ArticlemBio2023
Genome-Wide Mapping of the Escherichia coli PhoB Regulon Reveals Many Transcriptionally Inert, Intragenic Binding Sites.
Article in mBio, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
15 citing papers in PubMed, 21 citations in OpenAlex.
- Disentangling factors affecting bacterial transcriptional regulatory network inference.iScience · 2026Article
- Two-Component Systems inVeterinary sciences · 2025Review
- Analysis of stress-induced small proteins inScience signaling · 2025Article
- Analysis of stress-induced small proteins inbioRxiv : the preprint server for biology · 2025Article
- Genome-wide mapping of cyclic AMP receptor protein binding in EnteroaggregativebioRxiv : the preprint server for biology · 2025Article
- Genome-wide mapping of cAMP receptor protein binding in enteroaggregativeMicrobiology (Reading, England) · 2025Article
- Community Structure, Growth-Promoting Potential, and Genomic Analysis of Seed-Endophytic Bacteria inMicroorganisms · 2025Article
- Unveiling the role of the PhoP master regulator in arsenite resistance throughCurrent research in microbial sciences · 2025Article
- Transcription activation inEcoSal Plus · 2024Review
- An intracellular phosphorus-starvation signal activates the PhoB/PhoR two-component system inmBio · 2024Article
- Core Transcriptome of Hydrogen Producing Marine Vibrios Reveals Contribution of Glycolysis in Their Efficient Hydrogen Production.Current microbiology · 2024Article
- Phosphorus deficiency alleviates iron limitation in Synechocystis cyanobacteria through direct PhoB-mediated gene regulation.Nature communications · 2024Article
- Combined transcriptomic and ChIPseq analyses of themSystems · 2024Article
- Cbp1 and Cren7 form chromatin-like structures that ensure efficient transcription of long CRISPR arrays.Nature communications · 2024Article
- Phosphorus starvation response and PhoB-independent utilization of organic phosphate sources byMicrobiology spectrum · 2023Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Genome-scale analyses have revealed many transcription factor binding sites within, rather than upstream of, genes, raising questions as to the function of these binding sites. Here, we use complementary approaches to map the regulon of the Escherichia coli transcription factor PhoB, a response regulator that controls transcription of genes involved in phosphate homeostasis. Strikingly, the majority of PhoB binding sites are located within genes, but these intragenic sites are not associated with detectable transcription regulation and are not evolutionarily conserved. Many intragenic PhoB sites are located in regions bound by H-NS, likely due to shared sequence preferences of PhoB and H-NS. However, these PhoB binding sites are not associated with transcription regulation even in the absence of H-NS. We propose that for many transcription factors, including PhoB, binding sites not associated with promoter sequences are transcriptionally inert and hence are tolerated as genomic "noise."
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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.