The circadian clock is an internal timing mechanism that enables organisms to respond to, and even anticipate, changing environmental conditions associated with rotation of the earth. The output of these clocks results in circadian rhythms, which oscillate with circa 24-hr periods and control multiple aspects of behavior and physiology. Circadian rhythms can be entrained by daily environmental signals e.g. light/dark or temperature. Although circadian behaviors in C. elegans have been reported (1), no clock or clock-output genes have been identified. Homologs of animal clock genes are represented in the genome of C. elegans, but their only certain function is to regulate developmental timing. Thus, the nature, and existence of a C. elegans circadian clock remains uncertain. Since circadian transcripts exhibit rhythmic oscillations, genome-wide expression profiling is a powerful approach to identify clock and clock-output genes. We used microarrays to identify these cycling genes using temperature or light/dark as zeitgebers. Growth-synchronized populations of C. elegans were subjected to either 12:12 hr T-cycles (25:15degC) in constant darkness, or 12:12 hr photocycles at constant temperature. In order to identify 24-hr periodic gene expression, we determined the 24-hr spectral power and the probability of observing an equivalent or higher score from randomly permutated data. First, we find that in a 5-d dataset of temperature entrainment, T-cycles show a broad impact on global 24-hr periodicity (1900 transcripts,
p0.02). This result can be explained by either a temperature-driven clock-independent effect or by a temperature-entrained clock-dependent effect. To distinguish between these two possibilities, we analyzed a 6-d data set combining 3-d of temperature entrainment and 3-d of subsequent constant free-running conditions, and find at least 148 temperature-entrained circadian transcripts (
p0.02). Second, we identified a significant set of candidate light-entrained transcripts. Expression data from qRT-PCR suggests that these genes may represent bona fide cycling genes. Our results indicate that T-cycles directly evoke a global expression response broader than photocycles, and that a subset undergo cycling in a circadian manner. Since it is likely that the molecular components of the C. elegans clock are distinct from those of other organisms, C. elegans provides a new system for understanding circadian clocks as well as the evolution of circadian mechanisms.