ArticleProceedings of the National Academy of Sciences of the United States of America2009
Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 138 papers.
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138 citing papers in PubMed, 269 citations in OpenAlex.
- A hydrophobic vector association model of nucleosomes in chromatin.European biophysics journal : EBJ · 2026Article
- Chromatin remodeling coordinates chromosome compaction, synaptonemal complex architecture and meiotic crossing-over.Research square · 2026Article
- Free energy spectroscopy reveals the mechanistic landscape of chromatin compaction.Nucleic acids research · 2026Article
- Physics-based nucleosome-resolution modeling of epigenetic-driven chromatin domain dynamics.Nucleic acids research · 2026Article
- Conformations of Linker Histone H1 Bound to Nucleosome Arrays.Journal of molecular biology · 2026Article
- Contributions of Local Structural and Energetic Features of DNA to Large-scale Genomic Organization.Journal of molecular biology · 2026Review
- Selective binding of divalent cations reshapes nucleosome mechanics and unlocks histone tail dynamics.Communications biology · 2026Article
- Chromatin higher-order folding as influenced by preferred values of linker DNA.Current opinion in structural biology · 2025Review
- Nucleosome Linker Length and Distribution as Major Players in Epigenetic Regulation: Insights from Cryo-Electron Microscopy and Modeling of Retina Cell Maturation.DNA and cell biology · 2025Review
- Free energy spectroscopy reveals the mechanistic landscape of chromatin compaction.bioRxiv : the preprint server for biology · 2025Article
- All-atom MD simulations of the HPV16 capsid.bioRxiv : the preprint server for biology · 2025Article
- Compromised two-start zigzag chromatin folding in immature mouse retina cells driven by irregularly spaced nucleosomes with short DNA linkers.Nucleic acids research · 2025Article
- Regulation of Genome Architecture in Huntington's Disease.Biochemistry · 2025Article
- Geometric variations in nucleosomal DNA dictate higher-order chromatin structure and enhancer-promoter communication.The Journal of chemical physics · 2024Article
- Determining mesoscale chromatin structure parameters from spatially correlated cleavage data using a coarse-grained oligonucleosome model.bioRxiv : the preprint server for biology · 2024Article
- Regulation of chromatin architecture by protein binding: insights from molecular modeling.Biophysical reviews · 2024Review
- Article
- The role of cryptic ancestral symmetry in histone folding mechanisms across Eukarya and Archaea.PLoS computational biology · 2024Article
- Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization.bioRxiv : the preprint server for biology · 2023Article
- Structure of native chromatin fibres revealed by Cryo-ET in situ.Nature communications · 2023Article
78 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 4 institutions in 1 country.
Funding
Abstract
The architecture of the chromatin fiber, which determines DNA accessibility for transcription and other template-directed biological processes, remains unknown. Here we investigate the internal organization of the 30-nm chromatin fiber, combining Monte Carlo simulations of nucleosome chain folding with EM-assisted nucleosome interaction capture (EMANIC). We show that at physiological concentrations of monovalent ions, linker histones lead to a tight 2-start zigzag dominated by interactions between alternate nucleosomes (i +/- 2) and sealed by histone N-tails. Divalent ions further compact the fiber by promoting bending in some linker DNAs and hence raising sequential nucleosome interactions (i +/- 1). Remarkably, both straight and bent linker DNA conformations are retained in the fully compact chromatin fiber as inferred from both EMANIC and modeling. This conformational variability is energetically favorable as it helps accommodate DNA crossings within the fiber axis. Our results thus show that the 2-start zigzag topology and the type of linker DNA bending that defines solenoid models may be simultaneously present in a structurally heteromorphic chromatin fiber with uniform 30 nm diameter. Our data also suggest that dynamic linker DNA bending by linker histones and divalent cations in vivo may mediate the transition between tight nucleosome packing within discrete 30-nm fibers and self-associated higher-order chromosomal forms.
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