ArticleNature communications2015
The propagation of perturbations in rewired bacterial gene networks.
Article in Nature communications, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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Who cites it
11 citing papers in PubMed.
- Bacterial gene regulatory neural network as a biocomputing library of mathematical solvers.NPJ systems biology and applications · 2026Article
- Genetic properties underlying transcriptional variability across different perturbations.Nature communications · 2025Article
- Evolutionary innovation through transcription factor rewiring in microbes is shaped by levels of transcription factor activity, expression, and existing connectivity.PLoS biology · 2023Article
- Genome-wide promoter responses to CRISPR perturbations of regulators reveal regulatory networks in Escherichia coli.Nature communications · 2023Article
- Transcription factor expression levels and environmental signals constrain transcription factor innovation.Microbiology (Reading, England) · 2023Article
- Molecular basis for lethal cross-talk between two unrelated bacterial transcription factors - the regulatory protein of a restriction-modification system and the repressor of a defective prophage.Nucleic acids research · 2022Article
- Article
- Regulatory perturbations of ribosome allocation in bacteria reshape the growth proteome with a trade-off in adaptation capacity.iScience · 2022Article
- A quantitative method for proteome reallocation using minimal regulatory interventions.Nature chemical biology · 2020Article
- Scale free topology as an effective feedback system.PLoS computational biology · 2020Article
- Systematic and synthetic approaches to rewire regulatory networks.Current opinion in systems biology · 2018Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
What happens to gene expression when you add new links to a gene regulatory network? To answer this question, we profile 85 network rewirings in E. coli. Here we report that concerted patterns of differential expression propagate from reconnected hub genes. The rewirings link promoter regions to different transcription factor and σ-factor genes, resulting in perturbations that span four orders of magnitude, changing up to ∼ 70% of the transcriptome. Importantly, factor connectivity and promoter activity both associate with perturbation size. Perturbations from related rewirings have more similar transcription profiles and a statistical analysis reveals ∼ 20 underlying states of the system, associating particular gene groups with rewiring constructs. We examine two large clusters (ribosomal and flagellar genes) in detail. These represent alternative global outcomes from different rewirings because of antagonism between these major cell states. This data set of systematically related perturbations enables reverse engineering and discovery of underlying network interactions.
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Registered trials
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.