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E-GEOD-4201 - Transcription profiling of Zebrafish embryos investigating the effect of miR-430 microRNA on deadenylation and clearance of maternal mRNAs

Status
Submitted on 7 February 2006, released on 5 October 2007, last updated on 3 May 2014
Organism
Danio rerio
Samples (15)
Array (1)
Protocols (9)
Description
MicroRNAs comprise 1-3% of all vertebrate genes, but their in vivo functions and mechanisms of action remain largely unknown. Zebrafish miR-430 is expressed at the onset of zygotic transcription and regulates morphogenesis during early development. Using a microarray approach and in vivo target validation, we find that miR-430 directly regulates several hundred target mRNAs. Targets are highly enriched for maternal mRNAs that accumulate in the absence of miR-430. We also show that miR-430 accelerates the deadenylation of target mRNAs. These results suggest that miR-430 facilitates the deadenylation and clearance of maternal mRNAs during early embryogenesis. Experiment Overall Design: As a first step towards the identification of miR-430 targets, we compared the rate of mRNA degradation in wild type and maternal-zygotic (MZ) dicer mutant embryos, which are deficient in miRNA processing. We found that the rate of degradation of a target mRNA with partial complementarity to miR-430 is significantly reduced in MZdicer mutants. Providing miR-430 duplexes to MZdicer mutants restores the rate of target decay. These results indicate that miR-430 enhances the decay of target mRNAs. Experiment Overall Design: To identify miR-430 in vivo targets, we compared the mRNA expression profile of embryos that were wild-type, MZdicer, or MZdicer rescued with miR-430 (MZdicer+miR-430). This analysis identified ~600 genes that were upregulated in MZdicer, but not in MZdicer+miR-430. Experiment Overall Design: We have also analyzed the expression profile of the genes in the array at three different time points, one maternal stage(16 cell), and two Zygotic stages 5 hours and 9 hours
Experiment types
transcription profiling by array, cellular modification, co-expression, development or differentiation
Contact
Citation
Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Antonio J Giraldez, Yuichiro Mishima, Jason Rihel, Russell J Grocock, Stijn Van Dongen, Kunio Inoue, Anton J Enright, Alexander F Schier. Science 312(5770):75-9 (2006)
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-4201.idf.txt
Sample and data relationshipE-GEOD-4201.sdrf.txt
Raw data (1)E-GEOD-4201.raw.1.zip
Processed data (1)E-GEOD-4201.processed.1.zip
Array designA-AFFY-38.adf.txt
R ExpressionSetE-GEOD-4201.eSet.r
Links