Genome-wide mutation spectra of canonical and atypical UV photoproducts in  S. cerevisiae

UV exposure causes not only cytosine-to-thymine (C > T) substitutions in dipyrimidine sequences but also many non-canonical mutation classes (e.g. A > T, T > C, and AC > TT). While C > T substitutions are thought to arise from mutagenic bypass of cyclobutane pyrimidine dimers (CPDs), the photoproduct(s) that cause non-canonical mutation classes, which are responsible for key driver mutations in melanoma, are unclear. Here, we use lesion-specific photolyases and whole genome sequencing of yeast irradiated with predominately UVB light to dissect the origins of different classes of UV mutations. These data reveal that CPDs are responsible for ∼60% of all UV mutations and cause not only C > T mutations but also a subset of non-canonical mutation classes, particularly in CT sequence contexts. Our data also indicate that UV-induced pyrimidine (6–4) pyrimidone photoproducts (6–4PPs) are responsible for slightly less than half of all UV-induced mutations in yeast and are the primary cause of T > C substitutions in TT sequences and C > A substitutions. Finally, ∼5% of UV mutations are resistant to both CPD and 6–4PP photolyases, and these are comprised of A > T and AC > TT substitutions in purine-containing dinucleotides. Collectively, these findings define the photoproducts responsible for different UV mutation classes across a eukaryotic genome and indicate that many A > T and AC > TT substitutions arise from atypical UV photoproducts.