Genomic approaches for studying biological clocks

1. Time is an important dimension for any ecological niche. 2. Most higher organisms show adaptations that are related to daily or seasonal timing, and these adaptations are regulated by endogenous clocks. At the molecular level, these clocks are encoded by a network of proteins interacting with each other and with their own transcripts. 3. Recent expression studies suggested that a large fraction of the transcriptome and the proteome both in mammals and insects may show significant daily oscillations. Here, we review some of the recent genomic approaches to studying circadian clocks, including transcriptomic, proteomic and quantitative trait loci (QTL) analyses, in a wide variety of organisms, from plants to mammals. 4. We also discuss some of the methodological problems that are inherent in these types of studies. Understanding how the circadian system interacts with the environment at the molecular level is perhaps the most important challenge of chronobiology and we anticipate future developments with these methods using experimental paradigms that are more environmentally and ecologically focused. 5. The identification of novel clock genes using more ecologically relevant experimental designs will provide a reservoir of genetic variation whose function can be studied in natural populations.