ArticleProceedings of the National Academy of Sciences of the United States of America2013
Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 142 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
142 citing papers in PubMed, 306 citations in OpenAlex.
- Type II topoisomerase substrate geometry revealed through combined experiment and computation.bioRxiv : the preprint server for biology · 2026Article
- Bridging-driven condensation by eukaryotic SMC complexes is a conserved feature of genome organization.Nucleic acids research · 2026Article
- 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
- Supercoils Stabilize a "DNA Corset" Condensate with Torsion-Dependent Hysteretic Compaction.JACS Au · 2026Article
- Yeast condensin acts as a transient intermolecular crosslinker in entangled DNA.Nucleic acids research · 2026Article
- Multiplex mapping of protein-protein interaction interfaces.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Functional architecture of cardiac TF regulatory landscapes in control of mammalian heart development.bioRxiv : the preprint server for biology · 2025Article
- Decoding the role of DNA sequence on protein-DNA co-condensation.PLoS computational biology · 2025Article
- Bridging-mediated compaction of mitotic chromosomes.Nucleus (Austin, Tex.) · 2025Review
- Chromatin unfolding via loops can drive clustered transposon insertion.Biophysical journal · 2025Article
- Bridging-Induced Phase Separation and Loop Extrusion Drive Noise in Chromatin Transcription.Physical review letters · 2025Article
- Role of RNA in genome folding: It's all about affinity.Current opinion in structural biology · 2025Review
- Multiplex mapping of protein-protein interaction interfaces.bioRxiv : the preprint server for biology · 2025Article
- Multiphasic Organization and Differential Dynamics of Proteins within Protein-DNA Biomolecular Condensates.The journal of physical chemistry. B · 2025Article
- Article
82 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
Molecular dynamics simulations are used to model proteins that diffuse to DNA, bind, and dissociate; in the absence of any explicit interaction between proteins, or between templates, binding spontaneously induces local DNA compaction and protein aggregation. Small bivalent proteins form into rows [as on binding of the bacterial histone-like nucleoid-structuring protein (H-NS)], large proteins into quasi-spherical aggregates (as on nanoparticle binding), and cylinders with eight binding sites (representing octameric nucleosomal cores) into irregularly folded clusters (like those seen in nucleosomal strings). Binding of RNA polymerase II and a transcription factor (NFκB) to the appropriate sites on four human chromosomes generates protein clusters analogous to transcription factories, multiscale loops, and intrachromosomal contacts that mimic those found in vivo. We suggest that this emergent behavior of clustering is driven by an entropic bridging-induced attraction that minimizes bending and looping penalties in the template.
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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.