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Pause sequences facilitate entry into long-lived paused states by reducing RNA polymerase transcription rates

Author

Listed:
  • Ronen Gabizon

    (University of California)

  • Antony Lee

    (University of California)

  • Hanif Vahedian-Movahed

    (Rutgers University
    Harvard Medical School)

  • Richard H. Ebright

    (Rutgers University)

  • Carlos J. Bustamante

    (University of California
    University of California
    University of California)

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.

Suggested Citation

  • Ronen Gabizon & Antony Lee & Hanif Vahedian-Movahed & Richard H. Ebright & Carlos J. Bustamante, 2018. "Pause sequences facilitate entry into long-lived paused states by reducing RNA polymerase transcription rates," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
  • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-05344-9
    DOI: 10.1038/s41467-018-05344-9
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    Cited by:

    1. Jin Qian & Allison Cartee & Wenxuan Xu & Yan Yan & Bing Wang & Irina Artsimovitch & David Dunlap & Laura Finzi, 2024. "Reciprocating RNA Polymerase batters through roadblocks," Nature Communications, Nature, vol. 15(1), pages 1-11, December.

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