Transcription, nucleosome positioning and protein binding modulate nucleotide excision repair of the Saccharomyces cerevisiae MET17 promoter.

We have assessed how transcription, chromatin structure and protein binding modulate nucleotide excision repair in the upstream regulatory region and early coding region of the endogenous Saccharomyces cerevisiae gene MET17. Removal of UV-induced cyclobutane pyrimidine dimers was measured from these regions, in which transcription and chromatin structure could be regulated independently of each other. Distinct repair trends were apparent depending on transcriptional state. When transcription was repressed nucleosome positioning and protein binding as determined by chromatin immunoprecipitation and quantitative real-time PCR, were significant factors. Nucleosome positioning and/or protein binding effects were most apparent on the strand that becomes transcribed, with repair occurring fastest in a nucleosome free region but being retarded where regulatory proteins bound within this region. When transcription was derepressed the rate of repair increased on both strands in a region beginning 200 bp upstream of the TATA box and extending downstream into the coding region. This effect overrode the influences of nucleosome positioning and protein binding.