ArticleMolecular systems biology2013
Promoters maintain their relative activity levels under different growth conditions.
Article in Molecular systems biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers, 1 of them a synthesis that pooled it.
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Who cites it
91 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Analysing and meta-analysing time-series data of microbial growth and gene expression from plate readers.PLoS computational biology · 2022Pooled it
- Active-learning-guided optimization of cell-free systems for genome-wide transcriptomic profiling reveals progressive layers of regulation.Nature communications · 2026Article
- A constitutive promoter toolbox for tunable gene expression in Acinetobacter baumannii.Applied microbiology and biotechnology · 2026Article
- Exploring chromosomal position effects for predictable tuning of metabolic pathways in yeast.Nucleic acids research · 2026Article
- Revealing global stoichiometry conservation architecture in cells from Raman spectral patterns.eLife · 2026Article
- Engineering heterologous core promoters to optimize the SES expression system forSynthetic and systems biotechnology · 2026Article
- Construction of aACS omega · 2025Article
- The role of plasmid copy number and mutation rate in evolutionary outcomes.Nature ecology & evolution · 2025Article
- Live-cell omics with Raman spectroscopy.Microscopy (Oxford, England) · 2025Review
- Unraveling the regulatory dynamics of bidirectional promoters for modulating gene co-expression and metabolic flux in Saccharomyces cerevisiae.Nucleic acids research · 2025Article
- A CRISPR-Cas9 system for knock-out and knock-in of high molecular weight DNA enables module-swapping of the pikromycin synthase in its native host.Microbial cell factories · 2025Article
- Vibrio natriegens: Application of a Fast-Growing Halophilic Bacterium.Advances in biochemical engineering/biotechnology · 2025Review
- A comparative analysis of NADPH supply strategies inMetabolic engineering communications · 2024Article
- Single-cell heterogeneity in ribosome content and the consequences for the growth laws.bioRxiv : the preprint server for biology · 2024Article
- Functional predictability of universal gene circuits in diverse microbial hosts.Quantitative biology (Beijing, China) · 2024Article
- Species-aware DNA language models capture regulatory elements and their evolution.Genome biology · 2024Article
- Increased CONature communications · 2024Article
- Combinatorial optimization of gene expression through recombinase-mediated promoter and terminator shuffling in yeast.Nature communications · 2024Article
- Saccharomyces boulardii promoters for control of gene expression in vivo.Microbial cell factories · 2024Article
- Tradeoffs in bacterial physiology determine the efficiency of antibiotic killing.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
31 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
13 authors.
Funding
Abstract
Most genes change expression levels across conditions, but it is unclear which of these changes represents specific regulation and what determines their quantitative degree. Here, we accurately measured activities of ~900 S. cerevisiae and ~1800 E. coli promoters using fluorescent reporters. We show that in both organisms 60-90% of promoters change their expression between conditions by a constant global scaling factor that depends only on the conditions and not on the promoter's identity. Quantifying such global effects allows precise characterization of specific regulation-promoters deviating from the global scale line. These are organized into few functionally related groups that also adhere to scale lines and preserve their relative activities across conditions. Thus, only several scaling factors suffice to accurately describe genome-wide expression profiles across conditions. We present a parameter-free passive resource allocation model that quantitatively accounts for the global scaling factors. It suggests that many changes in expression across conditions result from global effects and not specific regulation, and provides means for quantitative interpretation of expression profiles.
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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.