ArticleBiophysical journal2022
Chromatin dynamics controls epigenetic domain formation.
Article in Biophysical journal, 2022. 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, 26 citations in OpenAlex.
- Formation of topologically associated chromatin domains using quantum annealing.Scientific reports · 2026Article
- A Self-Organized Liquid Reaction Container for Cellular Memory.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- How human-derived brain organoids are built differently from brain organoids derived from genetically-close relatives: a multi-scale hypothesis.Soft matter · 2026Article
- 3D genome folding in epigenetic regulation and cellular memory.Trends in cell biology · 2026Review
- Stretch regulated surface roughness controls macrophage inflammatory polarization through adhesion-chromatin coupling.Frontiers in pharmacology · 2026Article
- Epigenetic Regulation of Floral Transition.Plants (Basel, Switzerland) · 2025Review
- The Biological Function of Genome Organization.International journal of molecular sciences · 2025Review
- Polymer model integrates imaging and sequencing to reveal how nanoscale heterochromatin domains influence gene expression.Nature communications · 2025Article
- Role of diffusion and reaction of the constituents in spreading of histone modification marks.PLoS computational biology · 2024Article
- Active transcription and epigenetic reactions synergistically regulate meso-scale genomic organization.Nature communications · 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
- Polycomb repression of Hox genes involves spatial feedback but not domain compaction or phase transition.Nature genetics · 2024Article
- Design principles of 3D epigenetic memory systems.Science (New York, N.Y.) · 2023Article
- Regulation of the heterochromatin spreading reaction byOpen biology · 2023Review
- Heterogeneous interactions and polymer entropy decide organization and dynamics of chromatin domains.Biophysical journal · 2022Article
- Generation of dynamic three-dimensional genome structure through phase separation of chromatin.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- A Review of Mathematical and Computational Methods in Cancer Dynamics.Frontiers in oncology · 2022Review
- Multiscale modeling of genome organization with maximum entropy optimization.The Journal of chemical physics · 2021Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In multicellular organisms, nucleosomes carry epigenetic information that defines distinct patterns of gene expression, which are inherited over multiple generations. The enhanced capacity for information storage arises by nucleosome modifications, which are triggered by enzymes. Modified nucleosomes can transfer the mark to others that are in proximity by a positive-feedback (modification begets modification) mechanism. We created a generic polymer model, referred to as 3DSpreader, in which each bead, representing a nucleosome, stochastically switches between unmodified (U) and modified (M) states depending on the states of the neighbors. Modification begins at a specific nucleation site (NS) that is permanently in the M state, and could spread to other loci that is dictated by chromatin dynamics. Transfer of marks among the non-nucleation loci occurs stochastically as chromatin evolves in time. If the spreading rate is slower than the chromatin relaxation rate, which is biologically pertinent, then finite-sized domains form, driven by contacts between nucleosomes through a three-dimensional looping mechanism. Surprisingly, simulations based on the 3DSpreader model result in finite bounded domains that arise without the need for any boundary elements. Maintenance of spatially and temporally stable domains requires the presence of the NS, whose removal eliminates finite-sized modified domains. The theoretical predictions are in excellent agreement with experimental data for H3K9me3 spreading in mouse embryonic stem cells.
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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.