ArticleNature protocols2018
Mapping the small RNA interactome in bacteria using RIL-seq.
Article in Nature protocols, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed, 104 citations in OpenAlex.
- Loss of CsrA inProceedings of the National Academy of Sciences of the United States of America · 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
- TheInfection and immunity · 2026Article
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- A bacterial translation activator with an intrinsically disordered RNA-binding region.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
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- Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle.Molecular cell · 2025Article
- 3'UTR-derived small RNA couples acid resistance to metabolic reprogramming of Salmonella within macrophages.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
- Intramacrophage RIL-seq uncovers an RNA antagonist of the Salmonella virulence-associated small RNA PinT.Nucleic acids research · 2025Article
- An RNA sponge directs the transition from feast to famine in Caulobacter crescentus.Nature communications · 2025Article
- Article
- 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
- Improving prediction of bacterial sRNA regulatory targets with expression data.NAR genomics and bioinformatics · 2025Article
- Tiny but Mighty: Small RNAs-The Micromanagers of Bacterial Survival, Virulence, and Host-Pathogen Interactions.Non-coding RNA · 2025Review
- Modulation of protein activity by small RNA base pairing internal to coding sequences.Molecular cell · 2025Article
- Formation of a membraneless compartment regulates bacterial virulence.Nature communications · 2025Article
- DuplexDiscoverer: a computational method for the analysis of experimental duplex RNA-RNA interaction data.Nucleic acids research · 2025Article
- Small regulatory RNAs as key modulators of antibiotic resistance in pathogenic bacteria.Journal of microbiology (Seoul, Korea) · 2025Review
- Genomic insights into bacteriophages: a new frontier in AMR detection and phage therapy.Briefings in functional genomics · 2025Review
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) are major post-transcriptional regulators of gene expression in bacteria. To enable transcriptome-wide mapping of bacterial sRNA-target pairs, we developed RIL-seq (RNA interaction by ligation and sequencing). RIL-seq is an experimental-computational methodology for capturing sRNA-target interactions in vivo that takes advantage of the mutual binding of the sRNA and target RNA molecules to the RNA chaperone protein Hfq. The experimental part of the protocol involves co-immunoprecipitation of Hfq and bound RNAs, ligation of RNAs, library preparation and sequencing. The computational pipeline maps the sequenced fragments to the genome, reveals chimeric fragments (fragments comprising two ligated independent fragments) and determines statistically significant overrepresented chimeric fragments as interacting RNAs. The statistical filter is aimed at reducing the number of spurious interactions resulting from ligation of random neighboring RNA fragments, thus increasing the reliability of the determined sRNA-target pairs. A major advantage of RIL-seq is that it does not require overexpression of sRNAs; instead, it simultaneously captures the in vivo targets of all sRNAs in the native state of the cell. Application of RIL-seq to bacteria grown under different conditions provides distinctive snapshots of the sRNA interactome and sheds light on the dynamics and rewiring of the post-transcriptional regulatory network. As RIL-seq needs no prior information about the sRNA and target sequences, it can identify novel sRNAs, along with their targets. It can be adapted to detect protein-mediated RNA-RNA interactions in any bacterium with a sequenced genome. The experimental part of the RIL-seq protocol takes 7-9 d and the computational analysis takes ∼2 d.
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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.