ArticleGenome research2011
Genome-wide detection of novel regulatory RNAs in E. coli.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 107 papers.
What it found
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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.
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Who cites it
107 citing papers in PubMed, 143 citations in OpenAlex.
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- Twin Small RNAs and Divergent Fates: The Expansive Regulatory Networks of OmrA and OmrB.International journal of molecular sciences · 2025Review
- Escherichia coli phylogeny drives co-amoxiclav resistance through variable expression of TEM-1 beta-lactamase.Nature communications · 2025Article
- Genome-wide annotation of transcript boundaries using bacterial Rend-seq datasets.Microbial genomics · 2024Article
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- CRISPR-dCas13a system for programmable small RNAs and polycistronic mRNA repression in bacteria.Nucleic acids research · 2024Article
- MultipleFrontiers in cellular and infection microbiology · 2023Article
- Key players in regulatory RNA realm of bacteria.Biochemistry and biophysics reports · 2022Review
- A Sporulation-Specific sRNA Bvs196 Contributing to the Developing Spore inMicroorganisms · 2022Article
- Genome-Wide Identification of Novel sRNAs in Streptococcus mutans.Journal of bacteriology · 2022Article
- PhoP induces RyjB expression under acid stress in Escherichia coli.Journal of biochemistry · 2022Article
- A Peroxide-Responding sRNA Evolved from a Peroxidase mRNA.Molecular biology and evolution · 2022Article
- What Flips the Switch? Signals and Stress Regulating Extraintestinal PathogenicMicroorganisms · 2021Review
- A small RNA is functional inMicrobiology (Reading, England) · 2021Article
- Characterization of 475 Novel, Putative Small RNAs (sRNAs) in Carbon-StarvedAntibiotics (Basel, Switzerland) · 2021Article
- Transcriptome-Wide Analysis of Stationary Phase Small ncRNAs inInternational journal of molecular sciences · 2021Article
- Divergently Transcribed ncRNAs inFrontiers in molecular biosciences · 2021Article
- Uncovering Transcriptional Regulators and Targets of sRNAs Using an Integrative Data-Mining Approach: H-NS-Regulated RseX as a Case Study.Frontiers in cellular and infection microbiology · 2021Article
47 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
The intergenic regions in bacterial genomes can contain regulatory leader sequences and small RNAs (sRNAs), which both serve to modulate gene expression. Computational analyses have predicted the presence of hundreds of these noncoding regulatory RNAs in Escherichia coli; however, only about 80 have been experimentally validated. By applying a deep-sequencing approach, we detected and quantified the vast majority of the previously validated regulatory elements and identified 10 new sRNAs and nine new regulatory leader sequences in the intergenic regions of E. coli. Half of the newly discovered sRNAs displayed enhanced stability in the presence of the RNA-binding protein Hfq, which is vital to the function of many of the known E. coli sRNAs. Whereas previous methods have often relied on phylogenetic conservation to identify regulatory leader sequences, only five of the newly discovered E. coli leader sequences were present in the genomes of other enteric species. For those newly identified regulatory elements having orthologs in Salmonella, evolutionary analyses showed that these regions encoded new noncoding elements rather than small, unannotated protein-coding transcripts. In addition to discovering new noncoding regulatory elements, we validated 53 sRNAs that were previously predicted but never detected and showed that the presence, within intergenic regions, of σ(70) promoters and sequences with compensatory mutations that maintain stable RNA secondary structures across related species is a good predictor of novel sRNAs.
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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.