RNA polymerase II transcription suppresses nucleosomal modulation of UV-induced (6-4) photoproduct and cyclobutane pyrimidine dimer repair in yeast

The nucleotide excision repair (NER) pathway is able to remove a wide varie ty of structurally unrelated lesions from DNA. NER operates throughout the genome, but the efficiencies of lesion removal are not the same for differe nt genomic regions. Even within a single gene or DNA strand repair rates va ry, and this intragenic heterogeneity is of considerable interest with resp ect to the mutagenic potential of carcinogens, In this study, we have analy zed the removal of the two major types of genotoxic DNA adducts induced by UV light, i.e., the pyrimidine (6-4)-pyrimidone photoproduct (6-4PP) and th e cyclobutane pyrimidine dimer (CPD), from the Saccharomyces cerevisiae URA 3 gene at nucleotide resolution. In contrast to the fast and uniform remova l of CPDs from the transcribed strand, removal of lesions from the nontrans cribed strand is generally less efficient and is modulated by the chromatin environment of the damage, Removal of 6-4PPs from nontranscribed sequences is also profoundly influenced by positioned nucleosomes, but this type of lesion is repaired at a much higher rate, Still, the transcribed strand is repaired preferentially, indicating that, as in the removal of CPDs, transc ription-coupled repair predominates in the removal of 6-4PPs from transcrib ed DNA. The hypothesis that transcription machinery operates as the rate-de termining damage recognition entity in transcription-coupled repair is supp orted by the observation that this pathway removes both types of UV photopr oducts at equal rates without being profoundly influenced by the sequence o r chromatin context.