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Welcome. This web site accompanies our publication "Circadian Regulation of Gene Expression Systems in the Drosophila Head" (Claridge-Chang et al., Neuron, 2001, 32: 657-671).

Many organisms on earth have adapted to the daily environmental fluctuations in light and temperature by evolving internal, circadian clocks. Such clocks are known to regulate physiology and behavior at many levels. Clock-controlled functions in humans include sleep, cardiovascular function, respiration, endocrine function, gastrointestinal function, renal function, thermoregulation, immune function, vision, metabolism, and cognitive performance. Over the past three decades the fruit fly Drosophila melanogaster has emerged as an especially useful model for genetic and molecular studies of the animal clock. At its core the circadian clock contains a set of transcriptional feedback circuits. The identification of circadian transcript profiles provides us with a starting point from where we can trace signals connecting the molecular clock circuits to daily rhythms in physiology and behavior.

In this study, we observed circadian transcript profiles in adult Drosophila heads. Wild-type flies that had been kept in a 12-hr light/ 12-hr dark cycle for three days were harvested every four hours during an additional light/dark day (ZT) and a subsequent day in constant darkness (CT). This experiment was performed three times independently. Gene expression levels were measured using Affymetrix Drosophila Gene Chips containing 14010 probesets (about 13600 genes). Circadian oscillations were detected by fitting the separately normalized log-ratio data for the three time courses to 24-hr sine-waves of fixed phase in an amplitude-independent manner. Specifically, we used the 24-hr fourier components (F24) and associated probabilities (pF24) as quantitative indicators of circadian patterns. After discarding noisy patterns and patterns with low 24-hr autocorrelation, the remaining set was ranked using the pF24 values. Based on the results of independently conducted northern analyses we selected a set of 158 genes that exhibited particularly robust circadian rhythms. This subset contains genes with a wide variety of oscillatory phases and molecular functions including learning, memory, vision, olfaction, locomotion, detoxification, and areas of metabolism.

In order to distinguish different types of circadian regulation, we also collected expression profiles (one light/dark cycle, sampled every 6 hours) for three different types of arrhythmic mutants with defective clocks: period(per)-null, timeless(tim)-null, Clock(Clk)-jrk. Circadian transcripts directly controlled by the circadian transcription factor CLK tend to be constitutively down-regulated in the Clk-jrk mutant and constitutively up-regulated in the absence of the negative regulators PER and TIM, whereas another set of circadian transcripts shows the opposite behavior. Significant up- or down-regulation is indicated by Wilcoxon rank-sum tests comparing expression in each of the mutants relative to wild-type.

The search options available on this web-site allow exploration of the circadian expression data and annotated information for all genes represented on the Affymetrix Drosophila Gene Chips. Customized searches can be performed to recover subsets of the 158 circadian genes or to make independent selections.

The microarray expression data is available in downloadable format here or by clicking on the 'Data' link in the left navigation panel.