Nucleosome breathing facilitates cooperative binding of pluripotency factors Sox2 and Oct4 to DNA.

ABSTRACT: Critical lineage commitment events are staged by multiple transcription factors (TFs) binding to their cognate motifs, often positioned at nucleosome-enriched regions of chromatin. The underlying mechanism remains elusive due to difficulty in disentangling the heterogeneity in chromatin states. Using a novel coarse-grained model and molecular dynamics simulations, here we probe the association of Sox2 and Oct4 proteins that show clustered binding at the entry-exit region of a nucleosome. The model captures the conformational heterogeneity of nucleosome breathing dynamics that features repeated wrap-unwrap transitions of a DNA segment from one end of the nucleosome. During the dynamics, DNA forms bulges that diffuse stochastically and may regulate the target search dynamics of a protein by

SUBMITTER: Mondal A 

PROVIDER: S-EPMC9748375 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature