Skip to main content
SpringerLink
Log in

Multiple Approach to Analyzing the Role of MicroRNAs in Apoptosis

  • Protocol
  • First Online:
Apoptosis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 559))

Summary

MicroRNAs (miRNAs) are noncoding RNAs whose hallmarks are the very short sequences and the ability to repress the translation and/or transcription of target genes. miRNAs can have diverse functions, including regulation of cellular differentiation, proliferation, and embryogenesis. Over the past 5 years, an increasing number of studies have linked different miRNAs with programmed cell death or apoptosis. The principal aim of this chapter is to describe a method that (1) identifies miRNAs involved in apoptosis, using a validated array profiling approach, (2) assesses the direct involvement of candidate miRNAs in apoptosis, and (3) identifies the molecular mechanisms possibly involved in apoptotic response. To disclose the possible molecular targets of miRNAs, we propose the generation of a database created using a list of presumptive miRNA targets and the changes in the transcriptome after ectopic expression of the miRNAs. Our proposed method for doing this is suitable for both discovery of apoptotic pathways that regulate miRNAs and finding new miRNAs able to induce apoptosis.

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

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
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

Institutional subscriptions

References

  1. 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 

  2. 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 

  3. Valencia-Sanchez, M. A., Liu, J., Hannon, G. J., and Parker, R. (2006). Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev 20, 515–524.

    Article  PubMed  CAS  Google Scholar 

  4. Vasudevan, S., Tong, Y., and Steitz, J. A. (2007). Switching from repression to activation: microRNAs can up-regulate translation. Science 318, 1931–1934.

    Article  PubMed  CAS  Google Scholar 

  5. Georgantas, R. W., III, Hildreth, R., Morisot, S., Alder, J., Liu, C. G., Heimfeld, S., Calin, G. A., Croce, C. M., and Civin, C. I. (2007). CD34+ hematopoietic stem-progenitor cell microRNA expression and function: a circuit diagram of differentiation control. Proc Natl Acad Sci USA 104, 2750–2755.

    Article  PubMed  CAS  Google Scholar 

  6. Garzon, R., Pichiorri, F., Palumbo, T., Iuliano, R., Cimmino, A., Aqeilan, R., Volinia, S., Bhatt, D., Alder, H., Marcucci, G., Calin, G. A., Liu, C. G., Bloomfield, C. D., Andreeff, M., and Croce, C. M. (2006). MicroRNA fingerprints during human megakaryocytopoiesis. Proc Natl Acad Sci USA 103, 5078–5083.

    Article  PubMed  CAS  Google Scholar 

  7. Nakamoto, M., Jin, P., O’Donnell, W. T., and Warren, S. T. (2005). Physiological identification of human transcripts translationally regulated by a specific microRNA. Hum Mol Genet 14, 3813–3821.

    Article  PubMed  CAS  Google Scholar 

  8. Cheng, A. M., Byrom, M. W., Shelton, J., and Ford, L. P. (2005). Antisense inhibition of human miRNAs and indications for an involvement of miRNA in cell growth and apoptosis. Nucleic Acids Res 33, 1290–1297.

    Article  PubMed  CAS  Google Scholar 

  9. Leaman, D., Chen, P. Y., Fak, J., Yalcin, A., Pearce, M., Unnerstall, U., Marks, D. S., Sander, C., Tuschl, T., and Gaul, U. (2005). Antisense-mediated depletion reveals essential and specific functions of microRNAs in Drosophila development. Cell 121, 1097–1108.

    Article  PubMed  CAS  Google Scholar 

  10. Chang, T. C., Wentzel, E. A., Kent, O. A., Ramachandran, K., Mullendore, M., Lee, K. H., Feldmann, G., Yamakuchi, M., Ferlito, M., Lowenstein, C. J., Arking, D. E., Beer, M. A., Maitra, A., and Mendell, J. T. (2007). Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis. Mol Cell 26, 745–752.

    Article  PubMed  CAS  Google Scholar 

  11. He, L., He, X., Lim, L. P., de Stanchina, E., Xuan, Z., Liang, Y., Xue, W., Zender, L., Magnus, J., Ridzon, D., Jackson, A. L., Linsley, P. S., Chen, C., Lowe, S. W., Cleary, M. A., and Hannon, G. J. (2007). A microRNA component of the p53 tumour suppressor network. Nature 447, 1130–1134.

    Article  PubMed  CAS  Google Scholar 

  12. Raver-Shapira, N., Marciano, E., Meiri, E., Spector, Y., Rosenfeld, N., Moskovits, N., Bentwich, Z., and Oren, M. (2007). Transcriptional Activation of miR-34a Contributes to p53-Mediated Apoptosis. Mol Cell 26, 731–743.

    Article  PubMed  CAS  Google Scholar 

  13. Raver-Shapira, N., Marciano, E., Meiri, E., Spector, Y., Rosenfeld, N., Moskovits, N., Bentwich, Z., and Oren, M. (2007). Transcriptional activation of miR-34a contributes to p53-mediated apoptosis. Mol Cell 26, 731–743.

    Article  PubMed  CAS  Google Scholar 

  14. Welch, C., Chen, Y., and Stallings, R. L. (2007). MicroRNA-34a functions as a potential tumor suppressor by inducing apoptosis in neuroblastoma cells. Oncogene 26, 5017–5022.

    Article  PubMed  CAS  Google Scholar 

  15. Loffler, D., Brocke-Heidrich, K., Pfeifer, G., Stocsits, C., Hackermuller, J., Kretzschmar, A. K., Burger, R., Gramatzki, M., Blumert, C., Bauer, K., Cvijic, H., Ullmann, A. K., Stadler, P. F., and Horn, F. (2007). Interleukin-6 dependent survival of multiple myeloma cells involves the Stat3-mediated induction of microRNA-21 through a highly conserved enhancer. Blood 110, 1330–1333.

    Article  PubMed  Google Scholar 

  16. Cimmino, A., Calin, G. A., Fabbri, M., Iorio, M. V., Ferracin, M., Shimizu, M., Wojcik, S. E., Aqeilan, R. I., Zupo, S., Dono, M., Rassenti, L., Alder, H., Volinia, S., Liu, C. G., Kipps, T. J., Negrini, M., and Croce, C. M. (2005). miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc Natl Acad Sci USA 102, 13944–13949.

    Article  PubMed  CAS  Google Scholar 

  17. 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.

    Article  PubMed  CAS  Google Scholar 

  18. Gupta, A., Gartner, J. J., Sethupathy, P., Hatzigeorgiou, A. G., and Fraser, N. W. (2006). Anti-apoptotic function of a microRNA encoded by the HSV-1 latency-associated transcript. Nature 442, 82–85.

    PubMed  CAS  Google Scholar 

  19. Xu, C., Lu, Y., Pan, Z., Chu, W., Luo, X., Lin, H., Xiao, J., Shan, H., Wang, Z., and Yang, B. (2007). The muscle-specific microRNAs miR-1 and miR-133 produce opposing effects on apoptosis by targeting HSP60, HSP70 and caspase-9 in cardiomyocytes. J Cell Sci 120, 3045–3052.

    Article  PubMed  CAS  Google Scholar 

  20. Welch, C., Chen, Y., and Stallings, R. L. (2007). MicroRNA-34a functions as a potential tumor suppressor by inducing apoptosis in neuroblastoma cells. Oncogene 26, 5017–5022.

    Article  PubMed  CAS  Google Scholar 

  21. Tarasov, V., Jung, P., Verdoodt, B., Lodygin, D., Epanchintsev, A., Menssen, A., Meister, G., and Hermeking, H. (2007). Differential regulation of microRNAs by p53 revealed by massively parallel sequencing: miR-34a is a p53 target that induces apoptosis and G1-arrest. Cell cycle (Georgetown, Tex) 6, 1586–1593.

    Article  CAS  Google Scholar 

  22. Tazawa, H., Tsuchiya, N., Izumiya, M., and Nakagama, H. (2007). Tumor-suppressive miR-34a induces senescence-like growth arrest through modulation of the E2F pathway in human colon cancer cells. Proc Natl Acad Sci USA 104, 15472–15477.

    Article  PubMed  CAS  Google Scholar 

  23. Matsubara, H., Takeuchi, T., Nishikawa, E., Yanagisawa, K., Hayashita, Y., Ebi, H., Yamada, H., Suzuki, M., Nagino, M., Nimura, Y., Osada, H., and Takahashi, T. (2007). Apoptosis induction by antisense oligonucleotides against miR-17–5p and miR-20a in lung cancers overexpressing miR-17–92. Oncogene 26, 6099–6105.

    Article  PubMed  CAS  Google Scholar 

  24. Sylvestre, Y., De Guire, V., Querido, E., Mukhopadhyay, U. K., Bourdeau, V., Major, F., Ferbeyre, G., and Chartrand, P. (2007). An E2F/miR-20a autoregulatory feedback loop. J Biol Chem 282, 2135–2143.

    Article  PubMed  CAS  Google Scholar 

  25. Chan, J. A., Krichevsky, A. M., and Kosik, K. S. (2005). MicroRNA-21 is an antiapoptotic factor in human glioblastoma cells. Cancer Res 65, 6029–6033.

    Article  PubMed  CAS  Google Scholar 

  26. Meng, F., Henson, R., Lang, M., Wehbe, H., Maheshwari, S., Mendell, J. T., Jiang, J., Schmittgen, T. D., and Patel, T. (2006). Involvement of human micro-RNA in growth and response to chemotherapy in human cholangiocarcinoma cell lines. Gastroenterology 130, 2113–2129.

    Article  PubMed  CAS  Google Scholar 

  27. Si, M. L., Zhu, S., Wu, H., Lu, Z., Wu, F., and Mo, Y. Y. (2007). miR-21-mediated tumor growth. ,Oncogene 26, 2799–2803.

    Article  PubMed  CAS  Google Scholar 

  28. Corsten, M. F., Miranda, R., Kasmieh, R., Krichevsky, A. M., Weissleder, R., and Shah, K. (2007). MicroRNA-21 knockdown disrupts glioma growth in vivo and displays synergistic cytotoxicity with neural precursor cell delivered S-TRAIL in human gliomas. Cancer Res 67, 8994–9000.

    Article  PubMed  CAS  Google Scholar 

  29. Frankel, L. B., Christoffersen, N. R., Jacobsen, A., Lindow, M., Krogh, A., and Lund, A. H. (2007). Programmed cell death 4 (PDCD4) is an important functional target of the microRNA miR-21 in breast cancer cells. J Biol Chem 283, 1026–1033.

    Article  PubMed  Google Scholar 

  30. Ji, R., Cheng, Y., Yue, J., Yang, J., Liu, X., Chen, H., Dean, D. B., and Zhang, C. (2007). MicroRNA expression signature and antisense-mediated depletion reveal an essential role of MicroRNA in vascular neointimal lesion formation. Circ Res 100, 1579–1588.

    Article  PubMed  CAS  Google Scholar 

  31. Sathyan, P., Golden, H. B., and Miranda, R. C.(2007). Competing interactions between micro-RNAs determine neural progenitor survival and proliferation after ethanol exposure: evidence from an ex vivo model of the fetal cerebral cortical neuroepithelium. J Neurosci 27, 8546–8557.

    Article  PubMed  CAS  Google Scholar 

  32. Ovcharenko, D., Kelnar, K., Johnson, C., Leng, N., and Brown, D. (2007). Genome-scale microRNA and small interfering RNA screens identify small RNA modulators of TRAIL-induced apoptosis pathway. Cancer Res 67, 10782–10788.

    Article  PubMed  CAS  Google Scholar 

  33. Meng, F., Henson, R., Wehbe-Janek, H., Smith, H., Ueno, Y., and Patel, T. (2007). The MicroRNA let-7a modulates interleukin-6-dependent STAT-3 survival signaling in malignant human cholangiocytes. J Biol Chem 282, 8256–8264.

    Article  PubMed  CAS  Google Scholar 

  34. Nakagawa, Y., Iinuma, M., Naoe, T., Nozawa, Y., and Akao, Y. (2007). Characterized mechanism of alpha-mangostin-induced cell death: caspase-independent apoptosis with release of endonuclease-G from mitochondria and increased miR-143 expression in human colorectal cancer DLD-1 cells. Bioorg Med Chem 15, 5620–5628.

    Article  PubMed  CAS  Google Scholar 

  35. Mott, J. L., Kobayashi, S., Bronk, S. F., and Gores, G. J. (2007). mir-29 regulates Mcl-1 protein expression and apoptosis. Oncogene 26, 6133–6140.

    Article  PubMed  CAS  Google Scholar 

  36. Karres, J. S., Hilgers, V., Carrera, I., Treisman, J., and Cohen, S. M. (2007). The conserved microRNA miR-8 tunes atrophin levels to prevent neurodegeneration in Drosophila. Cell 131, 136–145.

    Article  PubMed  CAS  Google Scholar 

  37. 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 

  38. Nolo, R., Morrison, C. M., Tao, C., Zhang, X., and Halder, G. (2006). The bantam microRNA is a target of the hippo tumor-suppressor pathway. Curr Biol 16, 1895–1904.

    Article  PubMed  CAS  Google Scholar 

  39. Nairz, K., Rottig, C., Rintelen, F., Zdobnov, E., Moser, M., and Hafen, E. (2006). Overgrowth caused by misexpression of a microRNA with dispensable wild-type function. Dev Biol 291, 314–324.

    Article  PubMed  CAS  Google Scholar 

  40. 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 

  41. Gupta, A., Gartner, J. J., Sethupathy, P., Hatzigeorgiou, A. G., and Fraser, N. W. (2006). Anti-apoptotic function of a microRNA encoded by the HSV-1 latency-associated transcript. Nature 442, 82–85.

    PubMed  CAS  Google Scholar 

  42. Liu, C. G., Calin, G. A., Meloon, B., Gamliel, N., Sevignani, C., Ferracin, M., Dumitru, C. D., Shimizu, M., Zupo, S., Dono, M., Alder, H., Bullrich, F., Negrini, M., and Croce, C. M.(2004). An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc Natl Acad Sci USA 101, 9740–9744.

    Article  PubMed  CAS  Google Scholar 

  43. 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., Iuliano, R., Palumbo, T., Pichiorri, F., Roldo, C., Garzon, R., Sevignani, C., Rassenti, L., Alder, H., Volinia, S., Liu, C. G., Kipps, T. J., Negrini, M., and Croce, C. M. (2005). A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N Engl J Med 353, 1793–1801.

    Article  PubMed  CAS  Google Scholar 

  44. Esquela-Kerscher, A., and Slack, F. J. (2006). Oncomirs - microRNAs with a role in cancer. Nat Rev Cancer 6, 259–269.

    Article  PubMed  CAS  Google Scholar 

  45. Volinia, S., Calin, G. A., Liu, C. G., Ambs, S., Cimmino, A., Petrocca, F., Visone, R., Iorio, M., Roldo, C., Ferracin, M., Prueitt, R. L., Yanaihara, N., Lanza, G., Scarpa, A., Vecchione, A., Negrini, M., Harris, C. C., and Croce, C. M. (2006). A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci USA 103, 2257–2261.

    Article  PubMed  CAS  Google Scholar 

  46. Yanaihara, N., Caplen, N., Bowman, E., Seike, M., Kumamoto, K., Yi, M., Stephens, R. M., Okamoto, A., Yokota, J., Tanaka, T., Calin, G. A., Liu, C. G., Croce, C. M., and Harris, C. C. (2006). Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell 9, 189–198.

    Article  PubMed  CAS  Google Scholar 

  47. 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 

  48. Lu, J., Getz, G., Miska, E. A., Alvarez-Saavedra, E., Lamb, J., Peck, D., Sweet-Cordero, A., Ebert, B. L., Mak, R. H., Ferrando, A. A., Downing, J. R., Jacks, T., Horvitz, H. R., and Golub, T. R. (2005). MicroRNA expression profiles classify human cancers. Nature 435, 834–838.

    Article  PubMed  CAS  Google Scholar 

  49. Chen, C., Ridzon, D. A., Broomer, A. J., Zhou, Z., Lee, D. H., Nguyen, J. T., Barbisin, M., Xu, N. L., Mahuvakar, V. R., Andersen, M. R., Lao, K. Q., Livak, K. J., and Guegler, K. J. (2005). Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33, e179.

    Article  PubMed  Google Scholar 

  50. Kloosterman, W. P., Wienholds, E., de Bruijn, E., Kauppinen, S., and Plasterk, R. H. (2006). In situ detection of miRNAs in animal embryos using LNA-modified oligonucleotide probes. Nat Methods 3, 27–29.

    Article  PubMed  CAS  Google Scholar 

  51. Allawi, H. T., Dahlberg, J. E., Olson, S., Lund, E., Olson, M., Ma, W. P., Takova, T., Neri, B. P., and Lyamichev, V. I. (2004). Quantitation of microRNAs using a modified Invader assay. RNA 10, 1153–1161.

    Article  PubMed  CAS  Google Scholar 

  52. Nelson, P. T., Baldwin, D. A., Kloosterman, W. P., Kauppinen, S., Plasterk, R. H., and Mourelatos, Z. (2006). RAKE and LNA-ISH reveal microRNA expression and localization in archival human brain. RNA 12, 187–191.

    Article  PubMed  CAS  Google Scholar 

  53. Neely, L. A., Patel, S., Garver, J., Gallo, M., Hackett, M., McLaughlin, S., Nadel, M., Harris, J., Gullans, S., and Rooke, J. (2006). A single-molecule method for the quantitation of microRNA gene expression. Nat Methods 3, 41–46.

    Article  PubMed  CAS  Google Scholar 

  54. Liu, C. G., Spizzo, R., Calin, G. A., and Croce, C. M. (2008). Expression profiling of microRNA using oligo DNA arrays. Methods 44, 22–30.

    Article  PubMed  Google Scholar 

  55. Bejerano, G., Pheasant, M., Makunin, I., Stephen, S., Kent, W. J., Mattick, J. S., and Haussler, D. (2004). Ultraconserved elements in the human genome. Science 304, 1321–1325.

    Article  PubMed  CAS  Google Scholar 

  56. Calin, G. A., Liu, C. G., Ferracin, M., Hyslop, T., Spizzo, R., Sevignani, C., Fabbri, M., Cimmino, A., Lee, E. J., Wojcik, S. E., Shimizu, M., Tili, E., Rossi, S., Taccioli, C., Pichiorri, F., Liu, X., Zupo, S., Herlea, V., Gramantieri, L., Lanza, G., Alder, H., Rassenti, L., Volinia, S., Schmittgen, T. D., Kipps, T. J., Negrini, M., and Croce, C. M. (2007). Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas. Cancer Cell 12, 215–229.

    Article  PubMed  CAS  Google Scholar 

  57. Altuvia, Y., Landgraf, P., Lithwick, G., Elefant, N., Pfeffer, S., Aravin, A., Brownstein, M. J., Tuschl, T., and Margalit, H. (2005). Clustering and conservation patterns of human microRNAs. Nucleic Acids Res 33, 2697–2706.

    Article  PubMed  CAS  Google Scholar 

  58. 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.

    Article  PubMed  CAS  Google Scholar 

  59. Berezikov, E., Guryev, V., van de Belt, J., Wienholds, E., Plasterk, R. H., and Cuppen, E. (2005). Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120, 21–24.

    Article  PubMed  CAS  Google Scholar 

  60. Iorio, M. V., Ferracin, M., Liu, C. G., Veronese, A., Spizzo, R., Sabbioni, S., Magri, E., Pedriali, M., Fabbri, M., Campiglio, M., Menard, S., Palazzo, J. P., Rosenberg, A., Musiani, P., Volinia, S., Nenci, I., Calin, G. A., Querzoli, P., Negrini, M., and Croce, C. M. (2005). MicroRNA gene expression deregulation in human breast cancer. Cancer Res 65, 7065–7070.

    Article  PubMed  CAS  Google Scholar 

  61. Bloomston, M., Frankel, W. L., Petrocca, F., Volinia, S., Alder, H., Hagan, J. P., Liu, C. G., Bhatt, D., Taccioli, C., and Croce, C. M. (2007). MicroRNA expression patterns to differentiate pancreatic adenocarcinoma from normal pancreas and chronic pancreatitis. JAMA 297, 1901–1908.

    Article  PubMed  CAS  Google Scholar 

  62. Wu, W., Dave, N., Tseng, G. C., Richards, T., Xing, E. P., and Kaminski, N. (2005). Comparison of normalization methods for CodeLink Bioarray data. BMC Bioinformatics 6, 309.

    Article  PubMed  Google Scholar 

  63. 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., Calin, G. A., and Ivan, M. (2007). A microRNA signature of hypoxia. Mol Cell Biol 27, 1859–1867.

    Article  PubMed  CAS  Google Scholar 

  64. Calin, G. A., and Croce, C. M. (2006). MicroRNA signatures in human cancers. Nat Rev Cancer 6, 857–866.

    Article  PubMed  CAS  Google Scholar 

  65. Schmittgen, T. D., Jiang, J., Liu, Q., and Yang, L. (2004). A high-throughput method to monitor the expression of microRNA precursors. Nucleic Acids Res 32, e43.

    Article  PubMed  Google Scholar 

  66. Johnson, S. M., Grosshans, H., Shingara, J., Byrom, M., Jarvis, R., Cheng, A., Labourier, E., Reinert, K. L., Brown, D., and Slack, F. J. (2005). RAS is regulated by the let-7 microRNA family. Cell 120, 635–647.

    Article  PubMed  CAS  Google Scholar 

  67. Rajewsky, N. (2006). microRNA target predictions in animals. Nat Genet 38 Suppl, S8–S13.

    Article  PubMed  CAS  Google Scholar 

  68. Kiriakidou, M., Nelson, P. T., Kouranov, A., Fitziev, P., Bouyioukos, C., Mourelatos, Z., and Hatzigeorgiou, A. (2004). A combined computational-experimental approach predicts human microRNA targets. Genes Dev 18, 1165–1178.

    Article  PubMed  CAS  Google Scholar 

  69. 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.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  Google Scholar 

  71. Krek, A., Grun, D., Poy, M. N., Wolf, R., Rosenberg, L., Epstein, E. J., MacMenamin, P., da Piedade, I., Gunsalus, K. C., Stoffel, M., and Rajewsky, N. (2005). Combinatorial microRNA target predictions. Nat Genet ,37, 495–500.

    Article  PubMed  CAS  Google Scholar 

  72. Megraw, M., Sethupathy, P., Corda, B., and Hatzigeorgiou, A. G. (2007). miRGen: a database for the study of animal microRNA genomic organization and function. Nucleic Acids Res 35, D149–D155.

    Article  PubMed  CAS  Google Scholar 

  73. Kel, A., Voss, N., Jauregui, R., Kel-Margoulis, O., and Wingender, E. (2006). Beyond microarrays: Finding key transcription factors controlling signal transduction pathways. BMC Bioinformatics 7 Suppl 2, S13.

    Article  PubMed  Google Scholar 

  74. 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.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Experimental Therapeutics, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA

    Riccardo Spizzo

Authors
  1. Riccardo Spizzo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. George A. Calin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Riccardo Spizzo .

Editor information

Editors and Affiliations

  1. Boston Biomedical Research Institute, Grove Street 64, Watertown, 02472, U.S.A.

    Peter Erhardt

  2. Boston Biomedical Research Institute, Grove Street 64, Watertown, 02472, U.S.A.

    Ambrus Toth

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Humana Press, a part of Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Spizzo, R., Calin, G.A. (2009). Multiple Approach to Analyzing the Role of MicroRNAs in Apoptosis. In: Erhardt, P., Toth, A. (eds) Apoptosis. Methods in Molecular Biology, vol 559. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60327-017-5_16

Download citation

  • DOI: https://doi.org/10.1007/978-1-60327-017-5_16

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60327-016-8

  • Online ISBN: 978-1-60327-017-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation