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Comparative transcriptomics of pathogenic and non-pathogenic Listeria species. Mol Syst Biol 8:583

Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
Molecular Systems Biology (Impact Factor: 10.87). 05/2012; 8(1):583. DOI: 10.1038/msb.2012.11
Source: PubMed

ABSTRACT

Listeria monocytogenes is a human, food-borne pathogen. Genomic comparisons between L. monocytogenes and Listeria innocua, a closely related non-pathogenic species, were pivotal in the identification of protein-coding genes essential for virulence. However, no comprehensive comparison has focused on the non-coding genome. We used strand-specific cDNA sequencing to produce genome-wide transcription start site maps for both organisms, and developed a publicly available integrative browser to visualize and analyze both transcriptomes in different growth conditions and genetic backgrounds. Our data revealed conservation across most transcripts, but significant divergence between the species in a subset of non-coding RNAs. In L. monocytogenes, we identified 113 small RNAs (33 novel) and 70 antisense RNAs (53 novel), significantly increasing the repertoire of ncRNAs in this species. Remarkably, we identified a class of long antisense transcripts (lasRNAs) that overlap one gene while also serving as the 5' UTR of the adjacent divergent gene. Experimental evidence suggests that lasRNAs transcription inhibits expression of one operon while activating the expression of another. Such a lasRNA/operon structure, that we named 'excludon', might represent a novel form of regulation in bacteria.

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    • "Reads from the bisulfite strand-specific libraries were used to estimate antisense transcripts (asRNA) length according to the coverage they produced for the phage genome. Reads from the 5′-end libraries were used for determining transcriptional start sites across the phage genome, and were analyzed as previously described (Wurtzel et al., 2012a) with some minor modifications (Supplementary Text). Regions upstream of these transcriptional start sites were scanned for promoter motifs. "
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