Experimental identification of microRNA-140 targets by silencing and over-expressing miR-140

Nicolas Molina, Francisco Esteban, Pais, Helio, Schwach, Frank, Lindow, Morten, Kauppinen, Sakari, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2008) Experimental identification of microRNA-140 targets by silencing and over-expressing miR-140. RNA, 14. pp. 2513-2520. ISSN 1469-9001

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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. Twenty-one 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.

Item Type:	Article
Faculty \ School:	Faculty of Science > School of Computing Sciences Faculty of Science > School of Biological Sciences
UEA Research Groups:	Faculty of Science > Research Groups > Computational Biology Faculty of Science > Research Groups > Computational Biology > Computational biology of RNA (former - to 2018) Faculty of Science > Research Groups > Computational Biology > Phylogenetics (former - to 2018) Faculty of Science > Research Groups > Plant Sciences Faculty of Science > Research Groups > Norwich Epidemiology Centre Faculty of Medicine and Health Sciences > Research Groups > Norwich Epidemiology Centre
Depositing User:	EPrints Services
Date Deposited:	01 Oct 2010 13:36
Last Modified:	24 Sep 2024 09:27
URI:	https://ueaeprints.uea.ac.uk/id/eprint/145
DOI:	10.1261/rna.1221108

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