Chromatin Heterogeneity Modulates Nuclear Phase Behavior and Condensates Dynamics

The cell nucleus serves as a dynamic substrate responsible for storing and processing genetic material. This genetic material is intricately organized into dense, thread-like structures known as chromatin fibers, which, in turn, form a complex network with varying spatial densities. While extensive research has been conducted on the structural aspects of the chromatin network, the impact of its spatially heterogeneous mechanical properties on liquid-liquid phase separation within the nucleus remains enigmatic. In this study, we employ an optogenetic oligomerization system to investigate the role of the chromatin network in the phase separation dynamics within living cell nuclei. By modulating the spatial heterogeneity of the chromatin network through the use of a histone deacetylase inhibitor (HDACi) and inducing phase separation via blue light exposure to oligomerize proteins with different intrinsically disordered regions (IDRs), we reveal that the phase separation process is markedly inhibited when the chromatin network becomes globally homogeneous. Furthermore, we observe a reduction in the size of the phase-separated droplets and deviations from the typical coalescence-driven growth mechanism upon chromatin homogenization. Our study suggests alterations in the intranuclear mechanical properties concomitant with chromatin homogenization, which correlates with the change in the phase behavior in the nucleus. These findings emphasize the critical importance of the material state of the chromatin network in influencing liquid-liquid phase separation within the nucleus, and bear implications for the biophysical regulation of biomolecular condensates.