High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates

• DOI: 10.1371/journal.pgen.1003495
• Publication Date: 2013-05-16T21:23:58Z
• Authors: Gaurav Dugar; Alexander Herbig; Konrad U. Förstner; Nadja Heidrich; Richard Reinhardt; Kay Nieselt; Cynthia M. Sharma
• Keywords: RNA-Seq

Campylobacter jejuni is currently the leading cause of bacterial gastroenteritis in humans. Comparison multiple strains revealed a high genetic and phenotypic diversity. However, little known about differences transcriptome organization, gene expression, small RNA (sRNA) repertoires. Here we present first comparative primary analysis based on differential RNA-seq (dRNA-seq) four C. isolates. Our approach includes novel, generic method for automated annotation transcriptional start sites (TSS), which allowed us to provide genome-wide promoter maps analyzed strains. These global TSS are refined through integration SuperGenome that allows by mapping data into common coordinate system derived from whole-genome alignment. Considering steadily increasing amount studies, our will not only facilitate wider range pro- eukaryotes but can also be adapted among different growth or stress conditions. dRNA-seq conservation most TSS, single-nucleotide-polymorphisms (SNP) regions, lead strain-specific output. Furthermore, identified sRNA repertoires could contribute regulation In addition, novel minimal CRISPR-system type-II CRISPR subtype, relies host factor RNase III trans-encoded maturation crRNAs. This Campylobacter, seems active some strains, employs unique pathway, since crRNAs transcribed individual promoters upstream repeats thereby minimize requirements machinery. Overall, study provides new insights organization sRNAs, reveals genes modulate variation despite at DNA level.