ArticlePLoS genetics2015
Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding.
Article in PLoS genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 62 citations in OpenAlex.
- Article
- RpoN mediates biofilm formation by directly controllingBiofilm · 2025Article
- Expanding the σ54-dependent transcription process with orthogonal designs.Nucleic acids research · 2025Article
- ProPr54 web server: predicting σNAR genomics and bioinformatics · 2025Article
- Unveiling the novel regulatory roles of RpoD-family sigma factors in Salmonella Typhimurium heat shock response through systems biology approaches.PLoS genetics · 2024Article
- σCommunications biology · 2024Article
- Article
- Article
- A general mechanism for transcription bubble nucleation in bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Genome-wide mapping of thebioRxiv : the preprint server for biology · 2023Article
- Experimental promoter identification of a foodborne pathogenFrontiers in microbiology · 2023Article
- ChEAP: ChIP-exo analysis pipeline and the investigation ofComputational and structural biotechnology journal · 2023Article
- Review
- Automated model-predictive design of synthetic promoters to control transcriptional profiles in bacteria.Nature communications · 2022Article
- Genome-wide protein-DNA interaction site mapping in bacteria using a double-stranded DNA-specific cytosine deaminase.Nature microbiology · 2022Article
- Genome-wide promoter assembly inGenome research · 2022Article
- A Role for the RNA Polymerase Gene Specificity Factor σJournal of bacteriology · 2022Article
- The role of nitrogen-responsive regulators in controlling inorganic polyphosphate synthesis inMicrobiology (Reading, England) · 2022Article
- Methylation Motifs in Promoter Sequences May Contribute to the Maintenance of a ConservedMicroorganisms · 2021Article
- Whole set of constitutive promoters for RpoN sigma factor and the regulatory role of its enhancer protein NtrC inMicrobial genomics · 2021Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Bacterial RNA polymerases must associate with a σ factor to bind promoter DNA and initiate transcription. There are two families of σ factor: the σ70 family and the σ54 family. Members of the σ54 family are distinct in their ability to bind promoter DNA sequences, in the context of RNA polymerase holoenzyme, in a transcriptionally inactive state. Here, we map the genome-wide association of Escherichia coli σ54, the archetypal member of the σ54 family. Thus, we vastly expand the list of known σ54 binding sites to 135. Moreover, we estimate that there are more than 250 σ54 sites in total. Strikingly, the majority of σ54 binding sites are located inside genes. The location and orientation of intragenic σ54 binding sites is non-random, and many intragenic σ54 binding sites are conserved. We conclude that many intragenic σ54 binding sites are likely to be functional. Consistent with this assertion, we identify three conserved, intragenic σ54 promoters that drive transcription of mRNAs with unusually long 5' UTRs.
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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.