Hfq LiRIP-seq in Salmonella
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ABSTRACT:
PROVIDER: PRJNA983241 | ENA |
REPOSITORIES: ENA
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Project description:We have used the RIL-seq technique to map the global RNA-RNA interactome on the sRNA chaperone Hfq in Salmonella enterica.
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Project description:We have developed a novel approach named LiRIP-seq to profile the global RNA-RNA interactome in Salmonella enterica. By pulse expressing T4 RNA ligase from an inducible pBAD promoter, LiRIP-seq enables in vivo proximity ligation of Hfq-bound RNAs to their interaction partners. This is followed by enrichment of ligation products (RNA chimeras) using Hfq-coIP and subsequent RNA-seq analysis.
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Project description:The expression profile of an S. Typhimurium hfq mutant-strain was compared to the parental strain under 2 different growth conditions; early stationary phase and SPI-1 (Salmonella pathogenicity island 1) inducing condition. Keywords: Genetic modification
2008-08-23 | GSE8985 | GEO
Project description:The expression profile of an S. Typhimurium hfq mutant-strain was compared to the parental strain under 2 different growth conditions; early stationary phase and SPI-1 (Salmonella pathogenicity island 1) inducing condition. Keywords: Genetic modification This study comprises two separate experiments performed under different growth conditions, were the gene expression profile was compared to that of the parental strain. Three biological replicates were performed for each strain and condition. For this study, we used Salmonella genomic DNA as the comparator which also acted as the control for spot quality.
2008-08-23 | E-GEOD-8985 | biostudies-arrayexpress
Project description:The small RNAs associated with protein Hfq constitute one of the largest classes of post-transcriptional regulators known to date. Most previously investigated members of this class are encoded by conserved free-standing genes. Here, deep sequencing of Hfq-bound transcripts from multiple stages of growth of Salmonella Typhimurium revealed a plethora of new small RNA species from within mRNA loci, including DapZ which overlaps with the 3’ region of the biosynthetic gene, dapB. Synthesis of the DapZ small RNA is independent of DapB protein synthesis, and controlled by HilD, the master regulator of Salmonella invasion genes. DapZ carries a short G/U-rich domain similar to that of the globally acting GcvB small RNA, and uses GcvB-like seed pairing to repress translation of the major ABC transporters, DppA and OppA. This exemplifies double functional output from an mRNA locus by the production of both a protein and an Hfq-dependent trans-acting RNA. Our atlas of Hfq targets suggests that the 3’ regions of mRNA genes constitute a rich reservoir to feed the Hfq network with new regulatory small RNAs.
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Project description:The small RNAs associated with protein Hfq constitute one of the largest classes of post-transcriptional regulators known to date. Most previously investigated members of this class are encoded by conserved free-standing genes. Here, deep sequencing of Hfq-bound transcripts from multiple stages of growth of Salmonella Typhimurium revealed a plethora of new small RNA species from within mRNA loci, including DapZ which overlaps with the 3’ region of the biosynthetic gene, dapB. Synthesis of the DapZ small RNA is independent of DapB protein synthesis, and controlled by HilD, the master regulator of Salmonella invasion genes. DapZ carries a short G/U-rich domain similar to that of the globally acting GcvB small RNA, and uses GcvB-like seed pairing to repress translation of the major ABC transporters, DppA and OppA. This exemplifies double functional output from an mRNA locus by the production of both a protein and an Hfq-dependent trans-acting RNA. Our atlas of Hfq targets suggests that the 3’ regions of mRNA genes constitute a rich reservoir to feed the Hfq network with new regulatory small RNAs. Hfq-associated RNAs were systemically analyzed in Salmonella at 7 different growth stages in standard labortory condition (LB)
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