title: Comparative transcriptomics of pathogenic and non-pathogenic Listeria species.
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.
authors.affiliation: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Omri
authors.initials: O
authors.lastname: Wurtzel
authors.forename: Nina
authors.initials: N
authors.lastname: Sesto
authors.forename: J R
authors.initials: JR
authors.lastname: Mellin
authors.forename: Iris
authors.initials: I
authors.lastname: Karunker
authors.forename: Sarit
authors.initials: S
authors.lastname: Edelheit
authors.forename: Christophe
authors.initials: C
authors.lastname: Bécavin
authors.forename: Cristel
authors.initials: C
authors.lastname: Archambaud
authors.forename: Pascale
authors.initials: P
authors.lastname: Cossart
authors.forename: Rotem
authors.initials: R
authors.lastname: Sorek
mesh_terms: D020121:5' Untranslated Regions; D001483:Base Sequence; D005075:Biological Evolution; D017124:Conserved Sequence; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D008087:Listeria / Q000235:genetics* / Q000472:pathogenicity*; D008089:Listeria monocytogenes / Q000235:genetics / Q000472:pathogenicity; D008969:Molecular Sequence Data; D009876:Operon; D016372:RNA, Antisense / Q000235:genetics* / Q000378:metabolism; D012329:RNA, Bacterial; D022661:RNA, Untranslated / Q000235:genetics / Q000378:metabolism; D024363:Transcription Initiation Site; D059467:Transcriptome
chemical_list: D020121:5' Untranslated Regions; D016372:RNA, Antisense; D012329:RNA, Bacterial; D022661:RNA, Untranslated