Abstract
Increasing lines of evidence indicate that small non-coding RNAs including miRNAs, piRNAs, rasiRNAs, 21U endo-siRNAs, and snoRNAs are involved in many critical biological processes. Functional studies of these small RNAs require a simple, sensitive, and reliable method for detecting and quantifying levels of small RNAs. Here, we describe such a method that has been widely used for the validation of cloned small RNAs and also for quantitative analyses of small RNAs in both tissues and cells.
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References
Ambros, V. (2004) The functions of animal microRNAs. Nature, 431, 350–355.
Bartel, D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281–297.
Chang, T.C. and Mendell, J.T. (2007) The roles of microRNAs in vertebrate physiology and human disease. Annu Rev Genomics Hum Genet.
Kim, V.N. (2005) MicroRNA biogenesis: coordinated cropping and dicing. Nat Rev Mol Cell Biol, 6, 376–385.
Kim, V.N. (2006) Small RNAs just got bigger: Piwi-interacting RNAs (piRNAs) in mammalian testes. Genes Dev, 20, 1993–1997.
Kotaja, N., Bhattacharyya, S.N., Jaskiewicz, L., Kimmins, S., Parvinen, M., Filipowicz, W., and Sassone-Corsi, P. (2006) The chromatoid body of male germ cells: similarity with processing bodies and presence of Dicer and microRNA pathway components. Proc Natl Acad Sci U S A, 103, 2647–2652.
Aravin, A.A., Lagos-Quintana, M., Yalcin, A., Zavolan, M., Marks, D., Snyder, B., Gaasterland, T., Meyer, J., and Tuschl, T. (2003) The small RNA profile during Drosophila melanogaster development. Dev Cell, 5, 337–350.
Lee, R.C. and Ambros, V. (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science, 294, 862–864.
Lau, N.C., Lim, L.P., Weinstein, E.G., and Bartel, D.P. (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science, 294, 858–862.
Lagos-Quintana, M., Rauhut, R., Lendeckel, W., and Tuschl, T. (2001) Identification of novel genes coding for small expressed RNAs. Science, 294, 853–858.
Lau, N.C., Seto, A.G., Kim, J., Kuramochi-Miyagawa, S., Nakano, T., Bartel, D.P., and Kingston, R.E. (2006) Characterization of the piRNA complex from rat testes. Science, 313, 363–367.
Grivna, S.T., Beyret, E., Wang, Z., and Lin, H. (2006) A novel class of small RNAs in mouse spermatogenic cells. Genes Dev, 20, 1709–1714.
Girard, A., Sachidanandam, R., Hannon, G.J., and Carmell, M.A. (2006) A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature, 442, 199–202.
Aravin, A., Gaidatzis, D., Pfeffer, S., Lagos-Quintana, M., Landgraf, P., Iovino, N., Morris, P., Brownstein, M.J., Kuramochi-Miyagawa, S., Nakano, T., Chien, M., Russo, J.J., Ju, J., Sheridan, R., Sander, C., Zavolan, M., and Tuschl, T. (2006) A novel class of small RNAs bind to MILI protein in mouse testes. Nature, 442, 203–207.
Watanabe, T., Takeda, A., Tsukiyama, T., Mise, K., Okuno, T., Sasaki, H., Minami, N., and Imai, H. (2006) Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes. Genes Dev, 20, 1732–1743.
Vagin, V.V., Sigova, A., Li, C., Seitz, H., Gvozdev, V., and Zamore, P.D. (2006) A distinct small RNA pathway silences selfish genetic elements in the germline. Science, 313, 320–324.
Saito, K., Nishida, K.M., Mori, T., Kawamura, Y., Miyoshi, K., Nagami, T., Siomi, H., and Siomi, M.C. (2006) Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome. Genes Dev, 20, 2214–2222.
Ro, S., Song, R., Park, C., Zheng, H., Sanders, K.M., and Yan, W. (2007) Cloning and expression profiling of small RNAs expressed in the mouse ovary. RNA, 13, 2366–2380.
Ruby, J.G., Jan, C., Player, C., Axtell, M.J., Lee, W., Nusbaum, C., Ge, H., and Bartel, D.P. (2006) Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell, 127, 1193–1207.
Terns, M.P. and Terns, R.M. (2002) Small nucleolar RNAs: versatile trans-acting molecules of ancient evolutionary origin. Gene Expr, 10, 17–39.
Ouellet, D.L., Perron, M.P., Gobeil, L.A., Plante, P., and Provost, P. (2006) MicroRNAs in gene regulation: when the smallest governs it all. J Biomed Biotechnol, 2006, 69616.
Maatouk, D. and Harfe, B. (2006) MicroRNAs in development. ScientificWorldJournal, 6, 1828–1840.
Kim, V.N. and Nam, J.W. (2006) Genomics of microRNA. Trends Genet, 22, 165–173.
Bohnsack, M.T., Kos, M., and Tollervey, D. (2008) Quantitative analysis of snoRNA association with pre-ribosomes and release of snR30 by Rok1 helicase. EMBO Rep, 9, 1230–1236.
Hertel, J., de Jong, D., Marz, M., Rose, D., Tafer, H., Tanzer, A., Schierwater, B., and Stadler, P.F. (2009) Non-coding RNA annotation of the genome of Trichoplax adhaerens. Nucleic Acids Res, 37, 1602–1615.
Kim, M., Patel, B., Schroeder, K.E., Raza, A., and Dejong, J. (2008) Organization and transcriptional output of a novel mRNA-like piRNA gene (mpiR) located on mouse chromosome 10. RNA, 14, 1005–1011.
Mishima, T., Takizawa, T., Luo, S.S., Ishibashi, O., Kawahigashi, Y., Mizuguchi, Y., Ishikawa, T., Mori, M., Kanda, T., and Goto, T. (2008) MicroRNA (miRNA) cloning analysis reveals sex differences in miRNA expression profiles between adult mouse testis and ovary. Reproduction, 136, 811–822.
Papaioannou, M.D., Pitetti, J.L., Ro, S., Park, C., Aubry, F., Schaad, O., Vejnar, C.E., Kuhne, F., Descombes, P., Zdobnov, E.M., McManus, M.T., Guillou, F., Harfe, B.D., Yan, W., Jegou, B., and Nef, S. (2009) Sertoli cell Dicer is essential for spermatogenesis in mice. Dev Biol, 326, 250–259.
Ro, S., Park, C., Sanders, K.M., McCarrey, J.R., and Yan, W. (2007) Cloning and expression profiling of testis-expressed microRNAs. Dev Biol, 311, 592–602.
Ro, S., Park, C., Song, R., Nguyen, D., Jin, J., Sanders, K.M., McCarrey, J.R., and Yan, W. (2007) Cloning and expression profiling of testis-expressed piRNA-like RNAs. RNA, 13, 1693–1702.
Ro, S., Park, C., Young, D., Sanders, K.M., and Yan, W. (2007) Tissue-dependent paired expression of miRNAs. Nucleic Acids Res, 35, 5944–5953.
Siebolts, U., Varnholt, H., Drebber, U., Dienes, H.P., Wickenhauser, C., and Odenthal, M. (2009) Tissues from routine pathology archives are suitable for microRNA analyses by quantitative PCR. J Clin Pathol, 62, 84–88.
Smits, G., Mungall, A.J., Griffiths-Jones, S., Smith, P., Beury, D., Matthews, L., Rogers, J., Pask, A.J., Shaw, G., VandeBerg, J.L., McCarrey, J.R., Renfree, M.B., Reik, W., and Dunham, I. (2008) Conservation of the H19 noncoding RNA and H19-IGF2 imprinting mechanism in therians. Nat Genet, 40, 971–976.
Song, R., Ro, S., Michaels, J.D., Park, C., McCarrey, J.R., and Yan, W. (2009) Many X-linked microRNAs escape meiotic sex chromosome inactivation. Nat Genet, 41, 488–493.
Wang, W.X., Wilfred, B.R., Baldwin, D.A., Isett, R.B., Ren, N., Stromberg, A., and Nelson, P.T. (2008) Focus on RNA isolation: obtaining RNA for microRNA (miRNA) expression profiling analyses of neural tissue. Biochim Biophys Acta, 1779, 749–757.
Wu, F., Zikusoka, M., Trindade, A., Dassopoulos, T., Harris, M.L., Bayless, T.M., Brant, S.R., Chakravarti, S., and Kwon, J.H. (2008) MicroRNAs are differentially expressed in ulcerative colitis and alter expression of macrophage inflammatory peptide-2 alpha. Gastroenterology, 135(1624–1635), e24.
Wu, H., Neilson, J.R., Kumar, P., Manocha, M., Shankar, P., Sharp, P.A., and Manjunath, N. (2007) miRNA profiling of naive, effector and memory CD8 T cells. PLoS ONE, 2, e1020.
Yan, W., Morozumi, K., Zhang, J., Ro, S., Park, C., and Yanagimachi, R. (2008) Birth of mice after intracytoplasmic injection of single purified sperm nuclei and detection of messenger RNAs and microRNAs in the sperm nuclei. Biol Reprod, 78, 896–902.
Guryev, V. and Cuppen, E. (2009) Next-generation sequencing approaches in genetic rodent model systems to study functional effects of human genetic variation. FEBS Lett.
Li, W. and Ruan, K. (2009) MicroRNA detection by microarray. Anal Bioanal Chem.
Ro, S., Park, C., Jin, JL., Sanders, KM., and Yan, W. (2006) A PCR-based method for detection and quantification of small RNAs. Biochem and Biophys Res Commun, 351, 756–763.
Acknowledgments
The authors would like to thank Jonathan Cho for reading and editing the text. This work was supported by grants from the National Institute of Health (HD048855 and HD050281) to W.Y.
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Ro, S., Yan, W. (2010). Detection and Quantitative Analysis of Small RNAs by PCR. In: Sioud, M. (eds) RNA Therapeutics. Methods in Molecular Biology, vol 629. Humana Press. https://doi.org/10.1007/978-1-60761-657-3_19
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DOI: https://doi.org/10.1007/978-1-60761-657-3_19
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