ArticleNature communications2023
Predicting scale-dependent chromatin polymer properties from systematic coarse-graining.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Euchromatin forms condensed domains with short active regions on the surface.Nature genetics · 2026Article
- Physics-based nucleosome-resolution modeling of epigenetic-driven chromatin domain dynamics.Nucleic acids research · 2026Article
- An experimentally-informed polymer model reveals high resolution organization of genomic loci.Nature communications · 2026Article
- Multiscale chromatin modeling of chromosome X structural changes upon inactivation highlights the differential regulatory mechanism ofbioRxiv : the preprint server for biology · 2026Article
- Compaction of chromatin domains regulates target search times of proteins.PLoS computational biology · 2026Article
- Dynamical properties of chromatin provide insights into key folding principles.Biophysical journal · 2025Article
- Toward decoding the mechanisms that shape sub-megabase-scale genome organization.Current opinion in structural biology · 2025Review
- Bridging spatial and temporal scales of developmental gene regulation.Current opinion in genetics & development · 2025Review
- Chromatin structures from integrated AI and polymer physics model.PLoS computational biology · 2025Article
- ChromoGen: Diffusion model predicts single-cell chromatin conformations.Science advances · 2025Article
- Article
- The Role of Lamins in Genome Organisation: A Modelling Perspective.Sub-cellular biochemistry · 2025Review
- Article
- From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization.Annual review of biophysics · 2024Review
- OpenNucleome for high resolution nuclear structural and dynamical modeling.bioRxiv : the preprint server for biology · 2024Article
- Article
- Regulation of Chromatin Architecture by Transcription Factor Binding.bioRxiv : the preprint server for biology · 2023Article
- Predicting scale-dependent chromatin polymer properties from systematic coarse-graining.Nature communications · 2023Article
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6 authors.
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Abstract
Simulating chromatin is crucial for predicting genome organization and dynamics. Although coarse-grained bead-spring polymer models are commonly used to describe chromatin, the relevant bead dimensions, elastic properties, and the nature of inter-bead potentials are unknown. Using nucleosome-resolution contact probability (Micro-C) data, we systematically coarse-grain chromatin and predict quantities essential for polymer representation of chromatin. We compute size distributions of chromatin beads for different coarse-graining scales, quantify fluctuations and distributions of bond lengths between neighboring regions, and derive effective spring constant values. Unlike the prevalent notion, our findings argue that coarse-grained chromatin beads must be considered as soft particles that can overlap, and we derive an effective inter-bead soft potential and quantify an overlap parameter. We also compute angle distributions giving insights into intrinsic folding and local bendability of chromatin. While the nucleosome-linker DNA bond angle naturally emerges from our work, we show two populations of local structural states. The bead sizes, bond lengths, and bond angles show different mean behavior at Topologically Associating Domain (TAD) boundaries and TAD interiors. We integrate our findings into a coarse-grained polymer model and provide quantitative estimates of all model parameters, which can serve as a foundational basis for all future coarse-grained chromatin simulations.
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