Project description:CLK targets from fly heads using the TIM-GAL4; UAS-CLKGR line Experiment Overall Design: Fly heads were stimulated with vehicle + CHX or dexamethasone + CHX
Project description:This SuperSeries is composed of the following subset Series:; GSE7644: CLKGR in S2 cells; GSE7646: CLK targets from fly heads; GSE7651: Timepoints 5073 strain; GSE7652: Timepoints Control strain; GSE7653: S2 cells transfected with Clk Experiment Overall Design: Refer to individual Series
Project description: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.
Project description:Our objective was to identify candidate genes that contribute to the long 31-hour circadian period previously observed in DGRP_892. We performed transcriptional profiling of whole fly heads from two genotypes: DGRP_892, and Canton-S B, a line with a normal 24-hour circadian period. We collected fly heads every two hours over a 24-hour period. We quantified differential expression among genotype, time, and sex.
Project description: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.
Project description:To address the contribution of transcriptional regulation to Drosophila clock gene expression and to behavior, we generated a series of CRISPR-mediated deletions within two regions of the circadian gene timeless (tim), an intronic E box region and an upstream E box region that are both recognized by the key transcription factor Clock (Clk) and its heterodimeric partner Cycle. The upstream deletions but not an intronic deletion dramatically impact tim expression in fly heads; the biggest upstream deletion reduces peak RNA levels and tim RNA cycling amplitude to about 15% of normal, and there are similar effects on tim protein (TIM). The cycling amplitude of other clock genes is also strongly reduced, in these cases due to increases in trough levels. To examine the effect of promoter E-box deletions on Clk binding, we performed Clk-ChIP around the clock in wild-type and 126 mutant flies.
