Abstract
CLOCK is the master transcriptional regulator of the
Drosophila
circadian clock. Genome-wide analysis is used here to catalog a surprisingly large number of direct target genes of CLOCK and its partner, CYC. This study provides multiple insights into oscillating RNA Pol II occupancy and previously unobserved RNA cycling patterns, as well as temporal binding patterns and gene- and tissue-specific binding of CLOCK/CYC.
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 (ChIP) 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 h later by the transcriptional repressor PERIOD (PER), indicating that the majority of CLK targets are regulated similarly to core circadian genes. About 30% of target genes also show cycling RNA polymerase II (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.