLS) facilitates replication over damaged or difficult-to-replicate templates by employing specialized DNA polymerases. We investigate the effect on spontaneous mutagenesis of three main TLS control mechanisms: REV1 and PCNA ubiquitylation that recruit TLS polymerases and PRIMPOL that creates post-replicative gaps. Using whole-genome sequencing of cultured human RPE-1 cell clones, we find that REV1 and Polymerase ζ are wholly responsible for one component of base substitution mutagenesis that resembles homologous recombination deficiency, whereas the remaining component that approximates oxidative mutagenesis is reduced in PRIMPOL cells. Small deletions in short repeats appear in REV1PCNA double mutants, revealing an alternative TLS mechanism. Also, 500-5,000 bp deletions appear in REV1 and REV3L mutants, and chromosomal instability is detectable in REV1PRIMPOL cells. Our results indicate that TLS protects the genome from deletions and large rearrangements at the expense of being responsible for the majority of spontaneous base substitutions.