The circadian clock is a molecular and cellular oscillator found in most mammalian tissues that regulates rhythmic physiology and behavior. Numerous investigations have addressed the contribution of circadian rhythmicity to cellular, organ, and organismal physiology. We recently developed a method to look at transcriptional oscillations with unprecedented precision and accuracy using high-density time sampling. Here, we report a comparison of oscillating transcription from mouse liver, NIH3T3, and U2OS cells. Several surprising observations resulted from this study, including a 100-fold difference in the number of cycling transcripts in autonomous cellular models of the oscillator versus tissues harvested from intact mice. Strikingly, we found two clusters of genes that cycle at the second and third harmonic of circadian rhythmicity in liver, but not cultured cells. Validation experiments show that 12-hour oscillatory transcripts occur in several other peripheral tissues as well including heart, kidney, and lungs. These harmonics are lost ex vivo, as well as under restricted feeding conditions. Taken in sum, these studies illustrate the importance of time sampling with respect to multiple testing, suggest caution in use of autonomous cellular models to study clock output, and demonstrate the existence of harmonics of circadian gene expression in the mouse.
Circadian rhythms confer adaptive advantages by allowing organisms to anticipate daily changes in their environment. Over the last few years, many groups have used microarray technology to systematically identify genes under circadian regulation. We have extended on these studies by profiling the circadian transcriptome from the mouse liver and two immortalized cell lines at an unprecedentedly high temporal resolution. We identified over 3,000 different transcripts in the mouse liver that cycle with a period length of approximately 24 hours. To our surprise, we also identified two classes of genes which cycle with period lengths of 12 and 8 hours; i.e., harmonics of the circadian clock. Importantly, we were able to identify harmonics in five other tissue types; however, these rhythms were undetectable in disassociated cells. Moreover, harmonics were lost in the liver when mice are subjected to restricted feeding, suggesting that at least one component of circadian harmonics is driven by feeding.