ArticleNucleic acids research2022
Chromatin fiber breaks into clutches under tension and crowding.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- 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
- Nucleosome condensate and linker DNA alter chromatin folding pathways and rates.Biophysical journal · 2026Article
- Motorized chromosome models of mitotic chromosome folding.Nature communications · 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
- Article
- Characterizing DNA recognition preferences of transcription factors using global couplings and high-throughput sequencing.Nucleic acids research · 2025Article
- Toward decoding the mechanisms that shape sub-megabase-scale genome organization.Current opinion in structural biology · 2025Review
- Toward Predictive Coarse-Grained Simulations of Biomolecular Condensates.Biochemistry · 2025Review
- Connected Chromatin Amplifies Acetylation-Modulated Nucleosome Interactions.Biochemistry · 2025Article
- Dynamics of nucleosomes and chromatin fibers revealed by single-molecule measurements.BMB reports · 2025Review
- A Molecular View into the Structure and Dynamics of Phase-Separated Chromatin.The journal of physical chemistry. B · 2024Article
- From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization.Annual review of biophysics · 2024Review
- Article
- Transferable Implicit Solvation via Contrastive Learning of Graph Neural Networks.ACS central science · 2023Article
- Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization.bioRxiv : the preprint server for biology · 2023Article
- Transferable Coarse Graining via Contrastive Learning of Graph Neural Networks.bioRxiv : the preprint server for biology · 2023Article
- OpenABC enables flexible, simplified, and efficient GPU accelerated simulations of biomolecular condensates.PLoS computational biology · 2023Article
- Multiomic analysis of cohesin reveals that ZBTB transcription factors contribute to chromatin interactions.Nucleic acids research · 2023Article
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3 authors.
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Abstract
The arrangement of nucleosomes inside chromatin is of extensive interest. While in vitro experiments have revealed the formation of 30 nm fibers, most in vivo studies have failed to confirm their presence in cell nuclei. To reconcile the diverging experimental findings, we characterized chromatin organization using a residue-level coarse-grained model. The computed force-extension curve matches well with measurements from single-molecule experiments. Notably, we found that a dodeca-nucleosome in the two-helix zigzag conformation breaks into structures with nucleosome clutches and a mix of trimers and tetramers under tension. Such unfolded configurations can also be stabilized through trans interactions with other chromatin chains. Our study suggests that unfolding from chromatin fibers could contribute to the irregularity of in vivo chromatin configurations. We further revealed that chromatin segments with fibril or clutch structures engaged in distinct binding modes and discussed the implications of these inter-chain interactions for a potential sol-gel phase transition.
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