Transcriptomics

Dataset Information

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Hfq-coIP overgrowth


ABSTRACT: 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)

ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344  

SUBMITTER: Kai Papenfort   Yanjie Chao  Jörg Vogel  Cynthia M Sharma  Richard Reinhardt  Konrad U. Förstner 

PROVIDER: E-GEOD-38884 | ArrayExpress | 2012-10-01

SECONDARY ACCESSION(S): SRP013870GSE38884PRJNA169138

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

An atlas of Hfq-bound transcripts reveals 3' UTRs as a genomic reservoir of regulatory small RNAs.

Chao Yanjie Y   Papenfort Kai K   Reinhardt Richard R   Sharma Cynthia M CM   Vogel Jörg J  

The EMBO journal 20120824 20


The small RNAs associated with the 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 t  ...[more]

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