ArticleProceedings of the National Academy of Sciences of the United States of America2016
Grad-seq guides the discovery of ProQ as a major small RNA-binding protein.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 178 papers.
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Who cites it
178 citing papers in PubMed, 306 citations in OpenAlex.
- Identification of proteins exhibitingRNA biology · 2026Article
- Bacterial small regulatory RNAs.Nature reviews. Microbiology · 2026Review
- Cross-species R-DeeP profiling reveals a conserved core of RNA-dependent proteins in yeast.Nucleic acids research · 2026Article
- Regulation of cyclic lipopeptide orfamide A biosynthesis in Pseudomonas protegens by the Gac-Rsm-LuxR Cascade.Nucleic acids research · 2026Article
- SmallBARNA 2026: a kingdom-wide bacterial sRNA resource.Nucleic acids research · 2026Article
- A Two-Step Purification Strategy for RNA and RNA-Protein Complexes for Crystallization.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Structural dependence of ProQ-mRNA interactions in live bacterial cells.Communications biology · 2025Article
- A Small RNA Derived From the 5' End of the IS200 tnpA Transcript Regulates Multiple Virulence Regulons in Salmonella typhimurium.Molecular microbiology · 2025Article
- The Biology of Nucleus-Forming Jumbo Phages.Annual review of genetics · 2025Review
- RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics datasets.Nature communications · 2025Article
- Remodeling of RNA-binding proteome and RNA-mediated regulation as a new layer of control of sporulation.mSystems · 2025Article
- Adaptive genetics reveals constraints on protein structure/function by evolving E. coli under constant nutrient limitation.BMC biology · 2025Article
- 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
- Different RNA recognition by ProQ and FinO depends on the sequence surrounding intrinsic terminator hairpins.RNA (New York, N.Y.) · 2025Article
- RNA recognition by minimal ProQ fromRNA (New York, N.Y.) · 2025Article
- ProQ prevents mRNA degradation through inhibition of poly(A) polymerase.Nucleic acids research · 2025Article
- ProQ-associated small RNAs control motility in Vibrio cholerae.Nucleic acids research · 2025Article
- Improved constructs for bait RNA display in a bacterial three-hybrid assay.Scientific reports · 2025Article
- R-DeeP/TripepSVM identifies the RNA-binding OB-fold-like protein PatR as regulator of heterocyst patterning.Nucleic acids research · 2025Article
118 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The functional annotation of transcriptomes and identification of noncoding RNA (ncRNA) classes has been greatly facilitated by the advent of next-generation RNA sequencing which, by reading the nucleotide order of transcripts, theoretically allows the rapid profiling of all transcripts in a cell. However, primary sequence per se is a poor predictor of function, as ncRNAs dramatically vary in length and structure and often lack identifiable motifs. Therefore, to visualize an informative RNA landscape of organisms with potentially new RNA biology that are emerging from microbiome and environmental studies requires the use of more functionally relevant criteria. One such criterion is the association of RNAs with functionally important cognate RNA-binding proteins. Here we analyze the full ensemble of cellular RNAs using gradient profiling by sequencing (Grad-seq) in the bacterial pathogen Salmonella enterica, partitioning its coding and noncoding transcripts based on their network of RNA-protein interactions. In addition to capturing established RNA classes based on their biochemical profiles, the Grad-seq approach enabled the discovery of an overlooked large collective of structured small RNAs that form stable complexes with the conserved protein ProQ. We show that ProQ is an abundant RNA-binding protein with a wide range of ligands and a global influence on Salmonella gene expression. Given its generic ability to chart a functional RNA landscape irrespective of transcript length and sequence diversity, Grad-seq promises to define functional RNA classes and major RNA-binding proteins in both model species and genetically intractable organisms.
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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.