ArticleProceedings of the National Academy of Sciences of the United States of America2005
Electrostatic mechanism of nucleosomal array folding revealed by computer simulation.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed, 119 citations in OpenAlex.
- Conformations of Linker Histone H1 Bound to Nucleosome Arrays.Journal of molecular biology · 2026Article
- The influence of 10n and 10n+5 linker lengths on chromatin fiber topologies explored by mesoscale modeling.Biophysical journal · 2026Article
- Chromatin higher-order folding as influenced by preferred values of linker DNA.Current opinion in structural biology · 2025Review
- The impact of charge regulation and ionic intranuclear environment on the nucleosome core particle.The Journal of chemical physics · 2024Article
- The Impact of Charge Regulation and Ionic Intranuclear Environment on the Nucleosome Core Particle.bioRxiv : the preprint server for biology · 2024Article
- Structural insights into the cooperative nucleosome recognition and chromatin opening by FOXA1 and GATA4.Molecular cell · 2024Article
- From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization.Annual review of biophysics · 2024Review
- Multiscale modeling reveals the ion-mediated phase separation of nucleosome core particles.Biophysical journal · 2024Article
- Chromatin transitions triggered by LH density as epigenetic regulators of the genome.Nucleic acids research · 2022Article
- A Bottom-Up Coarse-Grained Model for Nucleosome-Nucleosome Interactions with Explicit Ions.Journal of chemical theory and computation · 2022Article
- Multiscale modeling of genome organization with maximum entropy optimization.The Journal of chemical physics · 2021Article
- Nucleosome Clutches are Regulated by Chromatin Internal Parameters.Journal of molecular biology · 2021Article
- Mesoscale Modeling and Single-Nucleosome Tracking Reveal Remodeling of Clutch Folding and Dynamics in Stem Cell Differentiation.Cell reports · 2021Article
- Ensembles of Breathing Nucleosomes: A Computational Study.Biophysical journal · 2020Article
- Irregular Chromatin: Packing Density, Fiber Width, and Occurrence of Heterogeneous Clusters.Biophysical journal · 2020Article
- Role of nucleosome positioning in 3D chromatin organization and loop formation.Journal of biosciences · 2020Article
- Article
- Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR.Current opinion in structural biology · 2019Review
- Force-extension behavior of DNA in the presence of DNA-bending nucleoid associated proteins.The Journal of chemical physics · 2018Article
- Effects of charge-modifying mutations in histone H2A α3-domain on nucleosome stability assessed by single-pair FRET and MD simulations.Scientific reports · 2017Article
3 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
Abstract
Although numerous experiments indicate that the chromatin fiber displays salt-dependent conformations, the associated molecular mechanism remains unclear. Here, we apply an irregular Discrete Surface Charge Optimization (DiSCO) model of the nucleosome with all histone tails incorporated to describe by Monte Carlo simulations salt-dependent rearrangements of a nucleosomal array with 12 nucleosomes. The ensemble of nucleosomal array conformations display salt-dependent condensation in good agreement with hydrodynamic measurements and suggest that the array adopts highly irregular 3D zig-zag conformations at high (physiological) salt concentrations and transitions into the extended "beads-on-a-string" conformation at low salt. Energy analyses indicate that the repulsion among linker DNA leads to this extended form, whereas internucleosome attraction drives the folding at high salt. The balance between these two contributions determines the salt-dependent condensation. Importantly, the internucleosome and linker DNA-nucleosome attractions require histone tails; we find that the H3 tails, in particular, are crucial for stabilizing the moderately folded fiber at physiological monovalent salt.
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