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The in vivo measurement of replication fork velocity and pausing by lag-time analysis

Author

Listed:
  • Dean Huang

    (University of Washington)

  • Anna E. Johnson

    (Vanderbilt University
    Vanderbilt University Medical Center)

  • Brandon S. Sim

    (University of Washington)

  • Teresa W. Lo

    (University of Washington)

  • Houra Merrikh

    (Vanderbilt University
    Vanderbilt University Medical Center)

  • Paul A. Wiggins

    (University of Washington
    University of Washington
    University of Washington)

Abstract

An important step towards understanding the mechanistic basis of the central dogma is the quantitative characterization of the dynamics of nucleic-acid-bound molecular motors in the context of the living cell. To capture these dynamics, we develop lag-time analysis, a method for measuring in vivo dynamics. Using this approach, we provide quantitative locus-specific measurements of fork velocity, in units of kilobases per second, as well as replisome pause durations, some with the precision of seconds. The measured fork velocity is observed to be both locus and time dependent, even in wild-type cells. In this work, we quantitatively characterize known phenomena, detect brief, locus-specific pauses at ribosomal DNA loci in wild-type cells, and observe temporal fork velocity oscillations in three highly-divergent bacterial species.

Suggested Citation

  • Dean Huang & Anna E. Johnson & Brandon S. Sim & Teresa W. Lo & Houra Merrikh & Paul A. Wiggins, 2023. "The in vivo measurement of replication fork velocity and pausing by lag-time analysis," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37456-2
    DOI: 10.1038/s41467-023-37456-2
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    References listed on IDEAS

    as
    1. Richard T. Pomerantz & Mike O’Donnell, 2008. "The replisome uses mRNA as a primer after colliding with RNA polymerase," Nature, Nature, vol. 456(7223), pages 762-766, December.
    2. Christian J. Rudolph & Amy L. Upton & Anna Stockum & Conrad A. Nieduszynski & Robert G. Lloyd, 2013. "Avoiding chromosome pathology when replication forks collide," Nature, Nature, vol. 500(7464), pages 608-611, August.
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    Cited by:

    1. Chen Zhang & Asha Mary Joseph & Laurent Casini & Justine Collier & Anjana Badrinarayanan & Suliana Manley, 2024. "Chromosome organization shapes replisome dynamics in Caulobacter crescentus," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

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