CLOCKWORK ORANGE promotes CLOCK-CYCLE activation via the Drosophila ortholog of CLOCK INTERACING PROTEIN, CIRCADIAN (ChIP-Seq)

CWO reinforces PER-TIM repression of core clock gene transcription by antagonizing CLK-CYC binding to E-boxes, but also functions to promote CLK-CYC transcription of core clock genes. To determine the relationship between CWO and CLK-CYC binding across the genome, we identified CWO and CLK binding sites via ChIP-seq. Overall design: ChIP-seq: to identify CWO target genes, HA antibody was used to IP CWO-HA from heads of cwo-HA; cwo5073 flies collected during transcriptional repression at Zeitgeber Time 2 (ZT2, where ZT0 is lights-on and ZT12 is lights-off during an LD cycle) and transcription activation at ZT14 for ChIP-seq analysis. CLK was IPed with anti-CLK antibody in parallel