Loop extrusion drives very different dynamics for Rouse chains in bulk solutions and at interfaces

¹ Department of Materials Physics, Nagoya University - Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
² PRESTO, Japan Science and Technology Agency (JST) - 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
³ Department of Physics and Mathematics, Aoyama Gakuin University - 5-10-1 Fuchinobe, Chuo- ku, Sagamihara, Kanagawa 252-5158, Japan
⁴ Instituut-Lorentz for Theoretical Physics, Leiden University - Niels Bohrweg 2, Leiden, 2333 CA, The Netherlands

Received: 3 April 2019
Accepted: 20 July 2019

Abstract

The loop extrusion theory predicts that the loops of chromosomes are produced by cohesin molecules that uni-directionally extrude a chromatin fiber. We here use an extension of the Rouse model to predict the chain conformational dynamics driven by the loop extrusion process. Our theory predicts that in a bulk solution, the mean square distance between the starting and ending sites of the loop extrusion process decreases with a constant rate. This is because the tension generated by the loop extrusion process drives the displacement of the starting site towards the ending site. In contrast, when the cohesin is entrapped at an interface, the mean square distance does not decrease until the tension generated by the loop extrusion process arrives at the ending site. This theory highlights the fact that the chain dynamics strongly depends on the mobility of the chain segments bound by cohesin.