Fluidification of Entangled Polymers by Loop Extrusion

Loop extrusion is one of the main processes shaping chromosome organisation across the cell cycle, yet its role in regulating DNA entanglement and nucleoplasm viscoelasticity remains overlooked. We simulate entangled solutions of linear polymers under the action of generic Loop Extruding Factors (LE...

Full description

Saved in:
Bibliographic Details
Published in:arXiv.org 2024-08
Main Authors: Conforto, Filippo, Yair Augusto Gutierrez Fosado, Michieletto, Davide
Format: Article
Language:English
Subjects:
Constraint modelling
Deoxyribonucleic acid
DNA
Entanglement
Extrusion
Polymers
Viscoelasticity
Viscosity
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Loop extrusion is one of the main processes shaping chromosome organisation across the cell cycle, yet its role in regulating DNA entanglement and nucleoplasm viscoelasticity remains overlooked. We simulate entangled solutions of linear polymers under the action of generic Loop Extruding Factors (LEF) with a model that fully accounts for topological constraints and LEF-DNA uncrossability. We discover that extrusion drives the formation of bottle-brush-like structures which significantly lower the entanglement and effective viscosity of the system through an active fluidification mechanism. Interestingly, this fluidification displays an optimum at one LEF every 300-3000 basepairs. In marked contrast with entangled linear chains, the viscosity of extruded chains scales linearly with polymer length, yielding up to 1000-fold fluidification. Our results illuminate how loop extrusion contributes to actively modulate genome entanglement and viscoelasticity in vivo.
ISSN:2331-8422
DOI:10.48550/arxiv.2401.17232