Epistasis between mutator alleles contributes to germline mutation spectra variability in laboratory mice

Abstract

Maintaining germline genome integrity is essential and enormously complex. Hundreds of proteins are involved in DNA replication and proofreading, and hundreds more are mobilized to repair DNA damage. While loss-of-function mutations in any of the genes encoding these proteins might lead to elevated mutation rates, mutator alleles have largely eluded detection in mammals. DNA replication and repair proteins often recognize particular sequence motifs or excise lesions at specific nucleotides. Thus, we might expect that the spectrum of de novo mutations - that is, the frequency of each individual mutation type (C>T, A>G, etc.) - will differ between genomes that harbor either a mutator or wild-type allele at a given locus. Previously, we used quantitative trait locus mapping to discover candidate mutator alleles in the DNA repair gene Mutyh that increased the C>A germline mutation rate in a family of inbred mice known as the BXDs. In this study we developed a new method, called "inter-haplotype distance," to detect alleles associated with mutation spectrum variation. By applying this approach to mutation data from the BXDs, we confirmed the presence of the germline mutator locus near Mutyh and discovered an additional C>A mutator locus on chromosome 6 that overlaps Ogg1 and Mbd4, two DNA glycosylases involved in base-excision repair. The effect of a chromosome 6 mutator allele depended on the presence of a mutator allele near Mutyh, and BXDs with mutator alleles at both loci had even greater numbers of C>A mutations than those with mutator alleles at either locus alone. Our new methods for analyzing mutation spectra reveal evidence of epistasis between germline mutator alleles, and may be applicable to mutation data from humans and other model organisms.