ArticleBiophysical journal2014
Macromolecular crowding as a regulator of gene transcription.
Article in Biophysical journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 90 citations in OpenAlex.
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- 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
- Chromatin Organization Governs Transcriptional Response and Plasticity of Cancer Stem Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Chromatin conformation, gene transcription, and nucleosome remodeling as an emergent system.Science advances · 2025Article
- The impact of charge regulation and ionic intranuclear environment on the nucleosome core particle.The Journal of chemical physics · 2024Article
- The Impact of Charge Regulation and Ionic Intranuclear Environment on the Nucleosome Core Particle.bioRxiv : the preprint server for biology · 2024Article
- Size Sensitivity of Metabolite Diffusion in Macromolecular Crowds.Nano letters · 2024Article
- The Role of Intracellular Potassium in Cell Quiescence, Proliferation, and Death.International journal of molecular sciences · 2024Review
- Mesenchymal Stem/Stromal Cells in Three-Dimensional Cell Culture: Ion Homeostasis and Ouabain-Induced Apoptosis.Biomedicines · 2023Article
- Surfactancy in a tadpole model of proteins.Journal of the Royal Society, Interface · 2022Article
- Evaluation of weak interactions of proteins and organic cations with DNA duplex structures.Biophysical journal · 2022Article
- Analysis of three-dimensional chromatin packing domains by chromatin scanning transmission electron microscopy (ChromSTEM).Scientific reports · 2022Article
- Monovalent ions and stress-induced senescence in human mesenchymal endometrial stem/stromal cells.Scientific reports · 2022Article
- Macromolecular crowding effects on the kinetics of opposing reactions catalyzed by alcohol dehydrogenase.Biochemistry and biophysics reports · 2021Article
- Nanoscale chromatin imaging and analysis platform bridges 4D chromatin organization with molecular function.Science advances · 2021Article
- Navigating the crowd: visualizing coordination between genome dynamics, structure, and transcription.Genome biology · 2020Review
- Transcription and Translation in Cytomimetic Protocells Perform Most Efficiently at Distinct Macromolecular Crowding Conditions.ACS synthetic biology · 2020Article
- Dynamic Crowding Regulates Transcription.Biophysical journal · 2020Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Studies of macromolecular crowding have shown its important effects on molecular transport and interactions in living cells. Less clear is the effect of crowding when its influence is incorporated into a complex network of interactions. Here, we explore the effects of crowding in the cell nucleus on a model of gene transcription as a network of reactions involving transcription factors, RNA polymerases, and DNA binding sites for these proteins. The novelty of our approach is that we determine the effects of crowding on the rates of these reactions using Brownian dynamics and Monte Carlo simulations, allowing us to integrate molecular-scale information, such as the shapes and sizes of each molecular species, into the rate equations of the model. The steady-state cytoplasmic mRNA concentration shows several regimes with qualitatively different dependences on the volume fraction, ϕ, of crowding agents in the nucleus, including a broad range of parameter values where it depends nonmonotonically on ϕ, with maximum mRNA production occurring at a physiologically relevant value. The extent of this crowding dependence can be modulated by a variety of means, suggesting that the transcriptional output of a gene can be regulated jointly by the local level of macromolecular crowding in the nucleus, together with the local concentrations of polymerases and DNA-binding proteins, as well as other properties of the gene's physical environment.
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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.