Diet and CLK-dependent expression changes in fly heads

This study aims to elucidate how the core circadian transcription factor, CLOCK (Clk), mediates diet-dependent transcriptional changes in fly heads. In particular, we sought to identify how CLK influences gene-level expression changes in fly heads from flies that had been reared on either a high nutrient or low nutrient (dietary restriction) diet. We performed RNA-Seq analyses of heads with inducible, pan-neuronal over-expression of dominant negative CLK protein lacking the basic-helix-loop-helix domain (DNA binding). Flies were heterozygous for the RU486-inducible Elav-GeneSwitch-GAL4 driver as well as a UAS-controlled dominant negative clock allele (CLK-D1). Flies were reared on either a nutrient rich (ad libitum, 5% yeast-extract) or dietary restriction (0.5% yeast-extract) diet with or without the addition of RU486 (200μM) in a 12:12h light-dark cycle at 25°C. mRNA was collected at ZT0 and ZT12 from three independent biological replicates (per genotype/diet) and deep-sequencing was performed (150 PE reads, read depth of 25 million).