ArticleNucleic acids research2016
Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers.
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Who cites it
86 citing papers in PubMed, 156 citations in OpenAlex.
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- GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors.Nature methods · 2026Article
- The MarR family regulator RmaH underlies the trade-off between acid sensitivity and antibiotic tolerance inJournal of bacteriology · 2026Article
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- LysR-type regulator LrhA promotes CRISPR-Cas immunity in Escherichia coli.Nucleic acids research · 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
- Posttranscriptional 3'-Terminal Modifications ofMicroorganisms · 2025Article
- The Environment-Dependent Regulatory Landscape of thebioRxiv : the preprint server for biology · 2025Article
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- High-resolution mapping of sigma factor DNA-binding sequences using artificial promoters, RNA aptamers, and deep sequencing.Nucleic acids research · 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
- A systematic survey of TF function in E. coli suggests RNAP stabilization is a prevalent strategy for both repressors and activators.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
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- Insights into the regulatory mechanisms and application prospects of the transcription factor Cra.Applied and environmental microbiology · 2024Review
- Dynamics design of a non-natural transcription factor responding to androst-4-ene-3,17-dione.Synthetic and systems biotechnology · 2024Article
- RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12.Nucleic acids research · 2024Article
- Regulatory Role of GgaR (YegW) for Glycogen Accumulation inMicroorganisms · 2024Article
26 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacterial genomes are transcribed by DNA-dependent RNA polymerase (RNAP), which achieves gene selectivity through interaction with sigma factors that recognize promoters, and transcription factors (TFs) that control the activity and specificity of RNAP holoenzyme. To understand the molecular mechanisms of transcriptional regulation, the identification of regulatory targets is needed for all these factors. We then performed genomic SELEX screenings of targets under the control of each sigma factor and each TF. Here we describe the assembly of 156 SELEX patterns of a total of 116 TFs performed in the presence and absence of effector ligands. The results reveal several novel concepts: (i) each TF regulates more targets than hitherto recognized; (ii) each promoter is regulated by more TFs than hitherto recognized; and (iii) the binding sites of some TFs are located within operons and even inside open reading frames. The binding sites of a set of global regulators, including cAMP receptor protein, LeuO and Lrp, overlap with those of the silencer H-NS, suggesting that certain global regulators play an anti-silencing role. To facilitate sharing of these accumulated SELEX datasets with the research community, we compiled a database, 'Transcription Profile of Escherichia coli' (www.shigen.nig.ac.jp/ecoli/tec/).
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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.