Pause sequences facilitate entry into long-lived paused states by reducing RNA polymerase transcription rates
Abstract
Transcription by RNA polymerase (RNAP) is interspersed with sequence-dependent pausing. The processes through which paused states are accessed and stabilized occur at spatiotemporal scales beyond the resolution of previous methods, and are poorly understood. Here, we combine high-resolution optical trapping with improved data analysis methods to investigate the formation of paused states at enhanced temporal resolution. We find that pause sites reduce the forward transcription rate of nearly all RNAP molecules, rather than just affecting the subset of molecules that enter long-lived pauses. We propose that the reduced rates at pause sites allow time for the elongation complex to undergo conformational changes required to enter long-lived pauses. We also find that backtracking occurs stepwise, with states backtracked by at most one base pair forming quickly, and further backtracking occurring slowly. Finally, we find that nascent RNA structures act as modulators that either enhance or attenuate pausing, depending on the sequence context.
- Authors:
-
[2];
[3];
[4];
[5]
- Univ. of California, Berkeley, CA (United States). California Institute for Quantitative Biosciences
- Univ. of California, Berkeley, CA (United States). Dept. of Physics
- Rutgers Univ., Piscataway, NJ (United States). Dept. of Chemistry and Waksman Institute; Harvard Medical School, Boston, MA (United States). Dept. of Biological Chemistry and Molecular Pharmacology
- Rutgers Univ., Piscataway, NJ (United States). Dept. of Chemistry and Waksman Institute
- Univ. of California, Berkeley, CA (United States). California Institute for Quantitative Biosciences; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Univ. of California, Berkeley, CA (United States). Dept. of Molecular and Cell Biology, and Kavli Energy Nanoscience Institute
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1624110
- Grant/Contract Number:
- AC02-05CH11231; R01GM032543; R01GM071552; GM041376
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Science & Technology - Other Topics
Citation Formats
Gabizon, Ronen, Lee, Antony, Vahedian-Movahed, Hanif, Ebright, Richard H., and Bustamante, Carlos J. Pause sequences facilitate entry into long-lived paused states by reducing RNA polymerase transcription rates. United States: N. p., 2018.
Web. doi:10.1038/s41467-018-05344-9.
Gabizon, Ronen, Lee, Antony, Vahedian-Movahed, Hanif, Ebright, Richard H., & Bustamante, Carlos J. Pause sequences facilitate entry into long-lived paused states by reducing RNA polymerase transcription rates. United States. https://doi.org/10.1038/s41467-018-05344-9
Gabizon, Ronen, Lee, Antony, Vahedian-Movahed, Hanif, Ebright, Richard H., and Bustamante, Carlos J. Thu .
"Pause sequences facilitate entry into long-lived paused states by reducing RNA polymerase transcription rates". United States. https://doi.org/10.1038/s41467-018-05344-9. https://www.osti.gov/servlets/purl/1624110.
@article{osti_1624110,
title = {Pause sequences facilitate entry into long-lived paused states by reducing RNA polymerase transcription rates},
author = {Gabizon, Ronen and Lee, Antony and Vahedian-Movahed, Hanif and Ebright, Richard H. and Bustamante, Carlos J.},
abstractNote = {Transcription by RNA polymerase (RNAP) is interspersed with sequence-dependent pausing. The processes through which paused states are accessed and stabilized occur at spatiotemporal scales beyond the resolution of previous methods, and are poorly understood. Here, we combine high-resolution optical trapping with improved data analysis methods to investigate the formation of paused states at enhanced temporal resolution. We find that pause sites reduce the forward transcription rate of nearly all RNAP molecules, rather than just affecting the subset of molecules that enter long-lived pauses. We propose that the reduced rates at pause sites allow time for the elongation complex to undergo conformational changes required to enter long-lived pauses. We also find that backtracking occurs stepwise, with states backtracked by at most one base pair forming quickly, and further backtracking occurring slowly. Finally, we find that nascent RNA structures act as modulators that either enhance or attenuate pausing, depending on the sequence context.},
doi = {10.1038/s41467-018-05344-9},
journal = {Nature Communications},
number = 1,
volume = 9,
place = {United States},
year = {Thu Jul 26 00:00:00 EDT 2018},
month = {Thu Jul 26 00:00:00 EDT 2018}
}
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