Role of protein-protein interactions on organization and dynamics of a model chromatin.

Abstract

The three-dimensional organization of chromatin is influenced by chromatin-binding proteins through both specific and non-specific interactions. However, the roles of chromatin sequence and the interactions between binding proteins in shaping chromatin structure remain elusive. By employing a simple polymer-based model of chromatin that explicitly considers sequence-dependent protein binding and protein-protein interactions, we elucidate a mechanism for chromatin organization. We find that tuning protein-protein interactions and protein concentration is sufficient to either promote or inhibit chromatin compartmentalization. Moreover, chromatin sequence and protein-protein attraction strongly affect the structural and dynamic exponents that describe the spatiotemporal organization of chromatin. Strikingly, our model's predictions for the exponents governing chromatin structure and dynamics successfully capture experimental observations, in sharp contrast to previous chromatin models. Overall, our findings have the potential to reinterpret data obtained from various chromosome conformation capture technologies, laying the groundwork for advancing our understanding of chromatin organization.