Drosophila CLOCK Target Gene Characterization: Implications for Circadian Tissue-Specific Gene Expression

CLOCK (CLK) is a master transcriptional regulator of the circadian clock in Drosophila. To identify CLK direct target genes and address circadian transcriptional regulation in Drosophila, we performed chromatin immunoprecipitation-tiling array assays (ChIP-chip) with a number of circadian proteins. CLK binding cycles on at least 800 sites with maximal binding in the early night. The CLK partner protein CYCLE (CYC) is on most of these sites. The CLK/CYC heterodimer is joined 4-6 hrs later by the transcriptional repressor PER, indicating that the majority of CLK targets are regulated similarly to core circadian genes (Menet et al. 2010). About 30% of target genes also show cycling Pol II binding. Many of these generate cycling RNAs despite not being documented in prior RNA cycling studies. This is due in part to different RNA isoforms and to fly head tissue heterogeneity. CLK has specific targets in different tissues, implying that important CLK partner proteins and/or mechanisms contribute to gene-specific and tissue-specific regulation. 5 different datasets are included including: CLK ChIP-chip (samples collected at 6 timepoints, 2 replicates each, input and IP samples), PER ChIP-chip (samples collected at 6 timepoints, 2 replicates each, input and IP samples), RNA Pol II ChIP-chip (samples collected at 6 timepoints, 2 replicates each, input and IP samples), CYC-ChIP-chip (samples from ZT14, samples in triplicate, input and IP samples), GMR-hid CLK ChIP-chip (2 replicates at ZT14 of both WT and GMR-hid, input and IP samples). Total of 62 arrays