Genome-wide Transcriptional Orchestration of Circadian Rhythms inDrosophila

Abstract

Circadian rhythms govern the behavior, physiology, and metabolism of living organisms. Recent studies have revealed the role of several genes in the clock mechanism both in Drosophila and in mammals. To study how gene expression is globally regulated by the clock mechanism, we used a high density oligonucleotide probe array (GeneChip) to profile gene expression patterns in Drosophila under light-dark and constant dark conditions. We found 712 genes showing a daily fluctuation in mRNA levels under light-dark conditions, and among these the expression of 115 genes was still cycling in constant darkness, i.e. under free-running conditions. Unexpectedly the expression of a large number of genes cycled exclusively under constant darkness. We found that cycling in most of these genes was lost in the arrhythmic Clock (Clk) mutant under lightdark conditions. Expression of periodically regulated genes is coordinated locally on chromosomes where small clusters of genes are regulated jointly. Our findings reveal that many genes involved in diverse functions are under circadian control and reveal the complexity of circadian gene expression in Drosophila.

Reciprocal regulation of carbon monoxide metabolism and the circadian clock

“…Because the expression of Alas1 and heme oxygenase has also been reported to be circadian in Drosophila melanogaster heads 19,20 , we investigated whether heme oxygenase (dHo (official symbol Ho), which is the only isoform of heme oxygenase in Drosophila and is essential for normal fly development 21 ) is also required for normal rhythms in this species. To this end, we examined behavioral rhythms in flies in which dHo expression was knocked down in various cell types by two independent UAS-dHo-RNAi lines by using the binary Gal4-UAS system 22 .…”

Perchance to dream: Solving the mystery of sleep through genetic analysis

“…Although the function of "clock" genes in generating circadian rhythms is now firmly established, their implication in other molecular pathways is likely given their wide-spread expression throughout the organism and the large number and diversity of genes controlling fundamental biologic processes that are under the influence of "clock" genes in Arabidopsis, Drosophila, and the mouse (Harmer et al, 2000;Claridge-Chang et al, 2001;McDonald and Rosbash, 2001;Rutter et al, 2001;Panda et al, 2002a;Storch et al, 2002;Ueda et al, 2002). The distinct roles of circadian and homeostatic components in sleep regulation are often difficult to discern (Dijk and Czeisler, 1994).…”

The role of microRNAs (miRNA) in circadian rhythmicity

“…Genomewide expression analysis from several microarray studies in different organisms indicates that the expression of as much as 5%-10% of transcripts in a specific tissue oscillates in a circadian manner (Claridge-Chang et al 2001;McDonald and Rosbash 2001;Akhtar et al 2002;Ceriani et al 2002;Lin et al 2002;Panda et al 2002;Storch et al 2002;Ueda et al 2002;Duffield 2003;Keegan et al 2007). …”