ArticleNature communications2023
In vivo RNA interactome profiling reveals 3'UTR-processed small RNA targeting a central regulatory hub.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 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
29 citing papers in PubMed, 34 citations in OpenAlex.
- Bacterial small regulatory RNAs.Nature reviews. Microbiology · 2026Review
- Modular small RNA drives the emergence of virulence traits and environmental trade-offs in Vibrio cholerae.Nature communications · 2026Article
- Regulation of RNase PH during nutrient deprivation: the role of proteases, GroEL, and RNase II.mBio · 2026Article
- Identification and characterization of small RNAs expressed by Leptospira borgpetersenii serovar Hardjo and their conservation in the genus Leptospira.BMC microbiology · 2026Article
- Codon bias shapes bacterial small RNA binding sites within protein-coding sequences.RNA (New York, N.Y.) · 2026Article
- Article
- Progress and challenges in profiling protein-RNA and protein-associated RNA-RNA interactions.RNA (New York, N.Y.) · 2026Review
- Article
- Global perspectives on Klebsiella epidemiology and biology: conference report on the KLEBS 2024 symposium.npj antimicrobials and resistance · 2026Article
- From environmental signals to adaptive phenotypes: signal-responsive regulation and network logic of bacterial small RNAs.FEMS microbiology reviews · 2026Review
- Origin and adaptive evolutionary trajectory of the 3' UTR-derived sRNA UhpU in Enterobacteriaceae.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- RNA-RNA interactome approaches provide in vivo evidence for a critical role of the Hfq rim face in sRNA-mRNA pairing.Nucleic acids research · 2025Article
- Intramacrophage RIL-seq uncovers an RNA antagonist of the Salmonella virulence-associated small RNA PinT.Nucleic acids research · 2025Article
- 3'UTR-derived small RNA couples acid resistance to metabolic reprogramming of Salmonella within macrophages.Nucleic acids research · 2025Article
- Development of two compatible plasmids to assess sRNA-mediated post-transcriptional regulation inMicrobiology (Reading, England) · 2025Article
- Conserved mycobacterial sRNA B11 regulates lipooligosaccharide synthesis at posttranscriptional level inmLife · 2025Article
- Global analysis of the Hfq-mediated RNA interactome discovers a MicA homolog that affects the cytotoxicity, biofilm formation, and resistance to complement of Bordetella pertussis.Nucleic acids research · 2025Article
- Bacterial Regulatory Circuits are Linked and Extended by Small RNAs.Journal of molecular biology · 2025Review
- TheJournal of bacteriology · 2025Article
- An RNase III-processed sRNA coordinates sialic acid metabolism ofProceedings of the National Academy of Sciences of the United States of America · 2025Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
Abstract
Small noncoding RNAs (sRNAs) are crucial regulators of gene expression in bacteria. Acting in concert with major RNA chaperones such as Hfq or ProQ, sRNAs base-pair with multiple target mRNAs and form large RNA-RNA interaction networks. To systematically investigate the RNA-RNA interactome in living cells, we have developed a streamlined in vivo approach iRIL-seq (intracellular RIL-seq). This generic approach is highly robust, illustrating the dynamic sRNA interactomes in Salmonella enterica across multiple stages of growth. We have identified the OmpD porin mRNA as a central regulatory hub that is targeted by a dozen sRNAs, including FadZ cleaved from the conserved 3'UTR of fadBA mRNA. Both ompD and FadZ are activated by CRP, constituting a type I incoherent feed-forward loop in the fatty acid metabolism pathway. Altogether, we have established an approach to profile RNA-RNA interactomes in live cells, highlighting the complexity of RNA regulatory hubs and RNA networks.
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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.