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Meta-analysis of studies using suppression subtractive hybridization and microarrays to investigate the effects of environmental stress on gene transcription in oysters.

Anderson K, Taylor DA, Thompson EL, Melwani AR, Nair SV, Raftos DA - PLoS ONE (2015)

Bottom Line: To address this shortfall, we conducted a meta-analysis of 14 studies that investigated the effects of different environmental stressors on gene expression in oysters.We found that the expression of over 400 genes in a range of oyster species changed significantly after exposure to environmental stress.In light of these findings, we put forward a consensus model of sub-cellular stress responses in oysters.

View Article: PubMed Central - PubMed

Affiliation: Sydney Institute of Marine Science, Chowder Bay, NSW, Australia; Department of Biological Sciences, Macquarie University, North Ryde, NSW, Australia.

ABSTRACT
Many microarray and suppression subtractive hybridization (SSH) studies have analyzed the effects of environmental stress on gene transcription in marine species. However, there have been no unifying analyses of these data to identify common stress response pathways. To address this shortfall, we conducted a meta-analysis of 14 studies that investigated the effects of different environmental stressors on gene expression in oysters. The stressors tested included chemical contamination, hypoxia and infection, as well as extremes of temperature, pH and turbidity. We found that the expression of over 400 genes in a range of oyster species changed significantly after exposure to environmental stress. A repeating pattern was evident in these transcriptional responses, regardless of the type of stress applied. Many of the genes that responded to environmental stress encoded proteins involved in translation and protein processing (including molecular chaperones), the mitochondrial electron transport chain, anti-oxidant activity and the cytoskeleton. In light of these findings, we put forward a consensus model of sub-cellular stress responses in oysters.

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Schematic representation of the workflow used in this study.
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pone.0118839.g001: Schematic representation of the workflow used in this study.

Mentions: Data for inclusion in the meta-analysis were selected by searching GenBank’s nucleotide and expressed sequence tag (EST) databases (http://www.ncbi.nlm.nih.gov) (Fig. 1). These databases were searched in 2013 for differentially expressed genes identified by SSH or cDNA microarray analyses of oysters from the genera Crassostrea, Ostrea and Saccostrea that had been exposed to environmental stressors (as defined by their GenBank annotations). Only microarray analyses that had been effectively validated by quantitative PCR were included in the analysis. Pertinent next generation transcriptomic and shotgun proteomic studies are discussed separately.


Meta-analysis of studies using suppression subtractive hybridization and microarrays to investigate the effects of environmental stress on gene transcription in oysters.

Anderson K, Taylor DA, Thompson EL, Melwani AR, Nair SV, Raftos DA - PLoS ONE (2015)

Schematic representation of the workflow used in this study.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4358831&req=5

pone.0118839.g001: Schematic representation of the workflow used in this study.
Mentions: Data for inclusion in the meta-analysis were selected by searching GenBank’s nucleotide and expressed sequence tag (EST) databases (http://www.ncbi.nlm.nih.gov) (Fig. 1). These databases were searched in 2013 for differentially expressed genes identified by SSH or cDNA microarray analyses of oysters from the genera Crassostrea, Ostrea and Saccostrea that had been exposed to environmental stressors (as defined by their GenBank annotations). Only microarray analyses that had been effectively validated by quantitative PCR were included in the analysis. Pertinent next generation transcriptomic and shotgun proteomic studies are discussed separately.

Bottom Line: To address this shortfall, we conducted a meta-analysis of 14 studies that investigated the effects of different environmental stressors on gene expression in oysters.We found that the expression of over 400 genes in a range of oyster species changed significantly after exposure to environmental stress.In light of these findings, we put forward a consensus model of sub-cellular stress responses in oysters.

View Article: PubMed Central - PubMed

Affiliation: Sydney Institute of Marine Science, Chowder Bay, NSW, Australia; Department of Biological Sciences, Macquarie University, North Ryde, NSW, Australia.

ABSTRACT
Many microarray and suppression subtractive hybridization (SSH) studies have analyzed the effects of environmental stress on gene transcription in marine species. However, there have been no unifying analyses of these data to identify common stress response pathways. To address this shortfall, we conducted a meta-analysis of 14 studies that investigated the effects of different environmental stressors on gene expression in oysters. The stressors tested included chemical contamination, hypoxia and infection, as well as extremes of temperature, pH and turbidity. We found that the expression of over 400 genes in a range of oyster species changed significantly after exposure to environmental stress. A repeating pattern was evident in these transcriptional responses, regardless of the type of stress applied. Many of the genes that responded to environmental stress encoded proteins involved in translation and protein processing (including molecular chaperones), the mitochondrial electron transport chain, anti-oxidant activity and the cytoskeleton. In light of these findings, we put forward a consensus model of sub-cellular stress responses in oysters.

Show MeSH
Related in: MedlinePlus