ArticleThe EMBO journal2017
Small RNA interactome of pathogenic E. coli revealed through crosslinking of RNase E.
Article in The EMBO journal, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 109 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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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.
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Who cites it
109 citing papers in PubMed, 180 citations in OpenAlex.
- Bacterial small regulatory RNAs.Nature reviews. Microbiology · 2026Review
- Phage-encoded sRNA counteracts xenogeneic silencing in pathogenic E. coli.PLoS pathogens · 2026Article
- Progress and challenges in profiling protein-RNA and protein-associated RNA-RNA interactions.RNA (New York, N.Y.) · 2026Review
- From environmental signals to adaptive phenotypes: signal-responsive regulation and network logic of bacterial small RNAs.FEMS microbiology reviews · 2026Review
- Intramacrophage RIL-seq uncovers an RNA antagonist of the Salmonella virulence-associated small RNA PinT.Nucleic acids research · 2025Article
- Adaptive genetics reveals constraints on protein structure/function by evolving E. coli under constant nutrient limitation.BMC biology · 2025Article
- The type 6 secretion system immunity protein RhsFI has been repurposed for small RNA regulation in pathogenic Escherichia coli.Nucleic acids research · 2025Article
- The Role of Bacteriophage-Derived Small RNA Molecules in Bacterial and Phage Interactions.Viruses · 2025Review
- Improving prediction of bacterial sRNA regulatory targets with expression data.NAR genomics and bioinformatics · 2025Article
- GNNs and ensemble models enhance the prediction of new sRNA-mRNA interactions in unseen conditions.BMC bioinformatics · 2025Article
- Small regulatory RNAs as key modulators of antibiotic resistance in pathogenic bacteria.Journal of microbiology (Seoul, Korea) · 2025Review
- Two temperature-responsive RNAs act in concert: the small RNA CyaR and the mRNA ompX.Nucleic acids research · 2025Article
- Cas9-independent tracrRNA cytotoxicity inmicroLife · 2025Article
- The RNA-binding protein ProQ directly binds and regulates virulence genes in enterohemorrhagicFrontiers in cellular and infection microbiology · 2025Article
- Advances in sRNA-mediated regulation ofFrontiers in cellular and infection microbiology · 2025Review
- A newly discovered sRNA is involved in the virulence regulation ofFrontiers in veterinary science · 2025Article
- Biological Insights from RNA-RNA Interactomes in Bacteria, as Revealed by RIL-seq.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Global analysis of the RNA-RNA interactome in Acinetobacter baumannii AB5075 uncovers a small regulatory RNA repressing the virulence-related outer membrane protein CarO.Nucleic acids research · 2024Article
- Unraveling the interplay between a small RNA and RNase E in bacteria.Nucleic acids research · 2024Article
- Interplay of two small RNAs fine-tunes hierarchical flagella gene expression in Campylobacter jejuni.Nature communications · 2024Article
49 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors at 5 institutions in 2 countries.
Funding
Abstract
RNA sequencing studies have identified hundreds of non-coding RNAs in bacteria, including regulatory small RNA (sRNA). However, our understanding of sRNA function has lagged behind their identification due to a lack of tools for the high-throughput analysis of RNA-RNA interactions in bacteria. Here we demonstrate that in vivo sRNA-mRNA duplexes can be recovered using UV-crosslinking, ligation and sequencing of hybrids (CLASH). Many sRNAs recruit the endoribonuclease, RNase E, to facilitate processing of mRNAs. We were able to recover base-paired sRNA-mRNA duplexes in association with RNase E, allowing proximity-dependent ligation and sequencing of cognate sRNA-mRNA pairs as chimeric reads. We verified that this approach captures bona fide sRNA-mRNA interactions. Clustering analyses identified novel sRNA seed regions and sets of potentially co-regulated target mRNAs. We identified multiple mRNA targets for the pathotype-specific sRNA Esr41, which was shown to regulate colicin sensitivity and iron transport in E. coli Numerous sRNA interactions were also identified with non-coding RNAs, including sRNAs and tRNAs, demonstrating the high complexity of the sRNA interactome.
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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.