Splicing-Dependent RNA Polymerase Pausing in Yeast

Ross D. Alexander, Steven A. Innocente, J. David Barrass, Jean D. Beggs

Research output: Contribution to journalArticlepeer-review

204 Citations (Scopus)
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In eukaryotic cells, there is evidence for functional coupling between transcription and processing of pre-mRNAs. To better understand this coupling, we performed a high-resolution kinetic analysis of transcription and splicing in budding yeast. This revealed that shortly after induction of transcription, RNA polymerase accumulates transiently around the 3' end of the intron on two reporter genes. This apparent transcriptional pause coincides with splicing factor recruitment and with the first detection of spliced mRNA and is repeated periodically thereafter. Pausing requires productive splicing, as it is lost upon mutation of the intron and restored by suppressing the splicing defect. The carboxy-terminal domain of the paused polymerase large subunit is hyperphosphorylated on serine 5, and phosphorylation of serine 2 is first detected here. Phosphorylated polymerase also accumulates around the 3' splice sites of constitutively expressed, endogenous yeast genes. We propose that transcriptional pausing is imposed by a checkpoint associated with cotranscriptional splicing.

Original languageEnglish
Pages (from-to)582-593
Number of pages12
JournalMolecular Cell
Issue number4
Publication statusPublished - 24 Nov 2010


  • Genes, Fungal/genetics
  • Genes, Reporter/genetics
  • Introns/genetics
  • Phosphorylation
  • Protein Structure, Tertiary
  • RNA Polymerase II/chemistry
  • RNA Splice Sites/genetics
  • RNA Splicing/genetics
  • Saccharomyces cerevisiae/enzymology
  • Saccharomyces cerevisiae Proteins/genetics
  • Transcription, Genetic


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