How enzymatic activity is involved in chromatin organization

Spatial organization of chromatin plays a critical role in genome regulation. Previously, various types of affinity mediators and enzymes have been attributed to regulate spatial organization of chromatin from a thermodynamics perspective. However, at the mechanistic level, enzymes act in their unique ways and perturb the chromatin. Here, we construct a polymer physics model following the mechanistic scheme of Topoisomerase-II, an enzyme resolving topological constraints of chromatin, and investigate how it affects interphase chromatin organization. Our computer simulations demonstrate Topoisomerase-II's ability to phase separate chromatin into eu- and heterochromatic regions with a characteristic wall-like organization of the euchromatic regions. We realized that the ability of the euchromatic regions to cross each other due to enzymatic activity of Topoisomerase-II induces this phase separation. This realization is based on the physical fact that partial absence of self-avoiding interaction can induce phase separation of a system into its self-avoiding and non-self-avoiding parts, which we reveal using a mean-field argument. Furthermore, motivated from recent experimental observations, we extend our model to a bidisperse setting and show that the characteristic features of the enzymatic activity-driven phase separation survive there. The existence of these robust characteristic features, even under the non-localized action of the enzyme, highlights the critical role of enzymatic activity in chromatin organization.

Automated summary

This study constructs a polymer physics model based on the mechanistic scheme of Topoisomerase-II to investigate its effect on the spatial organization of interphase chromatin. The simulations show that Topoisomerase-II can phase separate chromatin into eu- and heterochromatic regions, with a wall-like organization of the euchromatic regions. The ability of the euchromatic regions to cross each other, induced by the enzymatic activity of Topoisomerase-II, leads to this phase separation. The model is extended to a bidisperse setting, and the characteristic features of enzymatic activity-driven phase separation are observed. These findings highlight the critical role of enzymatic activity in chromatin organization.