ArticleNucleic acids research2014
Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 225 papers.
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Who cites it
225 citing papers in PubMed, 494 citations in OpenAlex.
- Chromatin remodelling: a driving force in reverse mechanotransduction.RNA biology · 2026Review
- Influence of Histone Acetylation on Chromatin 3D Organization inInternational journal of molecular sciences · 2026Article
- A scaffolding element rewires local 3D chromatin architecture during differentiation.Nature communications · 2026Article
- Article
- RepliSage: a stochastic graph-based framework for 3D chromatin modeling across the cell cycle.Nucleic acids research · 2026Article
- Physics-based nucleosome-resolution modeling of epigenetic-driven chromatin domain dynamics.Nucleic acids research · 2026Article
- The Fluid Mosaic Model of chromatin organization: integrating dynamics, conformational heterogeneity and multiscale organization.Communications biology · 2026Review
- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Architecture and regulation of nanoscale chromatin domains.Nature communications · 2026Review
- Unique territorial and compartmental organization of chromosomes in the holocentric silkworm.The EMBO journal · 2026Article
- Compaction of chromatin domains regulates target search times of proteins.PLoS computational biology · 2026Article
- Chromatin folding by the Polycomb group proteins and its elusive role in epigenetic repression.The FEBS journal · 2026Review
- Genome-wide modeling of DNA replication in space and time confirms the emergence of replication specific patterns in vivo in eukaryotes.Genome biology · 2025Article
- Dynamics of microcompartment formation at the mitosis-to-G1 transition.Nature structural & molecular biology · 2025Article
- Chromatin insulators in gene regulation and 3D genome organization.Biochemical Society transactions · 2025Review
- Dynamical properties of chromatin provide insights into key folding principles.Biophysical journal · 2025Article
- The emerging sequence grammar of 3D genome organisation.Human genetics · 2025Review
- RETRACTED: Kinetic organization of the genome revealed by ultraresolution multiscale live imaging.Science (New York, N.Y.) · 2025Article
- Article
- Polymer-derived distance penalties improve chromatin interaction predictions from single-cell data across crop genomes.bioRxiv : the preprint server for biology · 2025Article
165 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Genomes of eukaryotes are partitioned into domains of functionally distinct chromatin states. These domains are stably inherited across many cell generations and can be remodeled in response to developmental and external cues, hence contributing to the robustness and plasticity of expression patterns and cell phenotypes. Remarkably, recent studies indicate that these 1D epigenomic domains tend to fold into 3D topologically associated domains forming specialized nuclear chromatin compartments. However, the general mechanisms behind such compartmentalization including the contribution of epigenetic regulation remain unclear. Here, we address the question of the coupling between chromatin folding and epigenome. Using polymer physics, we analyze the properties of a block copolymer model that accounts for local epigenomic information. Considering copolymers build from the epigenomic landscape of Drosophila, we observe a very good agreement with the folding patterns observed in chromosome conformation capture experiments. Moreover, this model provides a physical basis for the existence of multistability in epigenome folding at sub-chromosomal scale. We show how experiments are fully consistent with multistable conformations where topologically associated domains of the same epigenomic state interact dynamically with each other. Our approach provides a general framework to improve our understanding of chromatin folding during cell cycle and differentiation and its relation to epigenetics.
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Registered trials
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.