1. Chromosomes and Gene Expression
  2. Physics of Living Systems
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The interplay between asymmetric and symmetric DNA loop extrusion

  1. Edward J Banigan  Is a corresponding author
  2. Leonid A Mirny  Is a corresponding author
  1. Massachusetts Institute of Technology, United States
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Cite this article as: eLife 2020;9:e63528 doi: 10.7554/eLife.63528

Abstract

Chromosome compaction is essential for reliable transmission of genetic information. Experiments suggest that ~ 1000-fold compaction is driven by condensin complexes that extrude chromatin loops, i.e., progressively collect chromatin fiber from one or both sides of the complex to form a growing loop. Theory indicates that symmetric two-sided loop extrusion can achieve such compaction, but recent single-molecule studies (Golfier et al., 2020) observed diverse dynamics of condensins that perform one-sided, symmetric two-sided, and asymmetric two-sided extrusion. We use simulations and theory to determine how these molecular properties lead to chromosome compaction. High compaction can be achieved if even a small fraction of condensins have two essential properties: a long residence time and the ability to perform two-sided (not necessarily symmetric) extrusion. In mixtures of condensins I and II, coupling two-sided extrusion and stable chromatin binding by condensin II promotes compaction. These results provide missing connections between single-molecule observations and chromosome-scale organization.

Data availability

Software used to perform simulations is publicly and freely available at https://github.com/mirnylab/one_sided_extrusion/tree/master/mitotic. Data analyzed from single-molecule experiments was previously published as part of Golfier et al. eLife 9:e53885 (2020).

The following previously published data sets were used

Article and author information

Author details

  1. Edward J Banigan

    Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, United States
    For correspondence
    ebanigan@mit.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5478-7425
  2. Leonid A Mirny

    Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, United States
    For correspondence
    lmirny@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0785-5410

Funding

National Institutes of Health (U54DK107980)

  • Edward J Banigan
  • Leonid A Mirny

National Institutes of Health (U54CA193419)

  • Edward J Banigan
  • Leonid A Mirny

National Institutes of Health (GM114190)

  • Edward J Banigan
  • Leonid A Mirny

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Adèle L Marston, University of Edinburgh, United Kingdom

Publication history

  1. Received: October 1, 2020
  2. Accepted: November 30, 2020
  3. Accepted Manuscript published: December 9, 2020 (version 1)
  4. Version of Record published: January 8, 2021 (version 2)

Copyright

© 2020, Banigan & Mirny

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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