Mammals underlie variations in their energy state, caused by the circadian rhythms in their feeding behavior. In mammals the liver serves as a metabolic hub buffering variations in the energy metabolism of the whole organism. To accommodate this, various ways of regulation are in place to make sure metabolic pathways are active and functional when needed. As one level of this regulation, various transcripts of key metabolic pathways show circadian variation in their redundancy.
In fact the circadian clock is known to be critical for the generation of rhythmicity of up to 10% of hepatic transcripts. It has been unclear though, whether these oscillations arise due to a direct effect of the molecular clock on gene promoters, a circadian gating on feeding behavior or a combination of both.
We dissected the relationship between the circadian oscillator and feeding cues in defining the temporal pattern of rhythmic transcripts in mouse liver. To achieve this, we used transcriptional profiling data from both wild-type and circadian clock-deficient, cry1-/-;cry2-/- mice (CrydKO) under ad libitum or temporally restricted feeding paradigms. We also investigated the effects of feeding after prolonged fasting on gene expression.
We used Affymetrix High Density Arrays MOE 430_2 to profile gene expression.
This database also features data accessible through the GEO accession GSE13093. The data for adlib fed WT mice is also available at http://wasabi.itmat.upenn.edu/circa/.
This database features data from 4 independent experiments.
- WT adlib (also at http://wasabi.itmat.upenn.edu/circa/)
- WT tRF
- WT fast/refed
- CrydKO adlib and tRF
Under adlib conditions food was available at all times(under this condition mice consume most of their food during nighttime), while food availability was restricted to the subjective daytime (CT1-CT9) under the tRF condition. In the ‘WT fast/refed‘ experiment, mice were fasted for 24 hour and then refed to investigate the direct effect of food intake on transcription. CrydKO mice are double Knock-Out mice for the Cryptochrome 1 and 2 genes. These mice do not have a functional circadian clock
The different feeding conditions and genotypes can be used to dissect the factors driving the expression of transcripts of interest. If i.e. a transcripts is induced by feeding, shows a circadian transcription pattern in WT mice with peak levels following the onset of feeding, but also shows rhythmic transcription in CrydKO mice under tRF condition, its rhythmical transcription is likely driven directly through food intake and not the hepatic circadian clock.
Expression levels should not be cross-compared between independent experiments since variations in the amplification and hybridization process can cause them to differ. Data will be presented as picture files which show variation of transcript levels. Data can be searched by various parameters under the advanced search or by keywords on the main search page.