The interplay between asymmetric and symmetric DNA loop extrusion

Abstract
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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

1. Golfier et al
(2020) Cohesin and condensin extrude DNA loops in a cell cycle-dependent manner
eLife, 53885.

https://cdn.elifesciences.org/articles/53885/elife-53885-data2-v2.zip

Article and author information

Author details

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.

"This ORCID iD identifies the author of this article:" 0000-0001-5478-7425
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.

"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.

Copyright

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.