ArticleScientific reports2016
Histone acetylation dependent energy landscapes in tri-nucleosome revealed by residue-resolved molecular simulations.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 44 citations in OpenAlex.
- Local acetyl-CoA metabolism and acetate recycling as epigenetic regulators of chromatin dynamics.FEMS yeast research · 2026Review
- Unveiling the Conformational Dynamics of the Histone Tails Using Markov State Modeling.Journal of chemical theory and computation · 2025Article
- In silico nanoscope to study the interplay of genome organization and transcription regulation.Nucleic acids research · 2025Article
- Conformational Dynamics of the Nucleosomal Histone H2B Tails Revealed by Molecular Dynamics Simulations.Journal of chemical information and modeling · 2024Article
- Coarse-Grained Models to Study Protein-DNA Interactions and Liquid-Liquid Phase Separation.Journal of chemical theory and computation · 2024Article
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- Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization.bioRxiv : the preprint server for biology · 2023Article
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- Now open: Evolving insights to the roles of lysine acetylation in chromatin organization and function.Molecular cell · 2022Review
- Non-enzymatic Covalent Modifications as a New Chapter in the Histone Code.Trends in biochemical sciences · 2021Review
- 3,4-dihydroxytoluene, a metabolite of rutin, suppresses the progression of nonalcoholic fatty liver disease in mice by inhibiting p300 histone acetyltransferase activity.Acta pharmacologica Sinica · 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
- Single-molecule and in silico dissection of the interaction between Polycomb repressive complex 2 and chromatin.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Bottom-Up Meets Top-Down: The Crossroads of Multiscale Chromatin Modeling.Biophysical journal · 2020Review
- Identification of histone acetylation markers in human fetal brains and increased H4K5ac expression in neural tube defects.Molecular genetics & genomic medicine · 2019Article
- Nucleosome Crowding in Chromatin Slows the Diffusion but Can Promote Target Search of Proteins.Biophysical journal · 2019Article
- Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR.Current opinion in structural biology · 2019Review
- Effect of in vivo post-translational modifications of the HMGB1 protein upon binding to platinated DNA: a molecular simulation study.Nucleic acids research · 2018Article
- Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA.PLoS computational biology · 2018Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Histone tail acetylation is a key epigenetic marker that tends to open chromatin folding and activate transcription. Despite intensive studies, precise roles of individual lysine acetylation in chromatin folding have only been poorly understood. Here, we revealed structural dynamics of tri-nucleosomes with several histone tail acetylation states and analyzed histone tail interactions with DNA by performing molecular simulations at an unprecedentedly high resolution. We found versatile acetylation-dependent landscapes of tri-nucleosome. The H4 and H2A tail acetylation reduced the contact between the first and third nucleosomes mediated by the histone tails. The H3 tail acetylation reduced its interaction with neighboring linker DNAs resulting in increase of the distance between consecutive nucleosomes. Notably, two copies of the same histone in a single nucleosome have markedly asymmetric interactions with DNAs, suggesting specific pattern of nucleosome docking albeit high inherent flexibility. Estimated transcription factor accessibility was significantly high for the H4 tail acetylated structures.
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