ArticleProceedings of the National Academy of Sciences of the United States of America2016
Generalized nucleation and looping model for epigenetic memory of histone modifications.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. 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.
- 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
- Discrete Subdomains Establish Epigenetic Diversity in Subtelomeric Heterochromatin.bioRxiv : the preprint server for biology · 2025Article
- Epigenetic memory: The role of the crosstalk between histone modifications and DNA methylation.Computational and structural biotechnology journal · 2025Review
- Role of diffusion and reaction of the constituents in spreading of histone modification marks.PLoS computational biology · 2024Article
- Interplay between epigenome and 3D chromatin structure.BMB reports · 2023Review
- Design principles of 3D epigenetic memory systems.Science (New York, N.Y.) · 2023Article
- Regulation of the heterochromatin spreading reaction byOpen biology · 2023Review
- Relationship between lysine methyltransferase levels and heterochromatin gene repression in living cells and in silico.PNAS nexus · 2023Article
- Dynamical modeling of the H3K27 epigenetic landscape in mouse embryonic stem cells.PLoS computational biology · 2022Article
- Species-specific chromatin landscape determines how transposable elements shape genome evolution.eLife · 2022Article
- Chromatin dynamics controls epigenetic domain formation.Biophysical journal · 2022Article
- Article
- Impact of chromosomal organization on epigenetic drift and domain stability revealed by physics-based simulations.Biophysical journal · 2021Article
- Multiscale modeling of genome organization with maximum entropy optimization.The Journal of chemical physics · 2021Article
- Using computational modelling to reveal mechanisms of epigenetic Polycomb control.Biochemical Society transactions · 2021Review
- Histone modifications form a cell-type-specific chromosomal bar code that persists through the cell cycle.Scientific reports · 2021Article
- Single-molecule and in silico dissection of the interaction between Polycomb repressive complex 2 and chromatin.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Chromosome Structural Mechanics Dictates the Local Spreading of Epigenetic Marks.Biophysical journal · 2020Article
- Physical modeling of the heritability and maintenance of epigenetic modifications.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
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2 authors.
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Abstract
Histone modifications can redistribute along the genome in a sequence-independent manner, giving rise to chromatin position effects and epigenetic memory. The underlying mechanisms shape the endogenous chromatin landscape and determine its response to ectopically targeted histone modifiers. Here, we simulate linear and looping-driven spreading of histone modifications and compare both models to recent experiments on histone methylation in fission yeast. We find that a generalized nucleation-and-looping mechanism describes key observations on engineered and endogenous methylation domains including intrinsic spatial confinement, independent regulation of domain size and memory, variegation in the absence of antagonists, and coexistence of short- and long-term memory at loci with weak and strong constitutive nucleation. These findings support a straightforward relationship between the biochemical properties of chromatin modifiers and the spatiotemporal modification pattern. The proposed mechanism gives rise to a phase diagram for cellular memory that may be generally applicable to explain epigenetic phenomena across different species.
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