Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast
Open accessAbstract
RNA Polymerase II pauses and backtracks during transcription, with many consequences for gene expression and cellular physiology. Here, we show that the energy required to melt double-stranded nucleic acids in the transcription bubble predicts pausing in Saccharomyces cerevisiae far more accurately than nucleosome roadblocks do. In addition, the same energy difference also determines when the RNA polymerase backtracks instead of continuing to move forward. This data-driven model corroborates-in a genome wide and quantitative manner-previous evidence that sequence-dependent thermodynamic features of nucleic acids influence both transcriptional pausing and backtracking.
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In budding yeast, RNA Pol II pauses correlate with the stability of the RNA:DNA hybrid, rather than the stability of the DNA:DNA duplex.
“Finally, in budding yeast, RNA Pol II pauses were found to correlate with the stability of the RNA:DNA hybrid, rather than the stability of the DNA:DNA duplex (Lukačišin et al, 2017).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Lukačišin et al, 2017
The Results section says pausing is associated with the difference between RNA:DNA and DNA:DNA basepairing energies, not RNA:DNA stability rather than DNA:DNA stability. The Discussion likewise says both stabilities must be considered comparatively. Page numbers are unavailable in our copy. (LLM, conf=0.88)
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RNA polymerase II speed: a key player in controlling and adapting transcriptome composition
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Auboeuf, D. (2020) · Life · doi:10.3390/life10020007 · Cited by 21 · see citing works
- Authors
- Lukačišin, M., Landon, M., & Jajoo, R.
- Affiliations
- Harvard University (US)
- Corresponding author
- Jajoo, Rishi
- Venue
- PLOS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2017-03-16
- Volume
- 12
- Issue
- 3
- Pages
- e0174066
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC5354634
- OpenAlex
- W2596014456
- Cited by
- 4
- References
- 42
- Citations by year
- 2021: 1 · 2020: 2 · 2019: 1
- FWCI
- 0.34
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS ONE (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- Foundation for the National Institutes of Health (GM08017)
- Jane Coffin Childs Memorial Fund for Medical Research
- Topics
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- transcriptional pausing, nucleic acid thermodynamics, transcription bubble, Saccharomyces cerevisiae, genome-wide analysis
- MeSH terms
- Genes, Fungal, Nucleic Acids, Saccharomyces cerevisiae, Thermodynamics, Transcription, Genetic, Base Pairing
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