Active Nucleosome Sliding, Eviction, and Reassembly Dynamics Can Regulate Chromatin Condensate Organization

Abstract

At the nucleosome scale, chromatin is an actively remodeled polymeric system whose organization is continuously reshaped by ATP-dependent remodelers that slide, evict, and reassemble nucleosomes along DNA. However, how the local structural rearrangements generated by such remodeling events influence condensate-scale organization and dynamics remains poorly understood. Here, we introduce a coarse-grained model of chromatin condensates composed of short polymers that explicitly incorporates enzyme-assisted nucleosome sliding together with nucleosome eviction and reassembly, coupled to Langevin relaxation dynamics. By explicitly accounting for the DNA length sequestered within individual nucleosomes, the model captures the steric constraints and local conformational relaxation that accompany nucleosome sliding, eviction, and reassembly. We find that nucleosome activity drives condensate swelling, enhances condensate-size fluctuations, and promotes internal mixing. In condensates containing both active and passive polymers, differences in nucleosome activity further induce radial segregation, with active polymers enriched near the periphery and passive polymers concentrated in the interior. These results identify active nucleosome remodeling as a physical mechanism for regulating chromatin condensate structure, fluidity, and spatial organization.