In 1971, Ron Konopka and Seymour Benzer published a landmark paper demonstrating that single-gene mutations could alter circadian behavior in the fruitfly Drosophila . This work laid the foundation for the explosion of molecular research on circadian rhythms in the following decades. Remarkably, the long period, short period, and arrhythmic behaviors observed resulted from mutations in the same gene, period (abbreviated “per”) . Another 13 years passed until the per gene was cloned [2,3]. The per RNA and PER protein were found to be rhythmically expressed and genetic experiments suggested that PER could feed back on its transcription [4,5]. Similar negative feedback loops were also described for the frequency gene in the fungus Neurospora crassa . A combination of forward genetics (from phenotype to genotype), reverse genetics (from genotype to phenotype), and brute force molecular characterizations identified new genes acting with per in the molecular clock [7,8]. Based on the per story, an early set of criteria was developed in the identification of new clock genes. The newly identified genes should: (1) have oscillatory products, (2) act as state variables, and (3) perturb the clock’s function when perturbed themselves. However, these criteria proved oversimplified, as the actual clock mechanism was eventually unraveled . For example, some integral clock components do not need to oscillate at least at the level of RNA or protein abundance . Also, because of redundancy of function in many mammalian genes, multiple gene paralogs (or variants of the same ancestral gene in one organism’s genome) could compromise the criterion of “necessity” if only one gene of a gene family was deleted. Despite these challenges, a molecular clock based on transcriptional/translational negative feedback has been described for many species including bacteria, fungi, plants, insects, and mammals [8,11,12; Figure 12.1A). Here we will focus on the mammalian clock mechanism and how it relates to human health.
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