title: Hypermutation signature reveals a slippage and realignment model of translesion synthesis by Rev3 polymerase in cisplatin-treated yeast.
abstract: Gene-gene or gene-drug interactions are typically quantified using fitness as a readout because the data are continuous and easily measured in high throughput. However, to what extent fitness captures the range of other phenotypes that show synergistic effects is usually unknown. UsingSaccharomyces cerevisiaeand focusing on a matrix of DNA repair mutants and genotoxic drugs, we quantify 76 gene-drug interactions based on both mutation rate and fitness and find that these parameters are not connected. Independent of fitness defects, we identified six cases of synthetic hypermutation, where the combined effect of the drug and mutant on mutation rate was greater than predicted. One example occurred when yeast lackingRAD1were exposed to cisplatin, and we characterized this interaction using whole-genome sequencing. Our sequencing results indicate mutagenesis by cisplatin inrad1Δ cells appeared to depend almost entirely on interstrand cross-links at GpCpN motifs. Interestingly, our data suggest that the following base on the template strand dictates the addition of the mutated base. This result differs from cisplatin mutation signatures in XPF-deficientCaenorhabditis elegansand supports a model in which translesion synthesis polymerases perform a slippage and realignment extension across from the damaged base. Accordingly, DNA polymerase ζ activity was essential for mutagenesis in cisplatin-treatedrad1Δ cells. Together these data reveal the potential to gain new mechanistic insights from nonfitness measures of gene-drug interactions and extend the use of mutation accumulation and whole-genome sequencing analysis to define DNA repair mechanisms.
authors.affiliation: Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada V5Z1L3.
authors.forename: Romulo
authors.initials: R
authors.lastname: Segovia
authors.affiliation: Michael Smith Genome Sciences Centre, Vancouver, BC, Canada V5Z4S6.
authors.forename: Yaoqing
authors.initials: Y
authors.lastname: Shen
authors.affiliation: Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709.
authors.forename: Scott A
authors.identifier: 0000-0003-2400-8325
authors.initials: SA
authors.lastname: Lujan
authors.affiliation: Michael Smith Genome Sciences Centre, Vancouver, BC, Canada V5Z4S6.|Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T1Z3.
authors.forename: Steven J M
authors.initials: SJ
authors.lastname: Jones
authors.affiliation: Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada V5Z1L3; pstirling@bccrc.ca.|Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T1Z3.
authors.forename: Peter C
authors.initials: PC
authors.lastname: Stirling
mesh_terms: D002945:Cisplatin / Q000627:therapeutic use / Q000633:toxicity*; D004249:DNA Damage / Q000187:drug effects; D004260:DNA Repair / Q000187:drug effects; D045643:DNA Repair Enzymes / Q000235:genetics*; D004261:DNA Replication / Q000187:drug effects; D004259:DNA-Directed DNA Polymerase / Q000235:genetics; D004720:Endonucleases / Q000235:genetics*; D056084:Genetic Fitness / Q000187:drug effects*; D016296:Mutagenesis / Q000187:drug effects*; D009152:Mutagenicity Tests; D059645:Mutation Rate; D012441:Saccharomyces cerevisiae / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics*; D000073336:Whole Genome Sequencing
chemical_list: D029701:Saccharomyces cerevisiae Proteins; D004259:DNA-Directed DNA Polymerase; D004720:Endonucleases; C069266:RAD1 protein, S cerevisiae; D045643:DNA Repair Enzymes; D002945:Cisplatin
keywords: DNA repair; gene–drug interaction; mutation signature; mutator; translesion synthesis