ArticleNucleic acids research2022
The transcription factor network of E. coli steers global responses to shifts in RNAP concentration.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Thermal Shifts Dominate Single-Gene Responses to Transcription-Targeting Antibiotics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Distinct transcription factor network dynamics underlie early and long-term adaptation to rifampicin inmSystems · 2026Article
- Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs.Nucleic acids research · 2025Article
- Dynamics of bacterial operons during genome-wide stresses is influenced by premature terminations and internal promoters.Science advances · 2025Article
- Bimodality in E. coli gene expression: Sources and robustness to genome-wide stresses.PLoS computational biology · 2025Article
- Biochemical characterization ofJournal of bacteriology · 2024Article
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- Global control of cellular physiology by biomolecular condensates through modulation of electrochemical equilibria.bioRxiv : the preprint server for biology · 2023Article
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18 authors.
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Abstract
The robustness and sensitivity of gene networks to environmental changes is critical for cell survival. How gene networks produce specific, chronologically ordered responses to genome-wide perturbations, while robustly maintaining homeostasis, remains an open question. We analysed if short- and mid-term genome-wide responses to shifts in RNA polymerase (RNAP) concentration are influenced by the known topology and logic of the transcription factor network (TFN) of Escherichia coli. We found that, at the gene cohort level, the magnitude of the single-gene, mid-term transcriptional responses to changes in RNAP concentration can be explained by the absolute difference between the gene's numbers of activating and repressing input transcription factors (TFs). Interestingly, this difference is strongly positively correlated with the number of input TFs of the gene. Meanwhile, short-term responses showed only weak influence from the TFN. Our results suggest that the global topological traits of the TFN of E. coli shape which gene cohorts respond to genome-wide stresses.
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