Generation of dynamic three-dimensional genome structure through phase separation of chromatin

Three-dimensional genome structure and dynamics play critical roles in regulating DNA functions. Flexible chromatin structure and movements suggested that the genome is dynamically phase-separated to form A (active) and B (inactive) compartments in interphase nuclei. Here, we examined this hypothesis by developing a polymer model of the whole genome of human cells and assessing the impact of phase separation on genome structure. Upon entry to the G1 phase, the simulated genome expanded according to heterogeneous repulsion among chromatin chains, which moved chromatin heterogeneously, inducing phase separation of chromatin. This repulsion-driven phase separation quantitatively reproduces the experimentally observed chromatin domains, A/B compartments, lamina-associated domains, and nucleolus-associated domains, consistently explaining nuclei of different human cells and predicting their dynamic fluctuations. We propose that phase separation induced by heterogeneous repulsive interactions among chromatin chains largely determines dynamic genome organization. SignificanceDNA functions in living cells are crucially affected by the three-dimensional genome structure and dynamics. We analyzed the whole genome of human cells by developing a polymer model of interphase nuclei. The model revealed the essential importance of the unfolding process of chromosomes from the condensed mitotic state for describing the interphase nuclei; through the unfolding process, heterogeneous repulsive interactions among chromatin chains induced phase separation of chromatin, which quantitatively explains the experimentally observed various genomic data. We can use this model structure as a platform to analyze the relationship among genome structure, dynamics, and functions.