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Series GSE17628 Query DataSets for GSE17628
Status Public on Aug 31, 2009
Title Tiling arrays from control and flies without Drosha or Pasha
Organism Drosophila melanogaster
Experiment type Expression profiling by genome tiling array
Summary Little is known about the contribution of translational control to circadian rhythms. To address this issue and in particular translational control by microRNAs (miRNAs), we knocked down the miRNA biogenesis pathway in Drosophila circadian tissues. In combination with an increase in circadian-mediated transcription, this severely affected Drosophila behavioral rhythms, indicating that miRNAs function in circadian timekeeping. To identify miRNA–mRNA pairs important for this regulation, immunoprecipitation of AGO1 followed by microarray analysis identified mRNAs under miRNA-mediated control. They included three core clock mRNAs—clock (clk), vrille (vri), and clockworkorange (cwo). To identify miRNAs involved in circadian timekeeping, we exploited circadian cell-specific inhibition of the miRNA biogenesis pathway followed by tiling array analysis. This approach identified miRNAs expressed in fly head circadian tissue. Behavioral and molecular experiments show that one of these miRNAs, the developmental regulator bantam, has a role in the core circadian pacemaker. S2 cell biochemical experiments indicate that bantam regulates the translation of clk through an association with three target sites located within the clk 39 untranslated region (UTR). Moreover, clk transgenes harboring mutated bantam sites in their 39 UTRs rescue rhythms of clk mutant flies much less well than wild-type CLK transgenes.
Tilling arrays were hybridized with cDNA from control or flies in which Drosha or Pasha was downregulated in the timeless-expressing neurons.
Overall design Control (Tim-gal4) , Tim-Drosha (Tim-gal4; UAS-Drosha IR) or Tim-Pasha (Tim-gal4; UAS-pasha IR) flies were entrained in 12h light:12h dark cycles and heads were collected at ZT3 and ZT15. For each strain, RNA extracted from those heads were mixed and used to prepare labeled cDNA that was hybridized to the tiling arrays. Then, the expression value for the Tim-pasha and Tim-Drosha samples was compared to control samples
Contributor(s) Kadener S, Sugino K
Citation(s) 19223442
Submission date Aug 13, 2009
Last update date Mar 21, 2012
Contact name Ken Sugino
Organization name Janelia Research Campus
Lab NeuroSeq
Street address 19700 Helix Dr
City Ashburn
State/province VA
ZIP/Postal code 20147
Country USA
Platforms (1)
GPL5919 [Dm35b_MR] Affymetrix Drosophila Tiling 1.0R Array
Samples (1)
GSM440112 Ctrol vs Pasha-Drosha
This SubSeries is part of SuperSeries:
GSE17629 Circadian analysis of miRNAs and their targets
BioProject PRJNA123391

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE17628_RAW.tar 89.2 Mb (http)(custom) TAR (of BAR, CEL, TXT)
Processed data provided as supplementary file

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