ArticleNucleic acids research2012
Crucial role of dynamic linker histone binding and divalent ions for DNA accessibility and gene regulation revealed by mesoscale modeling of oligonucleosomes.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 48 citations in OpenAlex.
- Free energy spectroscopy reveals the mechanistic landscape of chromatin compaction.Nucleic acids research · 2026Article
- Selective binding of divalent cations reshapes nucleosome mechanics and unlocks histone tail dynamics.Communications biology · 2026Article
- Local cation-clamping distorts and softens RNA duplex.Communications 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
- Phase Space Invaders' podcast episode with Tamar Schlick: a trajectory from mathematics to biology.Biophysical reviews · 2025Article
- From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization.Annual review of biophysics · 2024Review
- Regulation of chromatin architecture by protein binding: insights from molecular modeling.Biophysical reviews · 2024Review
- Brownian dynamics simulations of mesoscale chromatin fibers.Biophysical journal · 2023Article
- Chromatin transitions triggered by LH density as epigenetic regulators of the genome.Nucleic acids research · 2022Article
- Chromatin fiber breaks into clutches under tension and crowding.Nucleic acids research · 2022Article
- Nucleosome Clutches are Regulated by Chromatin Internal Parameters.Journal of molecular biology · 2021Article
- Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Irregular Chromatin: Packing Density, Fiber Width, and Occurrence of Heterogeneous Clusters.Biophysical journal · 2020Article
- Chromatin Compaction Multiscale Modeling: A Complex Synergy Between Theory, Simulation, and Experiment.Frontiers in molecular biosciences · 2020Review
- Sensitive effect of linker histone binding mode and subtype on chromatin condensation.Nucleic acids research · 2019Article
- Frozen-hydrated chromatin from metaphase chromosomes has an interdigitated multilayer structure.The EMBO journal · 2019Article
- Dynamics of Chromatin Fibers: Comparison of Monte Carlo Simulations with Force Spectroscopy.Biophysical journal · 2018Article
- Transfer-matrix calculations of the effects of tension and torque constraints on DNA-protein interactions.Nucleic acids research · 2018Article
- Dependence of the Linker Histone and Chromatin Condensation on the Nucleosome Environment.The journal of physical chemistry. B · 2017Article
- Electrophoretic stretching and imaging of single native chromatin fibers in nanoslits.Biomicrofluidics · 2017Article
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Authors and funding
2 authors at 2 institutions in 1 country.
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Abstract
Monte Carlo simulations of a mesoscale model of oligonucleosomes are analyzed to examine the role of dynamic-linker histone (LH) binding/unbinding in high monovalent salt with divalent ions, and to further interpret noted chromatin fiber softening by dynamic LH in monovalent salt conditions. We find that divalent ions produce a fiber stiffening effect that competes with, but does not overshadow, the dramatic softening triggered by dynamic-LH behavior. Indeed, we find that in typical in vivo conditions, dynamic-LH binding/unbinding reduces fiber stiffening dramatically (by a factor of almost 5, as measured by the elasticity modulus) compared with rigidly fixed LH, and also the force needed to initiate chromatin unfolding, making it consistent with those of molecular motors. Our data also show that, during unfolding, divalent ions together with LHs induce linker-DNA bending and DNA-DNA repulsion screening, which guarantee formation of heteromorphic superbeads-on-a-string structures that combine regions of loose and compact fiber independently of the characteristics of the LH-core bond. These structures might be important for gene regulation as they expose regions of the DNA selectively. Dynamic control of LH binding/unbinding, either globally or locally, in the presence of divalent ions, might constitute a mechanism for regulation of gene expression.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.