ArticleNucleic acids research2018
Epigenomics in 3D: importance of long-range spreading and specific interactions in epigenomic maintenance.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Single-cell chromatin state transitions during epigenetic memory formation.Science advances · 2026Article
- Article
- Graded versus ON/OFF control in quantitative gene expression and epigenetic memory.The EMBO journal · 2026Review
- A Self-Organized Liquid Reaction Container for Cellular Memory.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Characterising Epigenetic Tipping Points using a Spectral Dimension Reduction Approach.Bulletin of mathematical biology · 2026Article
- Stochastic modeling of epigenetic memory.NPJ systems biology and applications · 2026Review
- How chromosome folding records events of a cell's past.Nature genetics · 2026Article
- Transient histone deacetylase inhibition induces cellular memory of gene expression and 3D genome folding.Nature genetics · 2026Article
- 3D genome folding in epigenetic regulation and cellular memory.Trends in cell biology · 2026Review
- Dynamical properties of chromatin provide insights into key folding principles.Biophysical journal · 2025Article
- Role of diffusion and reaction of the constituents in spreading of histone modification marks.PLoS computational biology · 2024Article
- Two-way feedback between chromatin compaction and histone modification state explainsProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Design principles of 3D epigenetic memory systems.Science (New York, N.Y.) · 2023Article
- HP1-driven phase separation recapitulates the thermodynamics and kinetics of heterochromatin condensate formation.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Two-way feedback between chromatin compaction and histone modification state explainsbioRxiv : the preprint server for biology · 2023Article
- Epigenetic switching with asymmetric bridging interactions.Biophysical journal · 2023Article
- Dynamical modeling of the H3K27 epigenetic landscape in mouse embryonic stem cells.PLoS computational biology · 2022Article
- Chromatin dynamics controls epigenetic domain formation.Biophysical journal · 2022Article
- Dissecting cell fate dynamics in pediatric glioblastoma through the lens of complex systems and cellular cybernetics.Biological cybernetics · 2022Review
- Heterogeneous interactions and polymer entropy decide organization and dynamics of chromatin domains.Biophysical journal · 2022Article
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2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent progresses of genome-wide chromatin conformation capture techniques have shown that the genome is segmented into hierarchically organized spatial compartments. However, whether this non-random 3D organization only reflects or indeed contributes-and how-to the regulation of genome function remain to be elucidated. The observation in many species that 3D domains correlate strongly with the 1D epigenomic information along the genome suggests a dynamic coupling between chromatin organization and epigenetic regulation. Here, we posit that chromosome folding may contribute to the maintenance of a robust epigenomic identity via the formation of spatial compartments like topologically-associating domains. Using a novel theoretical framework, the living chromatin model, we show that 3D compartmentalization leads to the spatial colocalization of epigenome regulators, thus increasing their local concentration and enhancing their ability to spread an epigenomic signal at long-range. Interestingly, we find that the presence of 1D insulator elements, like CTCF, may contribute greatly to the stable maintenance of adjacent antagonistic epigenomic domains. We discuss the generic implications of our findings in the light of various biological contexts from yeast to human. Our approach provides a modular framework to improve our understanding and to investigate in details the coupling between the structure and function of chromatin.
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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.