Binder and monomer valencies determine the extent of collapse and reswelling of chromatin

Abstract

Multivalent DNA-bridging protein-mediated collapse of chromatin polymers have long been established as one of the driving factors in chromatin organization inside cells. These multivalent proteins can bind to distant binding sites along the chromatin backbone and bring them together in spatial proximity, leading to collapsed conformations. Recently, it has been suggested that these proteins not only drive the collapse of the chromatin polymer but also reswelling at higher concentrations. In this study, we investigate the physical mechanisms underlying this unexpected reswelling behavior. We use the Langevin dynamics simulation of a coarse-grained homopolymer to investigate the effects of the valencies of both the binders and the monomers on the polymer conformations. We find that while the extent of collapse of the polymer is strongly dependent on the binder valency, the extent of reswelling is largely determined by the monomer valency. Furthermore, we also discovered two different physical mechanisms that drive the reswelling of the polymer—excluded volume effects and loss of long-range loops. Finally, we obtain a classification map to determine the regimes in which each of these mechanisms is the dominant factor leading to polymer reswelling.