Predicting scale-dependent chromatin polymer properties from systematic coarse-graining.

ABSTRACT: Simulating chromatin is crucial for predicting genome organization and dynamics. Although coarse-grained bead-spring polymer models are commonly used to describe chromatin, the relevant bead dimensions, elastic properties, and the nature of inter-bead potentials are unknown. Using nucleosome-resolution contact probability (Micro-C) data, we systematically coarse-grain chromatin and predict quantities essential for polymer representation of chromatin. We compute size distributions of chromatin beads for different coarse-graining scales, quantify fluctuations and distributions of bond lengths between neighboring regions, and derive effective spring constant values. Unlike the prevalent notion, our findings argue that coarse-grained chromatin beads must be considered as soft particles that ca

SUBMITTER: Kadam S 

PROVIDER: S-EPMC10336007 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature