Genome-wide maps of deaminated CPDs (dCPDs) following UV-irradiation in cells and deamination as naked DNA in vitro

Here, we describe a genome-wide map of uracil lesions arising from deaminated UV-induced cyclobutane pyrimidine dimers (CPDs) that arose from UV irradiation of yeast cells (Saccharomyces cerevisiae) and deamination in vitro as isolated yeast genomic DNA (i.e., naked DNA control). Deaminated CPDs (dCPDs) were mapped at single nucleotide resolution across the yeast genome using the new dCPD-seq method in repair-deficient (rad14?), G2/M-arrested (cdc13-1) yeast cells immediately after UV irradiation (0 hour) and following 6 hour (6hr), 24hr, or 48hr of deamination in solution in vitro. We also generated a full deamination control, in which genomic DNA from a 48h deamination sample was incubated in vitro for an additional 16h at 67C. We used these data to analyze CPD deamination in different trinucleotide sequence contexts, yeast genes, transcription factor binding sites, and nucleosomes. Overall design: We used the new dCPD-seq method to map cytosine-containing UV-induced cyclobutane pyrimidine dimers (CPDs) that had undergone deamination to uracil. Deaminated CPDs were mapped at single nucleotide resolution across the yeast genome, both immediately after UV-irradiation of yeast cells (0 hour) and following 6 hour (6hr), 24hr, or 48hr deamination in vitro. We also mapped deamination in genomic DNA from a 48h deamination sample was incubated in vitro for an additional 16h at 67C, as a full deamination control.