Transcriptomics

Dataset Information

39

Transcription profiling of mouse mesenchymal derived cells with miR-140 silenced or over-expressed to identify mir-140 targets


ABSTRACT: MicroRNAs (miRNAs) are short noncoding RNA molecules regulating the expression of mRNAs. Target identification of miRNAs is computationally difficult due to the relatively low homology between miRNAs and their targets. We present here an experimental approach to target identification where the cartilage-specific miR-140 was overexpressed and silenced in cells it is normally expressed in separate experiments. Expression of mRNAs was profiled in both experiments and the intersection of mRNAs repressed by miR-140 overexpression and derepressed by silencing of miR-140 was identified. The intersection contained only 49 genes, although both treatments affected the accumulation of hundreds of mRNAs. These 49 genes showed a very strong enrichment for the miR-140 seed sequence implying that the approach is efficient and specific. 21 of these 49 genes were predicted to be direct targets based on the presence of the seed sequence. Interestingly, none of these were predicted by the published target prediction methods we used. One of the potential target mRNAs, Cxcl12, was experimentally validated by Northern blot analysis and a luciferase reporter assay. Experiment Overall Design: Each condition was profiled in triplicate. For over-expression experiment cells were transfected with siRNA-140 (miR-140 mimick) or siRNA-96 (as a control). For suppresion experiment cells were transfected with LNA-antimicroRNA-140 (suppressing endogenous miR-140) or LNA-antimicroRNA-449 (as a control).

INSTRUMENT(S): 418 [Affymetrix]

ORGANISM(S): Mus musculus  

SUBMITTER: Helio Pais   

PROVIDER: E-GEOD-13590 | ArrayExpress| 2012-03-27

SECONDARY ACCESSION(S): GSE13590PRJNA110699

REPOSITORIES: GEO, ArrayExpress

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Publications

Experimental identification of microRNA-140 targets by silencing and overexpressing miR-140.

Nicolas Francisco Esteban FE   Pais Helio H   Schwach Frank F   Lindow Morten M   Kauppinen Sakari S   Moulton Vincent V   Dalmay Tamas T  

RNA (New York, N.Y.) 20081022 12


MicroRNAs (miRNAs) are short noncoding RNA molecules regulating the expression of mRNAs. Target identification of miRNAs is computationally difficult due to the relatively low homology between miRNAs and their targets. We present here an experimental approach to target identification where the cartilage-specific miR-140 was overexpressed and silenced in cells it is normally expressed in separate experiments. Expression of mRNAs was profiled in both experiments and the intersection of mRNAs repre  ...[more]

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