ArticleProceedings of the National Academy of Sciences of the United States of America2020
Nucleosomal proofreading of activator-promoter interactions.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 35 citations in OpenAlex.
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- Invariant nonequilibrium dynamics in gene regulation optimize information flow.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Highly Constrained Kinetic Models for Single-Cell Gene Expression Analysis.bioRxiv : the preprint server for biology · 2026Article
- Chromatin enables precise and scalable gene regulation with factors of limited specificity.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Flexibility and sensitivity in gene regulation out of equilibrium.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Trade-offs and thermodynamics of energy-relay proofreading.Journal of the Royal Society, Interface · 2024Article
- The method in the madness: Transcriptional control from stochastic action at the single-molecule scale.Current opinion in structural biology · 2024Review
- Single gene analysis in yeast suggests nonequilibrium regulatory dynamics for transcription.Nature communications · 2024Article
- The Hill function is the universal Hopfield barrier for sharpness of input-output responses.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Governing principles of transcriptional logic out of equilibrium.Biophysical journal · 2024Article
- The Hill function is the universal Hopfield barrier for sharpness of input-output responses.bioRxiv : the preprint server for biology · 2024Article
- Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation.Developmental cell · 2023Article
- Dynamic epistasis analysis reveals how chromatin remodeling regulates transcriptional bursting.Nature structural & molecular biology · 2023Article
- Competing constraints shape the nonequilibrium limits of cellular decision-making.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Article
- A matter of time: Using dynamics and theory to uncover mechanisms of transcriptional bursting.Current opinion in cell biology · 2020Review
- Review
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2 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Specificity in transcriptional regulation is imparted by transcriptional activators that bind to specific DNA sequences from which they stimulate transcription. Specificity may be increased by slowing down the kinetics of regulation: by increasing the energy for dissociation of the activator-DNA complex or decreasing activator concentration. In general, higher dissociation energies imply longer DNA dwell times of the activator; the activator-bound gene may not readily turn off again. Lower activator concentrations entail longer pauses between binding events; the activator-unbound gene is not easily turned on again and activated transcription occurs in stochastic bursts. We show that kinetic proofreading of activator-DNA recognition-insertion of an energy-dissipating delay step into the activation pathway for transcription-reconciles high specificity of transcriptional regulation with fast regulatory kinetics. We show that kinetic proofreading results from the stochastic removal and reformation of promoter nucleosomes, at a distance from equilibrium.
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