ArticleNature communications2025
Polymer model integrates imaging and sequencing to reveal how nanoscale heterochromatin domains influence gene expression.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Nuclear mechanotransduction: tools for mechanical perturbation and chromatin characterization.Nucleus (Austin, Tex.) · 2026Review
- In Vivo Direct Reprogramming: Current Progress and Future Prospects from Mechanisms to Therapeutic Application.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- IntravChip: a vascularized and perfused microfluidic model of the primary tumor microenvironment to collect intravasated tumor cells.Biofabrication · 2026Article
- Power-law penalties correct distance bias in single-cell co-accessibility and deep-learning chromatin interaction predictions.NAR genomics and bioinformatics · 2026Article
- Architecture and regulation of nanoscale chromatin domains.Nature communications · 2026Review
- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- IntravChip: a vascularized and perfused microfluidic model of the primary tumor microenvironment to collect intravasated tumor cells.bioRxiv : the preprint server for biology · 2026Article
- Transient histone deacetylase inhibition induces cellular memory of gene expression and 3D genome folding.Nature genetics · 2026Article
- Scaling and self-similarity in the formation of the embryonic epigenome.Nature physics · 2026Article
- Transient histone deacetylase inhibition reveals cell type invariant and specific effects of chromatin decondensation on irradiation response.Frontiers in cell and developmental biology · 2026Article
- Revealing the biophysics of lamina-associated domain formation by integrating theoretical modeling and high-resolution imaging.Nature communications · 2025Article
- Polymer-derived distance penalties improve chromatin interaction predictions from single-cell data across crop genomes.bioRxiv : the preprint server for biology · 2025Article
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Authors and funding
8 authors.
Funding
Abstract
Chromatin organization regulates gene expression, with nanoscale heterochromatin domains playing a fundamental role. Their size varies with microenvironmental stiffness and epigenetic interventions, but how these factors regulate their formation and influence transcription remains unclear. To address this, we developed a sequencing-informed copolymer model that simulates chromatin evolution through diffusion and active epigenetic reactions. Our model predicts the formation of nanoscale heterochromatin domains and quantifies how domain size scales with epigenetic reaction rates, showing that epigenetic and compaction changes primarily occur at domain boundaries. We validated these predictions via Hi-C and super-resolution imaging of hyperacetylated melanoma cells and identified differential expression of metastasis-related genes through RNA-seq. We validated our findings in hMSCs, where epigenetic reaction rates respond to microenvironmental stiffness. Conclusively, our simulations reveal that heterochromatin domain boundaries regulate gene expression and epigenetic memory. These findings demonstrate how external cues drive chromatin organization and transcriptional memory in development and disease.
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