ArticleNucleic acids research2015
The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 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
24 citing papers in PubMed.
- Rewiring of cell morphology by Small protein B enhances stress tolerance and colonization in Aeromonas veronii under adverse conditions.Nucleic acids research · 2025Article
- ArgR-dependent bacterial resistance to host lipid droplets in Edwardsiella piscicida.Communications biology · 2025Article
- Klebsiella pneumoniae employs a type VI secretion system to overcome microbiota-mediated colonization resistance.Nature communications · 2025Article
- Decoding the regulatory networks ofFrontiers in cellular and infection microbiology · 2025Article
- A novel two-component system contributing the catabolism of c-di-GMP influences virulence inFrontiers in microbiology · 2025Article
- Identification of an ArgR-controlled promoter within the outermost region of the ISJournal of bacteriology · 2024Article
- Inferred regulons are consistent with regulator binding sequences in E. coli.PLoS computational biology · 2024Article
- The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets.Nucleic acids research · 2023Article
- Article
- Experimental promoter identification of a foodborne pathogenFrontiers in microbiology · 2023Article
- The Arginine Repressor ArgRMicrobiology spectrum · 2022Article
- The EcoCyc Database in 2021.Frontiers in microbiology · 2021Article
- l-Arginine sensing regulates virulence gene expression and disease progression in enteric pathogens.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Competitive Repression of theFrontiers in microbiology · 2019Article
- Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655.Nucleic acids research · 2018Article
- Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions.Applied and environmental microbiology · 2018Article
- Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism.Nature communications · 2018Article
- A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0.BMC biology · 2018Article
- Insights from resolving protein-DNA interactions at near base-pair resolution.Briefings in functional genomics · 2018Review
- Global transcriptional regulatory network forProceedings of the National Academy of Sciences of the United States of America · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA-binding motifs that are recognized by transcription factors (TFs) have been well studied; however, challenges remain in determining the in vivo architecture of TF-DNA complexes on a genome-scale. Here, we determined the in vivo architecture of Escherichia coli arginine repressor (ArgR)-DNA complexes using high-throughput sequencing of exonuclease-treated chromatin-immunoprecipitated DNA (ChIP-exo). The ChIP-exo has a unique peak-pair pattern indicating 5' and 3' ends of ArgR-binding region. We identified 62 ArgR-binding loci, which were classified into three groups, comprising single, double and triple peak-pairs. Each peak-pair has a unique 93 base pair (bp)-long (±2 bp) ArgR-binding sequence containing two ARG boxes (39 bp) and residual sequences. Moreover, the three ArgR-binding modes defined by the position of the two ARG boxes indicate that DNA bends centered between the pair of ARG boxes facilitate the non-specific contacts between ArgR subunits and the residual sequences. Additionally, our approach may also reveal other fundamental structural features of TF-DNA interactions that have implications for studying genome-scale transcriptional regulatory networks.
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.