Genomewide recruitment analysis of Rpb4, a subunit of polymerase II in Saccharomyces cerevisiae, reveals its involvement in transcription elongation

Eukaryot Cell. 2008 Jun;7(6):1009-18. doi: 10.1128/EC.00057-08. Epub 2008 Apr 25.


The Rpb4/Rpb7 subcomplex of yeast RNA polymerase II (Pol II) has counterparts in all multisubunit RNA polymerases from archaebacteria to higher eukaryotes. The Rpb4/7 subcomplex in Saccharomyces cerevisiae is unique in that it easily dissociates from the core, unlike the case in other organisms. The relative levels of Rpb4 and Rpb7 in yeasts affect the differential gene expression and stress response. Rpb4 is nonessential in S. cerevisiae and affects expression of a small number of genes under normal growth conditions. Here, using a chromatin immunoprecipitation ("ChIP on-chip") technique, we compared genomewide binding of Rpb4 to that of a core Pol II subunit, Rpb3. Our results showed that in spite of being nonessential for survival, Rpb4 was recruited on coding regions of most transcriptionally active genes, similar to the case with the core Pol II subunit, Rpb3, albeit to a lesser extent. The extent of Rpb4 recruitment increased with increasing gene length. We also observed Pol II lacking Rpb4 to be defective in transcribing long, GC-rich transcription units, suggesting a role for Rpb4 in transcription elongation. This role in transcription elongation was supported by the observed 6-azauracil (6AU) sensitivity of the rpb4Delta mutant. Unlike most phenotypes of rpb4Delta, the 6AU sensitivity of the rpb4Delta strain was not rescued by overexpression of RPB7. This report provides the first instance of a distinct role for Rpb4 in transcription, which is independent of its interacting partner, Rpb7.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Composition
  • Chromatin Immunoprecipitation
  • Gene Deletion
  • Genome, Fungal
  • Promoter Regions, Genetic
  • Protein Structure, Tertiary
  • RNA Polymerase II / chemistry*
  • RNA Polymerase II / genetics
  • RNA Polymerase II / metabolism*
  • Saccharomyces cerevisiae
  • Saccharomyces cerevisiae Proteins / chemistry*
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Transcription, Genetic* / drug effects
  • Uracil / analogs & derivatives
  • Uracil / pharmacology


  • Saccharomyces cerevisiae Proteins
  • Uracil
  • RNA Polymerase II
  • RPB3 protein, S cerevisiae
  • RPB4 protein, S cerevisiae
  • azauracil