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

被引：86

作者：

Vinther, Jeppe

Hedegaard, Mads M.

Gardner, Paul P.

Andersen, Jens S.

Arctander, Peter

机构：

[1] Univ Copenhagen, Inst Mol Biol & Physiol, Mol Evolut Grp, DK-2100 Copenhagen 0, Denmark

[2] Odense Univ, Dept Biochem & Mol Biol, Ctr Expt BioInformat, DK-5230 Odense M, Denmark

来源：

NUCLEIC ACIDS RESEARCH | 2006年 / 34卷 / 16期

关键词：

D O I：

10.1093/nar/gkl590

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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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页数：6

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共 20 条

[1] MicroRNAs: Genomics, biogenesis, mechanism, and function (Reprinted from Cell, vol 116, pg 281-297, 2004) [J].

Bartel, David P. .

CELL, 2007, 131 (04) :11-29

[2] 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets [J].

Birmingham, A ;

Anderson, EM ;

Reynolds, A ;

Ilsley-Tyree, D ;

Leake, D ;

Fedorov, Y ;

Baskerville, S ;

Maksimova, E ;

Robinson, K ;

Karpilow, J ;

Marshall, WS ;

Khvorova, A .

NATURE METHODS, 2006, 3 (03) :199-204

[3] Principles of MicroRNA-target recognition [J].

Brennecke, J ;

Stark, A ;

Russell, RB ;

Cohen, SM .

PLOS BIOLOGY, 2005, 3 (03) :404-418

[4] PACdb:: PolyA cleavage site and 3′-UTR database [J].

Brockman, JM ;

Singh, P ;

Liu, DL ;

Quinlan, S ;

Salisbury, J ;

Graber, JH .

BIOINFORMATICS, 2005, 21 (18) :3691-3693

[5] The widespread impact of mammalian microRNAs on mRNA repression and evolution [J].

Farh, KKH ;

Grimson, A ;

Jan, C ;

Lewis, BP ;

Johnston, WK ;

Lim, LP ;

Burge, CB ;

Bartel, DP .

SCIENCE, 2005, 310 (5755) :1817-1821

[6] Tropomyosin isoforms: divining rods for actin cytoskeleton function [J].

Gunning, PW ;

Schevzov, G ;

Kee, AJ ;

Hardeman, EC .

TRENDS IN CELL BIOLOGY, 2005, 15 (06) :333-341

[7] Regulation of actin filament network formation through Arp2/3 complex: Activation by a diverse array of proteins [J].

Higgs, HN ;

Pollard, TD .

ANNUAL REVIEW OF BIOCHEMISTRY, 2001, 70 :649-676

[8] Widespread siRNA "off-target'' transcript silencing mediated by seed region sequence complementarity [J].

Jackson, Aimee L. ;

Burchard, Julja ;

Schelter, Janell ;

Chau, B. Nelson ;

Cleary, Michele ;

Lim, Lee ;

Linsley, Peter S. .

RNA, 2006, 12 (07) :1179-1187

[9] Human MicroRNA targets [J].

John, B ;

Enright, AJ ;

Aravin, A ;

Tuschl, T ;

Sander, C ;

Marks, DS .

PLOS BIOLOGY, 2004, 2 (11) :1862-1879

[10] Combinatorial microRNA target predictions [J].

Krek, A ;

Grun, D ;

Poy, MN ;

Wolf, R ;

Rosenberg, L ;

Epstein, EJ ;

MacMenamin, P ;

da Piedade, I ;

Gunsalus, KC ;

Stoffel, M ;

Rajewsky, N .

NATURE GENETICS, 2005, 37 (05) :495-500