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Related Concept Videos

Operon Model01:23

Operon Model

The operon model represents a fundamental mechanism of gene regulation in prokaryotes, enabling coordinated expression of genes involved in related metabolic or functional pathways. Operons consist of structural genes, a promoter, and an operator, with transcription regulated by repressors, activators, and small effector molecules.Structure and Function of OperonsAn operon is a cluster of structural genes transcribed together under the control of a single promoter. The promoter region...
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Constitutive and Regulated Gene Expression

Gene expression in prokaryotes is governed by constitutive and regulated systems, allowing cells to balance the production of essential proteins with adaptive responses to environmental changes.Constitutive Gene ExpressionConstitutive, or housekeeping, genes are continuously expressed as they encode proteins vital for fundamental cellular processes. These include enzymes for glycolysis, ribosomal components for protein synthesis, and proteins involved in DNA replication. Their constant...
Non-equilibrium in the Cell01:16

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An important concept in studying metabolism and energy is that of chemical equilibrium. Most chemical reactions are reversible. They can proceed in both directions, releasing energy into their environment in one direction, and absorbing it from the environment in the other direction. The same is true for the chemical reactions involved in cell metabolism, such as the breaking down and building up of proteins into and from individual amino acids, respectively. Reactants within a closed system...
Translational Regulation01:29

Translational Regulation

Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
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The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the addition of a...
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Updated: Jul 8, 2026

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
10:44

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

Invariant nonequilibrium dynamics in gene regulation optimize information flow.

Benjamin Zoller1, Alexis Bénichou2, Thomas Gregor1,3

  • 1Department of Stem Cell and Developmental Biology, CNRS UMR3738 Paris Cité, Institut Pasteur, Paris FR-75015, France.

Proceedings of the National Academy of Sciences of the United States of America
|July 6, 2026
PubMed
Summary
This summary is machine-generated.

Eukaryotic gene regulation uses a switching correlation time (Tc) that remains constant across expression levels. This study reveals that nonequilibrium dynamics and at least four states are required to explain this observed invariance.

Keywords:
Markov modelsinformation theorypromoter switchingtranscriptional regulation

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Area of Science:

  • Molecular Biology
  • Systems Biology
  • Biophysics

Background:

  • Eukaryotic gene regulation involves promoter switching between active and inactive states.
  • A consistent "switching correlation time" (Tc) has been observed across various genes and organisms, lacking a clear biophysical explanation.

Purpose of the Study:

  • To investigate the biophysical requirements for the observed invariance of switching correlation time in eukaryotic gene regulation.
  • To develop and test models that explain the constant switching correlation time across different gene expression levels.

Main Methods:

  • Developed minimal yet realistic models of transcriptional regulation.
  • Utilized Bayesian inference on Drosophila gap gene expression data.
  • Analyzed nonequilibrium dynamics and detailed balance breaking in regulatory architectures.

Main Results:

  • Models with at least four internal states and broken detailed balance quantitatively reproduced the observed Tc-invariance.
  • The models demonstrated robustness to parameter perturbations.
  • The identified optimal strategy maximized information transmission from transcription factor concentration to gene expression.

Conclusions:

  • Eukaryotic transcriptional regulation likely operates in a nonequilibrium regime.
  • This nonequilibrium strategy balances precision, reaction-rate limitations, and energy dissipation.
  • The findings suggest near-optimal information transmission under fundamental physical constraints.