Skip to main content

A Brief Introduction to RNAi and MicroRNAs in Stem Cells

  • Protocol
  • First Online:

Part of the book series: Methods in Molecular Biology ((MIMB,volume 650))

Abstract

Recently, RNAi, including microRNAs (miRNAs), has become an important tool to investigate the regulatory mechanism of stem cell maintenance and differentiation. In this short chapter, we will give a brief overview of the discovery history, functions, and mechanisms of RNAi and miRNAs. We will also discuss RNAi as a tool to study stem cell function and the potential future practical applications.

This is a preview of subscription content, log in via an institution.

Buying options

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Napoli, C., Lemieux, C., and Jorgensen, R. (1990) Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans. Plant Cell 2, 279–289.

    PubMed  CAS  Google Scholar 

  2. Romano, N., and Macino, G. (1992) Quelling: Transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences. Mol Microbiol 6, 3343–3353.

    Article  PubMed  CAS  Google Scholar 

  3. Hannon, G. J. (2002) RNA interference. Nature 418, 244–251.

    Article  PubMed  CAS  Google Scholar 

  4. Fire, A., Xu, S., Montgomery, M. K., Kostas, S. A., Driver, S. E., and Mello, C. C. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806–811.

    Article  PubMed  CAS  Google Scholar 

  5. Boutla, A., Delidakis, C., Livadaras, I., Tsagris, M., and Tabler, M. (2001) Short 5'-phosphorylated double-stranded RNAs induce RNA interference in Drosophila. Curr Biol 11, 1776–1780.

    Article  PubMed  CAS  Google Scholar 

  6. Kennerdell, J. R., and Carthew, R. W. (1998) Use of dsRNA-mediated genetic interference to demonstrate that frizzled and frizzled 2 act in the wingless pathway. Cell 95, 1017–1026.

    Article  PubMed  CAS  Google Scholar 

  7. Duxbury, M. S., and Whang, E. E. (2004) RNA interference: A practical approach. J Surg Res 117, 339–344.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  9. Chen, S., Choo, A., Wang, N. D., Too, H. P., and Oh, S. K. (2007) Establishing efficient siRNA knockdown in mouse embryonic stem cells. Biotechnol Lett 29, 261–265.

    Article  PubMed  CAS  Google Scholar 

  10. Ambros, V. (2003) MicroRNA pathways in flies and worms: Growth, death, fat, stress, and timing. Cell 113, 673–676.

    Article  PubMed  CAS  Google Scholar 

  11. Cerutti, H. (2003) RNA interference: Traveling in the cell and gaining functions?, Trends Genet 19, 39–46.

    Article  PubMed  CAS  Google Scholar 

  12. Shi, Y. (2003) Mammalian RNAi for the masses. Trends Genet 19, 9–12.

    Article  PubMed  Google Scholar 

  13. McManus, M. T., and Sharp, P. A. (2002) Gene silencing in mammals by small interfering RNAs. Nat Rev Genet 3, 737–747.

    Article  PubMed  CAS  Google Scholar 

  14. Carrington, J. C., and Ambros, V. (2003) Role of microRNAs in plant and animal development. Science 301, 336–338.

    Article  PubMed  CAS  Google Scholar 

  15. Wienholds, E., Koudijs, M. J., van Eeden, F. J., Cuppen, E., and Plasterk, R. H. (2003) The microRNA-producing enzyme Dicer1 is essential for zebrafish development. Nat Genet 35, 217–218.

    Article  PubMed  CAS  Google Scholar 

  16. Rana, T. M. (2007) Illuminating the silence: Understanding the structure and function of small RNAs. Nat Rev 8, 23–36.

    Article  CAS  Google Scholar 

  17. Sharp, P. A., and Zamore, P. D. (2000) Molecular biology. RNA interference. Science 287, 2431–2433.

    Article  PubMed  CAS  Google Scholar 

  18. Hammond, S. M., Boettcher, S., Caudy, A. A., Kobayashi, R., and Hannon, G. J. (2001) Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 293, 1146–1150.

    Article  PubMed  CAS  Google Scholar 

  19. Meister, G., and Tuschl, T. (2004) Mechanisms of gene silencing by double-stranded RNA. Nature 431, 343–349.

    Article  PubMed  CAS  Google Scholar 

  20. Ishizuka, A., Siomi, M. C., and Siomi, H. (2002) A Drosophila fragile X protein interacts with components of RNAi and ribosomal proteins. Genes Dev 16, 2497–2508.

    Article  PubMed  CAS  Google Scholar 

  21. Caudy, A. A., Ketting, R. F., Hammond, S. M., Denli, A. M., Bathoorn, A. M., Tops, B. B., Silva, J. M., Myers, M. M., Hannon, G. J., and Plasterk, R. H. (2003) A micrococcal nuclease homologue in RNAi effector complexes. Nature 425, 411–414.

    Article  PubMed  CAS  Google Scholar 

  22. Mourelatos, Z., Dostie, J., Paushkin, S., Sharma, A., Charroux, B., Abel, L., Rappsilber, J., Mann, M., and Dreyfuss, G. (2002) miRNPs: A novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev 16, 720–728.

    Article  PubMed  CAS  Google Scholar 

  23. Dostie, J., Mourelatos, Z., Yang, M., Sharma, A., and Dreyfuss, G. (2003) Numerous microRNPs in neuronal cells containing novel microRNAs. RNA 9, 180–186.

    Article  PubMed  CAS  Google Scholar 

  24. Nelson, P. T., Hatzigeorgiou, A. G., and Mourelatos, Z. (2004) miRNP: mRNA association in polyribosomes in a human neuronal cell line. RNA 10, 387–394.

    Article  PubMed  CAS  Google Scholar 

  25. Chendrimada, T. P., Gregory, R. I., Kumaraswamy, E., Norman, J., Cooch, N., Nishikura, K., and Shiekhattar, R. (2005) TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 436, 740–744.

    Article  PubMed  CAS  Google Scholar 

  26. Lee, Y., Hur, I., Park, S. Y., Kim, Y. K., Suh, M. R., and Kim, V. N. (2006) The role of PACT in the RNA silencing pathway. EMBO J 25, 522–532.

    Article  PubMed  CAS  Google Scholar 

  27. Chu, C. Y., and Rana, T. M. (2006) Translation repression in human cells by microRNA-induced gene silencing requires RCK/p54. PLoS Biol 4, e210.

    Article  PubMed  CAS  Google Scholar 

  28. 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. Genes Dev 16, 2733–2742.

    Article  PubMed  CAS  Google Scholar 

  29. Sasaki, T., Shiohama, A., Minoshima, S., and Shimizu, N. (2003) Identification of eight members of the Argonaute family in the human genome small star, filled. Genomics 82, 323–330.

    Article  PubMed  CAS  Google Scholar 

  30. Williams, R. W., and Rubin, G. M. (2002) ARGONAUTE1 is required for efficient RNA interference in Drosophila embryos. Proc Natl Acad Sci USA 99, 6889–6894.

    Article  PubMed  CAS  Google Scholar 

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

    Google Scholar 

  32. Siomi, H., Ishizuka, A., and Siomi, M. C. (2004) RNA interference: A new mechanism by which FMRP acts in the normal brain? What can Drosophila teach us?, Ment Retard Dev Disabil Res Rev 10, 68–74.

    Article  PubMed  Google Scholar 

  33. Caudy, A. A., Myers, M., Hannon, G. J., and Hammond, S. M. (2002) Fragile X-related protein and VIG associate with the RNA interference machinery. Genes Dev 16, 2491–2496.

    Article  PubMed  CAS  Google Scholar 

  34. Hammond, S. M., Bernstein, E., Beach, D., and Hannon, G. J. (2000) An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404, 293–296.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  36. 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.

    Article  PubMed  CAS  Google Scholar 

  37. Ambros, V. (2001) MicroRNAs: Tiny regulators with great potential. Cell 107, 823–826.

    Article  PubMed  CAS  Google Scholar 

  38. Ambros, V. (2004) The functions of animal microRNAs. Nature 431, 350–355.

    Article  PubMed  CAS  Google Scholar 

  39. Bartel, D. P. (2004) MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116, 281–297.

    Article  PubMed  CAS  Google Scholar 

  40. Carrington, J. C., and Ambros, V. (2003) Role of microRNAs in plant and animal development. Science 301, 336–338.

    Article  PubMed  CAS  Google Scholar 

  41. Zhang, B. H., Stellwag, E. J., and Pan, X. P. (2009) Large-scale genome analysis reveals unique features of microRNAs. Gene 443, 100–109.

    Article  PubMed  CAS  Google Scholar 

  42. Yeom, K. H., Lee, Y., Han, J., Suh, M. R., and Kim, V. N. (2006) Characterization of DGCR8/Pasha, the essential cofactor for Drosha in primary miRNA processing. Nucleic Acids Res 34, 4622–4629.

    Article  PubMed  CAS  Google Scholar 

  43. Lund, E., Guttinger, S., Calado, A., Dahlberg, J. E., and Kutay, U. (2004) Nuclear export of microRNA precursors. Science 303, 95–98.

    Article  PubMed  CAS  Google Scholar 

  44. Gregory, R. I., Chendrimada, T. P., Cooch, N., and Shiekhattar, R. (2005) Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell 123, 631–640.

    Article  PubMed  CAS  Google Scholar 

  45. Gregory, R. I., Chendrimada, T. P., and Shiekhattar, R. (2006) MicroRNA biogenesis: Isolation and characterization of the microprocessor complex. Methods Mol Biol 342, 33–47.

    PubMed  CAS  Google Scholar 

  46. Eulalio, A., Behm-Ansmant, I., and Izaurralde, E. (2007) P bodies: At the crossroads of post-transcriptional pathways. Nat Reviews 8, 9–22.

    Article  CAS  Google Scholar 

  47. Lee, R. C., Feinbaum, R. L., and Ambros, V. (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843–854.

    Article  PubMed  CAS  Google Scholar 

  48. Wightman, B., Ha, I., and Ruvkun, G. (1993) Posttranscriptional regulation of the heterochronic gene Lin-14 by Lin-4 mediates temporal pattern-formation in C. elegans. Cell 75, 855–862.

    Article  PubMed  CAS  Google Scholar 

  49. Lee, R. C., and Ambros, V. (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294, 862–864.

    Article  PubMed  CAS  Google Scholar 

  50. Lagos-Quintana, M., Rauhut, R., Lendeckel, W., and Tuschl, T. (2001) Identification of novel genes coding for small expressed RNAs. Science 294, 853–858.

    Article  PubMed  CAS  Google Scholar 

  51. 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.

    Article  PubMed  CAS  Google Scholar 

  52. Reinhart, B. J., Slack, F. J., Basson, M., Pasquinelli, A. E., Bettinger, J. C., Rougvie, A. E., Horvitz, H. R., and Ruvkun, G. (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403, 901–906.

    Article  PubMed  CAS  Google Scholar 

  53. 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.

    Article  PubMed  CAS  Google Scholar 

  54. Brennecke, J., Hipfner, D. R., Stark, A., Russell, R. B., and Cohen, S. M. (2003) bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 113, 25–36.

    Article  PubMed  CAS  Google Scholar 

  55. Xu, P., Vernooy, S. Y., Guo, M., and Hay, B. A. (2003) The Drosophila microRNA Mir-14 suppresses cell death and is required for normal fat metabolism. Curr Biol 13, 790–795.

    Article  PubMed  CAS  Google Scholar 

  56. Baroukh, N., Ravier, M. A., Loder, M. K., Hill, E. V., Bounacer, A., Scharfmann, R., Rutter, G. A., and Van Obberghen, E. (2007) MicroRNA-124a regulates Foxa2 expression and intracellular signaling in pancreatic beta-cell lines. J Biol Chem 282, 19575–19588.

    Article  PubMed  CAS  Google Scholar 

  57. Webster, R. J., Giles, K. M., Price, K. J., Zhang, P. M., Mattick, J. S., and Leedman, P. J. (2009) Regulation of epidermal growth factor receptor signaling in human cancer cells by microRNA-7. J Biol Chem 284, 5731–5741.

    Article  PubMed  CAS  Google Scholar 

  58. Zhang, B. H., Pan, X. P., Cobb, G. P., and Anderson, T. A. (2007) MicroRNAs as oncogenes and tumor suppressors. Dev Biol 302, 1–12.

    Article  PubMed  CAS  Google Scholar 

  59. Saito, Y., Liang, G., Egger, G., Friedman, J. M., Chuang, J. C., Coetzee, G. A., and Jones, P. A. (2006) Specific activation of microRNA-127 with downregulation of the proto-oncogene BCL6 by chromatin-modifying drugs in human cancer cells. Cancer Cell 9, 435–443.

    Article  PubMed  CAS  Google Scholar 

  60. Pearson, J. C., Lemons, D., and McGinnis, W. (2005) Modulating Hox gene functions during animal body patterning. Nat Rev Genet 6, 893–904.

    Article  PubMed  CAS  Google Scholar 

  61. Hammond, S. M. (2006) MicroRNAs as oncogenes. Curr Opin Genet Dev 16, 4–9.

    Article  PubMed  CAS  Google Scholar 

  62. Hammond, S. M. (2006) MicroRNAs as oncogenes. Curr Opin Genet Dev 16, 4–9.

    Article  PubMed  CAS  Google Scholar 

  63. Kosik, K. S. (2006) The neuronal microRNA system. Nat Rev Neurosci 7, 911–920.

    Article  PubMed  CAS  Google Scholar 

  64. Kim, J., Krichevsky, A., Grad, Y., Hayes, G. D., Kosik, K. S., Church, G. M., and Ruvkun, G. (2004) Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc Natl Acad Sci USA 101, 360–365.

    Article  PubMed  CAS  Google Scholar 

  65. Krichevsky, A. M., King, K. S., Donahue, C. P., Khrapko, K., and Kosik, K. S. (2003) A microRNA array reveals extensive regulation of microRNAs during brain development. RNA 9, 1274–1281.

    Article  PubMed  CAS  Google Scholar 

  66. Giraldez, A. J., Cinalli, R. M., Glasner, M. E., Enright, A. J., Thomson, J. M., Baskerville, S., Hammond, S. M., Bartel, D. P., and Schier, A. F. (2005) MicroRNAs regulate brain morphogenesis in zebrafish. Science 308, 833–838.

    Article  PubMed  CAS  Google Scholar 

  67. Miska, E. A., Alvarez-Saavedra, E., Townsend, M., Yoshii, A., Sestan, N., Rakic, P., Constantine-Paton, M., and Horvitz, H. R. (2004) Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biol 5, R68.

    Article  PubMed  Google Scholar 

  68. 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.

    Article  PubMed  Google Scholar 

  69. Ashraf, S. I., and Kunes, S. (2006) A trace of silence: Memory and microRNA at the synapse. Curr Opin Neurobiol 16, 535–539.

    Article  PubMed  CAS  Google Scholar 

  70. Zhang, B. H., Pan, X. P., and Anderson, T. A. (2006) MicroRNA: A new player in stem cells. J Cell Physiol 209, 266–269.

    Article  PubMed  CAS  Google Scholar 

  71. Forstemann, K., Tomari, Y., Du, T. T., Vagin, V. V., Denli, A. M., Bratu, D. P., Klattenhoff, C., Theurkauf, W. E., and Zamore, P. D. (2005) Normal microRNA maturation and germ-line stem cell maintenance requires loquacious, a double-stranded RNA- binding domain protein. PLoS Biol 3, 1187–1201.

    Article  CAS  Google Scholar 

  72. Gangaraju, V. K., and Lin, H. F. (2009) MicroRNAs: Key regulators of stem cells. Nat Rev Mol Cell Biol 10, 116–125.

    Article  PubMed  CAS  Google Scholar 

  73. Greco, S. J., and Rameshwar, P. (2007) microRNAs regulate synthesis of the neurotransmitter substance P in human mesenchymal stem cell-derived neuronal cells. Proc Natl Acad Sci USA 104, 15484–15489.

    Article  PubMed  CAS  Google Scholar 

  74. Hammond, S. M., and Sharpless, N. E. (2008) HMGA2, microRNAs, and stem cell aging. Cell 135, 1013–1016.

    Article  PubMed  CAS  Google Scholar 

  75. Hatfield, S., and Ruohola-Baker, H. (2008) microRNA and stem cell function. Cell Tissue Res 331, 57–66.

    Article  PubMed  CAS  Google Scholar 

  76. Hatfield, S. D., Shcherbata, H. R., Fischer, K. A., Nakahara, K., Carthew, R. W., and Ruohola-Baker, H. (2005) Stem cell division is regulated by the microRNA pathway. Nature 435, 974–978.

    Article  PubMed  CAS  Google Scholar 

  77. Houbaviy, H. B., Murray, M. F., and Sharp, P. A. (2003) Embryonic stem cell-specific microRNAs. Dev Cell 5, 351–358.

    Article  PubMed  CAS  Google Scholar 

  78. Ivey, K. N., Muth, A., Amold, J., King, F. W., Yeh, R. F., Fish, J. E., Hsiao, E. C., Schwartz, R. J., Conklin, B. R., Bernstein, H. S., and Srivastava, D. (2008) microRNA regulation of cell lineages in mouse and human embryonic stem cells. Cell Stem Cell 2, 219–229.

    Article  PubMed  CAS  Google Scholar 

  79. Kanellopoulou, C., Muljo, S. A., Kung, A. L., Ganesan, S., Drapkin, R., Jenuwein, T., Livingston, D. M., and Rajewsky, K. (2005) Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev 19, 489–501.

    Article  PubMed  CAS  Google Scholar 

  80. Krichevsky, A. M., Sonntag, K. C., Isacson, O., and Kosik, K. S. (2006) Specific microRNAs modulate embryonic stem cell-derived neurogenesis. Stem Cells 24, 857–864.

    Article  PubMed  CAS  Google Scholar 

  81. Kuwabara, T., Hsieh, J., Nakashima, K., Taira, K., and Gage, F. H. (2004) A small modulatory dsRNA specifies the fate of adult neural stem cells. Cell 116, 779–793.

    Article  PubMed  CAS  Google Scholar 

  82. Lakshmipathy, U., Love, B., Goff, L. A., Jornsten, R., Graichen, R., Hart, R. P., and Chesnut, J. D. (2007) microRNA expression pattern of undifferentiated and differentiated human embryonic stem cells. Stem Cells Dev 16, 1003–1016.

    Article  PubMed  CAS  Google Scholar 

  83. Li, Q. T., and Gregory, R. I. (2008) microRNA regulation of stem cell fate. Cell Stem Cell 2, 195–196.

    Article  PubMed  CAS  Google Scholar 

  84. Murchison, E. P., Partridge, J. F., Tam, O. H., Cheloufi, S., and Hannon, G. J. (2005) Characterization of Dicer-deficient murine embryonic stem cells. Proc Natl Acad Sci USA 102, 12135–12140.

    Article  PubMed  CAS  Google Scholar 

  85. Park, J. K., Liu, X., Strauss, T. J., McKearin, D. M., and Liu, Q. H. (2007) The miRNA pathway intrinsically controls self-renewal of Drosophila germline stem cells. Curr Biol 17, 533–538.

    Article  PubMed  CAS  Google Scholar 

  86. Suh, M. R., Lee, Y., Kim, J. Y., Kim, S. K., Moon, S. H., Lee, J. Y., Cha, K. Y., Chung, H. M., Yoon, H. S., Moon, S. Y., Kim, V. N., and Kim, K. S. (2004) Human embryonic stem cells express a unique set of microRNAs. Dev Biol 270, 488–498.

    Article  PubMed  CAS  Google Scholar 

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

    Google Scholar 

  88. Wang, Y., Baskerville, S., Shenoy, A., Babiarz, J. E., Baehner, L., and Blelloch, R. (2008) Embryonic stem cell-specific microRNAs regulate the G1-S transition and promote rapid proliferation. Nat Genet 40, 1478–1483.

    Article  PubMed  CAS  Google Scholar 

  89. Wang, Y. L., Keys, D. N., Au-Young, J. K., and Chen, C. F. (2009) microRNAs in embryonic stem cells. J Cell Physiol 218, 251–255.

    Article  PubMed  CAS  Google Scholar 

  90. Zou, G. M., and Yoder, M. C. (2005) Application of RNA interference to study stem cell function: Current status and future perspectives. Biol Cell 97, 211–219.

    Article  PubMed  CAS  Google Scholar 

  91. Marson, A., Levine, S. S., Cole, M. F., Frampton, G. M., Brambrink, T., Johnstone, S., Guenther, M. G., Johnston, W. K., Wernig, M., Newman, J., Calabrese, J. M., Dennis, L. M., Volkert, T. L., Gupta, S., Love, J., Hannett, N., Sharp, P. A., Bartel, D. P., Jaenisch, R., and Young, R. A. (2008) Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 134, 521–533.

    Article  PubMed  CAS  Google Scholar 

  92. Mineno, J., Okamoto, S., Ando, T., Sato, M., Chono, H., Izu, H., Takayama, M., Asada, K., Mirochnitchenko, O., Inouye, M., and Kato, I. (2006) The expression profile of microRNAs in mouse embryos. Nucleic Acids Res 34, 1765–1771.

    Article  PubMed  CAS  Google Scholar 

  93. Bernstein, E., Kim, S. Y., Carmell, M. A., Murchison, E. P., Alcorn, H., Li, M. Z., Mills, A. A., Elledge, S. J., Anderson, K. V., and Hannon, G. J. (2003) Dicer is essential for mouse development. Nat Genet 35, 215–217.

    Article  PubMed  CAS  Google Scholar 

  94. Wang, Y., Medvid, R., Melton, C., Jaenisch, R., and Blelloch, R. (2007) DGCR8 is essential for microRNA biogenesis and silencing of embryonic stem cell self-renewal. Nat Genet 39, 380–385.

    Article  PubMed  CAS  Google Scholar 

  95. Stefani, G., and Slack, F. J. (2008) Small non-coding RNAs in animal development. Nat Rev 9, 219–230.

    Article  CAS  Google Scholar 

  96. Sinkkonen, L., Hugenschmidt, T., Berninger, P., Gaidatzis, D., Mohn, F., Artus-Revel, C. G., Zavolan, M., Svoboda, P., and Filipowicz, W. (2008) microRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells. Nat Struct Mol Biol 15, 259–267.

    Article  PubMed  CAS  Google Scholar 

  97. Velkey, J. M., and O’Shea, K. S. (2003) Oct4 RNA interference induces trophectoderm differentiation in mouse embryonic stem cells. Genesis 37, 18–24.

    Article  PubMed  CAS  Google Scholar 

  98. Hay, D. C., Sutherland, L., Clark, J., and Burdon, T. (2004) Oct-4 knockdown induces similar patterns of endoderm and trophoblast differentiation markers in human and mouse embryonic stem cells. Stem Cells 22, 225–235.

    Article  PubMed  CAS  Google Scholar 

  99. Ui-Tei, K., Zenno, S., Miyata, Y., and Saigo, K. (2000) Sensitive assay of RNA interference in Drosophila and Chinese hamster cultured cells using firefly luciferase gene as target. FEBS Lett 479, 79–82.

    Article  PubMed  CAS  Google Scholar 

  100. Gil, J., and Esteban, M. (2000) Induction of apoptosis by the dsRNA-dependent protein kinase (PKR): Mechanism of action. Apoptosis 5, 107–114.

    Article  PubMed  CAS  Google Scholar 

  101. Caplen, N. J., and Mousses, S. (2003) Short interfering RNA (siRNA)-mediated RNA interference (RNAi) in human cells. Ann N Y Acad Sci 1002, 56–62.

    Article  PubMed  CAS  Google Scholar 

  102. Michaelson, J. S., and Leder, P. (2003) RNAi reveals anti-apoptotic and transcriptionally repressive activities of DAXX. J Cell Sci 116, 345–352.

    Article  PubMed  CAS  Google Scholar 

  103. Brummelkamp, T. R., Bernards, R., and Agami, R. (2002) Stable suppression of tumorigenicity by virus-mediated RNA interference. Cancer Cell 2, 243–247.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Murashov, A.K. (2010). A Brief Introduction to RNAi and MicroRNAs in Stem Cells. In: Zhang, B., Stellwag, E. (eds) RNAi and microRNA-Mediated Gene Regulation in Stem Cells. Methods in Molecular Biology, vol 650. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-769-3_2

Download citation

  • DOI: https://doi.org/10.1007/978-1-60761-769-3_2

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60761-768-6

  • Online ISBN: 978-1-60761-769-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics