ArticleBiophysical journal2018
Chromatin Fiber Folding Directed by Cooperative Histone Tail Acetylation and Linker Histone Binding.
Article in Biophysical journal, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 34 citations in OpenAlex.
- Multiscale chromatin modeling of chromosome X structural changes upon inactivation highlights the differential regulatory mechanism ofbioRxiv : the preprint server for biology · 2026Article
- 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
- Unveiling the Conformational Dynamics of the Histone Tails Using Markov State Modeling.Journal of chemical theory and computation · 2025Article
- Regulation of Genome Architecture in Huntington's Disease.Biochemistry · 2025Article
- In silico nanoscope to study the interplay of genome organization and transcription regulation.Nucleic acids research · 2025Article
- Incorporating multiscale methylation effects into nucleosome-resolution chromatin models for simulating mesoscale fibers.The Journal of chemical physics · 2025Article
- Supercomputing in the biological sciences: Toward Zettascale and Yottascale simulations.Current opinion in structural biology · 2024Review
- Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics.Nucleic acids research · 2024Article
- Elucidating epigenetic mechanisms governing odontogenic differentiation in dental pulp stem cells: an in-depth exploration.Frontiers in cell and developmental biology · 2024Review
- Brownian dynamics simulations of mesoscale chromatin fibers.Biophysical journal · 2023Article
- Biophysical ordering transitions underlie genome 3D re-organization during cricket spermiogenesis.Nature communications · 2023Article
- Catching Nucleosome by Its Decorated Tails Determines Its Functional States.Frontiers in genetics · 2022Review
- Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails.Nature communications · 2021Article
- Histone Tail Conformations: A Fuzzy Affair with DNA.Trends in biochemical sciences · 2021Review
- H3K14 hyperacetylation‑mediated c‑Myc binding to the miR‑30a‑5p gene promoter under hypoxia postconditioning protects senescent cardiomyocytes from hypoxia/reoxygenation injury.Molecular medicine reports · 2021Article
- Nucleosome plasticity is a critical element of chromatin liquid-liquid phase separation and multivalent nucleosome interactions.Nature communications · 2021Article
- Elucidating the influence of linker histone variants on chromatosome dynamics and energetics.Nucleic acids research · 2020Article
- Epigenetic Regulation of Dental Pulp Stem Cell Fate.Stem cells international · 2020Review
- Molecular recognition of nucleosomes by binding partners.Current opinion in structural biology · 2019Review
- The Oligomerization Landscape of Histones.Biophysical journal · 2019Article
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
Abstract
In eukaryotic chromatin, islands of histone tail acetylation are found near transcription start sites and enhancers, whereas linker histones (LHs) are localized in intergenic regions with wild-type (WT) histone tails. However, the structural mechanisms by which acetylation, in combination with LH binding, modulates chromatin compaction and hence transcription regulation are unknown. To explore the folding propensity by which these features may govern gene expression, we analyze 20 kb fibers that contain regularly spaced acetylation islands of two sizes (2 or 5 kb) with various LH levels by mesoscale modeling. Specifically, we investigate the effect of acetylating each histone tail (H3, H4, H2A, and H2B) individually, in combination (H3 and H4, or all tails), and adding LH to WT regions. We find that fibers with acetylated H4 tails lose local contacts (<1 kb) and fibers with all tails acetylated have decreased long-range contacts in those regions. Tail interaction plots show that this opening of the fiber is driven by the loss of tail-tail interactions in favor of tail-parent core interactions and/or increase in free tails. When adding LH to WT regions, the fibers undergo hierarchical looping, enriching long-range contacts between WT and acetylated domains. For reference, adding LH to the entire fiber results in local condensation and loss of overall long-range contacts. These findings highlight the cooperation between histone tail acetylation and regulatory proteins like LH in directing folding and structural heterogeneity of chromatin fibers. The results advance our understanding of chromatin contact domains, which represent a pivotal part of the cell cycle, diseased states, and differentiation states in eukaryotic cells.
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