title: Comparative transcriptomics across the prokaryotic tree of life.
abstract: Whole-transcriptome sequencing studies from recent years revealed an unexpected complexity in transcriptomes of bacteria and archaea, including abundant non-coding RNAs, cis-antisense transcription and regulatory untranslated regions (UTRs). Understanding the functional relevance of the plethora of non-coding RNAs in a given organism is challenging, especially since some of these RNAs were attributed to 'transcriptional noise'. To allow the search for conserved transcriptomic elements we produced comparative transcriptome maps for multiple species across the microbial tree of life. These transcriptome maps are detailed in annotations, comparable by gene families, and BLAST-searchable by user provided sequences. Our transcriptome collection includes 18 model organisms spanning 10 phyla/subphyla of bacteria and archaea that were sequenced using standardized RNA-seq methods. The utility of the comparative approach, as implemented in our web server, is demonstrated by highlighting genes with exceptionally long 5'UTRs across species, which correspond to many known riboswitches and further suggest novel putative regulatory elements. Our study provides a standardized reference transcriptome to major clinically and environmentally important microbial phyla. The viewer is available at http://exploration.weizmann.ac.il/TCOL, setting a framework for comparative studies of the microbial non-coding genome.
authors.affiliation: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
authors.forename: Ofir
authors.initials: O
authors.lastname: Cohen
authors.affiliation: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
authors.forename: Shany
authors.initials: S
authors.lastname: Doron
authors.affiliation: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors.forename: Omri
authors.initials: O
authors.lastname: Wurtzel
authors.affiliation: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
authors.forename: Daniel
authors.initials: D
authors.lastname: Dar
authors.affiliation: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
authors.forename: Sarit
authors.initials: S
authors.lastname: Edelheit
authors.affiliation: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
authors.forename: Iris
authors.initials: I
authors.lastname: Karunker
authors.affiliation: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Eran
authors.initials: E
authors.lastname: Mick
authors.affiliation: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel rotem.sorek@weizmann.ac.il.
authors.forename: Rotem
authors.initials: R
authors.lastname: Sorek
mesh_terms: D020121:5' Untranslated Regions; D001105:Archaea / Q000145:classification / Q000235:genetics*; D001419:Bacteria / Q000145:classification / Q000235:genetics*; D002874:Chromosome Mapping; D003196:Computer Graphics; D010802:Phylogeny; D019642:RNA, Archaeal / Q000235:genetics*; D012329:RNA, Bacterial / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics*; D058928:Riboswitch; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D014584:User-Computer Interface
chemical_list: D020121:5' Untranslated Regions; D019642:RNA, Archaeal; D012329:RNA, Bacterial; D022661:RNA, Untranslated; D058928:Riboswitch