Base excision repair of N-methylpurines in a yeast minichromosome - Effects of transcription, DNA sequence, and nucleosome positioning

Base excision repair of dimethyl sulfate induced N-methylpurines (NMPs) was measured in a yeast minichromosome that has a galactose-inducible GAL1: UR A3 fusion gene, a constitutively expressed HIS3 gene, and varied regions of chromatin structure. Removal rates of NMPs varied dramatically (>20-fold) at different sites along three selected fragments encompassing a total leng th of 1775 base pairs. Repair of NMPs was not coupled to transcription, bec ause the transcribed strands of HIS3 and induced GAL1:URA3 were not repaire d faster than the nontranscribed strands. However, the repair rate of NMPs was significantly affected by the nearest neighbor nucleotides, Slow repair occurred at NMPs between purines, especially guanines, whereas fast repair occurred at NMPs between pyrimidines. NMPs between a purine and pyrimidine were repaired at moderate rates. Moreover, a rough correlation between nuc leosome positions and repair rates exists in some but not all regions that were analyzed.