ArticleProceedings of the National Academy of Sciences of the United States of America2020
Physical modeling of the heritability and maintenance of epigenetic modifications.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 54 citations in OpenAlex.
- Single-cell chromatin state transitions during epigenetic memory formation.Science advances · 2026Article
- A Self-Organized Liquid Reaction Container for Cellular Memory.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Physical models reveal indirect reader protein interactions that facilitate epigenetic crosstalk.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- 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
- Physical modeling of nucleosome clustering in euchromatin resulting from interactions between epigenetic reader proteins.Proceedings of the National Academy of Sciences of the United States of America · 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
- Single-cell chromatin state transitions during epigenetic memory formation.bioRxiv : the preprint server for biology · 2023Article
- Leveraging polymer modeling to reconstruct chromatin connectivity from live images.Biophysical journal · 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
- Chromatin accessibility: methods, mechanisms, and biological insights.Nucleus (Austin, Tex.) · 2022Review
- Chromatin dynamics controls epigenetic domain formation.Biophysical journal · 2022Article
- Heterogeneous interactions and polymer entropy decide organization and dynamics of chromatin domains.Biophysical journal · 2022Article
- Cell cycle arrest explains the observed bulk 3D genomic alterations in response to long-term heat shock in K562 cells.Genome research · 2022Article
- H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells.Genome research · 2022Article
- Roadmap on plasticity and epigenetics in cancer.Physical biology · 2022Review
- DNA sequence-dependent formation of heterochromatin nanodomains.Nature communications · 2022Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We develop a predictive theoretical model of the physical mechanisms that govern the heritability and maintenance of epigenetic modifications. This model focuses on a particular modification, methylation of lysine-9 of histone H3 (H3K9), which is one of the most representative and critical epigenetic marks that affects chromatin organization and gene expression. Our model combines the effect of segregation and compaction on chromosomal organization with the effect of the interaction between proteins that compact the chromatin (heterochromatin protein 1) and the methyltransferases that affect methyl spreading. Our chromatin model demonstrates that a block of H3K9 methylations in the epigenetic sequence determines the compaction state at any particular location in the chromatin. Using our predictive model for chromatin compaction, we develop a methylation model to address the reestablishment of the methylation sequence following DNA replication. Our model reliably maintains methylation over generations, thereby establishing the robustness of the epigenetic code.
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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.