ArticlePLoS biology2013
Promoter sequence determines the relationship between expression level and noise.
Article in PLoS biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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Who cites it
83 citing papers in PubMed.
- Molecular evolution in light of regulatory-coding epistasis.EMBO reports · 2026Review
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- CD28 and CTLA4 polymorphisms associated with ankylosing spondylitis: a study in the context of HLA-B27.BMC immunology · 2025Article
- Quantifying cell fate change under different stochastic gene activation frameworks.Quantitative biology (Beijing, China) · 2025Article
- The impact of phenotypic heterogeneity on fungal pathogenicity and drug resistance.FEMS microbiology reviews · 2025Review
- Anti-windup strategies for biomolecular control systems facilitated by model reduction theory for sequestration networks.Science advances · 2024Article
- What can we learn when fitting a simple telegraph model to a complex gene expression model?PLoS computational biology · 2024Article
- Promoters in Pichia pastoris: A Toolbox for Fine-Tuned Gene Expression.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development.Nature communications · 2023Article
- Multidimensional characterization of inducible promoters and a highly light-sensitive LOV-transcription factor.Nature communications · 2023Article
- Enhanced Transcriptional Strength of HIV-1 Subtype C Minimizes Gene Expression Noise and Confers Stability to the Viral Latent State.Journal of virology · 2023Article
- Genome-wide inference reveals that feedback regulations constrain promoter-dependent transcriptional burst kinetics.Nucleic acids research · 2023Article
- Controlling gene expression timing through gene regulatory architecture.PLoS computational biology · 2022Article
- Association between the side effect induced by COVID-19 vaccines and the immune regulatory gene polymorphism.Frontiers in immunology · 2022Article
- Genome-wide gene expression noise in Escherichia coli is condition-dependent and determined by propagation of noise through the regulatory network.PLoS biology · 2021Article
- Article
- Role of integrated noise in pathway-specific signal propagation in feed-forward loops.Theory in biosciences = Theorie in den Biowissenschaften · 2021Article
- Microbial metabolic noise.WIREs mechanisms of disease · 2021Review
- CD28 Gene Polymorphisms in the Promoter Region Are Associated with Transfusion Reactions: A Functional Study.Journal of clinical medicine · 2021Article
- Transcriptional and Epigenetic Bioinformatic Analysis of Claudin-9 Regulation in Gastric Cancer.Journal of oncology · 2021Article
23 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
The ability of cells to accurately control gene expression levels in response to extracellular cues is limited by the inherently stochastic nature of transcriptional regulation. A change in transcription factor (TF) activity results in changes in the expression of its targets, but the way in which cell-to-cell variability in expression (noise) changes as a function of TF activity, and whether targets of the same TF behave similarly, is not known. Here, we measure expression and noise as a function of TF activity for 16 native targets of the transcription factor Zap1 that are regulated by it through diverse mechanisms. For most activated and repressed Zap1 targets, noise decreases as expression increases. Kinetic modeling suggests that this is due to two distinct Zap1-mediated mechanisms that both change the frequency of transcriptional bursts. Notably, we found that another mechanism of repression by Zap1, which is encoded in the promoter DNA, likely decreases the size of transcriptional bursts, producing a unique transcriptional state characterized by low expression and low noise. In addition, we find that further reduction in noise is achieved when a single TF both activates and represses a single target gene. Our results suggest a global principle whereby at low TF concentrations, the dominant source of differences in expression between promoters stems from differences in burst frequency, whereas at high TF concentrations differences in burst size dominate. Taken together, we show that the precise amount by which noise changes with expression is specific to the regulatory mechanism of transcription and translation that acts at each gene.
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