ArticleNature communications2025
Nucleosome spacing can fine-tune higher-order chromatin assembly.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- AI-assisted Cryo-ET workflow for 3D visualization of chromatin during cellular differentiation.Biochemistry and biophysics reports · 2026Article
- Near-atomistic simulations reveal the molecular principles that control chromatin structure and phase separation.Nature communications · 2026Article
- Chromatin remodeling coordinates chromosome compaction, synaptonemal complex architecture and meiotic crossing-over.Research square · 2026Article
- Mixing chromatin fibers with different nucleosome repeat lengths changes dynamics of chromatin phase separation.The Journal of biological chemistry · 2026Article
- The roles of chromatin remodeling and 3D genome organization in cancers: from mechanistic insights to emerging treatment options.Molecular cancer · 2026Review
- Epigenetic remodeling during UV exposure: high resolution analysis of histone post-translational modifications in a DNA binding protein 2 mutant model.Histochemistry and cell biology · 2026Article
- A Chromatin Biology Assessment of AlphaFold3.bioRxiv : the preprint server for biology · 2026Article
- Single-molecule nucleosome spacing coordinates chromatin fiber interactions.bioRxiv : the preprint server for biology · 2026Article
- Histone modification cross-talk: analytical tools and molecular mechanisms.The Biochemical journal · 2026Review
- Quantifying the effect of magnesium ions on nucleosome stability in chromatin fibers.Biophysical journal · 2026Article
- Insights from single-molecule force spectroscopy into chromatin topology.Biophysical reviews · 2026Review
- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- From chromosomal protein disorder to chromatin phase separation.Epigenetics & chromatin · 2026Review
- Spindle pole proteins confine chromosomes to ensure their expulsion during female meiosis.bioRxiv : the preprint server for biology · 2026Article
- Nucleosome spacing regulates linker methylation by DNMT3A2/3B3.Molecular cell · 2026Article
- Contributions of Local Structural and Energetic Features of DNA to Large-scale Genomic Organization.Journal of molecular biology · 2026Review
- Nucleosome spacing across cell types, diseases, and ages.Nucleic acids research · 2026Review
- Histone H3 tail charge patterns govern nucleosome condensate formation and dynamics.Nucleic acids research · 2026Article
- Nucleosome condensate and linker DNA alter chromatin folding pathways and rates.Biophysical journal · 2026Article
- Direct measurement of sub-kilobase chromatin structure reveals that linker histone H1 broadly compacts chromatin, with differential impact amongst epigenetic states.bioRxiv : the preprint server for biology · 2025Article
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Abstract
Cellular chromatin displays heterogeneous structure and dynamics, properties that control diverse nuclear processes. Models invoke phase separation of conformational ensembles of chromatin fibers as a mechanism regulating chromatin organization in vivo. Here we combine biochemistry and molecular dynamics simulations to examine, at single base-pair resolution, how nucleosome spacing controls chromatin phase separation. We show that as DNA linkers extend from 25 bp to 30 bp, as exemplars of 10 N + 5 and 10 N (integer N) bp lengths, chromatin condensates become less thermodynamically stable and nucleosome mobility increases. Simulations reveal that this is due to trade-offs between inter- and intramolecular nucleosome stacking, favored by rigid 10 N + 5 and 10 N bp linkers, respectively. A remodeler can induce or inhibit phase separation by moving nucleosomes, changing the balance between intra- and intermolecular stacking. The intrinsic phase separation capacity of chromatin enables fine tuning of compaction and dynamics, likely contributing to heterogeneous chromatin organization in vivo.
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