ArticlePLoS computational biology2015
Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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47 citing papers in PubMed.
- DNA Sequence and Histone Variant H2A.Z Jointly Govern Nucleosome Unwrapping Pathways.bioRxiv : the preprint server for biology · 2026Article
- H2A.Z facilitates Sox2-nucleosome interaction by promoting DNA and histone H3 tail mobility.Nucleic acids research · 2026Article
- Time-Resolved Single-Molecule FRET Reveals Length-Dependent Nucleosome Decompaction by Poly(ADP-ribose).bioRxiv : the preprint server for biology · 2026Article
- DNA spontaneously wrapping around a histone core prefers negative supercoiling: A Brownian dynamics study.PLoS computational biology · 2025Article
- Coarse-Grained Models to Study Protein-DNA Interactions and Liquid-Liquid Phase Separation.Journal of chemical theory and computation · 2024Article
- Brewing COFFEE: A sequence-specific coarse-grained energy function for simulations of DNA-protein complexes.bioRxiv : the preprint server for biology · 2023Article
- Role of the histone tails in histone octamer transfer.Nucleic acids research · 2023Article
- Nucleosome breathing facilitates cooperative binding of pluripotency factors Sox2 and Oct4 to DNA.Biophysical journal · 2022Article
- DNA methylation cues in nucleosome geometry, stability and unwrapping.Nucleic acids research · 2022Article
- Release of linker histone from the nucleosome driven by polyelectrolyte competition with a disordered protein.Nature chemistry · 2022Article
- Molecular dynamics analysis of biomolecular systems including nucleic acids.Biophysics and physicobiology · 2022Article
- Molecular dynamics simulations reveal how H3K56 acetylation impacts nucleosome structure to promote DNA exposure for lesion sensing.DNA repair · 2021Article
- Surprising Twists in Nucleosomal DNA with Implication for Higher-order Folding.Journal of molecular biology · 2021Article
- Effect of DNA Flexibility on Complex Formation of a Cationic Nanoparticle with Double-Stranded DNA.ACS omega · 2021Article
- Multiscale modeling of genome organization with maximum entropy optimization.The Journal of chemical physics · 2021Article
- Histone Tail Conformations: A Fuzzy Affair with DNA.Trends in biochemical sciences · 2021Review
- The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study.PLoS computational biology · 2021Article
- Histone tails cooperate to control the breathing of genomic nucleosomes.PLoS computational biology · 2021Article
- Histone tails as signaling antennas of chromatin.Current opinion in structural biology · 2021Review
- Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface.Nature communications · 2021Article
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2 authors.
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Abstract
Nucleosomes, basic units of chromatin, are known to show spontaneous DNA unwrapping dynamics that are crucial for transcriptional activation, but its structural details are yet to be elucidated. Here, employing a coarse-grained molecular model that captures residue-level structural details up to histone tails, we simulated equilibrium fluctuations and forced unwrapping of single nucleosomes at various conditions. The equilibrium simulations showed spontaneous unwrapping from outer DNA and subsequent rewrapping dynamics, which are in good agreement with experiments. We found several distinct partially unwrapped states of nucleosomes, as well as reversible transitions among these states. At a low salt concentration, histone tails tend to sit in the concave cleft between the histone octamer and DNA, tightening the nucleosome. At a higher salt concentration, the tails tend to bound to the outer side of DNA or be expanded outwards, which led to higher degree of unwrapping. Of the four types of histone tails, H3 and H2B tail dynamics are markedly correlated with partial unwrapping of DNA, and, moreover, their contributions were distinct. Acetylation in histone tails was simply mimicked by changing their charges, which enhanced the unwrapping, especially markedly for H3 and H2B tails.
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