Determination of MiRNA targets in skeletal muscle cells

Methods in Molecular Biology

Volumn 798, Issue , 2012, Pages 475-490

  Huang, Zhan Peng ^a   Espinoza Lewis, Ramón ^a   Wang, Da Zhi ^a  

^a BOSTON CHILDREN S HOSPITAL   (United States)

Author keywords

Gene expression; MicroRNA; miRNA; Muscle; Muscle disease; Posttranscriptional regulation

Indexed keywords

LUCIFERASE; MICRORNA;

ANIMAL; ARTICLE; CELL LINE; CELL STRAIN HEK293; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE SILENCING; GENETICS; HUMAN; METABOLISM; MOUSE; NORTHERN BLOTTING; NUCLEOTIDE SEQUENCE; RAT; REAL TIME POLYMERASE CHAIN REACTION; REPORTER GENE; SKELETAL MUSCLE;

ANIMALS; BASE SEQUENCE; BLOTTING, NORTHERN; CELL LINE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE KNOCKDOWN TECHNIQUES; GENES, REPORTER; HEK293 CELLS; HUMANS; LUCIFERASES; MICE; MICRORNAS; MUSCLE, SKELETAL; RATS; REAL-TIME POLYMERASE CHAIN REACTION;

MAMMALIA;

EID: 84555196419     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-343-1_28     Document Type: Article

References (33)

1. Wagner, K.R. (2002) Genetic diseases of muscle. Neurol Clin. 20, 645-678. (Pubitemid 35154463)
2. Bartel, D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 116, 281-297.
3. He, L., Thomson, J.M., Hemann, M.T., Hernando-Monge, E., Mu, D., Goodson, S., Powers, S., Cordon-Cardo, C., Lowe, S.W., Hannon, G.J., and Hammond, S.M. (2005) A microRNA polycistron as a potential human oncogene. Nature. 435, 828-833. (Pubitemid 40839734)
4. Rodriguez, A., Griffiths-Jones, S., Ashurst, J.L., and Bradley, A. (2004) Identification of mammalian microRNA host genes and transcription units. Genome Res. 14, 1902-1910. (Pubitemid 39386503)
5. Ruby, J.G., Jan, C.H., and Bartel, D.P. (2007) Intronic microRNA precursors that bypass Drosha processing. Nature. 448, 83-86. (Pubitemid 47037009)
6. Yi, R., Qin, Y., Macara, I.G., and Cullen, B.R. (2003) Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev. 17, 3011-3016. (Pubitemid 38040764)
7. Hutvágner, G., McLachlan, J., Pasquinelli, A.E., Bálint, E., Tuschl, T., and Zamore, P.D. (2001) A cellular function for the RNAinterference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science. 293, 834-838. (Pubitemid 32743968)
8. Schwarz, D.S., Hutvágner. G., Du. T., Xu. Z., Aronin. N., and Zamore, P.D. (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell. 115, 199-208. (Pubitemid 37329583)
9. Lee, R.C., and Ambros, V. (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science. 294, 862-864. (Pubitemid 33032105)
10. Williams, A.H., Liu, N., van Rooij, E., and Olson, E.N. (2009) MicroRNA control of muscle development and disease. Curr Opin Cell Biol. 21, 461-469.
11. Zhao, Y., Samal, E., and Srivastava, D. (2005) Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature. 436, 214-220. (Pubitemid 41021266)
12. Chen, J.F., Mandel, E.M., Thomson, J.M., Wu, Q., Callis, T.E., Hammond, S.M., Conlon, F.L., and Wang, D.Z. (2006) The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nat Genet. 38, 228-233. (Pubitemid 43177239)
13. van Rooij, E., Sutherland, L.B., Qi, X., Richardson, J.A., Hill, J., and Olson, E.N. (2007) Control of stress-dependent cardiac growth and gene expression by a microRNA. Science. 316, 575-579. (Pubitemid 46683138)
14. Simon, D.J., Madison, J.M., Conery, A.L., Thompson-Peer, K.L., Soskis, M., Ruvkun, G.B., Kaplan, J.M., and Kim, J.K. (2008) The microRNA miR-1 regulates a MEF-2- dependent retrograde signal at neuromuscular junctions. Cell. 133, 903-915. (Pubitemid 351707687)
15. Kwon, C., Han, Z., Olson, E.N., and Srivastava, D. (2005) MicroRNA1 influences cardiac differentiation in Drosophila and regulates Notch signaling. Proc Natl Acad Sci USA. 102, 18986-18991. (Pubitemid 43049553)
16. Callis, T.E., and Wang, D.Z. (2008) Taking microRNAs to heart. Trends Mol Med. 14, 254-260.
17. Chen, J.F., Callis, T.E., and Wang, D.Z. (2009) microRNAs and muscle disorders. J Cell Sci. 122, 13-20.
18. Yang,B., Lin, H., Xiao, J., Lu, Y., Luo, X., Li, B., Zhang, Y., Xu, C., Bai, Y., Wang, H., Chen, G., and Wang, Z. (2007) The muscle-specific microRNA miR-1 regulates cardiac arrhythmogenic potential by targeting GJA1 and KCNJ2. Nat Med. 13, 486-91. (Pubitemid 46559834)
19. Callis, T.E., Pandya, K., Seok, H.Y., Tang, R.H., Tatsuguchi, M., Huang, Z.P., Chen, J.F., Deng, Z., Gunn, B., Shumate, J., Willis, M.S., Selzman, C.H., Wang, D.Z. (2009) MicroRNA-208a is a regulator of cardiac hypertrophy and conduction in mice. J Clin Invest. 119, 2772-86.
20. McCarthy, J.J. (2008) MicroRNA-206: the skeletal muscle-specific myomiR. Biochim Biophys Acta. 1779, 682-691.
21. Eisenberg, I., Eran, A., Nishino, I., Moggio, M., Lamperti, C., Amato, A.A., Lidov, H.G,, Kang, P.B., North, K.N., Mitrani-Rosenbaum, S., Flanigan, K.M., Neely, L.A., Whitney, D., Beggs, A.H., Kohane, I.S., and Kunkel, L.M. (2007) Distinctive patterns of microRNA expression in primary muscular disorders. Proc Natl Acad Sci. USA. 104, 17016-17021. (Pubitemid 350210983)
22. van Rooij, E., Sutherland, L.B., Liu, N., Williams, A.H., McAnally, J., Gerard, R.D., Richardson, J.A., and Olson, E.N. (2006) A signature pattern of stress-responsive microRNAs that can evoke cardiac hypertrophy and heart failure. Proc Natl Acad Sci. USA. 103, 18255-18260. (Pubitemid 44871645)
23. van Rooij, E., Sutherland, L.B., Thatcher, J.E., DiMaio, J.M., Naseem, R.H., Marshall, W.S., Hill, J.A., and Olson, E.N. (2008) Dysregulation of microRNAs after myocardial infarction reveals a role of miR-29 in cardiac fibrosis. Proc Natl Acad Sci. USA. 105, 13027-13032.
24. Tatsuguchi, M., Seok, H.Y., Callis, T.E., Thomson, J.M., Chen, J.F., Newman, M., Rojas, M., Hammond, S.M., and Wang, D.Z. (2007) Expression of microRNAs is dynamically regulated during cardiomyocyte hypertrophy. J Mol Cell Cardiol. 42, 1137-1141. (Pubitemid 46829201)
25. McCarthy, J.J., Esser, K.A., and Andrade, F.H. (2007) MicroRNA-206 is overexpressed in the diaphragm but not the hindlimb muscle of mdx mouse. Am J Physiol Cell Physiol. 293, C451-457. (Pubitemid 47105025)
26. Gentner, B., Schira, G., Giustacchini, A., Amendola, M., Brown, B.D., Ponzoni, M., and Naldini, L. (2009) Stable knockdown of microRNA in vivo by lentiviral vectors. Nat Methods. 6, 63-66.
27. Krützfeldt, J., Rajewsky, N., Braich, R., Rajeev, K.G., Tuschl, T., Manoharan, M., and Stoffel, M. (2005) Silencing of microRNAs in vivo with 'antagomirs'. Nature. 438, 685-689.
28. Krek, A., Grun, D., Poy, M.N., Wolf, R., Rosenberg, L., Epstein, E.J., MacMenamin, P., da Piedade, I., Gunsalus, K.C., Stoffel, M. & Rajewsky, N. (2005). Combinatorial microRNA target predictions. Nat Genet. 37, 495-500. (Pubitemid 40617277)
29. John, B., Enright, A.J., Aravin, A., Tuschl, T., Sander, C. & Marks, D.S. (2004). Human MicroRNA targets. PLoS Biol. 2, e363.
30. Lewis, B.P., Burge, C.B. & Bartel, D.P. (2005). Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 120, 15-20. (Pubitemid 40094598)
31. 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.
32. Baek, D., Villén, J., Shin, C., Camargo, F.D., Gygi, S.P., Bartel, D.P. (2008) The impact of microRNAs on protein output. Nature. 455, 64-71.
33. Stegmeier, F., Hu, G., Rickles, R.J., Hannon, G.J., Elledge, S.J. (2005) A lentiviral microRNA-based system for single-copy polymerase II-regulated RNA interference in mammalian cells. Proc Natl Acad Sci. USA. 102, 13212-13217. (Pubitemid 41325003)