ArticleMolecular cell2016
Global Mapping of Small RNA-Target Interactions in Bacteria.
Article in Molecular cell, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 245 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
245 citing papers in PubMed, 418 citations in OpenAlex.
- Bacterial small regulatory RNAs.Nature reviews. Microbiology · 2026Review
- A glycolytic intermediate gatekeeps global mRNA decay in Escherichia coli.Nature communications · 2026Article
- A 3'UTR-derived small RNA modulates the life cycle of the cholera toxin-encoding filamentous phage, CTXϕ.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Distribution of prophage-encoded Pas sRNAs across pathogenicbioRxiv : the preprint server for biology · 2026Article
- Codon bias shapes bacterial small RNA binding sites within protein-coding sequences.RNA (New York, N.Y.) · 2026Article
- rbpCNN: a biophysics-informed deep learning model for predicting piRNA and mRNA interactions.Scientific reports · 2026Article
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- SUPER: Upcycling Genetic Parts for Precise Gene Expression Control, Leakage Minimization, and Genetic Circuit Stability.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Article
- From environmental signals to adaptive phenotypes: signal-responsive regulation and network logic of bacterial small RNAs.FEMS microbiology reviews · 2026Review
- Machine Learning Approaches for Predicting RNA-RNA/DNA Interactions.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle.Molecular cell · 2025Article
- 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
- Coordination of the Fe-S cluster biogenesis network by the sRNA RyhB inRNA biology · 2025Article
- Intramacrophage RIL-seq uncovers an RNA antagonist of the Salmonella virulence-associated small RNA PinT.Nucleic acids research · 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
- 3'UTR-derived small RNA couples acid resistance to metabolic reprogramming of Salmonella within macrophages.Nucleic acids research · 2025Article
- An RNA sponge directs the transition from feast to famine in Caulobacter crescentus.Nature communications · 2025Article
- Article
- Adaptive genetics reveals constraints on protein structure/function by evolving E. coli under constant nutrient limitation.BMC biology · 2025Article
185 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Small RNAs (sRNAs) associated with the RNA chaperon protein Hfq are key posttranscriptional regulators of gene expression in bacteria. Deciphering the sRNA-target interactome is an essential step toward understanding the roles of sRNAs in the cellular networks. We developed a broadly applicable methodology termed RIL-seq (RNA interaction by ligation and sequencing), which integrates experimental and computational tools for in vivo transcriptome-wide identification of interactions involving Hfq-associated sRNAs. By applying this methodology to Escherichia coli we discovered an extensive network of interactions involving RNA pairs showing sequence complementarity. We expand the ensemble of targets for known sRNAs, uncover additional Hfq-bound sRNAs encoded in various genomic regions along with their trans encoded targets, and provide insights into binding and possible cycling of RNAs on Hfq. Comparison of the sRNA interactome under various conditions has revealed changes in the sRNA repertoire as well as substantial re-wiring of the network between conditions.
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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.