ArticleCell2016
Information Integration and Energy Expenditure in Gene Regulation.
Article in Cell, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 95 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
95 citing papers in PubMed, 191 citations in OpenAlex.
- Stable epigenetic states set single-cell activation thresholds in mammalian expression systems.bioRxiv : the preprint server for biology · 2026Article
- Invariant nonequilibrium dynamics in gene regulation optimize information flow.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Intrinsic promoter responsiveness dictates sensitivity to transcriptional activation by enhancers.bioRxiv : the preprint server for biology · 2026Article
- Decoupling between activation time and steady-state level in input-output responses.PLoS computational biology · 2026Article
- Modeling of gene regulatory networks: an annotated glossary.Trends in plant science · 2026Review
- Evolution of dominance in a Mendelian trait is linked to the evolution of environmental plasticity.Evolution; international journal of organic evolution · 2026Article
- Quantitative modulation of a spatial enhancer through the biophysical properties of a transcription factor binding site.Science advances · 2026Article
- How cells tame noise while maintaining ultrasensitive transcriptional responses.PLoS computational biology · 2025Article
- Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs.bioRxiv : the preprint server for biology · 2025Article
- Algebraic formulas for first-passage times of Markov processes in the linear framework.Bulletin of mathematical biology · 2025Article
- Emergence of activation or repression in transcriptional control under a fixed molecular context.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Decoupling between activation time and steady-state level in input-output responses.bioRxiv : the preprint server for biology · 2025Article
- Coordinated active repression operates via transcription factor cooperativity and multiple inactive promoter states in a developing organism.Nature communications · 2025Article
- Bicoid-nucleosome competition sets a concentration threshold for transcription constrained by genome replication.Cell reports · 2025Article
- Gene regulatory logic of the interferon-β enhancer is characterized by two selectively deployed modes of transcription factor synergy.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Article
- Evolution of dominance in a Mendelian trait is linked to the evolution of environmental plasticity.bioRxiv : the preprint server for biology · 2025Article
- Both the transcriptional activator, Bcd, and repressor, Cic, form small mobile oligomeric clusters.Biophysical journal · 2025Article
- Article
- Stochastic thermodynamics for biological functions.Quantitative biology (Beijing, China) · 2025Review
35 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
4 authors at 1 institution in 1 country.
Funding
Abstract
The quantitative concepts used to reason about gene regulation largely derive from bacterial studies. We show that this bacterial paradigm cannot explain the sharp expression of a canonical developmental gene in response to a regulating transcription factor (TF). In the absence of energy expenditure, with regulatory DNA at thermodynamic equilibrium, information integration across multiple TF binding sites can generate the required sharpness, but with strong constraints on the resultant "higher-order cooperativities." Even with such integration, there is a "Hopfield barrier" to sharpness; for n TF binding sites, this barrier is represented by the Hill function with the Hill coefficient n. If, however, energy is expended to maintain regulatory DNA away from thermodynamic equilibrium, as in kinetic proofreading, this barrier can be breached and greater sharpness achieved. Our approach is grounded in fundamental physics, leads to testable experimental predictions, and suggests how a quantitative paradigm for eukaryotic gene regulation can be formulated.
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What OpenQuestion holds
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.