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Comparative analysis of the primary transcriptome of Synechocystis sp. PCC 6803.
Kopf, Matthias; Klähn, Stephan; Scholz, Ingeborg; Matthiessen, Jasper K F; Hess, Wolfgang R; Voß, Björn.
Afiliación
  • Kopf M; Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg 79104, Germany.
  • Klähn S; Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg 79104, Germany.
  • Scholz I; Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg 79104, Germany.
  • Matthiessen JK; Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg 79104, Germany.
  • Hess WR; Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg 79104, Germany.
  • Voß B; Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg 79104, Germany bjoern.voss@biologie.uni-freiburg.de.
DNA Res ; 21(5): 527-39, 2014 Oct.
Article en En | MEDLINE | ID: mdl-24935866
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.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Synechocystis / Transcriptoma Tipo de estudio: Prognostic_studies Idioma: En Revista: DNA Res Asunto de la revista: BIOLOGIA MOLECULAR / GENETICA Año: 2014 Tipo del documento: Article País de afiliación: Alemania Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Synechocystis / Transcriptoma Tipo de estudio: Prognostic_studies Idioma: En Revista: DNA Res Asunto de la revista: BIOLOGIA MOLECULAR / GENETICA Año: 2014 Tipo del documento: Article País de afiliación: Alemania Pais de publicación: Reino Unido