ArticleNucleic acids research2016
Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 99 papers.
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99 citing papers in PubMed.
- Phase separation of ecDNA condensates establishes in-trans contact domains that boost selective MYC regulatory interactions.Nature communications · 2026Article
- Article
- Transcription clusters and developmental pathways - nature, nurture, noise.Journal of cell science · 2026Review
- Physics-Based Modeling of Sparse Single-Cell Hi-C Uncovers Structural and Epigenetic Variability.International journal of molecular sciences · 2026Article
- On the molecular basis of enduring memory in neurons, and cell fate in fibroblasts.Nucleic acids research · 2026Review
- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Compaction of chromatin domains regulates target search times of proteins.PLoS computational biology · 2026Article
- Bridging-mediated compaction of mitotic chromosomes.Nucleus (Austin, Tex.) · 2025Review
- Transcriptional condensates encode a "golden mean" to optimize enhancer-promoter communication across genomic distances.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Bridging-Induced Phase Separation and Loop Extrusion Drive Noise in Chromatin Transcription.Physical review letters · 2025Article
- Article
- Differential Crosslinking and Contractile Motors Drive Nuclear Chromatin Compaction.bioRxiv : the preprint server for biology · 2025Article
- Article
- Coarse-grained chromatin dynamics by tracking multiple similarly labeled gene loci.Biophysical journal · 2025Article
- TF Profiler: a transcription factor inference method that broadly measures transcription factor activity and identifies mechanistically distinct networks.Genome biology · 2025Article
- Article
- Cohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion.Genome biology · 2024Article
- Polymer Physics Models Reveal Structural Folding Features of Single-Molecule Gene Chromatin Conformations.International journal of molecular sciences · 2024Article
- Exploring protein-mediated compaction of DNA by coarse-grained simulations and unsupervised learning.Biophysical journal · 2024Article
- Regulation of chromatin architecture by protein binding: insights from molecular modeling.Biophysical reviews · 2024Review
39 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
Biophysicists are modeling conformations of interphase chromosomes, often basing the strengths of interactions between segments distant on the genetic map on contact frequencies determined experimentally. Here, instead, we develop a fitting-free, minimal model: bivalent or multivalent red and green 'transcription factors' bind to cognate sites in strings of beads ('chromatin') to form molecular bridges stabilizing loops. In the absence of additional explicit forces, molecular dynamic simulations reveal that bound factors spontaneously cluster-red with red, green with green, but rarely red with green-to give structures reminiscent of transcription factories. Binding of just two transcription factors (or proteins) to active and inactive regions of human chromosomes yields rosettes, topological domains and contact maps much like those seen experimentally. This emergent 'bridging-induced attraction' proves to be a robust, simple and generic force able to organize interphase chromosomes at all scales.
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