Mutational signatures are jointly shaped by DNA damage and repair
Mutations arise when DNA lesions escape DNA repair. To delineate the contributions of DNA damage and DNA repair deficiency to mutagenesis we sequenced 2,721 genomes of 54 C. elegans strains, each deficient for a specific DNA repair gene and wild-type, upon exposure to 12 different genotoxins. Combining genotoxins and repair deficiency leads to differential mutation rates or new mutational signatures in more than one third of experiments. Translesion synthesis polymerase deficiencies show dramatic and diverging effects. Knockout of Polκ dramatically exacerbates the mutagenicity of alkylating agents; conversely, Polζ deficiency reduces alkylation- and UV-induced substitution rates. Examples of DNA damage-repair deficiency interactions are also found in cancer genomes, although cases of hypermutation are surprisingly rare despite signs of positive selection in a number of DNA repair genes. Nevertheless, cancer risk may be substantially elevated even by small increases in mutagenicity according to evolutionary multi-hit theory. Overall, our data underscore how mutagenesis is a joint product of DNA damage and DNA repair, implying that mutational signatures may be more variable than currently anticipated.