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| 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
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| 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.
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| 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
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| Contributor(s) |
Kadener S, Sugino K |
| Citation(s) |
19223442 |
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| Submission date |
Aug 13, 2009 |
| Last update date |
Mar 21, 2012 |
| Contact name |
Ken Sugino |
| Organization name |
Janelia Research Campus
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| Lab |
NeuroSeq
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| Street address |
19700 Helix Dr
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| City |
Ashburn |
| State/province |
VA |
| ZIP/Postal code |
20147 |
| Country |
USA |
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| Platforms (1) |
| GPL5919 |
[Dm35b_MR] Affymetrix Drosophila Tiling 1.0R Array |
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| Samples (1) |
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| This SubSeries is part of SuperSeries: |
| GSE17629 |
Circadian analysis of miRNAs and their targets |
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| Relations |
| BioProject |
PRJNA123391 |
| 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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