  Chromatin is known to be organized 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 them to predict chromatin
organization and dynamics. Taking two domains on the human chromosome as
examples, we investigate its 3D organization, size/shape fluctuations, and
dynamics of different segments within a domain, accounting for hydrodynamic
effects. Considering different cell types, we quantify changes in interaction
strengths and chromatin shape fluctuations in different epigenetic states.
Perturbing the interaction strengths systematically, we further investigate how
epigenetic-like changes can alter the spatio-temporal nature of the domains.
Our results show that heterogeneous weak interactions are crucial in
determining the organization of the domains. Computing effective stiffness and
relaxation times, we investigate how perturbations in interactions affect the
solid-like and liquid-like nature of chromatin domains. 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.
