title: Comparative analysis of the primary transcriptome of Synechocystis sp. PCC 6803.
abstract: RNA-seq and especially differential RNA-seq-type transcriptomic analyses (dRNA-seq) are powerful analytical tools, as they not only provide insights into gene expression changes but also provide detailed information about all promoters active at a given moment, effectively giving a deep insight into the transcriptional landscape. Synechocystis sp. PCC 6803 (Synechocystis 6803) is a unicellular model cyanobacterium that is widely used in research fields from ecology, photophysiology to systems biology, modelling and biotechnology. Here, we analysed the response of the Synechocystis 6803 primary transcriptome to different, environmentally relevant stimuli. We established genome-wide maps of the transcriptional start sites active under 10 different conditions relevant for photosynthetic growth and identified 4,091 transcriptional units, which provide information about operons, 5' and 3' untranslated regions (UTRs). Based on a unique expression factor, we describe regulons and relevant promoter sequences at single-nucleotide resolution. Finally, we report several sRNAs with an intriguing expression pattern and therefore likely function, specific for carbon depletion (CsiR1), nitrogen depletion (NsiR4), phosphate depletion (PsiR1), iron stress (IsaR1) or photosynthesis (PsrR1). This dataset is accompanied by comprehensive information providing extensive visualization and data access to allow an easy-to-use approach for the design of experiments, the incorporation into modelling studies of the regulatory system and for comparative analyses.
authors.affiliation: Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg 79104, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Kopf
authors.affiliation: Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg 79104, Germany.
authors.forename: Stephan
authors.initials: S
authors.lastname: Klähn
authors.affiliation: Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg 79104, Germany.
authors.forename: Ingeborg
authors.initials: I
authors.lastname: Scholz
authors.affiliation: Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg 79104, Germany.
authors.forename: Jasper K F
authors.initials: JK
authors.lastname: Matthiessen
authors.affiliation: Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg 79104, Germany.
authors.forename: Wolfgang R
authors.initials: WR
authors.lastname: Hess
authors.affiliation: Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg 79104, Germany bjoern.voss@biologie.uni-freiburg.de.
authors.forename: Björn
authors.initials: B
authors.lastname: Voß
mesh_terms: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D009876:Operon; D010788:Photosynthesis / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism; D046939:Synechocystis / Q000235:genetics* / Q000378:metabolism; D024363:Transcription Initiation Site; D059467:Transcriptome
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D012329:RNA, Bacterial
keywords: comparative transcriptome analysis; cyanobacteria; regulation of gene expression; sRNA; transcriptional unit