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Fluorescence microscopy reveals that the contents of many (membrane-free)nuclear "bodies" exchange rapidly with the soluble pool whilst the underlyingstructure persists; such observations await a satisfactory biophysicalexplanation. To shed light on this, we perform large-scale Brownian dynamicssimulations of a chromatin fiber interacting with an ensemble of (multivalent)DNA-binding proteins; these proteins switch between two states -- active(binding) and inactive (non-binding). This system provides a model for anyDNA-binding protein that can be modified post-translationally to change itsaffinity for DNA (e.g., like the phosphorylation of a transcription factor).Due to this out-of-equilibrium process, proteins spontaneously assemble intoclusters of self-limiting size, as individual proteins in a cluster exchangewith the soluble pool with kinetics like those seen in photo-bleachingexperiments. This behavior contrasts sharply with that exhibited by"equilibrium", or non-switching, proteins that exist only in the binding state;when these bind to DNA non-specifically, they form clusters that growindefinitely in size. Our results point to post-translational modification ofchromatin-bridging proteins as a generic mechanism driving the self-assembly ofhighly dynamic, non-equilibrium, protein clusters with the properties ofnuclear bodies. Such active modification also reshapes intra-chromatin contactsto give networks resembling those seen in topologically-associating domains, asswitching markedly favors local (short-range) contacts over distant ones.

Ephemeral protein binding to DNA shapes stable nuclear bodies and chromatin domains