ArticleBiophysical journal2020
Dynamic Crowding Regulates Transcription.
Article in Biophysical journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.
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.
The trial behind it
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
17 citing papers in PubMed, 1 synthesis or guideline pooled it, 32 citations in OpenAlex.
- Macromolecular Crowding in Cytoplasm and Cellular Organelles.Sub-cellular biochemistry · 2025Pooled it
- Chromatin Packing Domain Engineering Through the Manipulation of Nuclear Cationic States.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- HCR-Proxy resolves site-specific proximal RNA microenvironments at subcompartmental resolution.Nucleic acids research · 2026Article
- Geometrically Encoded Positioning of Introns, Intergenic Segments, and Exons in the Human Genome.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Leveraging chromatin packing domains to target chemoevasion in vivo.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Geometrically encoded positioning of introns, intergenic segments, and exons in the human genome.bioRxiv : the preprint server for biology · 2025Article
- The impact of cell density variations on nanoparticle uptake across bioprinted A549 gradients.Frontiers in bioengineering and biotechnology · 2025Article
- Molecular Crowding by Computational Approaches.Sub-cellular biochemistry · 2025Review
- Hypothesis: bacteria live on the edge of phase transitions with a cell cycle regulated by a water-clock.Theory in biosciences = Theorie in den Biowissenschaften · 2024Article
- A life off the beaten track in biomechanics: Imperfect elasticity, cytoskeletal glassiness, and epithelial unjamming.Biophysics reviews · 2023Review
- Regulation of organelle size and organization during development.Seminars in cell & developmental biology · 2023Review
- Progress on Crowding Effect in Cell-like Structures.Membranes · 2022Review
- Investigating molecular crowding during cell division and hyperosmotic stress in budding yeast with FRET.Current topics in membranes · 2021Article
- Effect of Different Crowding Agents on the Architectural Properties of the Bacterial Nucleoid-Associated Protein HU.International journal of molecular sciences · 2020Article
- Navigating the crowd: visualizing coordination between genome dynamics, structure, and transcription.Genome biology · 2020Review
- Multiscale Genome Organization: Dazzling Subject and Inventive Methods.Biophysical journal · 2020Article
- The self-stirred genome: large-scale chromatin dynamics, its biophysical origins and implications.Current opinion in genetics & development · 2020Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
The nuclear environment is highly crowded by biological macromolecules, including chromatin and mobile proteins, which alter the kinetics and efficiency of transcriptional machinery. These alterations have been described, both theoretically and experimentally, for steady-state crowding densities; however, temporal changes in crowding density ("dynamic crowding") have yet to be integrated with gene expression. Dynamic crowding is pertinent to nuclear biology because processes such as chromatin translocation and protein diffusion lend to highly mobile biological crowders. Therefore, to capture such dynamic crowding and investigate its influence on transcription, we employ a three-pronged, systems-molecular approach. A system of chemical reactions represents the transcription pathway, the rates of which are determined by molecular-scale simulations; Brownian dynamics and Monte Carlo simulations quantify protein diffusion and DNA-protein binding affinity, dependent on macromolecular density. Altogether, this approach shows that transcription depends critically on dynamic crowding as the gene expression resultant from dynamic crowding can be profoundly different than that of steady-state crowding. In fact, expression levels can display both amplification and suppression and are notably different for genes or gene populations with different chemical and structural properties. These properties can be exploited to impose circadian expression, which is asymmetric and varies in strength, or to explain expression in cells under biomechanical stress. Therefore, this work demonstrates that dynamic crowding nontrivially alters transcription kinetics and presents dynamic crowding within the bulk nuclear nanoenvironment as a novel regulatory framework for gene expression.
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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.