ArticleNucleic acids research2018
Shaping epigenetic memory via genomic bookmarking.
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 32 papers.
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Who cites it
32 citing papers in PubMed, 80 citations in OpenAlex.
- Graded versus ON/OFF control in quantitative gene expression and epigenetic memory.The EMBO journal · 2026Review
- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- A Self-Organized Liquid Reaction Container for Cellular Memory.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- 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
- Environmental conditions elicit a slow but enduring response of histone post-translational modifications in Mozambique tilapia.Environmental epigenetics · 2024Article
- Design principles of 3D epigenetic memory systems.Science (New York, N.Y.) · 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
- Individual Genetic Heterogeneity.Genes · 2022Review
- Chromatin dynamics controls epigenetic domain formation.Biophysical journal · 2022Article
- Article
- DNA sequence-dependent formation of heterochromatin nanodomains.Nature communications · 2022Article
- High fidelity epigenetic inheritance: Information theoretic model predicts threshold filling of histone modifications post replication.PLoS computational biology · 2022Article
- Predictive Polymer Models for 3D Chromosome Organization.Methods in molecular biology (Clifton, N.J.) · 2022Review
- Impact of chromosomal organization on epigenetic drift and domain stability revealed by physics-based simulations.Biophysical journal · 2021Article
- The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study.PLoS computational biology · 2021Article
- Unfolding of the chromatin fiber driven by overexpression of noninteracting bridging factors.Biophysical journal · 2021Article
- A DNA Sequence Based Polymer Model for Chromatin Folding.International journal of molecular sciences · 2021Article
- Review
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Reconciling the stability of epigenetic patterns with the rapid turnover of histone modifications and their adaptability to external stimuli is an outstanding challenge. Here, we propose a new biophysical mechanism that can establish and maintain robust yet plastic epigenetic domains via genomic bookmarking (GBM). We model chromatin as a recolourable polymer whose segments bear non-permanent histone marks (or colours) which can be modified by 'writer' proteins. The three-dimensional chromatin organisation is mediated by protein bridges, or 'readers', such as Polycomb Repressive Complexes and Transcription Factors. The coupling between readers and writers drives spreading of biochemical marks and sustains the memory of local chromatin states across replication and mitosis. In contrast, GBM-targeted perturbations destabilise the epigenetic patterns. Strikingly, we demonstrate that GBM alone can explain the full distribution of Polycomb marks in a whole Drosophila chromosome. We finally suggest that our model provides a starting point for an understanding of the biophysics of cellular differentiation and reprogramming.
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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.