Chromosomes are systematically packaged and encapsulated within the nucleus. In the absence of membrane-delineated subnuclear structures, phase separation-mediated biomolecular condensation emerges as a critical organizing principle. Previous investigations have established that the formation of both heterochromatin and super-enhancer condensates is contingent upon phase separation mechanisms. However, the degree to which various chromosomal regions depend on phase separation remains unclear, as does the feasibility of quantitatively characterizing these differences under physiological conditions. Consequently, there is a pressing need for high-throughput, quantitative analyses of the phase separation dependence of chromatin higher-order structures in physiologically relevant contexts. Employing 1,6-hexanediol (1,6-HD) perturbation coupled with quantitative assessment of chromatin three-dimensional structural alterations, we elucidated the impact of phase separation on chromatin architecture at multiple hierarchical levels: chromosome compartments, topologically associating domains (TADs), and chromatin loops. Our findings reveal that chromosome compartment stability exhibits a "neighbor effect," while TAD stability is modulated by both CTCF-cohesin binding and phase separation phenomena.

The integrity of chromatin higher-order structure is profoundly influenced by its associated proteins. Under physiological conditions, proteins display diverse aggregation propensities, executing specific functions and orchestrating physiological processes. Conversely, in senescent states, dysregulation of protein liquid-solid aggregation dynamics precipitates cellular homeostatic imbalance and aging. To elucidate the mechanisms by which aberrant protein liquid-solid aggregation states induce cellular senescence, we investigated the liquid-solid state transition of the FUS protein in murine hematopoietic stem cells. This study uncovered its profound impact on three-dimensional genome organization and the consequent induction of hematopoietic stem cell aging.
 

Biomolecular Condensates,Chromatin Architecture