ArticleNucleic acids research2021
Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 54 citations in OpenAlex.
- Genome-wide screening of the Keio collection identifies genetic determinants of Escherichia coli sensitivity and tolerance to benzoic acid.World journal of microbiology & biotechnology · 2026Article
- Approaches for accelerating microbial gene function discovery using artificial intelligence.Nature microbiology · 2026Review
- Transcription Factor HusR (YnfL) Is a Novel Regulator for Hydroxyurea Sensitivity inMicroorganisms · 2026Article
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- Identification of gene targets regulated by the IclR-like regulator SL1344_3500 inJournal of bacteriology · 2025Article
- Genome-Wide Screen using Escherichia coli Keio knockout mutant line reveals genes related to the antimicrobial properties of trans-Cinnamic Acid.World journal of microbiology & biotechnology · 2025Article
- The Environment-Dependent Regulatory Landscape of thebioRxiv : the preprint server for biology · 2025Article
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- A transcription factor from the cryptic Escherichia coli Rac prophage controls both phage and host operons.Nucleic acids research · 2025Article
- Identification of a comprehensive set of transcriptional regulators involved in the long-term survivability of Escherichia coli in soil.Scientific reports · 2025Article
- ChIP-mini: a low-input ChIP-exo protocol for elucidating DNA-binding protein dynamics in intracellular pathogens.Nucleic acids research · 2025Article
- Raiding nature's genetic toolbox for UV-C resistance by functional metagenomics.Scientific reports · 2025Article
- Transcriptional Regulation in Bacteria.Microorganisms · 2024Article
- Deciphering regulatory architectures of bacterial promoters from synthetic expression patterns.PLoS computational biology · 2024Article
- Diversity of Transcriptional Regulatory Adaptation in E. coli.Molecular biology and evolution · 2024Article
- The Y-ome Conundrum: Insights into Uncharacterized Genes and Approaches for Functional Annotation.Molecular and cellular biochemistry · 2024Review
- Bacterial chromatin proteins, transcription, and DNA topology: Inseparable partners in the control of gene expression.Molecular microbiology · 2024Review
- Article
- Deciphering regulatory architectures from synthetic single-cell expression patterns.bioRxiv : the preprint server for biology · 2024Article
- RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12.Nucleic acids research · 2024Article
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacteria regulate gene expression to adapt to changing environments through transcriptional regulatory networks (TRNs). Although extensively studied, no TRN is fully characterized since the identity and activity of all the transcriptional regulators comprising a TRN are not known. Here, we experimentally evaluate 40 uncharacterized proteins in Escherichia coli K-12 MG1655, which were computationally predicted to be transcription factors (TFs). First, we used a multiplexed chromatin immunoprecipitation method combined with lambda exonuclease digestion (multiplexed ChIP-exo) assay to characterize binding sites for these candidate TFs; 34 of them were found to be DNA-binding proteins. We then compared the relative location between binding sites and RNA polymerase (RNAP). We found 48% (283/588) overlap between the TFs and RNAP. Finally, we used these data to infer potential functions for 10 of the 34 TFs with validated DNA binding sites and consensus binding motifs. Taken together, this study: (i) significantly expands the number of confirmed TFs to 276, close to the estimated total of about 280 TFs; (ii) provides putative functions for the newly discovered TFs and (iii) confirms the functions of four representative TFs through mutant phenotypes.
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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.