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

Jeppe Vinther; Mads Marquardt Hedegaard; Paul Phillip Gardner; Jens S. Andersen; Peter Arctander

doi:10.1093/nar/gkl590

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

Jeppe Vinther, Mads Marquardt Hedegaard, Paul Phillip Gardner, Jens S. Andersen, Peter Arctander

Functional Genomics

102 Citations (Scopus)

Abstract

miRNAs are small noncoding RNAs that regulate gene expression.We have used stable isotope labeling by amino acids in cellculture (SILAC) to investigate the effect of miRNA-1 on theHeLa cell proteome. Expression of 12 out of 504 investigatedproteins was repressed by miRNA-1 transfection. This repressedset of genes significantly overlaps with miRNA-1 regulated genesthat have been identified with DNA array technology and arepredicted by computational methods. Moreover, we find that the3'-untranslated region for the repressed set are enriched inmiRNA-1 complementary sites. Our findings demonstrate that SILACcan be used for miRNA target identification and that one highlyexpressed miRNA can regulate the levels of many different proteins.

Original language	English
Journal	Nucleic Acids Research
Volume	34
Issue number	16
Pages (from-to)	e107
ISSN	0305-1048
DOIs	https://doi.org/10.1093/nar/gkl590
Publication status	Published - 2006

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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. ",

author = "Jeppe Vinther and Hedegaard, {Mads Marquardt} and Gardner, {Paul Phillip} and Andersen, {Jens S.} and Peter Arctander",

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T1 - Identification of miRNA targets with stable isotope labeling by amino acids in cell culture.

AU - Vinther, Jeppe

AU - Hedegaard, Mads Marquardt

AU - Gardner, Paul Phillip

AU - Andersen, Jens S.

AU - Arctander, Peter

PY - 2006

Y1 - 2006

N2 - 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.

AB - 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.

U2 - 10.1093/nar/gkl590

DO - 10.1093/nar/gkl590

M3 - Journal article

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VL - 34

SP - e107

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - 16

ER -

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

Abstract

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