ArticleiScience2021
Mathematical modeling of histone modifications reveals the formation mechanism and function of bivalent chromatin.
Article in iScience, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Clinical response to azacitidine in MDS is associated with distinct DNA methylation changes in HSPCs.Nature communications · 2025Trial
- Stochastic modeling of epigenetic memory.NPJ systems biology and applications · 2026Review
- Large-scale reorganization of DNA methylation and upregulation of extracellular matrix genes in the dorsal dentate gyrus following cocaine taking.bioRxiv : the preprint server for biology · 2026Article
- Bivalent chromatin accommodates survivin and BRG1/SWI complex to activate DNA damage response in CD4Cell communication and signaling : CCS · 2024Article
- Stochastic nucleosome disassembly mediated by remodelers and histone fragmentation.The Journal of chemical physics · 2023Article
- Epigenetic factor competition reshapes the EMT landscape.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Network design principle for robust oscillatory behaviors with respect to biological noise.eLife · 2022Article
- The nonequilibrium mechanism of noise-enhanced drug synergy in HIV latency reactivation.iScience · 2022Article
- Emergent dynamics of a three-node regulatory network explain phenotypic switching and heterogeneity: a case study of Th1/Th2/Th17 cell differentiation.Molecular biology of the cell · 2022Article
- Bivalent Regulation and Related Mechanisms of H3K4/27/9me3 in Stem Cells.Stem cell reviews and reports · 2022Review
- NRF2-dependent Epigenetic Regulation can Promote the Hybrid Epithelial/Mesenchymal Phenotype.Frontiers in cell and developmental biology · 2021Article
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Authors and funding
5 authors.
Funding
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Abstract
Bivalent chromatin is characterized by occupation of both activating and repressive histone modifications. Here, we develop a mathematical model that involves antagonistic histone modifications H3K4me3 and H3K27me3 to capture the key features of bivalent chromatin. Three necessary conditions for the emergence of bivalent chromatin are identified, including advantageous methylating activity over demethylating activity, frequent noise conversions of modifications, and sufficient nonlinearity. The first condition is further confirmed by analyzing the existing experimental data. Investigation of the composition of bivalent chromatin reveals that bivalent nucleosomes carrying both H3K4me3 and H3K27me3 account for no more than half of nucleosomes at the bivalent chromatin domain. We identify that bivalent chromatin not only allows transitions to multiple states but also serves as a stepping stone to facilitate a stepwise transition between repressive chromatin state and activating chromatin state and thus elucidate crucial roles of bivalent chromatin in mediating phenotypical plasticity during cell fate determination.
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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.