title: Identification of miRNA targets with stable isotope labeling by amino acids in cell culture.
abstract: 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.
authors.affiliation: Molecular Evolution Group, Institute of Molecular Biology and Physiology, University of Copenhagen, Universitetsparken 15, Building 10 DK-2100 Copenhagen Ø, Denmark. jvinther@bi.ku.dk
authors.forename: Jeppe
authors.initials: J
authors.lastname: Vinther
authors.forename: Mads M
authors.initials: MM
authors.lastname: Hedegaard
authors.forename: Paul P
authors.initials: PP
authors.lastname: Gardner
authors.forename: Jens S
authors.initials: JS
authors.lastname: Andersen
authors.forename: Peter
authors.initials: P
authors.lastname: Arctander
mesh_terms: D020413:3' Untranslated Regions / Q000737:chemistry*; D000596:Amino Acids / Q000737:chemistry; D002247:Carbon Isotopes; D005786:Gene Expression Regulation; D006367:HeLa Cells; D006801:Humans; D013058:Mass Spectrometry; D035683:MicroRNAs / Q000502:physiology*; D009587:Nitrogen Isotopes; D020543:Proteome / Q000737:chemistry / Q000235:genetics*; D040901:Proteomics / Q000379:methods*
chemical_list: D020413:3' Untranslated Regions; D000596:Amino Acids; D002247:Carbon Isotopes; D035683:MicroRNAs; D009587:Nitrogen Isotopes; D020543:Proteome