Nonequilibrium Switching of Segmental States Can Influence Compaction of Chromatin

Abstract

Knowledge about the dynamic nature of chromatin organization is essential to understand the regulation of processes like DNA transcription and repair. While most models assume protein organization and chemical states along chromatin as static, experiments have shown that these are dynamic and lead to the switching of chromatin segments between different physical states. To understand the implications of this inherent nonequilibrium switching, we present a diblock copolymer model of chromatin, with switching of its segmental states between two states, mimicking active/repressed or protein unbound/bound states. We show that competition between switching timescale Tt , polymer relaxation timescale τp , and segmental relaxation timescale τs can lead to non-trivial changes in chromatin organization, leading to changes in local compaction and contact probabilities. Radius of gyration of chromatin shows a non-monotonic behavior with Tt. We find that polymers with a small segment length (Ns) exhibit a more compact structure than those with larger segment lengths. Also, we observe that the switching can lead to higher contact probability and better mixing of far-away segments