A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi.

Perkins, Timothy T; Kingsley, Robert A; Fookes, Maria C; Gardner, Paul P; James, Keith D; Yu, Lu; Assefa, Samuel A; He, Miao; Croucher, Nicholas J; Pickard, Derek J; +5 more...Maskell, Duncan J; Parkhill, Julian; Choudhary, Jyoti; Thomson, Nicholas RORCID logo; and Dougan, Gordon (2009) A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLOS GENETICS, 5 (7). e1000569-. ISSN 1553-7404 DOI: 10.1371/journal.pgen.1000569
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High-density, strand-specific cDNA sequencing (ssRNA-seq) was used to analyze the transcriptome of Salmonella enterica serovar Typhi (S. Typhi). By mapping sequence data to the entire S. Typhi genome, we analyzed the transcriptome in a strand-specific manner and further defined transcribed regions encoded within prophages, pseudogenes, previously un-annotated, and 3'- or 5'-untranslated regions (UTR). An additional 40 novel candidate non-coding RNAs were identified beyond those previously annotated. Proteomic analysis was combined with transcriptome data to confirm and refine the annotation of a number of hpothetical genes. ssRNA-seq was also combined with microarray and proteome analysis to further define the S. Typhi OmpR regulon and identify novel OmpR regulated transcripts. Thus, ssRNA-seq provides a novel and powerful approach to the characterization of the bacterial transcriptome.


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A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi.pdf
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