Near-atomistic modeling reconciles difference between irregular and regular chromatin

Abstract

Three-dimensional genome organization lays the foundation for biological processes involving gene expression and epigenetic regulation. Nevertheless, it is unclear how chromatin is structured at the fundamental level. There is a heated debate over the existence of chromatin fibril structure and its regulation by multiple chromatin factors. Controversy also remains on the sol-gel properties of chromatin subject to different environmental conditions. Here, building upon our recently developed near-atomistic chromatin model, we combined exhaustive molecular dynamics simulations with deep-learning techniques to study the detailed folding landscape of a string of nucleosomes.