High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates
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{"title"=>"High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates", "type"=>"journal", "authors"=>[{"first_name"=>"Gaurav", "last_name"=>"Dugar", "scopus_author_id"=>"55755061500"}, {"first_name"=>"Alexander", "last_name"=>"Herbig", "scopus_author_id"=>"35589705200"}, {"first_name"=>"Konrad U.", "last_name"=>"Förstner", "scopus_author_id"=>"14032724100"}, {"first_name"=>"Nadja", "last_name"=>"Heidrich", "scopus_author_id"=>"6507414569"}, {"first_name"=>"Richard", "last_name"=>"Reinhardt", "scopus_author_id"=>"7101612726"}, {"first_name"=>"Kay", "last_name"=>"Nieselt", "scopus_author_id"=>"55887593200"}, {"first_name"=>"Cynthia M.", "last_name"=>"Sharma", "scopus_author_id"=>"9943575900"}], "year"=>2013, "source"=>"PLoS Genetics", "identifiers"=>{"scopus"=>"2-s2.0-84878482772", "issn"=>"15537390", "pmid"=>"23696746", "pui"=>"369039814", "isbn"=>"1553-7404 (Electronic) 1553-7390 (Linking)", "sgr"=>"84878482772", "doi"=>"10.1371/journal.pgen.1003495"}, "id"=>"d8c5611a-7699-319a-9849-5c0b3d84d68f", "abstract"=>"Campylobacter jejuni is currently the leading cause of bacterial gastroenteritis in humans. 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Figshare

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

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