90 / 2024-10-21 17:36:28

Steric repulsion introduced by loop constraints modulates the microphase separation of chromatins

steric repulsion,chromatin loop,microphase separation,molecular modeling,deep learning

Within the confines of a densely populated cell nucleus, chromatin undergoes intricate folding, forming loops, domains, and compartments under the governance of topological constraints and phase separation. This coordinated process inevitably introduces interference between different folding strategies. In this study, we model interphase chromatins as block copolymers with hetero-hierarchical loops within a confined system. Employing dissipative particle dynamics simulations and scaling analysis, we aim to explain how the structure and distribution of loop domains modulate the microphase separation of chromatins. Our results highlight the correlation between the microphase separation of the copolymer and the length, heterogeneity, and hierarchically nested levels of the loop domains. This correlation arises from steric repulsion intrinsic to loop domains. The steric repulsion induces variations in chain stiffness (including local orientation correlations and the persistence length), thereby influencing the degree of phase separation. Through simulations of block copolymers with distinct groups of hetero-hierarchical loop anchors, we successfully reproduce changes in phase separation across diverse cell lines, under fixed interaction parameters. These findings, in qualitative alignment with Hi-C data, suggest that the variations of loop constraints alone possess the capacity to regulate higher-order structures and the gene expressions of interphase chromatins. We also introduce a deep learning framework that predicts genome organizations across different cell types and spatial scales. The model enables in silico testing of genetic or epigenetic perturbations on genome architecture. Perturbation results reveal unexpected linear correlations between loop properties and genome organizations at various levels, including insulation degree, compartmentalization, and contact intensity above 10-Mb genomic distance.