Local Volume Concentration, Packing Domains and Scaling Properties of Chromatin

TL;DR

The paper introduces the SR-EV model for chromatin structure, capturing its organization as a bi-continuous, corrugated system with dense and dilute regions, aligning well with experimental observations across scales.

Contribution

It presents a novel stochastic model that reproduces chromatin's hierarchical organization and domain features, bridging theoretical predictions with experimental data.

Findings

Model accurately predicts chromatin volume concentration and contact probability.

Chromatin organization is robust to cell type and external perturbations.

The model reveals intrinsic bi-continuous packing domains in chromatin.

Abstract

We propose the Self Returning Excluded Volume (SR-EV) model for the structure of chromatin based on stochastic rules and physical interactions. The SR-EV rules of return generate conformationally-defined domains observed by single cell imaging techniques. From nucleosome to chromosome scales, the model captures the overall chromatin organization as a corrugated system, with dense and dilute regions alternating in a manner that resembles the mixing of two disordered bi-continuous phases. This particular organizational topology is a consequence of the multiplicity of interactions and processes occurring in the nuclei, and mimicked by the proposed return rules. Single configuration properties and ensemble averages show a robust agreement between theoretical and experimental results including chromatin volume concentration, contact probability, packing domain identification and size characterization, and packing scaling behavior. Model and experimental results suggest that there is an inherent chromatin organization regardless of the cell character and resistant to an external forcing such as Rad21 degradation.