Spontaneous mutagenesis in human cells is controlled by REV1-Polymerase z 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 z 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 REV1-/-PCNAK164R/K164R 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 REV1-/- PRIMPOL-/- 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.

Automated summary

Translesion DNA synthesis (TLS) using specialized DNA polymerases facilitates replication over damaged or difficult-to-replicate templates. Investigating three main TLS control mechanisms, REV1 and PCNA ubiquitylation recruit TLS polymerases while PRIMPOL creates post-replicative gaps. Whole-genome sequencing of human RPE-1 cell clones reveals REV1 and Polymerase z as responsible for base substitution mutagenesis resembling homologous recombination deficiency, while PRIMPOL-/- cells show reduced component resembling oxidative mutagenesis. Small deletions in short repeats appear in REV1-/-PCNAK164R/K164R double mutants, revealing an alternative TLS mechanism. REV1-/- and REV3L-/- mutants exhibit 500-5,000 bp deletions, and REV1-/- PRIMPOL-/- cells show chromosomal instability. TLS protects against deletions and large rearrangements but contributes to spontaneous base substitutions.