Genome-wide role of Rad26 in promoting transcription-coupled nucleotide excision repair in yeast chromatin

Proc Natl Acad Sci U S A. 2020 Aug 4;117(31):18608-18616. doi: 10.1073/pnas.2003868117. Epub 2020 Jul 20.


Transcription-coupled nucleotide excision repair (TC-NER) is an important DNA repair mechanism that removes RNA polymerase (RNAP)-stalling DNA damage from the transcribed strand (TS) of active genes. TC-NER deficiency in humans is associated with the severe neurological disorder Cockayne syndrome. Initiation of TC-NER is mediated by specific factors such as the human Cockayne syndrome group B (CSB) protein or its yeast homolog Rad26. However, the genome-wide role of CSB/Rad26 in TC-NER, particularly in the context of the chromatin organization, is unclear. Here, we used single-nucleotide resolution UV damage mapping data to show that Rad26 and its ATPase activity is critical for TC-NER downstream of the first (+1) nucleosome in gene coding regions. However, TC-NER on the transcription start site (TSS)-proximal half of the +1 nucleosome is largely independent of Rad26, likely due to high occupancy of the transcription initiation/repair factor TFIIH in this nucleosome. Downstream of the +1 nucleosome, the combination of low TFIIH occupancy and high occupancy of the transcription elongation factor Spt4/Spt5 suppresses TC-NER in Rad26-deficient cells. We show that deletion of SPT4 significantly restores TC-NER across the genome in a rad26∆ mutant, particularly in the downstream nucleosomes. These data demonstrate that the requirement for Rad26 in TC-NER is modulated by the distribution of TFIIH and Spt4/Spt5 in transcribed chromatin and Rad26 mainly functions downstream of the +1 nucleosome to remove TC-NER suppression by Spt4/Spt5.

Keywords: Cockayne syndrome; DNA repair; Spt4/Spt5; TFIIH; nucleosome.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adenosine Triphosphatases* / genetics
  • Adenosine Triphosphatases* / metabolism
  • DNA Helicases
  • DNA Repair / genetics*
  • DNA Repair Enzymes
  • Genome, Fungal / genetics
  • Humans
  • Nucleosomes / genetics*
  • Nucleosomes / metabolism
  • Poly-ADP-Ribose Binding Proteins
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins* / genetics
  • Saccharomyces cerevisiae Proteins* / metabolism


  • Nucleosomes
  • Poly-ADP-Ribose Binding Proteins
  • Saccharomyces cerevisiae Proteins
  • Adenosine Triphosphatases
  • RAD26 protein, S cerevisiae
  • DNA Helicases
  • ERCC6 protein, human
  • DNA Repair Enzymes