News and Publications

Genetics and Genomics of Circadian Clocks

* Genomics Institute of the Novartis Research Foundation, San Diego, California

Numerous cellular processes fluctuate with a 24-hour periodicity, and an endogenous molecular oscillator known as the circadian clock generates these biological rhythms. Circadian rhythms are found in all kingdoms of life and control diverse events ranging from the sleep-wake cycles in mammals to the overall rate of photosynthesis in plants. Many pathologic changes in humans, such as sleep disorders, most likely are due to a defect in circadian rhythms, so understanding how the circadian clock operates within the cell will have significance for both plants and animals. To study how circadian clocks are built inside of cells, we use molecular, genetic, and genomic approaches in 3 model systems: mouse, Arabidopsis, and Drosophila.

In mammals, the circadian clock plays an integral role in timing daily rhythms of behavior, such as the sleep-wake cycle, and physiology, including body temperature and liver metabolism, in anticipation to changes in light as the Earth rotates around the sun. The master circadian clock resides within a region of the brain that receives light information from the eyes. However, this region can keep time even in the absence of light, as occurs in some visually blind persons. Mutations in the genes that encode components of the circadian clock are manifested as abnormal activity rhythms in rodents and as sleeping disorders in humans, although which photoreceptors set the clock is unclear. Thus, although significant advances have been made in understanding how the mammalian clock itself runs, little is known about the how light transduces synchronizing signals to the clock.

To address this major question, we are using genetic and genomic approaches to identify new gene functions in circadian biology. We are generating a number of mouse strains with mutations in known and potential photoreceptors and are testing the mice for defects in circadian rhythm. Thus far, we have determined that one photoreceptor, melanopsin, is an important contributor in maintaining synchrony between the clock and environmental light conditions. With the recently completed sequencing of the human and mouse genomes, we now know the sequences of more than 30,000 genes that can be investigated for potential roles in circadian function. We developed large-scale, in vitro, cell-based assays that can be used to rapidly determine if genes control clock activity. Combining this approach with genetic analysis will enable us to further dissect the connection between environmental stimuli, in the form of light, and the behavioral and physiologic events regulated by the circadian clock.

In the fruit fly Drosophila, we are interested in elucidating how circadian clocks are organized to control behavior and physiology. The master clock in Drosophila is located in specific neurons within the brain. At the molecular level, the core molecular oscillator is composed of an autoregulatory feedback loop involving a set of clock genes, including period, timeless, clock, and cycle. We are interested in the mechanisms by which the molecular oscillator transduces timing information to regulate diverse physiologic and behavioral outputs. Therefore, we used gene chips to assay clock-controlled gene expression at a genome-wide level. Among several interesting candidate genes, we identified a clock-regulated, calcium-activated potassium channel. We are determining whether this ion channel is a direct link between the molecular oscillator and rhythmic control of behavior.

Flowering is a major event in the life cycle of higher plants. Many plants use seasonal changes in the length of days as a signal to flower, and higher plants use their circadian clocks to perceive these changes. Recently, we defined a molecular link between the circadian clock and day length-dependent regulation of flowering. CONSTANS, a gene involved in flowering time, was identified several years ago and is regulated by the circadian clock. We showed that clock regulation of CONSTANS expression is the key to seasonal control of flowering in Arabidopsis. We are extending these studies by comparing gene expression profiles under conditions of long days and short days to identify other components involved in perception of day length.

By combining molecular, genetic, and genomic approaches, we are beginning to define a number of molecular links between the circadian clock and rhythmic regulation of behavior and development. Analysis of circadian rhythms in multiple organisms provides a unique opportunity to define molecular controls for the behavior of whole organisms. These results will provide targets for clinical and agricultural applications to improve the quality of life.

Publications

Beachy, R., Bennetzen, J.L., Chassy, B.M., Chrispeels, M., Chory, J., Ecker, J.R., Noel, J.P., Kay, S.A., Dean, C., Lamb, C., Jones, J., Santerre, C.R., Schroeder, J.I., Umen, J., Yanofsky, M., Wessler, S., Zhao, Y., Parrott, W. Divergent perspectives on GM food. Nat. Biotechnol. 20:1195, 2002.

Ceriani, M.F., Hogenesch, J.B., Yanovsky, M., Villella, A., Panda, S., Straume, M., Kay, S.A. Genome-wide expression analysis in Drosophila predicts genes controlling circadian behavior. J. Neurosci. 22:9305, 2002.

Panda, S., Hogenesch, J.B., Kay, S.A. Circadian rhythms from flies to human. Nature 417:329, 2002.

Scully, A.L., Zehhof, A.C., Kay, S.A. A P element with a novel fusion of reporters identifies regular, a C₂H₂ zinc-finger gene downstream of the circadian clock. Mol. Cell. Neurosci. 19:501, 2002.

Yanovsky, M.J., Kay, S.A. Molecular basis of seasonal time measurement in Arabidopsis. Nature 419:308, 2002.