ArticlePLoS computational biology2022
Epigenetic cell memory: The gene's inner chromatin modification circuit.
Article in PLoS computational biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 42 citations in OpenAlex.
- Epigenetic insights of Olympic champions: nuclear and mitochondrial DNA methylation and regulators of aging.GeroScience · 2026Article
- Review
- Condensates and cell states: A new paradigm for understanding tumor biology.Biophysical journal · 2026Review
- Nonlinearities and Switch-Like Behavior in Gene Expression: From Genetics to Biochemistry and Back.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Review
- Beyond The Nucleus: Translating Engineered Protein Localization To Chromatin Modifying Enzymes.Current opinion in biomedical engineering · 2026Article
- Stochastic modeling of epigenetic memory.NPJ systems biology and applications · 2026Review
- Analog epigenetic memory revealed by targeted chromatin editing.Cell genomics · 2025Article
- Coclique level structure for stochastic chemical reaction networks.Journal of mathematical biology · 2025Article
- Reversing transgene silencing via targeted chromatin editing.bioRxiv : the preprint server for biology · 2025Article
- Review
- Epigenetic erosion of H4K20me1 induced by inflammation drives aged stem cell ferroptosis.Nature aging · 2025Article
- Epigenetic memory: The role of the crosstalk between histone modifications and DNA methylation.Computational and structural biotechnology journal · 2025Review
- Asymmetric autocatalytic reactions and their stationary distribution.Royal Society open science · 2024Article
- The evolutionary theory of cancer: challenges and potential solutions.Nature reviews. Cancer · 2024Review
- Induced Pluripotent Stem Cells as a Possible Approach for Exploring the Pathophysiology of Polycystic Ovary Syndrome (PCOS).Stem cell reviews and reports · 2024Review
- Nutrigenomics and redox regulation: Concepts relating to the Special Issue on nutrigenomics.Redox biology · 2023Review
- Aberrant Expression of TET2 Accounts for DNA Hypomethylation in Varicocele.Cell journal · 2023Article
- Tuning Methylation-Dependent Silencing Dynamics by Synthetic Modulation of CpG Density.ACS synthetic biology · 2023Article
- Tuning methylation-dependent silencing dynamics by synthetic modulation of CpG density.bioRxiv : the preprint server for biology · 2023Article
- Remembering through the genome: the role of chromatin states in brain functions and diseases.Translational psychiatry · 2023Review
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Epigenetic cell memory allows distinct gene expression patterns to persist in different cell types despite a common genotype. Although different patterns can be maintained by the concerted action of transcription factors (TFs), it was proposed that long-term persistence hinges on chromatin state. Here, we study how the dynamics of chromatin state affect memory, and focus on a biologically motivated circuit motif, among histones and DNA modifications, that mediates the action of TFs on gene expression. Memory arises from time-scale separation among three circuit's constituent processes: basal erasure, auto and cross-catalysis, and recruited erasure of modifications. When the two latter processes are sufficiently faster than the former, the circuit exhibits bistability and hysteresis, allowing active and repressed gene states to coexist and persist after TF stimulus removal. The duration of memory is stochastic with a mean value that increases as time-scale separation increases, but more so for the repressed state. This asymmetry stems from the cross-catalysis between repressive histone modifications and DNA methylation and is enhanced by the relatively slower decay rate of the latter. Nevertheless, TF-mediated positive autoregulation can rebalance this asymmetry and even confers robustness of active states to repressive stimuli. More generally, by wiring positively autoregulated chromatin modification circuits under time scale separation, long-term distinct gene expression patterns arise, which are also robust to failure in the regulatory links.
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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.