Microarray analysis and organization of circadian gene expression Drosophila

We have used high-density oligonucleotide arrays to study global circadian gene expression in Drosophila melanogaster. Coupled with an analysis of clo ck mutant (Clk) flies, a cell line designed to identify direct targets of t he CLOCK (CLK) transcription factor and differential display, we uncovered several striking features of circadian gene networks. These include the ide ntification of 134 cycling genes, which contribute to a wide range of diver se processes. Many of these clock or clock-regulated genes are located in g ene clusters, which appear subject to transcriptional coregulation. All osc illating gene expression is under clk control, indicating that Drosophila h as no clk-independent circadian systems. An even larger number of genes is affected in Clk flies, suggesting that clk affects other genetic networks. As we identified a small number of direct target genes, the data suggest th at most of the circadian gene network is indirectly regulated by clk.