A Strand-Specific RNA�CSeq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi

High-density, strand-specific cDNA sequencing (ssRNA�Cseq) 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�Cseq was also combined with microarray and proteome analysis to further define the S. Typhi OmpR regulon and identify novel OmpR regulated transcripts. Thus, ssRNA�Cseq provides a novel and powerful approach to the characterization of the bacterial transcriptome.本研究采用高密度链特异性cDNA测序（strand-specific cDNA sequencing, ssRNA-seq）分析了伤寒沙门氏菌（Salmonella enterica serovar Typhi, S. Typhi）的转录组。通过将测序数据比对至完整的伤寒沙门氏菌基因组，我们以链特异性方式解析了其转录组，并进一步明确了前噬菌体、假基因、此前未注释区域以及3'-或5'-非翻译区（untranslated region, UTR）所编码的转录区域。除已注释的非编码RNA（non-coding RNAs）外，本研究还额外鉴定出40种新型候选非编码RNA。结合蛋白质组分析与转录组数据，我们对多个假定基因（hypothetical genes）的注释进行了验证与细化。此外，本研究还将ssRNA-seq与微阵列及蛋白质组分析相结合，进一步明确了伤寒沙门氏菌的OmpR调节子，并鉴定出受OmpR调控的新型转录本。综上，ssRNA-seq为细菌转录组的特征解析提供了一种全新且高效的研究手段。