Alladi Ramakrishnan Hall

Predicting polymer properties of chromatin from contact map data

Ranjith Padinhateeri

IIT Bombay

It is common to model chromatin as a bead spring chain. However, the polymer properties of the chromatin -- its stretching elasticity, bending elasticity, the nature of inter-bead interactions, etc. -- are not well understood. To bridge this gap, we simulated a large ensemble of chromatin configurations at near-nucleosome (200bp) resolution, consistent with recently published contact map data. We then systematically coarse-grained the configurations and predicted quantities essential for the polymer representation of chromatin. Unlike the prevalent notion, we show that coarse-grained chromatin polymer beads should be considered as soft particles that can overlap, and we propose an overlap parameter. We show that accounting for such overlap is necessary to predict 3D distances from simulations in a self-consistent manner.