Mapping Hap2/Hap3/Hap5 binding sites in yeast using CPD-seq data

Here, we used the cyclobutane pyrimidine dimer-sequencing (CPD-seq) method to map UV damage footprints associated with transcription factor binding to DNA in yeast. We analyzed CPD-seq data from UV-irradiated wild-type yeast cells that were immediately isolated and analyzed (0hr time point) and compared these data to isolated yeast genomic DNA that was UV-irradiated in vitro (naked DNA control). We analyze these data with a machine learning algorithm to identify binding sites of the Hap2/Hap3/Hap5 transcription factor complex across the yeast genome, based on their UV damage footprint. As a control, we UV-irradiated hap5 mutant cells, which renders the complex unable to bind DNA, and mapped UV damage patterns using CPD-seq. Overall design: We used the CPD-seq method to map UV-induced cyclobutane pyrimidine dimers (CPDs) at single-nucleotide resolution across the yeast genome, both immediately after UV-irradiation of yeast cells (0hr) and in isolated yeast genomic DNA that was UV-irradiated in vitro.