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Small RNA Technologies: siRNA, miRNA, antagomiR, Target Mimicry, miRNA Sponge and miRNA Profiling

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Current Perspectives in microRNAs (miRNA)

The breakthrough discovery of RNA interference (RNAi) by Fire and Mello in 1998 has ushered in a new wave of RNA-based technological advances in the life sciences. Small RNAs, namely small interfering RNA (siRNA) and microRNA (miRNA), not only play key roles in down regulating gene expression, controlling growth and development, stress response, and various diseases, but also serve as essential tools for the study of gene functions. In this chapter, we provide an overview of the technological aspects of siRNAs and miRNAs and common methods for studying their functions.

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References

  1. Alvarez, J.P., Pekker, I., Goldshmidt, A., Blum, E., Amsellem, Z., and Eshed, Y. (2006). Endogenous and synthetic microRNAs stimulate simultaneous, efficient, and localized regula-tion of multiple targets in diverse species. Plant cell 18, 1134-1151.

    CAS  PubMed  Google Scholar 

  2. Amarzguioui, M., Rossi, J.J., and Kim, D. (2005). Approaches for chemically synthesized siRNA and vector-mediated RNAi. FEBS Lett 579, 5974-5981.

    CAS  PubMed  Google Scholar 

  3. Ambros, V. (2001). microRNAs: tiny regulators with great potential. Cell 107, 823-826.

    CAS  PubMed  Google Scholar 

  4. Aravin, A.A., Hannon, G.J., and Brennecke, J. (2007a). The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science (New York, NY) 318, 761-764.

    CAS  Google Scholar 

  5. Aravin, A.A., Sachidanandam, R., Girard, A., Fejes-Toth, K., and Hannon, G.J. (2007b). Developmentally regulated piRNA clusters implicate MILI in transposon control. Science (New York, NY) 316, 744-747.

    CAS  Google Scholar 

  6. Babak, T., Zhang, W., Morris, Q., Blencowe, B.J., and Hughes, T.R. (2004). Probing microRNAs with microarrays: tissue specificity and functional inference. RNA (New York, NY) 10, 1813-1819.

    CAS  Google Scholar 

  7. Bartel, D.P. (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297.

    CAS  PubMed  Google Scholar 

  8. Betel, D., Sheridan, R., Marks, D.S., and Sander, C. (2007). Computational analysis of mouse piRNA sequence and biogenesis. PLoS Comput Biol 3, e222.

    PubMed  Google Scholar 

  9. Boden, D., Pusch, O., Silbermann, R., Lee, F., Tucker, L., and Ramratnam, B. (2004). Enhanced gene silencing of HIV-1 specific siRNA using microRNA designed hairpins. Nucleic Acids Res 32, 1154-1158.

    CAS  PubMed  Google Scholar 

  10. Brennecke, J., Stark, A., Russell, R.B., and Cohen, S.M. (2005). Principles of MicroRNA– Target Recognition. PLoS Biol 3, e85.

    PubMed  Google Scholar 

  11. Calin, G.A., and Croce, C.M. (2006). MicroRNA signatures in human cancers. Nature Rev 6, 857-866.

    CAS  Google Scholar 

  12. Calin, G.A., Ferracin, M., Cimmino, A., Di Leva, G., Shimizu, M., Wojcik, S.E., Iorio, M.V., Visone, R., Sever, N.I., Fabbri, M., et al. (2005). A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. New Engl J Med 353, 1793-1801.

    CAS  PubMed  Google Scholar 

  13. Calin, G.A., Liu, C.G., Sevignani, C., Ferracin, M., Felli, N., Dumitru, C.D., Shimizu, M., Cimmino, A., Zupo, S., Dono, M., et al. (2004). MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. Proc Natl Acad Sci USA 101, 11755-11760.

    CAS  PubMed  Google Scholar 

  14. Carmell, M.A., Xuan, Z., Zhang, M.Q., and Hannon, G.J. (2002). The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Gene Dev 16, 2733-2742.

    CAS  PubMed  Google Scholar 

  15. Castoldi, M., Schmidt, S., Benes, V., Noerholm, M., Kulozik, A.E., Hentze, M.W., and Muckenthaler, M.U. (2006). A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA). RNA (New York, NY) 12, 913-920.

    CAS  Google Scholar 

  16. Chaudhuri, K., and Chatterjee, R. (2007). MicroRNA detection and target prediction: integra-tion of computational and experimental approaches. DNA Cell Biol 26, 321-337.

    CAS  PubMed  Google Scholar 

  17. Chen, C.Z. (2005). MicroRNAs as oncogenes and tumor suppressors. New Engl J Med 353, 1768-1771.

    CAS  PubMed  Google Scholar 

  18. Chitwood, D.H., and Timmermans, M.C. (2007). Target mimics modulate miRNAs. Nat Genet 39, 935-936.

    CAS  PubMed  Google Scholar 

  19. Davison, T.S., Johnson, C.D., and Andruss, B.F. (2006). Analyzing micro-RNA expression using microarrays. Methods Enzymol 411, 14-34.

    CAS  PubMed  Google Scholar 

  20. Doench, J.G., Petersen, C.P., and Sharp, P.A. (2003). siRNAs can function as miRNAs. Gene Dev 17, 438-442.

    CAS  PubMed  Google Scholar 

  21. Ebert, M.S., Neilson, J.R., and Sharp, P.A. (2007). MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nat Methods 4, 721-726.

    CAS  PubMed  Google Scholar 

  22. Elbashir, S.M., Harborth, J., Lendeckel, W., Yalcin, A., Weber, K., and Tuschl, T. (2001a). Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494-498.

    CAS  Google Scholar 

  23. Elbashir, S.M., Lendeckel, W., and Tuschl, T. (2001b). RNA interference is mediated by 21- and 22-nucleotide RNAs. Gene Dev 15, 188-200.

    CAS  Google Scholar 

  24. Elbashir, S.M., Martinez, J., Patkaniowska, A., Lendeckel, W., and Tuschl, T. (2001c). Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J 20, 6877-6888.

    CAS  Google Scholar 

  25. Enright, A.J., John, B., Gaul, U., Tuschl, T., Sander, C., and Marks, D.S. (2003). MicroRNA targets in Drosophila. Genome Biol 5, R1.

    PubMed  Google Scholar 

  26. Fewell, G.D., and Schmitt, K. (2006). Vector-based RNAi approaches for stable, inducible and genome-wide screens. Drug Discov Today 11, 975-982.

    CAS  PubMed  Google Scholar 

  27. Filichkin, S.A., DiFazio, S.P., Brunner, A.M., Davis, J.M., Yang, Z.K., Kalluri, U.C., Arias, R.S., Etherington, E., Tuskan, G.A., and Strauss, S.H. (2007). Efficiency of gene silencing in Arabidopsis: direct inverted repeats vs. transitive RNAi vectors. Plant Biotechnol J 5, 615-626.

    CAS  PubMed  Google Scholar 

  28. Filipowicz, W. (2005). RNAi: the nuts and bolts of the RISC machine. Cell 122, 17-20.

    CAS  PubMed  Google Scholar 

  29. Forstemann, K., Horwich, M.D., Wee, L., Tomari, Y., and Zamore, P.D. (2007). Drosophila microRNAs are sorted into functionally distinct argonaute complexes after production by dicer-1. Cell 130, 287-297.

    PubMed  Google Scholar 

  30. Franco-Zorrilla, J.M., Valli, A., Todesco, M., Mateos, I., Puga, M.I., Rubio-Somoza, I., Leyva, A., Weigel, D., Garcia, J.A., and Paz-Ares, J. (2007). Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet 39, 1033-1037.

    CAS  PubMed  Google Scholar 

  31. Gasciolli, V., Mallory, A.C., Bartel, D.P., and Vaucheret, H. (2005). Partially redundant func-tions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs. Curr Biol 15, 1494-1500.

    CAS  PubMed  Google Scholar 

  32. Griffiths-Jones, S. (2006). miRBase: the microRNA sequence database. Method Mol Biol (Clifton, NJ) 342, 129-138.

    CAS  Google Scholar 

  33. Griffiths-Jones, S., Grocock, R.J., van Dongen, S., Bateman, A., and Enright, A.J. (2006). miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34, D140-D144.

    CAS  PubMed  Google Scholar 

  34. Grivna, S.T., Pyhtila, B., and Lin, H. (2006). MIWI associates with translational machinery and PIWI-interacting RNAs (piRNAs) in regulating spermatogenesis. Proc Natl Acad Sci USA 103, 13415-13420.

    CAS  PubMed  Google Scholar 

  35. Grosshans, H., and Svoboda, P. (2007). miRNA, piRNA, siRNA- Kleine Wiener Ribonukleinsauren. Bioessays 29, 940-943.

    PubMed  Google Scholar 

  36. Grundhoff, A., Sullivan, C.S., and Ganem, D. (2006). A combined computational and microarray-based approach identifies novel microRNAs encoded by human gamma-herpesviruses. RNA (New York, NY) 12, 733-750.

    CAS  Google Scholar 

  37. Gunawardane, L.S., Saito, K., Nishida, K.M., Miyoshi, K., Kawamura, Y., Nagami, T., Siomi, H., and Siomi, M.C. (2007). A slicer-mediated mechanism for repeat-associated siRNA 5′ end formation in Drosophila. Science (New York, NY) 315, 1587-1590.

    CAS  Google Scholar 

  38. Haley, B., Tang, G., and Zamore, P.D. (2003). In vitro analysis of RNA interference in Drosophila melanogaster. Methods (San Diego, CA) 30, 330-336.

    CAS  Google Scholar 

  39. Hamilton, A.J., and Baulcombe, D.C. (1999). A species of small antisense RNA in posttran-scriptional gene silencing in plants. Science (New York, NY) 286, 950-952.

    CAS  Google Scholar 

  40. Henderson, I.R., Zhang, X., Lu, C., Johnson, L., Meyers, B.C., Green, P.J., and Jacobsen, S.E. (2006). Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat Genet 38, 721-725.

    CAS  PubMed  Google Scholar 

  41. Hobert, O. (2004). Common logic of transcription factor and microRNA action. Trends Biochem Sci 29, 462-468.

    CAS  PubMed  Google Scholar 

  42. Hon, L., and Zhang, Z. (2007). The roles of binding site arrangement and combinatorial tar-geting in microRNA repression of gene expression. Genome Biol 8, R166.

    PubMed  Google Scholar 

  43. Howell, M.D., Fahlgren, N., Chapman, E.J., Cumbie, J.S., Sullivan, C.M., Givan, S.A., Kasschau, K.D., and Carrington, J.C. (2007). Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. Plant Cell 19, 926-942.

    CAS  PubMed  Google Scholar 

  44. Hutvagner, G., McLachlan, J., Pasquinelli, A.E., Balint, 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 (New York, NY) 293, 834-838.

    CAS  Google Scholar 

  45. Hutvagner, G., Simard, M.J., Mello, C.C., and Zamore, P.D. (2004). Sequence-specific inhibi-tion of small RNA function. PLoS Biol 2, E98.

    PubMed  Google Scholar 

  46. Iorio, M.V., Ferracin, M., Liu, C.G., Veronese, A., Spizzo, R., Sabbioni, S., Magri, E., Pedriali, M., Fabbri, M., Campiglio, M., et al. (2005). MicroRNA gene expression deregulation in human breast cancer. Cancer Res 65, 7065-7070.

    CAS  PubMed  Google Scholar 

  47. Jiang, J., Lee, E.J., Gusev, Y., and Schmittgen, T.D. (2005). Real-time expression profiling of microRNA precursors in human cancer cell lines. Nucleic Acids Res 33, 5394-5403.

    CAS  PubMed  Google Scholar 

  48. John, B., Enright, A.J., Aravin, A., Tuschl, T., Sander, C., and Marks, D.S. (2004). Human MicroRNA targets. PLoS Biol 2, e363.

    PubMed  Google Scholar 

  49. Kasahara, H., and Aoki, H. (2005). Gene silencing using adenoviral RNAi vector in vascular smooth muscle cells and cardiomyocytes. Method Mol Med 112, 155-172.

    CAS  Google Scholar 

  50. Khvorova, A., Reynolds, A., and Jayasena, S.D. (2003). Functional siRNAs and miRNAs exhibit strand bias. Cell 115, 209-216.

    CAS  PubMed  Google Scholar 

  51. Kim, S.K., Nam, J.W., Rhee, J.K., Lee, W.J., and Zhang, B.T. (2006). miTarget: microRNA target gene prediction using a support vector machine. BMC Bioinformatics 7, 411.

    PubMed  Google Scholar 

  52. Klattenhoff, C., Bratu, D.P., McGinnis-Schultz, N., Koppetsch, B.S., Cook, H.A., and Theurkauf, W.E. (2007). Drosophila rasiRNA pathway mutations disrupt embryonic axis specification through activation of an ATR/Chk2 DNA damage response. Dev Cell 12, 45-55.

    CAS  PubMed  Google Scholar 

  53. Klenov, M.S., Lavrov, S.A., Stolyarenko, A.D., Ryazansky, S.S., Aravin, A.A., Tuschl, T., and Gvozdev, V.A. (2007). Repeat-associated siRNAs cause chromatin silencing of retrotrans-posons in the Drosophila melanogaster germline. Nucleic Acids Res 35, 5430-5438.

    CAS  PubMed  Google Scholar 

  54. Kloosterman, W.P., Lagendijk, A.K., Ketting, R.F., Moulton, J.D., and Plasterk, R.H. (2007). Targeted inhibition of miRNA maturation with morpholinos reveals a role for miR-375 in pancreatic islet development. PLoS Biol 5, e203.

    PubMed  Google Scholar 

  55. Krichevsky, A.M., King, K.S., Donahue, C.P., Khrapko, K., and Kosik, K.S. (2003). A micro-RNA array reveals extensive regulation of microRNAs during brain development. RNA (New York, NY) 9, 1274-1281.

    CAS  Google Scholar 

  56. Kruger, J., and Rehmsmeier, M. (2006). RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res 34, W451-W454.

    PubMed  Google Scholar 

  57. Krutzfeldt, J., Kuwajima, S., Braich, R., Rajeev, K.G., Pena, J., Tuschl, T., Manoharan, M., and Stoffel, M. (2007). Specificity, duplex degradation and subcellular localization of antago-mirs. Nucleic Acids Res 35, 2885-2892.

    CAS  PubMed  Google Scholar 

  58. Krutzfeldt, J., Poy, M.N., and Stoffel, M. (2006). Strategies to determine the biological func-tion of microRNAs. Nat Genet 38 Suppl, S14-S19.

    PubMed  Google Scholar 

  59. Krutzfeldt, 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.

    PubMed  Google Scholar 

  60. Kulshreshtha, R., Ferracin, M., Negrini, M., Calin, G.A., Davuluri, R.V., and Ivan, M. (2007a). Regulation of microRNA expression: the hypoxic component. Cell Cycle 6, 1426-1431.

    CAS  Google Scholar 

  61. Kulshreshtha, R., Ferracin, M., Wojcik, S.E., Garzon, R., Alder, H., Agosto-Perez, F.J., Davuluri, R., Liu, C.G., Croce, C.M., Negrini, M., et al. (2007b). A microRNA signature of hypoxia. Mol Cell Biol 27, 1859-1867.

    CAS  Google Scholar 

  62. Lacomme, C., Hrubikova, K., and Hein, I. (2003). Enhancement of virus-induced gene silenc-ing through viral-based production of inverted-repeats. Plant J 34, 543-553.

    CAS  PubMed  Google Scholar 

  63. Lagos-Quintana, M., Rauhut, R., Meyer, J., Borkhardt, A., and Tuschl, T. (2003). New micro-RNAs from mouse and human. RNA (New York, NY) 9, 175-179.

    CAS  Google Scholar 

  64. Lagos-Quintana, M., Rauhut, R., Yalcin, A., Meyer, J., Lendeckel, W., and Tuschl, T. (2002). Identification of tissue-specific microRNAs from mouse. Curr Biol 12, 735-739.

    CAS  PubMed  Google Scholar 

  65. Landgraf, P., Rusu, M., Sheridan, R., Sewer, A., Iovino, N., Aravin, A., Pfeffer, S., Rice, A., Kamphorst, A.O., Landthaler, M., et al. (2007). A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129, 1401-1414.

    CAS  PubMed  Google Scholar 

  66. 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 (New York, NY) 313, 363-367.

    CAS  Google Scholar 

  67. Lee, E.J., Gusev, Y., Jiang, J., Nuovo, G.J., Lerner, M.R., Frankel, W.L., Morgan, D.L., Postier, R.G., Brackett, D.J., and Schmittgen, T.D. (2007). Expression profiling identifies microRNA signature in pancreatic cancer. Int J Cancer 120, 1046-1054.

    CAS  PubMed  Google Scholar 

  68. Lee, Y.S., and Carthew, R.W. (2003). Making a better RNAi vector for Drosophila: use of intron spacers. Methods (San Diego, CA) 30, 322-329.

    CAS  Google Scholar 

  69. Lee, Y.S., Nakahara, K., Pham, J.W., Kim, K., He, Z., Sontheimer, E.J., and Carthew, R.W. (2004). Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 117, 69-81.

    CAS  PubMed  Google Scholar 

  70. Leuschner, P.J., Ameres, S.L., Kueng, S., and Martinez, J. (2006). Cleavage of the siRNA passenger strand during RISC assembly in human cells. EMBO Rep 7, 314-320.

    CAS  PubMed  Google Scholar 

  71. Lewis, B.P., Burge, C.B., and Bartel, D.P. (2005). Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15-20.

    CAS  PubMed  Google Scholar 

  72. Lewis, B.P., Shih, I.H., Jones-Rhoades, M.W., Bartel, D.P., and Burge, C.B. (2003). Prediction of mammalian microRNA targets. Cell 115, 787-798.

    CAS  PubMed  Google Scholar 

  73. Liang, R.Q., Li, W., Li, Y., Tan, C.Y., Li, J.X., Jin, Y.X., and Ruan, K.C. (2005). An oligonu-cleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe. Nucleic Acids Res 33, e17.

    PubMed  Google Scholar 

  74. Lim, L.P., Lau, N.C., Garrett-Engele, P., Grimson, A., Schelter, J.M., Castle, J., Bartel, D.P., Linsley, P.S., and Johnson, J.M. (2005). Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433, 769-773.

    CAS  PubMed  Google Scholar 

  75. Liu, C.G., Calin, G.A., Meloon, B., Gamliel, N., Sevignani, C., Ferracin, M., Dumitru, C.D., Shimizu, M., Zupo, S., Dono, M., et al. (2004a). An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc Natl Acad Sci USA 101, 9740-9744.

    CAS  Google Scholar 

  76. Liu, J., Carmell, M.A., Rivas, F.V., Marsden, C.G., Thomson, J.M., Song, J.J., Hammond, S.M., Joshua-Tor, L., and Hannon, G.J. (2004b). Argonaute2 is the catalytic engine of mammalian RNAi. Science (New York, NY) 305, 1437-1441.

    CAS  Google Scholar 

  77. Liu, X., Jiang, F., Kalidas, S., Smith, D., and Liu, Q. (2006). Dicer-2 and R2D2 coordinately bind siRNA to promote assembly of the siRISC complexes. RNA (New York, NY) 12, 1514-1520.

    CAS  Google Scholar 

  78. Llave, C., Xie, Z., Kasschau, K.D., and Carrington, J.C. (2002). Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science (New York, NY) 297, 2053-2056.

    CAS  Google Scholar 

  79. Lu, S., Shi, R., Tsao, C.C., Yi, X., Li, L., and Chiang, V.L. (2004). RNA silencing in plants by the expression of siRNA duplexes. Nucleic Acids Res 32, e171.

    PubMed  Google Scholar 

  80. Ma, L., Teruya-Feldstein, J., and Weinberg, R.A. (2007). Tumour invasion and metastasis ini-tiated by microRNA-10b in breast cancer. Nature 449, 682-688.

    CAS  PubMed  Google Scholar 

  81. Martinez, J., Patkaniowska, A., Urlaub, H., Luhrmann, R., and Tuschl, T. (2002). Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell 110, 563-574.

    CAS  PubMed  Google Scholar 

  82. Matranga, C., Tomari, Y., Shin, C., Bartel, D.P., and Zamore, P.D. (2005). Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes. Cell 123, 607-620.

    CAS  PubMed  Google Scholar 

  83. Matranga, C., and Zamore, P.D. (2004). Plant RNA interference in vitro. Cold Spring Harbor Sym 69, 403-408.

    CAS  Google Scholar 

  84. Mattie, M.D., Benz, C.C., Bowers, J., Sensinger, K., Wong, L., Scott, G.K., Fedele, V., Ginzinger, D., Getts, R., and Haqq, C. (2006). Optimized high-throughput microRNA expres-sion profiling provides novel biomarker assessment of clinical prostate and breast cancer biopsies. Mol Cancer 5, 24.

    PubMed  Google Scholar 

  85. Mellits, K.H., Pe’ery, T., Manche, L., Robertson, H.D., and Mathews, M.B. (1990). Removal of double-stranded contaminants from RNA transcripts: synthesis of adenovirus VA RNAI from a T7 vector. Nucleic Acids Res 18, 5401-5406.

    CAS  PubMed  Google Scholar 

  86. Monticelli, S., Ansel, K.M., Xiao, C., Socci, N.D., Krichevsky, A.M., Thai, T.H., Rajewsky, N., Marks, D.S., Sander, C., Rajewsky, K., et al. (2005). MicroRNA profiling of the murine hematopoietic system. Genome Biol 6, R71.

    PubMed  Google Scholar 

  87. Nelson, P.T., Baldwin, D.A., Scearce, L.M., Oberholtzer, J.C., Tobias, J.W., and Mourelatos, Z. (2004). Microarray-based, high-throughput gene expression profiling of microRNAs. Nat Methods 1, 155-161.

    CAS  PubMed  Google Scholar 

  88. Nishida, K.M., Saito, K., Mori, T., Kawamura, Y., Nagami-Okada, T., Inagaki, S., Siomi, H., and Siomi, M.C. (2007). Gene silencing mechanisms mediated by Aubergine piRNA complexes in Drosophila male gonad. RNA (New York, NY) 13, 1911-1922.

    CAS  Google Scholar 

  89. Niu, Q.W., Lin, S.S., Reyes, J.L., Chen, K.C., Wu, H.W., Yeh, S.D., and Chua, N.H. (2006). Expression of artificial microRNAs in transgenic Arabidopsis thaliana confers virus resist-ance. Nat Biotechnol 24, 1420-1428.

    CAS  PubMed  Google Scholar 

  90. Nogueira, F.T., Sarkar, A.K., Chitwood, D.H., and Timmermans, M.C. (2006). Organ polar-ity in plants is specified through the opposing activity of two distinct small regulatory RNAs. Cold Spring Harbor Sym 71, 157-164.

    CAS  Google Scholar 

  91. Okamura, K., Ishizuka, A., Siomi, H., and Siomi, M.C. (2004). Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways. Gene Dev 18, 1655-1666.

    CAS  PubMed  Google Scholar 

  92. Pelisson, A., Sarot, E., Payen-Groschene, G., and Bucheton, A. (2007). A novel repeat-associated small interfering RNA-mediated silencing pathway downregulates complemen-tary sense gypsy transcripts in somatic cells of the Drosophila ovary. J Virol 81, 1951-1960.

    CAS  PubMed  Google Scholar 

  93. Qi, Y., Denli, A.M., and Hannon, G.J. (2005). Biochemical specialization within Arabidopsis RNA silencing pathways. Mol Cell 19, 421-428.

    CAS  PubMed  Google Scholar 

  94. Qu, J., Ye, J., and Fang, R. (2007). Artificial microRNA-mediated virus resistance in plants. J Virol 81, 6690-6699.

    CAS  PubMed  Google Scholar 

  95. Rand, T.A., Petersen, S., Du, F., and Wang, X. (2005). Argonaute2 cleaves the anti-guide strand of siRNA during RISC activation. Cell 123, 621-629.

    CAS  PubMed  Google Scholar 

  96. Rehmsmeier, M., Steffen, P., Hochsmann, M., and Giegerich, R. (2004). Fast and effective prediction of microRNA/target duplexes. RNA (New York, NY) 10, 1507-1517.

    CAS  Google Scholar 

  97. Reichhart, J.M., Ligoxygakis, P., Naitza, S., Woerfel, G., Imler, J.L., and Gubb, D. (2002). Splice-activated UAS hairpin vector gives complete RNAi knockout of single or double tar-get transcripts in Drosophila melanogaster. Genesis 34, 160-164.

    CAS  PubMed  Google Scholar 

  98. Rhoades, M.W., Reinhart, B.J., Lim, L.P., Burge, C.B., Bartel, B., and Bartel, D.P. (2002). Prediction of plant microRNA targets. Cell 110, 513-520.

    CAS  PubMed  Google Scholar 

  99. 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 (New York, NY) 13, 1693-1702.

    CAS  Google Scholar 

  100. Saetrom, O., Snove, O., Jr., and Saetrom, P. (2005). Weighted sequence motifs as an improved seeding step in microRNA target prediction algorithms. RNA (New York, NY) 11, 995-1003.

    CAS  Google Scholar 

  101. Schwab, R., Ossowski, S., Riester, M., Warthmann, N., and Weigel, D. (2006). Highly spe- cific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18, 1121-1133.

    CAS  PubMed  Google Scholar 

  102. Schwarz, D.S., Hutvagner, 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.

    CAS  PubMed  Google Scholar 

  103. Sempere, L.F., Freemantle, S., Pitha-Rowe, I., Moss, E., Dmitrovsky, E., and Ambros, V. (2004). Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation. Genome Biol 5, R13.

    PubMed  Google Scholar 

  104. Shingara, J., Keiger, K., Shelton, J., Laosinchai-Wolf, W., Powers, P., Conrad, R., Brown, D., and Labourier, E. (2005). An optimized isolation and labeling platform for accurate micro-RNA expression profiling. RNA (New York, NY) 11, 1461-1470.

    CAS  Google Scholar 

  105. Sioud, M., and Rosok, O. (2004). Profiling microRNA expression using sensitive cDNA probes and filter arrays. BioTechniques 37, 574-576, 578-580.

    Google Scholar 

  106. Smalheiser, N.R., and Torvik, V.I. (2006). Complications in mammalian microRNA target prediction. Method Mol Biol (Clifton, NJ) 342, 115-127.

    CAS  Google Scholar 

  107. Smith, N.A., Singh, S.P., Wang, M.B., Stoutjesdijk, P.A., Green, A.G., and Waterhouse, P.M. (2000). Total silencing by intron-spliced hairpin RNAs. Nature 407, 319-320.

    CAS  PubMed  Google Scholar 

  108. Song, J.J., Smith, S.K., Hannon, G.J., and Joshua-Tor, L. (2004). Crystal structure of Argonaute and its implications for RISC slicer activity. Science (New York, NY) 305, 1434-1437.

    CAS  Google Scholar 

  109. Sui, G., and Shi, Y. (2005). Gene silencing by a DNA vector-based RNAi technology. Method Mol Biol (Clifton, NJ) 309, 205-218.

    CAS  Google Scholar 

  110. Sui, G., Soohoo, C., Affar el, B., Gay, F., Shi, Y., Forrester, W.C., and Shi, Y. (2002). A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc Natl Acad Sci USA 99, 5515-5520.

    CAS  PubMed  Google Scholar 

  111. Sun, D., Melegari, M., Sridhar, S., Rogler, C.E., and Zhu, L. (2006). Multi-miRNA hairpin method that improves gene knockdown efficiency and provides linked multi-gene knock-down. BioTechniques 41, 59-63.

    CAS  PubMed  Google Scholar 

  112. Szafranska, A.E., Davison, T.S., John, J., Cannon, T., Sipos, B., Maghnouj, A., Labourier, E., and Hahn, S.A. (2007). MicroRNA expression alterations are linked to tumorigenesis and non-neoplastic processes in pancreatic ductal adenocarcinoma. Oncogene 26, 4442-4452.

    CAS  PubMed  Google Scholar 

  113. Tang, F., Hajkova, P., Barton, S.C., Lao, K., and Surani, M.A. (2006). MicroRNA expression profiling of single whole embryonic stem cells. Nucleic Acids Res 34, e9.

    PubMed  Google Scholar 

  114. Tang, G. (2005). siRNA and miRNA: an insight into RISCs. Trends Biochem Sci 30, 106-114.

    CAS  PubMed  Google Scholar 

  115. Tang, G., Reinhart, B.J., Bartel, D.P., and Zamore, P.D. (2003). A biochemical framework for RNA silencing in plants. Gene Dev 17, 49-63.

    CAS  PubMed  Google Scholar 

  116. Tang, X., Gal, J., Zhuang, X., Wang, W., Zhu, H., and Tang, G. (2007). A simple array plat-form for microRNA analysis and its application in mouse tissues. RNA (New York, NY) 13, 1803-1822.

    CAS  Google Scholar 

  117. Tomari, Y., Du, T., and Zamore, P.D. (2007). Sorting of Drosophila small silencing RNAs. Cell 130, 299-308.

    CAS  PubMed  Google Scholar 

  118. 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 (New York, NY) 313, 320-324.

    CAS  Google Scholar 

  119. . Vaucheret, H. (2005). MicroRNA-dependent trans-acting siRNA production. Sci STKE 2005, pe43.

    Google Scholar 

  120. Volinia, S., Calin, G.A., Liu, C.G., Ambs, S., Cimmino, A., Petrocca, F., Visone, R., Iorio, M., Roldo, C., Ferracin, M., et al. (2006). A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci USA 103, 2257-2261.

    CAS  PubMed  Google Scholar 

  121. Wakiyama, M., Takimoto, K., Ohara, O., and Yokoyama, S. (2007). Let-7 microRNA-mediated mRNA deadenylation and translational repression in a mammalian cell-free sys-tem. Gene Dev 21, 1857-1862.

    CAS  PubMed  Google Scholar 

  122. Wang, H., Ach, R.A., and Curry, B. (2007). Direct and sensitive miRNA profiling from low-input total RNA. RNA (New York, NY) 13, 151-159.

    CAS  Google Scholar 

  123. Wang, X., and Wang, X. (2006). Systematic identification of microRNA functions by com-bining target prediction and expression profiling. Nucleic Acids Res 34, 1646-1652.

    CAS  PubMed  Google Scholar 

  124. Watanabe, Y., Tomita, M., and Kanai, A. (2007). Computational methods for MicroRNA target prediction. Methods Enzymol 427, 65-86.

    CAS  PubMed  Google Scholar 

  125. Wesley, S.V., Helliwell, C.A., Smith, N.A., Wang, M.B., Rouse, D.T., Liu, Q., Gooding, P.S., Singh, S.P., Abbott, D., Stoutjesdijk, P.A., et al. (2001). Construct design for efficient, effec-tive and high-throughput gene silencing in plants. Plant J 27, 581-590.

    CAS  PubMed  Google Scholar 

  126. Wielopolska, A., Townley, H., Moore, I., Waterhouse, P., and Helliwell, C. (2005). A high-throughput inducible RNAi vector for plants. Plant Biotechnol J 3, 583-590.

    CAS  PubMed  Google Scholar 

  127. Williams, L., Carles, C.C., Osmont, K.S., and Fletcher, J.C. (2005). A database analysis method identifies an endogenous trans-acting short-interfering RNA that targets the Arabidopsis ARF2, ARF3, and ARF4 genes. Proc Natl Acad Sci USA 102, 9703-9708.

    CAS  PubMed  Google Scholar 

  128. Wu, M.T., Wu, R.H., Hung, C.F., Cheng, T.L., Tsai, W.H., and Chang, W.T. (2005). Simple and efficient DNA vector-based RNAi systems in mammalian cells. Biochem Biophys Res Commun 330, 53-59.

    CAS  PubMed  Google Scholar 

  129. Xia, X.G., Zhou, H., Ding, H., Affar el, B., Shi, Y., and Xu, Z. (2003). An enhanced U6 promoter for synthesis of short hairpin RNA. Nucleic Acids Res 31, e100.

    PubMed  Google Scholar 

  130. Xie, X., Lu, J., Kulbokas, E.J., Golub, T.R., Mootha, V., Lindblad-Toh, K., Lander, E.S., and Kellis, M. (2005). Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434, 338-345.

    CAS  PubMed  Google Scholar 

  131. Yan, X., Chao, T., Tu, K., Zhang, Y., Xie, L., Gong, Y., Yuan, J., Qiang, B., and Peng, X. (2007). Improving the prediction of human microRNA target genes by using ensemble algo-rithm. FEBS Lett 581, 1587-1593.

    CAS  PubMed  Google Scholar 

  132. Yanaihara, N., Caplen, N., Bowman, E., Seike, M., Kumamoto, K., Yi, M., Stephens, R.M., Okamoto, A., Yokota, J., Tanaka, T., et al. (2006). Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell 9, 189-198.

    CAS  PubMed  Google Scholar 

  133. Yin, H., and Lin, H. (2007). An epigenetic activation role of Piwi and a Piwi-associated piRNA in Drosophila melanogaster. Nature 450, 304-308.

    CAS  PubMed  Google Scholar 

  134. Yoon, S., and De Micheli, G. (2005). Prediction of regulatory modules comprising microR-NAs and target genes. Bioinformatics (Oxford, England) 21 Suppl 2, ii93-ii100.

    CAS  Google Scholar 

  135. Zamore, P.D. (2006). RNA interference: big applause for silencing in Stockholm. Cell 127, 1083-1086.

    CAS  PubMed  Google Scholar 

  136. Zamore, P.D. (2007). RNA silencing: genomic defence with a slice of pi. Nature 446, 864-865.

    CAS  PubMed  Google Scholar 

  137. Zamore, P.D., and Haley, B. (2005). Ribo-gnome: the big world of small RNAs. Science (New York, NY) 309, 1519-1524.

    CAS  Google Scholar 

  138. Zamore, P.D., Tuschl, T., Sharp, P.A., and Bartel, D.P. (2000). RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101, 25-33.

    CAS  PubMed  Google Scholar 

  139. Zeng, Y., Cai, X., and Cullen, B.R. (2005). Use of RNA polymerase II to transcribe artificial microRNAs. Methods Enzymol 392, 371-380.

    CAS  PubMed  Google Scholar 

  140. Zeng, Y., Wagner, E.J., and Cullen, B.R. (2002). Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells. Mol Cell 9, 1327-1333.

    CAS  PubMed  Google Scholar 

  141. Zhang, Y. (2005). miRU: an automated plant miRNA target prediction server. Nucleic Acids Res 33, W701-704.

    CAS  PubMed  Google Scholar 

  142. Zhao, J.J., Hua, Y.J., Sun, D.G., Meng, X.X., Xiao, H.S., and Ma, X. (2006). Genome-wide microRNA profiling in human fetal nervous tissues by oligonucleotide microarray. Childs Nerv Syst 22, 1419-1425.

    PubMed  Google Scholar 

  143. Zhu, S., Si, M.L., Wu, H., and Mo, Y.Y. (2007). MicroRNA-21 targets the tumor suppressor gene tropomyosin 1 (TPM1). J Biol Chem 282, 14328-14336.

    CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Gene Suppression Laboratory, Department of Plant and Soil Sciences and KTRDC, University of Kentucky, Lexington, KY 40546, USA

    Guiliang Tang, Venugopal Mendu, Xiaohu Tang, Xiaoyun Jia & Qi-Jun Chen

  2. Pacific Agri-Food Research Centre, Agriculture and Agri-Food Canada, 4200 Highway 97, Box 5000, Summerland, BC V0H1Z0, Canada

    Yu Xiang

  3. College of Plant Protection, Shaanxi Provincial Key Lab of Molecular Biology for Agriculture, Northwest Agriculture and Forestry (A & F) University, Yangling, 712100, China

    Zhensheng Kang

  4. Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, 741 South Limestone, Lexington, KY 40536, USA

    Xiaoqing Tang

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  1. Guiliang Tang
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  1. University of Southern California, Los Angeles, CA, USA

    Shao-Yao Ying

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Tang, G. et al. (2008). Small RNA Technologies: siRNA, miRNA, antagomiR, Target Mimicry, miRNA Sponge and miRNA Profiling. In: Ying, SY. (eds) Current Perspectives in microRNAs (miRNA). Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-8533-8_2

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