ArticleProceedings of the National Academy of Sciences of the United States of America2022
Generation of dynamic three-dimensional genome structure through phase separation of chromatin.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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36 citing papers in PubMed.
- Deep learning enabled prediction of nuclear lamina-associated chromatin.Patterns (New York, N.Y.) · 2026Article
- Multiaxial Biophysical Control of Oncogenic Phase Separation by Indoleamines: A Proof-of-Concept Synthesis of Landscape-Level Regulation.Journal of pineal research · 2026Review
- Physics-based nucleosome-resolution modeling of epigenetic-driven chromatin domain dynamics.Nucleic acids research · 2026Article
- The Fluid Mosaic Model of chromatin organization: integrating dynamics, conformational heterogeneity and multiscale organization.Communications biology · 2026Review
- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- A Facile Platform for One-Step Generation of Uniform Microdroplets through Dehydration-Driven Phase Separation in Microfluidics.Small methods · 2026Article
- Compaction of chromatin domains regulates target search times of proteins.PLoS computational biology · 2026Article
- Chromatin conformation, gene transcription, and nucleosome remodeling as an emergent system.Science advances · 2025Article
- Construction of Coarse-Grained Molecular Dynamics Model of Nuclear Global Chromosomes Dynamics in Mammalian Cells.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Understanding and Simulating the Dynamics of a Polymer-Like Chromatin.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Three-Dimensional Simulation of Whole-Genome Structuring Through the Transition from Anaphase to Interphase.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Integrative Modeling of 3D Genome Organization by Bayesian Molecular Dynamics Simulations with Hi-C Metainference.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Interplay of chromatin organization and mechanics of the cell nucleus.Biophysical journal · 2024Article
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- Multiscale Bayesian simulations reveal functional chromatin condensation of gene loci.PNAS nexus · 2024Article
- OpenNucleome for high resolution nuclear structural and dynamical modeling.bioRxiv : the preprint server for biology · 2024Article
- Computational methods for analysing multiscale 3D genome organization.Nature reviews. Genetics · 2024Review
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2 authors.
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Abstract
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 examine 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.
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