ArticleBiophysical journal2006
Entropy-driven genome organization.
Article in Biophysical journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 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
70 citing papers in PubMed.
- Phase separation of ecDNA condensates establishes in-trans contact domains that boost selective MYC regulatory interactions.Nature communications · 2026Article
- The Fluid Mosaic Model of chromatin organization: integrating dynamics, conformational heterogeneity and multiscale organization.Communications biology · 2026Review
- Reversible Bacterial Depletion Aggregation and Restabilization by Water-Soluble Polymers.Langmuir : the ACS journal of surfaces and colloids · 2025Article
- Accelerated amyloid fibril formation at the interface of liquid-liquid phase-separated droplets by depletion interactions.Protein science : a publication of the Protein Society · 2025Article
- Understanding and Simulating the Dynamics of a Polymer-Like Chromatin.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Entropy-Driven, Integrative Bioinformatics Approaches Reveal the Recent Transmission of the Monkeypox Virus from Nigeria to Multiple Non-African Countries.Molecular biotechnology · 2024Article
- Orientation-independent-DIC imaging reveals that a transient rise in depletion attraction contributes to mitotic chromosome condensation.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Morphological control of bundled actin networks subject to fixed-mass depletion.The Journal of chemical physics · 2024Article
- Modeling the compaction of bacterial chromosomes by biomolecular crowding and the cross-linking protein H-NS.Scientific reports · 2024Article
- Consistencies and contradictions in different polymer models of chromatin architecture.Computational and structural biotechnology journal · 2023Review
- DNA sliding and loop formation byBiochemistry and biophysics reports · 2022Article
- Entropy Perspectives of Molecular and Evolutionary Biology.International journal of molecular sciences · 2022Review
- Molecular dynamics analysis of biomolecular systems including nucleic acids.Biophysics and physicobiology · 2022Article
- Weak interactions in higher-order chromatin organization.Nucleic acids research · 2020Review
- Confinement Geometry Tunes Fascin-Actin Bundle Structures and Consequently the Shape of a Lipid Bilayer Vesicle.Frontiers in molecular biosciences · 2020Article
- Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR.Current opinion in structural biology · 2019Review
- Physical principles of retroviral integration in the human genome.Nature communications · 2019Article
- From 1D sequence to 3D chromatin dynamics and cellular functions: a phase separation perspective.Nucleic acids research · 2018Article
- Formation of Chromatin Subcompartments by Phase Separation.Biophysical journal · 2018Review
- Entropic effect of macromolecular crowding enhances binding between nucleosome clutches in heterochromatin, but not in euchromatin.Scientific reports · 2018Article
10 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
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA and RNA polymerases active on bacterial and human genomes in the crowded environment of a cell are modeled as beads spaced along a string. Aggregation of the large polymerizing complexes increases the entropy of the system through an increase in entropy of the many small crowding molecules; this occurs despite the entropic costs of looping the intervening DNA. Results of a quantitative cost/benefit analysis are consistent with observations that active polymerases cluster into replication and transcription "factories" in both pro- and eukaryotes. We conclude that the second law of thermodynamics acts through nonspecific entropic forces between engaged polymerases to drive the self-organization of genomes into loops containing several thousands (and sometimes millions) of basepairs.
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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.