Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases
Open accessAbstract
RNA polymerase pausing represents an important mechanism of transcriptional regulation. In this study, we use a single-molecule transcription assay to investigate the effect of template base-pair composition on pausing by RNA polymerase II and the evolutionarily distinct mitochondrial polymerase Rpo41. For both enzymes, pauses are shorter and less frequent on GC-rich templates. Significantly, incubation with RNase abolishes the template dependence of pausing. A kinetic model, wherein the secondary structure of the nascent RNA poses an energetic barrier to pausing by impeding backtracking along the template, quantitatively predicts the pause densities and durations observed. The energy barriers extracted from the data correlate well with RNA folding energies obtained from cotranscriptional folding simulations. These results reveal that RNA secondary structures provide a cis -acting mechanism by which sequence modulates transcriptional elongation.
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The role played by GC content in RNA Pol II speed in cellulo might be more complex than anticipated.
“As GC rich templates have been shown to increase RNA pol II speed in vitro (Zamft et al, 2012), the role played by the GC content in RNA pol II speed in cellulo might be more complex than anticipated.”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Zamft et al, 2012
The Experimental Setup reports that higher GC content reduces Pol II pause duration and pause density, which can increase transcriptional throughput in the in vitro experiment. But it also says pause-free velocity is template-independent; the cited finding is reduced pausing, not an increase in Pol II's pause-free speed. The statement about complexity in cellulo is the citing authors’ inference, not a finding attributed to this source. (LLM, conf=0.86)
Experimental — accuracy not yet measuredCo-transcriptional folding of nascent RNA at GC-rich sequences may impose an energy barrier to pausing by impeding backtracking along DNA.
“This is probably due to co‐transcriptional folding of nascent RNA which, at GC‐rich sequences, may impose an energy barrier to pausing by impeding backtracking along the DNA (Zamft et al, 2012).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Zamft et al, 2012
In vitro transcription assays showed that RNA Pol II pauses are shorter and less frequent on GC-rich templates.
“Indeed, in vitro transcription assays showed that RNA Pol II pauses are shorter and less frequent on GC‐rich templates.”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Zamft et al, 2012
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- Authors
- Zamft, B., Bintu, L., Ishibashi, T., & Bustamante, C.
- Affiliations
- University of California, Berkeley (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Bustamante, Carlos
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2012-05-21
- Volume
- 109
- Issue
- 23
- Pages
- 8948-8953
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC3384149
- OpenAlex
- W2129738296
- Cited by
- 117
- References
- 49
- Citations by year
- 2026: 3 · 2025: 8 · 2024: 7 · 2023: 4 · 2022: 8 · 2021: 7 · 2020: 14 · 2019: 9 · 2018: 6 · 2017: 14 · 2016: 9 · 2015: 5 · 2014: 11 · 2013: 9 · 2012: 2
- FWCI
- 3.47
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Rare & Special e-Zone (The Hong Kong University of Science and Technology) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- U.S. Department of Energy (DEAC03-76SF00098)
- National Institutes of Health
- Japan Society for the Promotion of Science
- National Institute of General Medical Sciences (R01-GM0325543)
- Lawrence Berkeley National Laboratory
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- RNA polymerase pausing, RNA polymerase II, transcription elongation, backtracking, ribonuclease, kinetic model, cis-acting regulation
- MeSH terms
- Base Composition, Computer Simulation, Models, Biological, Oligonucleotides, RNA, RNA Polymerase II, DNA-Directed RNA Polymerases, Saccharomyces cerevisiae, Transcription, Genetic, Polymerase Chain Reaction, Myxococcus xanthus, Mitochondrial Proteins, Saccharomyces cerevisiae Proteins, RNA Folding
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