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Identification and validation of gene expression changes upon removal of Dicer in the murine limb mesenchyme

ABSTRACT: Wild type and Dicer null embryonic mouse limbs were analaysed using Affymetrix arrays to identify gene expression changes. Genes that were up-regulated in Dicer-null limbs were canidates for being miRNA targets. Potential miRNA target genes were validated using qRTPCR.

ORGANISM(S): Mus musculus

PROVIDER: GSE13807 | GEO | 2011/01/31

SECONDARY ACCESSION(S): PRJNA110575

REPOSITORIES: GEO

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Identification and validation of gene expression changes upon removal of Dicer in the murine limb mesenchyme

Project description:Wild type and Dicer null embryonic mouse limbs were analaysed using Affymetrix arrays to identify gene expression changes. Genes that were up-regulated in Dicer-null limbs were canidates for being miRNA targets. Potential miRNA target genes were validated using qRTPCR. Mice carrying a heterozygous Dicer floxed allele and the prxcre driver allele were crossed to homozygous Dicer Floxed mice. Embryos were harvested from pregent moms and genotyped to determine heterozygous, Wild type and mutant limb buds. These limb buds were used to prepare RNA for array analysis.

2011-01-31 | E-GEOD-13807 | biostudies-arrayexpress

DICER-interacting partners in juvenile mouse testes

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Phosphoproteomic analysis of liver of Dicer knockout mice

Project description:Dicer is an essential ribonuclease involved in the biogenesis of miRNA. Previous studies have reported that Dicer is dysregulated in multiple types of cancers. To investigate the downstream phosphoproteome of Dicer, we carried out phosphotyrosine profiling of the liver of Dicer knockout of mice. We employed antibody-based enrichment of phosphotyrosine containing peptides coupled with spike-in SILAC-based quantitation. Over 400 phosphoisites were identified in each condition while 290 phosphosites were quantitated in common. Amongst these, several key signaling molecules like receptor tyrosine kinase MET, MET, PDGFR, EPHA2, EPHB4 and IGF1R/INSR were hyperphosphorylated. Also, non-receptor tyrosine kinases of Src family and their downstream effector signaling partners including IRS2 and STAT3were found to be hyperphosphorylated. Our study indicates that there is significant alteration in the signaling pathways upon ablation of Dicer.

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Project description:A hallmark of RNA silencing is a class of ~22 nt RNAs which are processed from dsRNA precursor by Dicer. Accurate processing by Dicer is critical for the functionality of microRNAs (miRNAs). According to the current model, Dicer measures the length by anchoring the 3' overhang of the dsRNA terminus. Here we find that human Dicer binds to the 5' end of RNA and utilizes the 5' end as an additional reference point for cleavage site selection (5' counting rule). We further identify a novel motif (5'-pocket) in Dicer, which recognizes the 5' end of RNA. By analyzing miRNA population from 5'-pocket mutant Dicer expressing Dicer-null mES, we provide that the 5' pocket is significant for Dicer processing in vivo.

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The effects of the 5' pocket motif of Dicer on miRNA biogenesis

2011-07-12 | E-GEOD-27903 | biostudies-arrayexpress

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Proliferation and Tumorigenesis of a Murine Sarcoma Cell Line in the Absence of Dicer

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Project description:Dicer is required for miRNA processing and RNA interference. Here we knocked out Dicer in SV40 T antigen immortalized subcutaneous preadipocytes isolated from Dicer flox mice by transducing these cells with adenoviruses harboring Cre recombinase. Control cells were transduced with adenovirus harboring GFP. We used microarrays to detail the gene expression profile of Dicer knockout preadipocytes.

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Expression data from Dicer and Ago2-knockdown HeLa cells

Project description:Dicer and Argonaute2 (Ago2) gene is involving in microRNA (miRNA) maturation. Knockdown of these genes has great impact on miRNA expression profiles. We used microarrays to detail the miRNA expression profiles in Dicer- and Ago2-knockdown HeLa cells and demonstarted that the significant difference between Ago2-knockdown and Dicer- and Ago2-co-knockdown HeLa cells were not found.

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