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1 Biological Sciences, University of Liverpool, Liverpool, Merseyside, United Kingdom
2 Medicine, University of Colorado, Aurora, Colorado, USA
3 Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
4 Biological Sciences, University of Liverpool, Liverpool, Merseyside, United Kingdom; Biological Sciences, University of Southern California, Los Angeles, California, USA
* To whom correspondence should be addressed. E-mail: gracey{at}usc.edu.
Hibernation is a seasonally entrained and profound phenotypic transition to conserve energy in winter. It involves significant biochemical reprogramming, though our understanding of the underpinning molecular events is fragmentary and selective. We have conducted a large-scale gene expression screen of the golden-mantled ground squirrel, Spermophilus lateralis, to identify transcriptional responses associated specifically with the summer-winter transition and the torpid-arousal transition in winter. We used 112 cDNA microarrays comprising 12,288 probes that cover at least 5,109 genes. In liver the profiles of torpid and active states in the winter were almost identical though we identified 102 cDNAs that were differentially expressed between winter and summer, 90% of which were down-regulated in the winter states. By contrast, in cardiac tissue 59 and 115 cDNAs were elevated in interbout arousal and torpor, respectively, relative to the summer active condition, but only 7 were common to both winter states, and during arousal none were down-regulated. In brain 78 cDNAs were found to change in winter, 44 of which were up-regulated. Thus transcriptional changes associated with hibernation are qualitatively modest and, since these changes are generally less than 2-fold, also quantitatively modest. Unbiased gene ontology profiling of the transcripts suggests a winter switch to 
-oxidation of lipids in liver and heart, a reduction in metabolism of toxic compounds and the urea cycle in liver, and down-regulated electron transport in the brain. We identified just one strongly winter-induced transcript common to all tissues, namely an RNA-binding protein, RBM3. This analysis clearly differentiates responses of the principal tissues, identifies a large number of new genes undergoing regulation and broadens our understanding of affected cellular processes that in part account for the winter-adaptive hibernating phenotype.
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