Modulation of UV damage formation and repair in nucleosomes in distinct chromatin states in Drosophila

Here, we describe a new genome-wide map of UV-induced cyclobutane pyrimidine dimers (CPDs) in Drosophila S2 cells and a naked DNA control using CPD-seq. We used this data to analyze CPD formation in nucleosomes and different chromatin states across the Drosophila genome. We analyzed CPD formation alongside existing excision repair-sequencing (XR-seq) data to compare CPD damage and repair rates in five distinct chromatin types in Drosophila. This analysis revealed that CPD repair varied in different chromatin domains, while CPD formation was largely unaffected. Moreover, we observed distinct patterns of repair activity in nucleosomes in different chromatin types. Overall design: We used the CPD-seq method to map UV-induced cyclobutane pyrimidine dimers (CPDs) a single nucleotide resolution across the Drosophila genome, immediately after UV-radiation of Drosophila S2 cells (UV 0hr) and in Drosophila genomic DNA that was UV irradiated in vitro (naked DNA control). The no UV control represents unirradated sample.