Uniform transitions of the general RNA polymerase II transcription complex

Nat Struct Mol Biol. 2010 Oct;17(10):1272-8. doi: 10.1038/nsmb.1903. Epub 2010 Sep 5.


We present genome-wide occupancy profiles for RNA polymerase (Pol) II, its phosphorylated forms and transcription factors in proliferating yeast. Pol II exchanges initiation factors for elongation factors during a 5' transition that is completed 150 nucleotides downstream of the transcription start site (TSS). The resulting elongation complex is composed of all the elongation factors and shows high levels of Ser7 and Ser5 phosphorylation on the C-terminal repeat domain (CTD) of Pol II. Ser2 phosphorylation levels increase until 600-1,000 nucleotides downstream of the TSS and do not correlate with recruitment of Spt6 and Pcf11, which bind the Ser2-phosphorylated CTD in vitro. This indicates CTD-independent recruitment mechanisms and CTD masking in vivo. Elongation complexes are productive and disassemble in a two-step 3' transition. Paf1, Spt16 (part of the FACT complex), and the CTD kinases Bur1 and Ctk1 exit upstream of the polyadenylation site, whereas Spt4, Spt5, Spt6, Spn1 (also called Iws1) and Elf1 exit downstream. Transitions are uniform and independent of gene length, type and expression.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Division
  • Chromatin / genetics
  • Chromatin / metabolism
  • Chromatin Immunoprecipitation
  • Chromatography, Affinity
  • Genes, Fungal*
  • Genome-Wide Association Study
  • Macromolecular Substances
  • Models, Genetic*
  • Phosphorylation
  • Phosphoserine / metabolism
  • Protein Kinases / metabolism
  • Protein Processing, Post-Translational
  • RNA Polymerase II / metabolism*
  • RNA, Fungal / metabolism
  • RNA, Messenger / metabolism
  • Saccharomyces cerevisiae / enzymology
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Transcription Factors, TFII / metabolism
  • Transcription, Genetic*
  • Transcriptional Elongation Factors / metabolism
  • mRNA Cleavage and Polyadenylation Factors / metabolism


  • Chromatin
  • Macromolecular Substances
  • PCF11 protein, S cerevisiae
  • RNA, Fungal
  • RNA, Messenger
  • Saccharomyces cerevisiae Proteins
  • Transcription Factors, TFII
  • Transcriptional Elongation Factors
  • mRNA Cleavage and Polyadenylation Factors
  • Phosphoserine
  • Protein Kinases
  • carboxy-terminal domain kinase
  • RNA Polymerase II
  • RPB3 protein, S cerevisiae