BRCA1 deficiency specific base substitution mutagenesis is dependent on translesion synthesis and regulated by 53BP1

Dan Chen,Eszter Németh,Zsolt Gyüre,Zoltan Szallasi,Andrea L Richardson,Judit Z Gervai,Ádám Póti,Fabrizio D’Adda Di Fagagna,Zoltán Szeltner,Bernadett Szikriszt,Marta Ceccon,Dávid Szüts,Judit Zámborszky

doi:10.1038/s41467-021-27872-7

Abstract

Defects in BRCA1, BRCA2 and other genes of the homology-dependent DNA repair (HR) pathway cause an elevated rate of mutagenesis, eliciting specific mutation patterns including COSMIC signature SBS3. Using genome sequencing of knock-out cell lines we show that Y family translesion synthesis (TLS) polymerases contribute to the spontaneous generation of base substitution and short insertion/deletion mutations in BRCA1 deficient cells, and that TLS on DNA adducts is increased in BRCA1 and BRCA2 mutants. The inactivation of 53BP1 in BRCA1 mutant cells markedly reduces TLS-specific mutagenesis, and rescues the deficiency of template switch–mediated gene conversions in the immunoglobulin V locus of BRCA1 mutant chicken DT40 cells. 53BP1 also promotes TLS in human cellular extracts in vitro. Our results show that HR deficiency–specific mutagenesis is largely caused by TLS, and suggest a function for 53BP1 in regulating the choice between TLS and error-free template switching in replicative DNA damage bypass.

Highlights

Defects in BRCA1, BRCA2 and other genes of the homology-dependent DNA repair (HR) pathway cause an elevated rate of mutagenesis, eliciting specific mutation patterns including COSMIC signature SBS3
To test whether translesion synthesis (TLS) is responsible for mutagenesis associated with HR deficiency (HRD), we created double mutant DT40 cell lines by homologous gene targeting, disrupting BRCA1 in POLH−/−, POLK−/− and REV1−/− cell lines that carry homozygous deletions in the Y family polymerases Polη, Polκ and REV1, respectively
SBS mutagenesis was lower in BRCA1−/− POLH−/− cells (p = 0.004, t-test), BRCA1−/− POLK−/− cells (p = 0.055), and BRCA1−/− REV1−/− cells (p = 0.0001) than in BRCA1−/− controls, suggesting that Y family TLS polymerases are responsible for at least part of the increased base substitution mutagenesis in BRCA1 deficient cells

Summary

Introduction

Defects in BRCA1, BRCA2 and other genes of the homology-dependent DNA repair (HR) pathway cause an elevated rate of mutagenesis, eliciting specific mutation patterns including COSMIC signature SBS3. Using genome sequencing of knock-out cell lines we show that Y family translesion synthesis (TLS) polymerases contribute to the spontaneous generation of base substitution and short insertion/deletion mutations in BRCA1 deficient cells, and that TLS on DNA adducts is increased in BRCA1 and BRCA2 mutants. The analysis of tumour wholeexome or whole-genome sequences revealed associations between specific mutation patterns and the loss of BRCA1 function. These comprise a broad-spectrum base substitution signature termed. Mutational analyses of tumours and knock-out cell lines indicated that the inactivation of BRCA2, PALB2 and other genes encoding proteins responsible for homology-dependent repair (HR) elicits. BRCA1 and BRCA2 help protect stalled and reversed replication forks through recruiting

Methods

Results

Conclusion