Abstract
MicroRNAs (miRNAs) are a class of small ∼22 nucleotide noncoding RNAs which regulate gene expression at the posttranscriptional level by either destabilizing and consequently degrading their targeted mRNAs or by repressing their translation. Emerging evidence has demonstrated that miRNAs are essential for normal mammalian development, homeostasis, and many other functions. In addition, deleterious changes in miRNA expression were associated with human diseases. Several muscle-specific miRNAs, including miR-1, miR-133, miR-206, and miR-208, have been shown to be important for normal myoblast differentiation, proliferation, and muscle remodeling in response to stress. They have also been implicated in various cardiac and skeletal muscular diseases. miRNA-based gene therapies hold great potential for the treatment of cardiac and skeletal muscle diseases. Herein, we describe methods commonly applied to study the biological role of miRNAs, as well as techniques utilized to manipulate miRNA expression and to investigate their target regulation.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Wagner, K.R. (2002) Genetic diseases of muscle. Neurol Clin. 20, 645–678.
Bartel, D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 116, 281–297.
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.
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.
Ruby, J.G., Jan, C.H., and Bartel, D.P. (2007) Intronic microRNA precursors that bypass Drosha processing. Nature. 448, 83–86.
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.
Hutvágner, G., McLachlan, J., Pasquinelli, A.E., Bálint, E., Tuschl, T., and Zamore, P.D. (2001) A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science. 293, 834–838.
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.
Lee, R.C., and Ambros, V. (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science. 294, 862–864.
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.
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.
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.
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.
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.
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.
Callis, T.E., and Wang, D.Z. (2008) Taking microRNAs to heart. Trends Mol Med. 14, 254–260.
Chen, J.F., Callis, T.E., and Wang, D.Z. (2009) microRNAs and muscle disorders. J Cell Sci. 122, 13–20.
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.
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.
McCarthy, J.J. (2008) MicroRNA-206: the skeletal muscle-specific myomiR. Biochim Biophys Acta. 1779, 682–691.
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.
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.
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.
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.
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.
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.
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.
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.
John, B., Enright, A.J., Aravin, A., Tuschl, T., Sander, C. & Marks, D.S. (2004). Human MicroRNA targets. PLoS Biol. 2, e363.
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.
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.
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.
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.
Acknowledgments
We thank members of the Wang laboratory for discussion and support. Research in the Wang lab was supported by the March of Dimes Birth Defect Foundation, National Institutes of Health and Muscular Dystrophy Association. ZP Huang is a postdoctoral fellow and DZ Wang is an Established Investigator of the American Heart Association.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Huang, ZP., Espinoza-Lewis, R., Wang, DZ. (2012). Determination of MiRNA Targets in Skeletal Muscle Cells. In: DiMario, J. (eds) Myogenesis. Methods in Molecular Biology, vol 798. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-343-1_28
Download citation
DOI: https://doi.org/10.1007/978-1-61779-343-1_28
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-61779-342-4
Online ISBN: 978-1-61779-343-1
eBook Packages: Springer Protocols