Chromatin Mechanics Dictates Subdiffusion and Coarsening Dynamics of Embedded Condensates

Abstract

DNA is organized into chromatin, a complex polymeric material which stores information and controls gene expression. An emerging mechanism for biological organization, particularly within the crowded nucleus, is biomolecular phase separation into condensed droplets of protein and nucleic acids. However, the way in which chromatin impacts the dynamics of phase separation and condensate formation is poorly understood. Here, we utilize a powerful optogenetic strategy to examine the interplay of droplet coarsening with the surrounding viscoelastic chromatin network. We demonstrate that droplet growth dynamics are directly inhibited by the chromatin-dense environment, which gives rise to an anomalously slow coarsening exponent, ~0.12, contrasting with the classical prediction of ~1 3 ⁄ . Using scaling arguments and simulations, we show how this arrested growth can arise due to subdiffusion of individual condensates, predicting ~/3 , where is the diffusion exponent. Tracking the fluctuating motion of condensates within chromatin reveals a subdiffusive exponent, ~0.5, which explains the anomalous coarsening behavior and is also consistent with Rouse-like dynamics arising from the entangled chromatin. Our findings have implications for the biophysical regulation of the size and shape of biomolecular condensates, and suggest that condensate emulsions can be used to probe the viscoelastic mechanical environment within living cells.

Phase separation of tunable biomolecular condensates predicted by an interacting particle model

“…4f) and exactly coincide with 〈 〉. These distributions are relevant for the general case of soft-matter systems, but reflect an oversimplified scenario for living-cells, where we expect to find a limit to condensate size 45,47 .…”

“…Condensates in living cells can only grow up to a given size 45,47 , therefore we impose an upper limit to condensate size in our model: condensates rapidly dissolve after reaching QER particles, i.e. , exponentially decreases for condensates with size above QER .…”

Properties of repression condensates in living Ciona embryos

“…We suggest that the wild-type Hes repressor exhibits different properties upon binding to DNA. Recent work supporting this possibility comes from observations that condensate growth within a nucleus is limited by the surrounding chromatin 38 , if a condensate is bound to DNA this effect could be amplified. Additionally, classical genetic studies have identified several examples of insulators delimiting the spreading of silencers into neighboring, active loci 13,39,40 .…”

The nucleolus as a multiphase liquid condensate

“…Both mechanisms predict that the average droplet size, <R>, will increase with time, t, according to <R> ~ t 1/3 . The growth dynamics of in vitro nucleolar protein condensates, as well as nucleoli observed in developing Caenorhabditis elegans embryos, exhibits such t 1/3 coarsening dynamics; interestingly, emerging evidence suggests that the surrounding viscoelastic chromatin can decrease the scaling exponent for coarsening nuclear condensates 46 . Evidence of a saturation concentration, below which nucleolar phases do not assemble (Box 2) and that was shown to be important for several nucleolar proteins, provides additional quantitative support for the LLPS model in nucleolar organization 20,44 .…”