ArticleThe EMBO journal2016
Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo.
Article in The EMBO journal, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 191 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
191 citing papers in PubMed, 305 citations in OpenAlex.
- Bacterial small regulatory RNAs.Nature reviews. Microbiology · 2026Review
- Small Regulatory RNAs in Prokaryotes: Key Features, Identification, Environmental Roles, and Applications.Microorganisms · 2026Review
- Identification of highly immunogenic endogenous dsRNAs from cellular MDA5 filaments.bioRxiv : the preprint server for biology · 2026Article
- SmallBARNA 2026: a kingdom-wide bacterial sRNA resource.Nucleic acids research · 2026Article
- Structural dependence of ProQ-mRNA interactions in live bacterial cells.Communications biology · 2025Article
- 3'UTR-derived small RNA couples acid resistance to metabolic reprogramming of Salmonella within macrophages.Nucleic acids research · 2025Article
- Intramacrophage RIL-seq uncovers an RNA antagonist of the Salmonella virulence-associated small RNA PinT.Nucleic acids research · 2025Article
- A Small RNA Derived From the 5' End of the IS200 tnpA Transcript Regulates Multiple Virulence Regulons in Salmonella typhimurium.Molecular microbiology · 2025Article
- KH-R3H domain cooperation in RNA recognition by the global RNA-binding protein KhpB.Nature communications · 2025Article
- Article
- RNA-binding protein YebC enhances translation of proline-rich amino acid stretches in bacteria.Nature communications · 2025Article
- What makes a small RNA work?Nucleic acids research · 2025Review
- The Power Duo: How the Interplay Between Nucleoid-Associated Proteins and Small Noncoding RNAs Orchestrates the Cellular Regulatory Symphony.Molecular microbiology · 2025Review
- Dynamic and intricate regulation by the Csr sRNAs in the Arctic Pseudoalteromonas fuliginea.Communications biology · 2025Article
- Improved constructs for bait RNA display in a bacterial three-hybrid assay.Scientific reports · 2025Article
- The global RNA-binding protein RbpB is a regulator of polysaccharide utilization in Bacteroides thetaiotaomicron.Nature communications · 2025Article
- RBProkCNN: Deep learning on appropriate contextual evolutionary information for RNA binding protein discovery in prokaryotes.Computational and structural biotechnology journal · 2024Article
- Improved constructs for bait RNA display in a bacterial three-hybrid assay.bioRxiv : the preprint server for biology · 2024Article
- Biospecific Chemistry for Covalent Linking of Biomacromolecules.Chemical reviews · 2024Review
- Co-transcriptional gene regulation in eukaryotes and prokaryotes.Nature reviews. Molecular cell biology · 2024Review
131 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The molecular roles of many RNA-binding proteins in bacterial post-transcriptional gene regulation are not well understood. Approaches combining in vivo UV crosslinking with RNA deep sequencing (CLIP-seq) have begun to revolutionize the transcriptome-wide mapping of eukaryotic RNA-binding protein target sites. We have applied CLIP-seq to chart the target landscape of two major bacterial post-transcriptional regulators, Hfq and CsrA, in the model pathogen Salmonella Typhimurium. By detecting binding sites at single-nucleotide resolution, we identify RNA preferences and structural constraints of Hfq and CsrA during their interactions with hundreds of cellular transcripts. This reveals 3'-located Rho-independent terminators as a universal motif involved in Hfq-RNA interactions. Additionally, Hfq preferentially binds 5' to sRNA-target sites in mRNAs, and 3' to seed sequences in sRNAs, reflecting a simple logic in how Hfq facilitates sRNA-mRNA interactions. Importantly, global knowledge of Hfq sites significantly improves sRNA-target predictions. CsrA binds AUGGA sequences in apical loops and targets many Salmonella virulence mRNAs. Overall, our generic CLIP-seq approach will bring new insights into post-transcriptional gene regulation by RNA-binding proteins in diverse bacterial species.
Indexed as
Identifiers
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.