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Annual Review of Physical Chemistry

Volume 76, 2025

Organization and Dynamics of Chromosomes

  • D. Thirumalai1,2, Guang Shi1, Sucheol Shin1 and Changbong Hyeon3
  • 1Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA; email: [email protected] 2Department of Physics, The University of Texas at Austin, Austin, Texas, USA 3School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea
  • Vol. 76:565-588 (Volume publication date April 2025)
  • First published as a Review in Advance on February 19, 2025
  • Copyright © 2025 by the author(s).
    This work is licensed under a Creative Commons Attribution 4.0 International License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. See credit lines of images or other third-party material in this article for license information.

Abstract

How long thread-like eukaryotic chromosomes fit tidily in the small volume of the nucleus without significant entanglement is just beginning to be understood, thanks to major advances in experimental techniques. Several polymer models, which reproduce contact maps that measure the probabilities that two loci are in spatial contact, have predicted the 3D structures of interphase chromosomes. Data-driven approaches, using contact maps as input, predict that mitotic helical chromosomes are characterized by a switch in handedness, referred to as perversion. By using experimentally derived effective interactions between chromatin loci in simulations, structures of conventional and inverted nuclei have been accurately predicted. Polymer theory and simulations show that the dynamics of individual loci in chromatin exhibit subdiffusive behavior but the diffusion exponents are broadly distributed, which accords well with experiments. Although coarse-grained models are successful, many challenging problems remain, which require the creation of new experimental and computational tools to understand genome biology.

Keyword(s): chromosome statistical potential, contact maps, distance maps, glass-like dynamics, polymer models, random helix perversion, structural heterogeneity
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2025-04-21
2025-06-20
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Organization and Dynamics of Chromosomes
Annual Review of Physical Chemistry 76, 565 (2025); https://doi.org/10.1146/annurev-physchem-082423-024123
/content/journals/10.1146/annurev-physchem-082423-024123
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