Cold exposure has a profound impact on almost all aspects of organismal physiology. Responses to cold are most easily identified in species that naturally experience large and potentially debilitating fluctuations in environmental conditions, where they constitute a crucial component of both survival and fitness. The common carp, Cyprinus carpioL., belongs to the same Cyprinid family of fish as zebrafish, but originates in a continental climate with extremes of winter and summer. It is an economically important farmed fish, and carp species account for much of world aquaculture production. It is hardy and tolerant of a wide range of temperatures for which it exhibits an extremely plastic thermal phenotype.
Using carp, we have undertaken a broad, system-wide gene expression screen to investigate the physiological mechanisms underlying cold adaptation. This data set provides a basis to explore a range of specific mechanistic hypotheses at all levels of organization, from individual biochemical pathways to the level of the whole organism.
Carp were exposed to increasing levels of cold, and responses across seven tissues were assessed by using a microarray composed of 13,440 cDNA probes. The microarrays were fabricated using a collection of carp cDNA clones that was enriched for environmentally regulated genes. The cDNA collection can be explored at CarpBase and Build 2.0 was used for this publication.
We discovered that a large set of unique cDNAs (~3,400) were affected by cold. These cDNAs included an expression signature common to all tissues of 252 up-regulated genes involved in RNA processing, translation initiation, mitochondrial metabolism, proteasomal function, and modification of higher-order structures of lipid membranes and chromosomes. A detailed heatmap showing the genes that were represented in the common response can be downloaded from the PNAS journal website.
We also identified a large set of genes that were differentially expressed in at least one tissue in response to cold. A detailed heatmap showing the genes that weredifferentially expressed in the tissue specific response can be downloaded from the PNAS journal website.
Publications:
Gracey, A.Y., Fraser, E.J., Li, W., Fang, Y., Taylor, R.R., Rogers, J., & Brass, A. (2004) Coping with cold: An integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate. Proc. Natl. Acad. Sci. USA, 101: 16970-16975. PubMed.
Tiku, P.E., Gracey, A.Y., Macartney, A.I., Beynon, R.B., & Cossins, A.R. (1996) Cold-inducible expression of desaturase by transcriptional and post-translational mechanisms. Science, 271: 815-818. PubMed.