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Genome organization via loop extrusion, insights from polymer physics models

Surya Ghosh 1, 2 Daniel Jost 1, 3
1 TIMC-BCM - Biologie Computationnelle et Mathématique
TIMC - Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525
Abstract : Understanding how genomes fold and organize is one of the main challenges in modern biology. Recent high-throughput techniques like Hi-C, in combination with cutting-edge polymer physics models, have provided access to precise information on 3D chromosome folding to decipher the mechanisms driving such multi-scale organization. In particular, Structural Maintenance of Chromosomes (SMC) proteins play an important role in the local structuration of chromatin, putatively via a loop extrusion process. Here, we review the different polymer physics models that investigate the role of SMCs in the formation of topologically-associated domains (TADs) during interphase via the formation of dynamic loops. We describe the main physical ingredients, compare them and discuss their relevance against experimental observations. Summary key points • SMC-mediated chromatin loops may be formed via a loop extrusion process. • Polymer physics models have been instrumental in studying loop extrusion. • Loop extrusion may be driven by: directed translocation of active motors, diffusion of slip-links, transcription-induced supercoiling. • We describe the main physical ingredients and parameters to better understand and compare these three classes of models.
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https://hal.archives-ouvertes.fr/hal-03012763
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Soumis le : mercredi 18 novembre 2020 - 17:26:15
Dernière modification le : mercredi 9 décembre 2020 - 03:29:10
Archivage à long terme le : : vendredi 19 février 2021 - 20:31:55

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Surya Ghosh, Daniel Jost. Genome organization via loop extrusion, insights from polymer physics models. Briefings in Functional Genomics and Proteomics, Oxford University Press, 2020, 19 (2), pp.119-127. ⟨10.1093/bfgp/elz023⟩. ⟨hal-03012763⟩

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