ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2014
Comparative analysis of the primary transcriptome of Synechocystis sp. PCC 6803.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 153 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
153 citing papers in PubMed.
- ModifiedMicroorganisms · 2026Article
- Deletion of the gene for a cyanobacterial ribosome-associated protein affects the carbon/nitrogen metabolism.bioRxiv : the preprint server for biology · 2026Article
- The (Glg)ABCs of cyanobacteria: modelling of glycogen synthesis and functional divergence of glycogen synthases in Synechocystis sp. PCC 6803.FEBS letters · 2026Article
- Systematic and Functional Identification of Small Non-Coding RNAs Associated with Excess Ammonium Stress in CyanobacteriumInternational journal of molecular sciences · 2026Article
- Antisense RNA controls the degradation of phycobilisomes in heterocyst-forming cyanobacteria by a transcriptional interference mechanism.Nucleic acids research · 2026Article
- Utilization of phosphate-responsive promoters for auto-inducible management of biotechnological processes based on cyanobacteria.Metabolic engineering communications · 2026Article
- Transfer of the synechan biosynthesis and regulatory pathway enables sulfated polysaccharide production in Synechococcus elongatus PCC 7942.Scientific reports · 2026Article
- From pond to platform: howJournal of bacteriology · 2026Review
- Impact of SliP4 deletion on the high-light acclimation inmicroLife · 2026Article
- Deciphering guanidine assimilation and riboswitch-based gene regulation in cyanobacteria for synthetic biology applications.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Genomic and transcriptomic insights into the molecular responses of a biocrust-derived oleaginous microalgaSynthetic and systems biotechnology · 2025Article
- Deep Generative Model-Driven Design of Microbial Synthetic Promoters.Journal of microbiology and biotechnology · 2025Review
- Partial photoswitching of rod-shaped phycobilisome production in the cyanobacterium Synechocystis sp. PCC 6803.Plant & cell physiology · 2025Article
- Diurnal rhythm causes metabolic crises in the cyanobacterial mutants of c-di-AMP signaling cascade.iScience · 2025Article
- Establishing a Malonyl-CoA Biosensor for the Two Model CyanobacteriaACS synthetic biology · 2025Article
- Alkane biosynthesis gene expression and its increased production in recombinant cyanobacteria.FEBS open bio · 2025Article
- Development of a CRISPR activation system for targeted gene upregulation in Synechocystis sp. PCC 6803.Communications biology · 2025Article
- Self-sustained rhythmic behavior ofPNAS nexus · 2025Article
- Integrative bioinformatics approaches reveal key hub genes in cyanobacteria: insights from Synechocystis sp. PCC 6803 and Geminocystis sp. NIES-3708 under abiotic stress conditions.Genes & genomics · 2025Article
- Photosynthesis in Synechocystis sp. PCC 6803 is not optimally regulated under very high COApplied microbiology and biotechnology · 2025Article
93 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.