Transcriptomics,Genomics

Dataset Information

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Environmental stress in an ectothermic vertebrate, the coral reef fish Pomacentrus moluccensis


ABSTRACT: Transcriptional profiling of gene responses in liver in the coral reef fish Pomacentrus moluccensis in response to different types of environmental stress: cold, heat, hypoxic and hyposmotic shock. Goal was to determine the common effects of different types of environmental stress on gene expression as well as responses unique to different stressors. Abstract from Kassahn et al. BMC Genomics (2007) 8:358 Background While our understanding of the importance of transcriptional regulation for biological function is continuously growing, we still know comparatively little about how environmentally-induced stress affects gene expression in vertebrates and how consistent transcriptional stress responses are across different types of environmental stress. Results In this study, we looked for a genetic measure of environmental stress and used a multi-stressor approach to identify components of a common stress response as well as components unique to different types of environmental stress. We exposed individuals of the coral reef fish Pomacentrus moluccensis to hypoxic, hyposmotic, cold and heat shock and measured the responses of approximately 16,000 genes in liver. We also compared winter and summer responses to heat shock to examine the capacity for such responses to vary with acclimation to different ambient temperatures. We identified a series of gene functions that were consistently involved in all stress responses examined here, suggesting common effects of stress on biological function. These common responses were achieved by the regulation of largely independent sets of genes and the responses of individual genes varied greatly across different stress types. However, we were able to identify groups of co-regulated genes, the genes within which shared similar functions. Given current estimates of climatic change, we were particularly interested in the response to prolonged heat exposure. In total, 324 gene loci were differentially expressed following exposure to heat over five days. The functions of these heat-responsive genes suggest that prolonged heat stress leads to oxidative stress and protein damage, challenge of the immune system, and a re-allocation of energy sources. Conclusion This is the first environmental genomic study to measure gene regulation in response to different environmental stressors in a natural population of a warm-adapted ectothermic vertebrate. This study offers insight into the effects of environmental stress on biological function and sheds light on the expected sensitivity of coral reef fishes to elevated temperatures in the future. Keywords: Stress response Overall design: Balanced design with dye-swaps and biological replicates representing comparisons of environmentally-stressed fish compared against fish kept at ambient conditions and comparisons involving fish exposed to different types of environmental stress. No technical replicates were employed. In total 59 dual channel microarray hybridisations were performed using 118 different individuals. Thus, each microarray hybridisation employed two individual fish (no sample pooling).

INSTRUMENT(S): Compugen Zebrafish 16K

SUBMITTER: Karin Sonja Kassahn  

PROVIDER: GSE7499 | GEO | 2007-10-15

SECONDARY ACCESSION(S): PRJNA100481

REPOSITORIES: GEO

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From transcriptome to biological function: environmental stress in an ectothermic vertebrate, the coral reef fish Pomacentrus moluccensis.

Kassahn Karin S KS   Crozier Ross H RH   Ward Alister C AC   Stone Glenn G   Caley M Julian MJ  

BMC genomics 20071005


BACKGROUND: Our understanding of the importance of transcriptional regulation for biological function is continuously improving. We still know, however, comparatively little about how environmentally induced stress affects gene expression in vertebrates, and the consistency of transcriptional stress responses to different types of environmental stress. In this study, we used a multi-stressor approach to identify components of a common stress response as well as components unique to different typ  ...[more]

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