Analyzing mRNA expression identifies Smad3 as a microRNA-140 target regulated only at protein level

RNA

Volumn 16, Issue 3, 2010, Pages 489-494

  Pais, Helio ^a   Nicolas, Francisco Esteban ^a   Soond, Surinder M ^a   Swingler, Tracey E ^a   Clark, Ian M ^a   Chantry, Andrew ^a   Moulton, Vincent ^a   Dalmay, Tamas ^a  

^a UNIVERSITY OF EAST ANGLIA   (United Kingdom)

Author keywords

microRNA target identification; microRNA 140; Smad; TGF

Indexed keywords

MESSENGER RNA; MICRORNA; MICRORNA 140; PROTEIN; SMAD3 PROTEIN; TRANSFORMING GROWTH FACTOR BETA; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; EMBRYO; FEEDBACK SYSTEM; GENE REPRESSION; GENE TARGETING; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; MOUSE; NEGATIVE FEEDBACK; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN EXPRESSION;

ANIMALS; CELL LINE; COMPUTATIONAL BIOLOGY; MICE; MICRORNAS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS, GENETIC; SMAD3 PROTEIN; TRANSFORMING GROWTH FACTOR BETA;

EID: 77149122720     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.1701210     Document Type: Article

References (28)

1. Baek D, Villén J, Shin C, Camargo FD, Gygi SP, Bartel DP. 2008. The impact of microRNAs on protein output. Nature 455: 64-71.
2. Bartel DP. 2004. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
3. Behm-Ansmant I, Rehwinkel J, Doerks T, Stark A, Bork P, Izaurralde E. 2006. mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes. Genes & Dev 20: 1885-1898.
4. Brennecke J, Stark A, Russell RB, Cohen SM. 2005. Principles of microRNA-target recognition. PLoS Biol 3: e85. doi: 10.1371/journal.pbio.0030085.
5. Dai Y-S, Cserjesi P. 2002. The basic helix-loop-helix factor, HAND2, functions as a transcriptional activator by binding to e-boxes as a heterodimer. J Biol Chem 277: 12604-12612.
6. Davis BN, Hilyard AC, Lagna G, Hata A. 2008. SMAD proteins control DROSHA-mediated microRNA maturation. Nature 454: 56-61.
7. Dennler S, Itoh S, Vivien D, ten Dijke P, Huet S, Gauthier JM. 1998. Direct binding of Smad3 and Smad4 to critical TGF β-inducible elements in the promoter of human plasminogen activator inhibitor-type 1 gene. EMBO J 17: 3091-3100.
8. Eberhart JK, He X, Swartz ME, Yan YL, Song H, Boling TC, Kunerth AK, Walker MB, Kimmel CB, Postlethwait JH. 2008. MicroRNA Mirn140 modulates Pdgf signaling during palatogenesis. Nat Genet 40: 290-298.
9. Eulalio A, Rehwinkel J, Stricker M, Huntzinger E, Yang SF, Doerks T, Dorner S, Bork P, Boutros M, Izaurralde E. 2007. Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing. Genes & Dev 21: 2558-2570.
10. Eulalio A, Huntzinger E, Nishihara T, Rehwinkel J, Fauser M, Izaurralde E. 2009. Deadenylation is a widespread effect of miRNA regulation. RNA 15: 21-32.
11. Giraldez AJ, Mishima Y, Rihel J, Grocock RJ, Van Dongen S, Inoue K, Enright AJ, Schier AF. 2006. Zebrafish MiR-430 promotes dead-enylation and clearance of maternal mRNAs. Science 312: 75-79.
12. Heldin CH, Miyazono K, ten Dijke P. 1997. TGF-β signalling from cell membrane to nucleus through SMAD proteins. Nature 390: 465-471.
13. Kobayashi T, Lu J, Cobb BS, Rodda SJ, McMahon AP, Schipani E, Merkenschlager M, Kronenberg HM. 2008. Dicer-dependent pathways regulate chondrocyte proliferation and differentiation. Proc Natl Acad Sci 105: 1949-1954.
14. Kong W, Yang H, He L, Zhao JJ, Coppola D, Dalton WS, Cheng JQ. 2008. MicroRNA-155 is regulated by the transforming growth factor β/Smad pathway and contributes to epithelial cell plasticity by targeting RhoA. Mol Cell Biol 28: 6773-6784.
15. Li Z, Hassan MQ, Volinia S, van Wijnen AJ, Stein JL, Croce CM, Lian JB, Stein GS. 2008. A microRNA signature for a BMP2-induced osteoblast lineage commitment program. Proc Natl Acad Sci 105: 13906-13911.
16. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM. 2005. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 443: 769-773.
17. Luzi E, Marini F, Sala SC, Tognarini I, Galli G, Brandi ML. 2008. Osteogenic differentiation of human adipose tissue-derived stem cells is modulated by the miR-26a targeting of the SMAD1 transcription factor. J Bone Miner Res 23: 287-295.
18. Nicolas FE, Pais H, Schwach F, Lindow M, Kauppinen S, Moulton V, Dalmay T. 2008. Experimental identification of microRNA-140 targets by silencing and overexpressing miR-140. RNA 14: 2513-2520.
19. Petrocca F, Vecchione A, Croce CM. 2008. Emerging role of miR-106b-25/miR-17-92 clusters in the control of transforming growth factor β signaling. Cancer Res 68: 8191-8194.
20. Rehwinkel J, Behm-Ansmant I, Gatfield D, Izaurralde E. 2005. A crucial role for GW182 and the DCP1:DCP2 decapping complex in miRNA-mediated gene silencing. RNA 11: 1640-1647.
21. Selbach M, Schwanhäusser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N. 2008. Widespread changes in protein synthesis induced by microRNAs. Nature 455: 58-63.
22. Sethupathy P, Megraw M, Hatzigeorgiou AG. 2006. A guide through present computational approaches for the identification of mammalian microRNA targets. Nat Methods 3: 881-886.
23. Sun Q, Zhang Y, Yang G, Chen X, Zhang Y, Cao G, Wang J, Sun Y, Zhang P, Fan M, et al. 2008. Transforming growth factor-β-regulated miR-24 promotes skeletal muscle differentiation. Nucleic Acids Res 36: 2690-2699.
24. Tuddenham L, Wheeler G, Ntounia-Fousara S, Waters J, Hajihosseini MK, Clark I, Dalmay T. 2006. The cartilage specific microRNA-140 targets histone deacetylase 4 in mouse cells. FEBS Lett 580: 4214-4217.
25. Wienholds E, Kloosterman WP, Miska E, Alvarez-Saavedra E, Berezikov E, de Bruijn E, Horvitz HR, Kauppinen S, Plasterk RH. 2005. MicroRNA expression in zebrafish embryonic development. Science 309: 310-311.
26. Wu L, Fan J, Belasco JG. 2006. MicroRNAs direct rapid deadenylation of mRNA. Proc Natl Acad Sci 103: 4034-4039.
27. Yang X, Chen L, Xu X, Li C, Huang C, Deng CX. 2001. TGF-β/Smad3 signals repress chondrocyte hypertrophic differentiation and are required for maintaining articular cartilage. J Cell Biol 153: 35-46.
28. Zhao Y, Samal E, Srivastava D. 2005. Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 436: 214-220.