Tight correlation between inhibition of DNA repair in vitro and transcription factor IIIA binding in a 5S ribosomal RNA gene

UV-induced photoproducts (cyclobutane pyrimidine dimers, CPDs) in DNA are r emoved by nucleotide excision repair (NER), and the presence of transcripti on factors on DNA can restrict the accessibility of NER enzymes. We have in vestigatigated the modulation of NER in a gene promoter using the Xenopus t ranscription factor IIIA (TFIIIA)-5S rDNA complex and Xenopus oocyte nuclea r extracts. TFIIIA alters CPD formation primarily in the transcribed strand of the 50 bp internal control region (ICR) of 5S rDNA, During NER in vitro , CPD removal is reduced at most sites in both strands of the ICR when TFII IA is bound. Efficient repair occurs just outside the TFIIIA-binding site ( within 10 bp), and in the absence of 5S rRNA transcription, Interestingly, three CPD sites within the ICR [+56, +75 (transcribed strand) and +73 (non- transcribed strand)] are repaired rapidly when TFIIIA is bound, while CPDs within similar to 5 bases of these sites are repaired much more slowly. CPD s at these three sites may partially displace TFIIIA, thereby enabling rapi d repair, However, TFIIIA is not completely displaced during NER, at least at sites outside the ICR, even though the NER complex could be sterically h indered by TFIIIA, Such inefficient repair of transcription factor binding sites could increase mutation frequency in regulatory regions of genes.