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Nucleic Acids Research Advance Access originally published online on August 31, 2006
Nucleic Acids Research 2006 34(16):e107; doi:10.1093/nar/gkl590
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Nucleic Acids Research, 2006, Vol. 34, No. 16 e107
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Identification of miRNA targets with stable isotope labeling by amino acids in cell culture

Jeppe Vinther1,*, Mads M. Hedegaard1, Paul P. Gardner1, Jens S. Andersen2 and Peter Arctander1

1 Molecular Evolution Group, Institute of Molecular Biology and Physiology, University of Copenhagen, Universitetsparken 15, Building 10 DK-2100 Copenhagen Ø, Denmark 2 Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark–Odense University Campusvej 55, DK-5230 Odense M, Denmark

*To whom correspondence should be addressed. Tel: +45 35321310; Fax: +45 35321300; Email: jvinther{at}bi.ku.dk

Received June 19, 2006. Revised July 27, 2006. Accepted August 1, 2006.

miRNAs are small noncoding RNAs that regulate gene expression. We have used stable isotope labeling by amino acids in cell culture (SILAC) to investigate the effect of miRNA-1 on the HeLa cell proteome. Expression of 12 out of 504 investigated proteins was repressed by miRNA-1 transfection. This repressed set of genes significantly overlaps with miRNA-1 regulated genes that have been identified with DNA array technology and are predicted by computational methods. Moreover, we find that the 3'-untranslated region for the repressed set are enriched in miRNA-1 complementary sites. Our findings demonstrate that SILAC can be used for miRNA target identification and that one highly expressed miRNA can regulate the levels of many different proteins.


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