Chromatin constrains the formation, diffusion, and coarsening of phase-separated condensates

In the nucleus of a eukaryotic cell, DNA is organized into chromatin – a complex polymeric material which stores information and controls gene expression. An emerging mechanism for biological organization, including within the nucleus, is biomolecular phase separation into condensed droplets of protein and nucleic acids. We utilized an optogenetic strategy to examine how chromatin influences droplet coarsening in the nucleus. We found that droplet growth dynamics are directly inhibited by the chromatin-dense environment, which gives rise to an anomalously slow coarsening exponent, , contrasting with the classical prediction of. This slowdown of growth could arise due to subdiffusion of individual droplets, which would predict , where  is the subdiffusive exponent. Tracking the fluctuating motion of droplets within chromatin revealed a subdiffusive exponent, , which combined with a lack of observable Ostwald ripening accounts for the anomalous coarsening behavior. We further combine theory and molecular dynamics simulations to show that cross-linked chromatin can not only mechanically suppress droplets’ coalescence and ripening but also quantitatively control their number, size, and placement. Our results highlight the role of the subcellular mechanical environment on the regulation of biomolecular condensates and demonstrate the use of condensate emulsions to probe the intracellular environment.