ArticleJournal of molecular biology2016
Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions.
Article in Journal of molecular biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
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Who cites it
82 citing papers in PubMed.
- Physics-based nucleosome-resolution modeling of epigenetic-driven chromatin domain dynamics.Nucleic acids research · 2026Article
- Kaiso reads methylated CpGs at nucleosome entry/exit and displaces the H3 tail.bioRxiv : the preprint server for biology · 2026Article
- Linker histone H1 represses H3 tail acetylation induced by H4 tail acetylation and alters its dynamics.Communications biology · 2026Article
- Energy Landscapes and Structural Plasticity of Intrinsically Disordered Histones.Journal of chemical information and modeling · 2025Article
- Structural and thermodynamic impact of oncogenic mutations on the nucleosome core particle.Biophysical journal · 2025Article
- Unveiling the Conformational Dynamics of the Histone Tails Using Markov State Modeling.Journal of chemical theory and computation · 2025Article
- Histone tetrasome dynamics affects chromatin transcription.Nucleic acids research · 2025Article
- Unveiling nucleosome dynamics: A comparative study using all-atom and coarse-grained simulations enhanced by principal component analysis.The Journal of chemical physics · 2025Article
- Molecular basis of global promoter sensing and nucleosome capture by the SWR1 chromatin remodeler.Cell · 2024Article
- Molecular Dynamics Simulations of Nucleosomes Containing Histone Variant H2A.J.International journal of molecular sciences · 2024Article
- Unveiling Nucleosome Dynamics: A Comparative Study Using All-Atom and Coarse-Grained Simulations Enhanced by Principal Component Analysis.bioRxiv : the preprint server for biology · 2024Article
- What tunes guanine ionization potential in a nucleosome? An all-in-one systematic QM/MM assessment.Biophysical journal · 2024Article
- Conformational Dynamics of the Nucleosomal Histone H2B Tails Revealed by Molecular Dynamics Simulations.Journal of chemical information and modeling · 2024Article
- Structural dynamics in chromatin unraveling by pioneer transcription factors.Biophysical reviews · 2024Review
- Sequence Dependence in Nucleosome Dynamics.The journal of physical chemistry. B · 2024Article
- Coarse-Grained Models to Study Protein-DNA Interactions and Liquid-Liquid Phase Separation.Journal of chemical theory and computation · 2024Article
- Structure and Dynamics of Compact Dinucleosomes: Analysis by Electron Microscopy and spFRET.International journal of molecular sciences · 2023Article
- Machines on Genes through the Computational Microscope.Journal of chemical theory and computation · 2023Review
- C-B-A Test of DNA Force Fields.ACS omega · 2023Article
- Histone variant H2A.Z modulates nucleosome dynamics to promote DNA accessibility.Nature communications · 2023Article
22 more citing papers are in PubMed but not listed here.
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6 authors.
Funding
Abstract
An octamer of histone proteins wraps about 200bp of DNA into two superhelical turns to form nucleosomes found in chromatin. Although the static structure of the nucleosomal core particle has been solved, details of the dynamic interactions between histones and DNA remain elusive. We performed extensively long unconstrained, all-atom microsecond molecular dynamics simulations of nucleosomes including linker DNA segments and full-length histones in explicit solvent. For the first time, we were able to identify and characterize the rearrangements in nucleosomes on a microsecond timescale including the coupling between the conformation of the histone tails and the DNA geometry. We found that certain histone tail conformations promoted DNA bulging near its entry/exit sites, resulting in the formation of twist defects within the DNA. This led to a reorganization of histone-DNA interactions, suggestive of the formation of initial nucleosome sliding intermediates. We characterized the dynamics of the histone tails upon their condensation on the core and linker DNA and showed that tails may adopt conformationally constrained positions due to the insertion of "anchoring" lysines and arginines into the DNA minor grooves. Potentially, these phenomena affect the accessibility of post-translationally modified histone residues that serve as important sites for epigenetic marks (e.g., at H3K9, H3K27, H4K16), suggesting that interactions of the histone tails with the core and linker DNA modulate the processes of histone tail modifications and binding of the effector proteins. We discuss the implications of the observed results on the nucleosome function and compare our results to different experimental studies.
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