ArticlePLoS biology2021
Genome-wide gene expression noise in Escherichia coli is condition-dependent and determined by propagation of noise through the regulatory network.
Article in PLoS biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 51 citations in OpenAlex.
- E. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients.Molecular systems biology · 2026Article
- Heterogeneity in microbial antibiotic responses: genetic basis and within-host evolution.Trends in genetics : TIG · 2026Review
- Inter-individual gene expression variability implies stable regulation of brain-biased genes across organs in three ray-finned fishes.bioRxiv : the preprint server for biology · 2026Article
- Single-cell approach dissecting agr quorum sensing dynamics in Staphylococcus aureus.Nature communications · 2026Article
- Single-cell phenotypic heterogeneity shapes quorum signaling dynamics in Pseudomonas aeruginosa.Nature communications · 2026Article
- Dissecting microbial communities with single-cell transcriptome analysis.Science (New York, N.Y.) · 2025Review
- Congruence between noise and plasticity in protein expression.Scientific reports · 2025Article
- Growth rate controls the sensitivity of gene regulatory circuits.Science advances · 2025Article
- Gene syntaxes modulate gene expression and circuit behavior on plasmids.Journal of biological engineering · 2025Article
- Stress-Induced Constraint on Expression Noise of Essential Genes in E. coli.Journal of molecular evolution · 2024Article
- Progressive decline in old pole gene expression signal enhances phenotypic heterogeneity in bacteria.Science advances · 2024Article
- Genetically encoded transcriptional plasticity underlies stress adaptation in Mycobacterium tuberculosis.Nature communications · 2024Article
- Genetically encoded transcriptional plasticity underlies stress adaptation in Mycobacterium tuberculosis.Research square · 2023Article
- Growth-dependent Gene Expression Variation Influences the Strength of Codon Usage Biases.Molecular biology and evolution · 2023Article
- Genetically encoded transcriptional plasticity underlies stress adaptation in Mycobacterium tuberculosis.bioRxiv : the preprint server for biology · 2023Article
- Growth-dependent gene expression variation influences the strength of codon usage biases.bioRxiv : the preprint server for biology · 2023Article
- The Influence of Heteroresistance on Minimum Inhibitory Concentration, Investigated Using Weak-Acid Stress in Food Spoilage Yeasts.Applied and environmental microbiology · 2023Article
- Being noisy in a crowd: Differential selective pressure on gene expression noise in model gene regulatory networks.PLoS computational biology · 2023Article
- Effective bet-hedging through growth rate dependent stability.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Variable DNA topology is an epigenetic generator of physiological heterogeneity in bacterial populations.Molecular microbiology · 2023Review
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although it is well appreciated that gene expression is inherently noisy and that transcriptional noise is encoded in a promoter's sequence, little is known about the extent to which noise levels of individual promoters vary across growth conditions. Using flow cytometry, we here quantify transcriptional noise in Escherichia coli genome-wide across 8 growth conditions and find that noise levels systematically decrease with growth rate, with a condition-dependent lower bound on noise. Whereas constitutive promoters consistently exhibit low noise in all conditions, regulated promoters are both more noisy on average and more variable in noise across conditions. Moreover, individual promoters show highly distinct variation in noise across conditions. We show that a simple model of noise propagation from regulators to their targets can explain a significant fraction of the variation in relative noise levels and identifies TFs that most contribute to both condition-specific and condition-independent noise propagation. In addition, analysis of the genome-wide correlation structure of various gene properties shows that gene regulation, expression noise, and noise plasticity are all positively correlated genome-wide and vary independently of variations in absolute expression, codon bias, and evolutionary rate. Together, our results show that while absolute expression noise tends to decrease with growth rate, relative noise levels of genes are highly condition-dependent and determined by the propagation of noise through the gene regulatory network.
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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.