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Nucleic Acids Res. 2006;34(16):e107. Epub 2006 Aug 31.

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

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  • 1Molecular Evolution Group, Institute of Molecular Biology and Physiology, University of Copenhagen, Universitetsparken 15, Building 10 DK-2100 Copenhagen Ø, Denmark. jvinther@bi.ku.dk


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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