Spatiotemporal organization of chromatin domains: role of interaction energy and polymer entropy

Chromatin is known to be organised into multiple domains of varying sizes and compaction. While these domains are often imagined as static structures, they are highly dynamic and show cell-to-cell variability. Since processes such as gene regulation and DNA replication occur in the context of these domains, it is important to understand their organization, fluctuation and dynamics. To simulate chromatin domains, one requires knowledge of interaction strengths among chromatin segments. Here, we derive interaction strength parameters from experimentally known contact maps, and use it to predict chromatin organization and dynamics. Taking -globin domain as an example, we investigate its 3D organization, size/shape fluctuations, and dynamics of different segments within a domain, accounting for hydrodynamic effects. Perturbing the interaction strengths systematically, we quantify how epigenetic changes can alter the spatio-temporal nature of the domains. Computing distance-distributions and relaxation times for different chromatin states, we show that weak and strong interactions cooperatively determine the organization of the domains and how the solid-like and liquid-like nature of chromatin gets altered as we vary epigenetic states. Quantifying dynamics of chromatin segments within a domain, we show how the competition between polymer entropy and interaction energy influence the timescales of loop formation and maintenance of stable loops. PACS numbers: