The transcript catalogue of the short-lived fish Nothobranchius furzeri provides insights into age-dependent changes of mRNA levels
| Autor: | Dmitry Shagin, Kathrin Reichwald, Nils Hartmann, Matthias Platzer, Marco Groth, Steffen Priebe, Christoph Englert, Andreas Petzold, Stefan Taudien |
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| Rok vydání: | 2012 |
| Předmět: |
Aging
RNA-Seq Biology Nothobranchius furzeri Cyprinodontiformes Genetics Coding region Animals RNA Messenger Gene Zebrafish Gene Library Transcriptome assembly Transcript catalogue cDNA library Gene Expression Profiling Gene Expression Regulation Developmental High-Throughput Nucleotide Sequencing Molecular Sequence Annotation biology.organism_classification Gene expression profiling Ageing Gene expression DNA microarray Model fish species RNA-seq Biotechnology Research Article |
| Zdroj: | BMC Genomics BASE-Bielefeld Academic Search Engine |
| ISSN: | 1471-2164 |
| Popis: | Background The African annual fish Nothobranchius furzeri has over recent years been established as a model species for ageing-related studies. This is mainly based on its exceptionally short lifespan and the presence of typical characteristics of vertebrate ageing. To substantiate its role as an alternative vertebrate ageing model, a transcript catalogue is needed, which can serve e.g. as basis for identifying ageing-related genes. Results To build the N. furzeri transcript catalogue, thirteen cDNA libraries were sequenced using Sanger, 454/Roche and Solexa/Illumina technologies yielding about 39 Gb. In total, 19,875 protein-coding genes were identified and annotated. Of these, 71% are represented by at least one transcript contig with a complete coding sequence. Further, transcript levels of young and old fish of the strains GRZ and MZM-0403, which differ in lifespan by twofold, were studied by RNA-seq. In skin and brain, 85 differentially expressed genes were detected; these have a role in cell cycle control and proliferation, inflammation and tissue maintenance. An RNA-seq experiment for zebrafish skin confirmed the ageing-related relevance of the findings in N. furzeri. Notably, analyses of transcript levels between zebrafish and N. furzeri but also between N. furzeri strains differed largely, suggesting that ageing is accelerated in the short-lived N. furzeri strain GRZ compared to the longer-lived strain MZM-0403. Conclusions We provide a comprehensive, annotated N. furzeri transcript catalogue and a first transcriptome-wide insight into N. furzeri ageing. This data will serve as a basis for future functional studies of ageing-related genes. |
| Databáze: | OpenAIRE |
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