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

Zsolt Gyüre; Ádám Póti; Eszter Németh; Bernadett Szikriszt; Rita Lózsa; Michał Krawczyk; Andrea L Richardson; Dávid Szüts

doi:10.1016/j.celrep.2023.112887

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

Cell Rep. 2023 Aug 29;42(8):112887. doi: 10.1016/j.celrep.2023.112887. Epub 2023 Jul 26.

Authors

Zsolt Gyüre¹, Ádám Póti², Eszter Németh², Bernadett Szikriszt², Rita Lózsa², Michał Krawczyk², Andrea L Richardson³, Dávid Szüts⁴

Affiliations

¹ Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; Doctoral School of Molecular Medicine, Semmelweis University, 1085 Budapest, Hungary; Turbine Simulated Cell Technologies, 1027 Budapest, Hungary.
² Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary.
³ Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. Electronic address: aricha58@jhu.edu.
⁴ Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; National Laboratory for Drug Research and Development, 1117 Budapest, Hungary. Electronic address: szuts.david@ttk.hu.

PMID: 37498746
DOI: 10.1016/j.celrep.2023.112887

Abstract

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 REV1^-/-PCNA^K164R/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.

Keywords: CP: Molecular biology; PRIMPOL; REV1; REV3L; RPE-1 cell line; base substitution mutation; deletion mutation; spontaneous mutagenesis; translesion synthesis; whole genome sequencing.