ArticleNature communications2021
Nucleosome plasticity is a critical element of chromatin liquid-liquid phase separation and multivalent nucleosome interactions.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 115 papers.
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115 citing papers in PubMed, 177 citations in OpenAlex.
- Near-atomistic simulations reveal the molecular principles that control chromatin structure and phase separation.Nature communications · 2026Article
- Cross-Scale Convergence in Epigenetic Gene Regulation: A Perspective on Functional Enrichment Analytics for Cancer.Current issues in molecular biology · 2026Article
- The role of the 2'-OH group in phase separation and percolation transitions of RNA.Nature communications · 2026Article
- The Critical Role of the 2'-OH group in Phase Separation and Percolation Transitions of RNA.bioRxiv : the preprint server for biology · 2026Article
- Single-molecule nucleosome spacing coordinates chromatin fiber interactions.bioRxiv : the preprint server for biology · 2026Article
- Argonaute proteins orchestrate Meiotic Sex Chromosome Inactivation and timing of the spermatogenic transcriptional program.PLoS genetics · 2026Article
- 5-Formylcytosine functions as a chemical regulator of nucleosome positioning.Nature communications · 2026Article
- 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
- NEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA Simulations.Journal of chemical theory and computation · 2026Article
- Linker histone H1 functions as a liquid-like glue to organize chromatin in living human cells.Science advances · 2026Article
- Quantifying the effect of magnesium ions on nucleosome stability in chromatin fibers.Biophysical journal · 2026Article
- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Contributions of Local Structural and Energetic Features of DNA to Large-scale Genomic Organization.Journal of molecular biology · 2026Review
- Time-Resolved Single-Molecule FRET Reveals Length-Dependent Nucleosome Decompaction by Poly(ADP-ribose).bioRxiv : the preprint server for biology · 2026Article
- In vitro reconstitution of heterochromatin compartments reveals the spontaneous formation of tunable liquid-liquid interfaces.Nucleic acids research · 2026Article
- Histone H3 tail charge patterns govern nucleosome condensate formation and dynamics.Nucleic acids research · 2026Article
- Selective binding of divalent cations reshapes nucleosome mechanics and unlocks histone tail dynamics.Communications biology · 2026Article
- An experimentally-informed polymer model reveals high resolution organization of genomic loci.Nature communications · 2026Article
- Nucleosome condensate and linker DNA alter chromatin folding pathways and rates.Biophysical journal · 2026Article
55 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Liquid-liquid phase separation (LLPS) is an important mechanism that helps explain the membraneless compartmentalization of the nucleus. Because chromatin compaction and LLPS are collective phenomena, linking their modulation to the physicochemical features of nucleosomes is challenging. Here, we develop an advanced multiscale chromatin model-integrating atomistic representations, a chemically-specific coarse-grained model, and a minimal model-to resolve individual nucleosomes within sub-Mb chromatin domains and phase-separated systems. To overcome the difficulty of sampling chromatin at high resolution, we devise a transferable enhanced-sampling Debye-length replica-exchange molecular dynamics approach. We find that nucleosome thermal fluctuations become significant at physiological salt concentrations and destabilize the 30-nm fiber. Our simulations show that nucleosome breathing favors stochastic folding of chromatin and promotes LLPS by simultaneously boosting the transient nature and heterogeneity of nucleosome-nucleosome contacts, and the effective nucleosome valency. Our work puts forward the intrinsic plasticity of nucleosomes as a key element in the liquid-like behavior of nucleosomes within chromatin, and the regulation of chromatin LLPS.
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