The DOI matches its Crossref record; 49 of the 49 references it cites were found in a registry or an index.
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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“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
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“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
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“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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Cites
Entropic Elasticity of λ-Phage DNA
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Self-citationA Slow RNA Polymerase II Affects Alternative Splicing In Vivo
de la Mata, M., Alonso, C. R., Kadener, S., Fededa, J. P., Blaustein, M., Pelisch, F., Cramer, P., Bentley, D., & Kornblihtt, A. R. (2003) · Molecular Cell · doi:10.1016/j.molcel.2003.08.001 · Cited by 683
Transcription Against an Applied Force
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Base composition bias might result from competition for metabolic resources
Rocha, E. P. C., & Danchin, A. (2002) · Trends in Genetics · doi:10.1016/s0168-9525(02)02690-2 · Cited by 481
High Guanine and Cytosine Content Increases mRNA Levels in Mammalian Cells
Kudla, G., Lipinski, L., Caffin, F., Helwak, A., & Zylicz, M. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040180 · Cited by 476
Evolution of multisubunit RNA polymerases in the three domains of life
Werner, F., & Grohmann, D. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2507 · Cited by 431
Yeast mitochondrial RNA polymerase is homologous to those encoded by bacteriophages T3 and T7.
Masters, B. S., Stohl, L. L., & Clayton, D. A. (1987) · Cell · doi:10.1016/0092-8674(87)90013-4 · Cited by 410
Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals
Artsimovitch, I., & Landick, R. C. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.13.7090 · Cited by 405
Structural basis of RNA polymerase II backtracking, arrest and reactivation
Cheung, A. C. M., & Cramer, P. (2011) · Nature · doi:10.1038/nature09785 · Cited by 373
Backtracking by single RNA polymerase molecules observed at near-base-pair resolution
Shaevitz, J. W., Abbondanzieri, E. A., Landick, R. C., & Block, S. M. (2003) · Nature · doi:10.1038/nature02191 · Cited by 372
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Coupling mRNA processing with transcription in time and space
Bentley, D. L. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3662 · Cited by 828
Zhou, Z., Dang, Y., Zhou, M., Li, L., Yu, C., Fu, J., Chen, S., & Liu, Y. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1606724113 · Cited by 441
Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing
Saldi, T. K., Cortázar, M. A., Sheridan, R. M., & Bentley, D. L. (2016) · Journal of Molecular Biology · doi:10.1016/j.jmb.2016.04.017 · Cited by 266
Causes and consequences of RNA polymerase II stalling during transcript elongation
González, M. N., Blears, D., & Svejstrup, J. Q. (2020) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-020-00308-8 · Cited by 262
Optical Tweezers Analysis of DNA–Protein Complexes
Heller, I., Hoekstra, T. P., King, G. A., Peterman, E. J. G., & Wuite, G. J. L. (2014) · Chemical Reviews · doi:10.1021/cr4003006 · Cited by 212
Metadata
- 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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