Genome-wide mapping of yeast RNA polymerase II termination

PLoS Genet. 2014 Oct 9;10(10):e1004632. doi: 10.1371/journal.pgen.1004632. eCollection 2014 Oct.


Yeast RNA polymerase II (Pol II) terminates transcription of coding transcripts through the polyadenylation (pA) pathway and non-coding transcripts through the non-polyadenylation (non-pA) pathway. We have used PAR-CLIP to map the position of Pol II genome-wide in living yeast cells after depletion of components of either the pA or non-pA termination complexes. We show here that Ysh1, responsible for cleavage at the pA site, is required for efficient removal of Pol II from the template. Depletion of Ysh1 from the nucleus does not, however, lead to readthrough transcription. In contrast, depletion of the termination factor Nrd1 leads to widespread runaway elongation of non-pA transcripts. Depletion of Sen1 also leads to readthrough at non-pA terminators, but in contrast to Nrd1, this readthrough is less processive, or more susceptible to pausing. The data presented here provide delineation of in vivo Pol II termination regions and highlight differences in the sequences that signal termination of different classes of non-pA transcripts.

Publication types

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

MeSH terms

  • DNA Helicases / genetics
  • DNA Helicases / metabolism
  • Genome, Fungal
  • RNA Helicases / genetics
  • RNA Helicases / metabolism
  • RNA Polymerase II / genetics*
  • RNA Polymerase II / metabolism*
  • RNA Stability
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism
  • mRNA Cleavage and Polyadenylation Factors / genetics
  • mRNA Cleavage and Polyadenylation Factors / metabolism


  • NRD1 protein, S cerevisiae
  • RNA-Binding Proteins
  • Saccharomyces cerevisiae Proteins
  • YSH1 protein, S cerevisiae
  • mRNA Cleavage and Polyadenylation Factors
  • RNA Polymerase II
  • SEN1 protein, S cerevisiae
  • DNA Helicases
  • RNA Helicases

Associated data

  • GEO/GSE56435