ArticlePLoS genetics2013
Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding.
Article in PLoS genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 123 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
123 citing papers in PubMed, 204 citations in OpenAlex.
- EnterotoxigenicProceedings of the National Academy of Sciences of the United States of America · 2018Trial
- Ability ofMicroorganisms · 2026Article
- The AadR-FixK hierarchy coordinates iron-responsive metabolism via Fur-family regulators inbioRxiv : the preprint server for biology · 2026Article
- ThebioRxiv : the preprint server for biology · 2026Article
- Revealing transcriptomic responses inmSystems · 2026Article
- Understanding Iron and Oxidative Stress Response inbioRxiv : the preprint server for biology · 2026Article
- The molecular basis of the synergistic toxicity of nickel and copper, common environmental co-contaminants.Applied and environmental microbiology · 2025Article
- Anoxia activates CRISPR-Cas immunity in the mouse intestine.Nature microbiology · 2025Article
- Laboratory Evolution Reveals Transcriptional Mechanisms Underlying Thermal Adaptation of Escherichia coli.Genome biology and evolution · 2025Article
- The Evolution of Function in the DNA-Binding Domain of the CRP/FNR Family.Genome biology and evolution · 2025Article
- Article
- Genome-Wide Analysis of DtxR and HrrA Regulons Reveals Novel Targets and a High Level of Interconnectivity Between Iron and Heme Regulatory Networks in Corynebacterium glutamicum.Molecular microbiology · 2025Article
- Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs.Nucleic acids research · 2025Article
- Klebsiella pneumoniae employs a type VI secretion system to overcome microbiota-mediated colonization resistance.Nature communications · 2025Article
- Dynamic quinone repertoire accompanied the diversification of energy metabolism in Pseudomonadota.The ISME journal · 2025Article
- Marine-derived L-asparaginase: unlocking marine power in anti-tumor therapeutics.Frontiers in immunology · 2025Review
- Article
- Tyrosol blocks E. coli anaerobic biofilm formation via YbfA and FNR to increase antibiotic susceptibility.Nature communications · 2024Article
- Alternate routes to mnmJournal of bacteriology · 2024Article
- Iron limitation indirectly reduces theMicrobiology spectrum · 2024Article
63 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
FNR is a well-studied global regulator of anaerobiosis, which is widely conserved across bacteria. Despite the importance of FNR and anaerobiosis in microbial lifestyles, the factors that influence its function on a genome-wide scale are poorly understood. Here, we report a functional genomic analysis of FNR action. We find that FNR occupancy at many target sites is strongly influenced by nucleoid-associated proteins (NAPs) that restrict access to many FNR binding sites. At a genome-wide level, only a subset of predicted FNR binding sites were bound under anaerobic fermentative conditions and many appeared to be masked by the NAPs H-NS, IHF and Fis. Similar assays in cells lacking H-NS and its paralog StpA showed increased FNR occupancy at sites bound by H-NS in WT strains, indicating that large regions of the genome are not readily accessible for FNR binding. Genome accessibility may also explain our finding that genome-wide FNR occupancy did not correlate with the match to consensus at binding sites, suggesting that significant variation in ChIP signal was attributable to cross-linking or immunoprecipitation efficiency rather than differences in binding affinities for FNR sites. Correlation of FNR ChIP-seq peaks with transcriptomic data showed that less than half of the FNR-regulated operons could be attributed to direct FNR binding. Conversely, FNR bound some promoters without regulating expression presumably requiring changes in activity of condition-specific transcription factors. Such combinatorial regulation may allow Escherichia coli to respond rapidly to environmental changes and confer an ecological advantage in the anaerobic but nutrient-fluctuating environment of the mammalian gut.
Indexed as
Identifiers
What OpenQuestion holds
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.