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| Status |
Public on Aug 31, 2009 |
| Title |
AGO 1 IMMUNOPRECIPITATION MICROARRAYS |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by 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.
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| Overall design |
Ago IP immunoprecipitation was performed from fly heads collected at different circadian timpoints. For wild type samples 2 biological replicates were collected for each of the six analyzed timepoints from the head protein extract (INPUT) and AGO 1-immunoprecipitated samples (IP). Gene expression was analyzed from both samples by the use of oligonucleotide microarrays. The INPUT sample corresponding to ZT3 has only one replica.
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| Contributor(s) |
Kadener S, Sugino K |
| Citation(s) |
19696147 |
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| Submission date |
Aug 13, 2009 |
| Last update date |
Aug 28, 2018 |
| 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) |
| GPL1322 |
[Drosophila_2] Affymetrix Drosophila Genome 2.0 Array |
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| Samples (27)
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| GSM440088 |
INPUT ZT11, replica 1 |
| GSM440089 |
INPUT ZT11, replica 2 |
| GSM440090 |
INPUT ZT15, replica 1 |
| GSM440091 |
INPUT ZT15, replica 2 |
| GSM440092 |
INPUT ZT19, replica 1 |
| GSM440093 |
INPUT ZT19, replica 2 |
| GSM440094 |
INPUT ZT23, replica 1 |
| GSM440095 |
INPUT ZT23, replica 2 |
| GSM440096 |
IP ZT3, replica 1 |
| GSM440097 |
IP ZT3, replica 2 |
| GSM440098 |
IP ZT7, replica 1 |
| GSM440099 |
IP ZT7, replica 2 |
| GSM440100 |
IP ZT11, replica 1 |
| GSM440101 |
IP ZT11, replica 2 |
| GSM440102 |
IP ZT15, replica 1 |
| GSM440103 |
IP ZT15, replica 2 |
| GSM440104 |
IP ZT19, replica 1 |
| GSM440105 |
IP ZT19, replica 2 |
| GSM440106 |
IP ZT23, replica 1 |
| GSM440107 |
IP ZT23, replica 2 |
| GSM440108 |
INP Tim-Dcr ZT3 |
| GSM440109 |
INP Tim-Dcr ZT15 |
| GSM440110 |
IP Tim-Dcr ZT3 |
| GSM440111 |
IP Tim-Dcr ZT15 |
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| This SubSeries is part of SuperSeries: |
| GSE17629 |
Circadian analysis of miRNAs and their targets |
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| Relations |
| BioProject |
PRJNA123389 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE17627_RAW.tar |
49.9 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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