ArticleNature communications2024
Single gene analysis in yeast suggests nonequilibrium regulatory dynamics for transcription.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- scYeast: a biological-knowledge-guided foundation model on yeast single-cell transcriptomics.Synthetic and systems biotechnology · 2027Article
- 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
- RiboScreenBiomedicines · 2026Review
- Highly Constrained Kinetic Models for Single-Cell Gene Expression Analysis.bioRxiv : the preprint server for biology · 2026Article
- RNA polymerase II initiation factors show different dynamic behaviour upon induced transcription in live cells.bioRxiv : the preprint server for biology · 2025Article
- Identification and understanding of allostery hotspots in proteins: Integration of deep mutational scanning and multi-faceted computational analyses.Journal of molecular biology · 2025Review
- Timing is everything: transcription bursting in development.Genes & development · 2025Review
- Quantification and potential functional relevance of binding cooperativity of adjacent transcription factors on DNA.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Machine learning in molecular biophysics: Protein allostery, multi-level free energy simulations, and lipid phase transitions.Biophysics reviews · 2025Review
- Inferring transcriptional bursting kinetics from single-cell snapshot data using a generalized telegraph model.Royal Society open science · 2023Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Fluctuations in the initiation rate of transcription, the first step in gene expression, ensue from the stochastic behavior of the molecular process that controls transcription. In steady state, the regulatory process is often assumed to operate reversibly, i.e., in equilibrium. However, reversibility imposes fundamental limits to information processing. For instance, the assumption of equilibrium is difficult to square with the precision with which the regulatory process executes its task in eukaryotes. Here we provide evidence - from microscopic analyses of the transcription dynamics at a single gene copy of yeast - that the regulatory process for transcription is cyclic and irreversible (out of equilibrium). The necessary coupling to reservoirs of free energy occurs via sequence-specific transcriptional activators and the recruitment, in part, of ATP-dependent chromatin remodelers. Our findings may help explain how eukaryotic cells reconcile the dual but opposing requirements for fast regulatory kinetics and high regulatory specificity.
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