ArticleNature communications2021
Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Near-atomistic simulations reveal the molecular principles that control chromatin structure and phase separation.Nature communications · 2026Article
- Molecular dynamics guided all-atom reconstruction of cryo-ET maps reveals mechanisms of histone tail mediated chromatin compaction.Nature communications · 2026Article
- Free energy spectroscopy reveals the mechanistic landscape of chromatin compaction.Nucleic acids research · 2026Article
- NEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA Simulations.Journal of chemical theory and computation · 2026Article
- Bayesian Optimization for High-Dimensional Coarse-Grained Model Parameterization: A Case Study on Pebax Polymer.Journal of chemical theory and computation · 2026Article
- Nucleosome condensate and linker DNA alter chromatin folding pathways and rates.Biophysical journal · 2026Article
- Direct measurement of sub-kilobase chromatin structure reveals that linker histone H1 broadly compacts chromatin, with differential impact amongst epigenetic states.bioRxiv : the preprint server for biology · 2025Article
- NEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA Simulations.bioRxiv : the preprint server for biology · 2025Article
- Free energy spectroscopy reveals the mechanistic landscape of chromatin compaction.bioRxiv : the preprint server for biology · 2025Article
- How chromatin-binding proteins direct distinct folding pathways of tetra-nucleosomes: Insights from coarse-grained simulations.bioRxiv : the preprint server for biology · 2025Article
- Article
- Toward Predictive Coarse-Grained Simulations of Biomolecular Condensates.Biochemistry · 2025Review
- Connected Chromatin Amplifies Acetylation-Modulated Nucleosome Interactions.Biochemistry · 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
- Dynamics of nucleosomes and chromatin fibers revealed by single-molecule measurements.BMB reports · 2025Review
- 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
- A Molecular View into the Structure and Dynamics of Phase-Separated Chromatin.The journal of physical chemistry. B · 2024Article
- Determining mesoscale chromatin structure parameters from spatially correlated cleavage data using a coarse-grained oligonucleosome model.bioRxiv : the preprint server for biology · 2024Article
- From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization.Annual review of biophysics · 2024Review
- Angle between DNA linker and nucleosome core particle regulates array compaction revealed by individual-particle cryo-electron tomography.Nature communications · 2024Article
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3 authors.
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Abstract
The three-dimensional organization of chromatin is expected to play critical roles in regulating genome functions. High-resolution characterization of its structure and dynamics could improve our understanding of gene regulation mechanisms but has remained challenging. Using a near-atomistic model that preserves the chemical specificity of protein-DNA interactions at residue and base-pair resolution, we studied the stability and folding pathways of a tetra-nucleosome. Dynamical simulations performed with an advanced sampling technique uncovered multiple pathways that connect open chromatin configurations with the zigzag crystal structure. Intermediate states along the simulated folding pathways resemble chromatin configurations reported from in situ experiments. We further determined a six-dimensional free energy surface as a function of the inter-nucleosome distances via a deep learning approach. The zigzag structure can indeed be seen as the global minimum of the surface. However, it is not favored by a significant amount relative to the partially unfolded, in situ configurations. Chemical perturbations such as histone H4 tail acetylation and thermal fluctuations can further tilt the energetic balance to stabilize intermediate states. Our study provides insight into the connection between various reported chromatin configurations and has implications on the in situ relevance of the 30 nm fiber.
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