Splicing-Dependent RNA Polymerase Pausing in Yeast
Open accessAbstract
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.
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RNA Pol II ChIP on chip and ChIP-seq data showed that RNA Pol II accumulates on exons in yeast and human, suggesting that RNA Pol II pauses over exons.
“Indeed, RNA Pol II ChIP on chip and ChIP‐seq data showed that RNA Pol II accumulates on exons in yeast and human, suggesting that RNA Pol II pauses over exons (Brodsky et al, 2005; Schwartz et al, 2009; Alexander et al, 2010; Carrillo Oesterreich et al, 2010; Kwak et al, 2013; Mayer et al, 2015; Nojima et al, 2015; Harlen et al, 2016).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Alexander et al, 2010
The Results and Discussion report RNAPII accumulation and brief pausing near 3′ splice sites in yeast, in regions that overlap the start of an exon. The Discussion also reports exon-associated accumulation in humans. But this paper’s own experiments used ChIP-qPCR, not ChIP-on-chip or ChIP-seq, and its yeast finding is localized near 3′ splice sites rather than established broadly across exons. No page numbers are supplied in our copy. (LLM, conf=0.88)
Experimental — accuracy not yet measuredTranscriptional pausing over the 3′ splice site is splicing-dependent, since it was lost upon introduction of a mutation in the 5′ or 3′ splice sites.
“This transcriptional pausing over the 3′ splice site is splicing‐dependent, since it was lost upon introduction of a mutation in the 5′ or 3′ splice sites (Alexander et al, 2010; Chathoth et al, 2014).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Alexander et al, 2010
A mutation in the branch site of the intron inhibited RNA Pol II pausing, which was restored by introducing a complementary mutation in the U2 snRNA.
“A mutation in the branch site of the intron also inhibited this RNA Pol II pausing, which was restored by introducing a complementary mutation in the U2 snRNA (Alexander et al, 2010).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Alexander et al, 2010
In budding yeast, RNA Pol II ChIP qPCR allowed observation of RNA Pol II pausing at the 3′ splice site.
“Furthermore, in budding yeast, RNA Pol II ChIP qPCR allowed observation of RNA Pol II pausing at the 3′ splice site (Alexander et al, 2010).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Alexander et al, 2010
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References 49 · Cited by 251
- Authors
- Alexander, R. D., Innocente, S. A., Barrass, J. D., & Beggs, J. D.
- Affiliations
- Wellcome Centre for Cell Biology (GB)
- Corresponding author
- Beggs, Jean D.
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2010-11
- Volume
- 40
- Issue
- 4
- Pages
- 582-593
- ISSN
- 1097-2765 (ISSN-L)
- PMC
- PMC3000496
- OpenAlex
- W2153849837
- Cited by
- 251
- References
- 49
- Citations by year
- 2026: 2 · 2025: 4 · 2024: 9 · 2023: 17 · 2022: 7 · 2021: 14 · 2020: 13 · 2019: 18 · 2018: 7 · 2017: 21 · 2016: 25 · 2015: 12 · 2014: 18 · 2013: 20 · 2012: 25
- FWCI
- 10.73
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Molecular Cell (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
- Funders
- Wellcome Trust (087551)
- European Commission
- Darwin Trust of Edinburgh
- Directorate for Biological Sciences
- Biotechnology and Biological Sciences Research Council (BB/D019621/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- RNA polymerase pausing, co-transcriptional splicing, pre-mRNA splicing, introns, 3' splice site, C-terminal domain, Saccharomyces cerevisiae, transcription kinetics
- MeSH terms
- Genes, Fungal, Introns, Phosphorylation, RNA Polymerase II, RNA Splicing, Saccharomyces cerevisiae, Transcription, Genetic, Protein Structure, Tertiary, Genes, Reporter, RNA Splice Sites, Saccharomyces cerevisiae Proteins
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