ArticlePLoS genetics2008
Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq.
Article in PLoS genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 326 papers.
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Who cites it
326 citing papers in PubMed, 564 citations in OpenAlex.
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- A global survey of small RNA interactors identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum.Nucleic acids research · 2024Article
- A widely conserved protein Rof inhibits transcription termination factor Rho and promotes Salmonella virulence program.Nature communications · 2024Article
- Hfq-Antisense RNA I Binding Regulates RNase E-Dependent RNA Stability and ColE1 Plasmid Copy Number.International journal of molecular sciences · 2024Article
- Genome-wide annotation of transcript boundaries using bacterial Rend-seq datasets.Microbial genomics · 2024Article
- Contribution of Hfq to gene regulation and virulence inInfection and immunity · 2024Article
- Identification and Characterization of Non-protein Coding RNA Homologs inIndian journal of microbiology · 2024Article
- Exploring the transcriptional landscape of phage-host interactions using novel high-throughput approaches.Current opinion in microbiology · 2024Review
- Methodologies for bacterial ribonuclease characterization using RNA-seq.FEMS microbiology reviews · 2023Review
- Phylogenetic Relationships among TnpB-Containing Mobile Elements in Six Bacterial Species.Genes · 2023Article
- Identification and initial characterization of Hfq-associated sRNAs in Histophilus somni strain 2336.PloS one · 2023Article
- The small RNA STnc1480 contributes to the regulation of biofilm formation and pathogenicity in Salmonella typhimurium.Archives of microbiology · 2022Article
266 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 3 countries.
Funding
Abstract
Recent advances in high-throughput pyrosequencing (HTPS) technology now allow a thorough analysis of RNA bound to cellular proteins, and, therefore, of post-transcriptional regulons. We used HTPS to discover the Salmonella RNAs that are targeted by the common bacterial Sm-like protein, Hfq. Initial transcriptomic analysis revealed that Hfq controls the expression of almost a fifth of all Salmonella genes, including several horizontally acquired pathogenicity islands (SPI-1, -2, -4, -5), two sigma factor regulons, and the flagellar gene cascade. Subsequent HTPS analysis of 350,000 cDNAs, derived from RNA co-immunoprecipitation (coIP) with epitope-tagged Hfq or control coIP, identified 727 mRNAs that are Hfq-bound in vivo. The cDNA analysis discovered new, small noncoding RNAs (sRNAs) and more than doubled the number of sRNAs known to be expressed in Salmonella to 64; about half of these are associated with Hfq. Our analysis explained aspects of the pleiotropic effects of Hfq loss-of-function. Specifically, we found that the mRNAs of hilD (master regulator of the SPI-1 invasion genes) and flhDC (flagellar master regulator) were bound by Hfq. We predicted that defective SPI-1 secretion and flagellar phenotypes of the hfq mutant would be rescued by overexpression of HilD and FlhDC, and we proved this to be correct. The combination of epitope-tagging and HTPS of immunoprecipitated RNA detected the expression of many intergenic chromosomal regions of Salmonella. Our approach overcomes the limited availability of high-density microarrays that have impeded expression-based sRNA discovery in microorganisms. We present a generic strategy that is ideal for the systems-level analysis of the post-transcriptional regulons of RNA-binding proteins and for sRNA discovery in a wide range of bacteria.
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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.