A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi.
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.
Perkins
Timothy T
TT
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Kingsley
Robert A
RA
Fookes
Maria C
MC
Gardner
Paul P
PP
James
Keith D
KD
Yu
Lu
L
Assefa
Samuel A
SA
He
Miao
M
Croucher
Nicholas J
NJ
Pickard
Derek J
DJ
Maskell
Duncan J
DJ
Parkhill
Julian
J
Choudhary
Jyoti
J
Thomson
Nicholas R
NR
Dougan
Gordon
G
D001426:Bacterial Proteins / Q000032:analysis; D018076:DNA, Complementary; D020869:Gene Expression Profiling; D040901:Proteomics; D012329:RNA, Bacterial / Q000032:analysis / Q000235:genetics; D012485:Salmonella typhi / Q000235:genetics*; D017423:Sequence Analysis, RNA
D001426:Bacterial Proteins; D018076:DNA, Complementary; D012329:RNA, Bacterial