Abstract
MicroRNAs (miRNAs), an abundant class of approx 22-nucleotide (nt) small RNAs that control gene expression at the posttranscriptional level, may play important roles during normal hematopoiesis and leukemogenesis. This chapter focuses on the methods and strategies for dissecting miRNA function during hematopoietic lineage differentiation. We describe a modified miRNA cloning method and expression analysis approach for determining miRNA expression during hematopoietic lineage differentiation. We illustrate a retroviral vector and a general strategy for the ectopic expression of miRNAs in hematopoietic stem/progenitor cells. We discuss in vitro and in vivo functional assays that can be used to examine the roles of miRNAs during hematopoietic lineage differentiation. The methods and principles described here should also be applicable to study the roles of miRNAs in the differentiation and function of nonhematopoietic cell types.
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References
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.
Wightman, B., Ha, I.and Ruvkun, G. (1993) Posttranscriptional regulation of the hetero-chronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75, 855–862.
Ambros, V. (2003) MicroRNA pathways in flies and worms: growth, death, fat, stress, and timing. Cell 113, 673–676.
Bartel, D. P. and Chen, C. Z. (2004) Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat. Rev. Genet. 5, 396–400.
Bartel, D. P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281–297.
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.
Lagos-Quintana, M., Rauhut, R., Meyer, J., Borkhardt, A., and Tuschl, T. (2003) New microRNAs from mouse and human. RNA 9, 175–179.
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.
Mourelatos, Z., Dostie, J., Paushkin, S., et al. (2002) miRNPs: a novel class of ribonucle-oproteins containing numerous microRNAs. Genes Dev. 16, 720–728.
Ambros, V., Lee, R. C., Lavanway, A., Williams, P. T., and Jewell, D. (2003) MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr. Biol. 13, 807–818.
Dostie, J., Mourelatos, Z., Yang, M., Sharma, A., and Dreyfuss, G. (2003) Numerous microRNPs in neuronal cells containing novel microRNAs. RNA 9, 180–186.
Houbaviy, H. B., Murray, M. F., and Sharp, P. A. (2003) Embryonic stem cell-specific MicroRNAs. Dev. Cell 5, 351–358.
Michael, M. Z., O’Connor, S. M., van Holst Pellekaan N. G., Young G. P., and James R. J. (2003) Reduced accumulation of specific microRNAs in colorectal neoplasia. Mol. Cancer Res. 1, 882–891.
Lim, L. P., Lau, N. C., Weinstein, E. G., et al. (2003) The microRNAs of Caenorhabditis elegans. Genes Dev. 17, 991–1008.
Lim, L. P., Glasner, M. E., Yekta, S., Burge, C. B., and Bartel, D. P. (2003) Vertebrate microRNA genes. Science 299, 1540.
Lai, E. C., Tomancak, P., Williams, R. W., and Rubin, G. M. (2003) Computational iden-tification of Drosophila microRNA genes. Genome Biol. 4, R42.
Grad, Y., Aach, J., Hayes, G. D., et al. (2003) Computational and experimental identifica-tion of C. elegans microRNAs. Mol. Cell 11, 1253–1263.
Kim, J., Krichevsky, A., Grad, Y., et al. 2004 Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc. Natl. Acad. Sci. USA 101, 360–365.
Aukerman, M. J. and Sakai, H. (2003) Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell 15, 2730–2741.
Chen, X. (2004) A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303, 2022–2025.
Emery, J. F., Floyd, S. K., Alvarez, J., et al. (2003) Radial patterning of Arabidopsis shoots by class III HD-ZIP and KANADI genes. Curr. Biol. 13, 1768–1774.
Palatnik, J. F., Allen, E., Wu, X., et al. (2003) Control of leaf morphogenesis by microRNAs. Nature 425, 257–263.
Reinhart, B. J., Slack, F. J., Basson, M., et al. (2000) The 21 nucleotide let-7 RNA regu-lates developmental timing in Caenorhabditis elegans. Nature 403, 901–906.
Pasquinelli, A. E., Reinhart, B. J., Slack, F., et al. (2000) Conservation across animal phylogeny of the sequence and temporal regulation of the 21 nucleotide let-7 heterochronic regulatory RNA. Nature 408, 86–89.
Chang, S., Johnston, R. J. Jr., Frokjaer-Jensen, C., Lockery, S., and Hobert, O. (2004) MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode. Nature 430, 785–789.
Johnston, R. J. and Hobert, O. (2003) A microRNA controlling left/right neuronal asym-metry in Caenorhabditis elegans. Nature 426, 845–849.
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 regu-lates the proapoptotic gene hid in Drosophila. Cell 113, 25–36.
Hipfner, D. R., Weigmann, K., and Cohen, S. M. (2002) The bantam gene regulates Droso-phila growth. Genetics 161, 1527–1537.
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.
Chen, C. Z., Li, L., Lodish, H. F., and Bartel, D. P. (2004) MicroRNAs modulate hemato-poietic lineage differentiation. Science 303, 83–86.
Poy, M. N., Eliasson, L., Krutzfeldt, J., et al. (2004) A pancreatic islet-specific microRNA regulates insulin secretion. Nature 432, 226–230.
Esau, C., Kang, X., Peralta, E., et al. (2004) MicroRNA-143 regulates adipocyte differen-tiation. J. Biol. Chem. 279, 52,361–52,365.
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.
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.
Stark, A., Brennecke, J., Russell, R. B., and Cohen, S. M. (2003) Identification of Droso-phila MicroRNA Targets. PLoS Biol. 1, E60.
Lai, E. C. (2004) Predicting and validating microRNA targets. Genome Biol. 5, 115.
John, B., Enright, A. J., Aravin, A., Tuschl, T., Sander, C., and Marks, D. S. (2004) Human MicroRNA targets. PLoS Biol. 2, e363.
Kiriakidou, M., Nelson, P. T., Kouranov, A., et al. (2004) A combined computational-experimental approach predicts human microRNA targets. Genes Dev. 18, 1165–1178.
Enright, A. J., John, B., Gaul, U., Tuschl, T., Sander, C., and Marks, D. S. (2003) MicroRNA targets in Drosophila. Genome Biol. 5, R1.
Rajewsky, N. and Socci, N. D. (2004) Computational identification of microRNA targets. Dev. Biol. 267, 529–535.
Krek, A., Grun, D., Poy, M. N., et al. (2005) Combinatorial microRNA target predictions. Nat. Genet. 37, 495–500.
Naviaux, R. K., Costanzi, E., Haas, M., and Verma, I. M. (1996) The pCL vector system: rapid production of helper-free, high-titer, recombinant retroviruses. J. Virol. 70, 5701–5705.
Liang, R. Q., Li, W., Li, Y., et al. (2005) An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe. Nucleic Acids Res. 33, e17.
Baskerville, S. and Bartel, D. P. (2005) Microarray profiling of microRNAs reveals fre-quent coexpression with neighboring miRNAs and host genes. RNA 11, 241–247.
Sioud, M. and Rosok, O. (2004) Profiling microRNA expression using sensitive cDNA probes and filter arrays. Biotechniques 37, 574–576, 578-580.
Miska, E. A., Alvarez-Saavedra, E., Townsend, M., et al. (2004) Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biol. 5, R68.
Liu, C. G., Calin, G. A., Meloon, B., et al. (2004) An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc. Natl. Acad. Sci. USA 101, 9740–9744.
Barad, O., Meiri, E., Avniel, A., et al. (2004) MicroRNA expression detected by oligo-nucleotide microarrays: system establishment and expression profiling in human tissues. Genome Res. 14, 2486–2494.
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.
Allawi, H. T., Dahlberg, J. E., Olson, S., et al. (2004) Quantitation of microRNAs using a modified Invader assay. RNA 10, 1153–1161.
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.
Aravin, A. A., Lagos-Quintana, M., Yalcin, A., et al. (2003) The small RNA profile dur-ing Drosophila melanogaster development. Dev. Cell 5, 337–350.
Pui, J. C., Allman, D., Xu, L., et al. (1999) Notch1 expression in early lymphopoiesis influ-ences B versus T lineage determination. Immunity 11, 299–308.
Shivdasani, R. A. and Orkin, S. H. (1996) The transcriptional control of hematopoiesis. Blood 87, 4025–4039.
Gauwerky, C. E. and Croce, C. M. (1993) Chromosomal translocations in leukaemia. Semin. Cancer Biol. 4, 333–340.
Maillard, I., Adler, S. H., and Pear, W. S. (2003) Notch and the immune system. Immunity 19, 781–791.
Lee, Y., Ahn, C., Han, J., et al. (2003) The nuclear RNase III Drosha initiates microRNA processing. Nature 425, 415–419.
Denli, A. M., Tops, B. B., Plasterk, R. H., Ketting, R. F., and Hannon, G. J. (2004) Processing of primary microRNAs by the Microprocessor complex. Nature 432, 231–235.
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.
Lund, E., Guttinger, S., Calado, A., Dahlberg, J. E., and Kutay, U. (2004) Nuclear export of microRNA precursors. Science 303, 95–98.
Grishok, A., Pasquinelli, A. E., Conte, D., et al. (2001) Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106, 23–24.
Ketting, R. F., Fischer, S. E., Bernstein, E., Sijen, T., Hannon, G. J., and Plasterk, R. H. (2001) Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev. 15, 2654–2659.
Hutvágner, 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 293, 834–838.
Metcalf, D. and Nicola, N. A. (1995) The Hematopoietic Colony-Stimulating Factors. In: Biology to Clinical Applications, Cambridge University Press Cambridge, UK.
Eaves, A. C. and Eaves, C. J. (1988) Maintenance and proliferation control of primitive hemopoietic progenitors in long-term cultures of human marrow cells. Blood Cells 14, 355–368.
Collins, L. S. and Dorshkind, K. (1987) A stromal cell line from myeloid long-term bone marrow cultures can support myelopoiesis and B lymphopoiesis. J. Immunol. 138, 1082–1087.
Nakano, T., Kodama, H., and Honjo, T. (1994) Generation of lymphohematopoietic cells from embryonic stem cells in culture. Science 265, 1098–1101.
Jenkinson, E. J. and Anderson, G. (1994) Fetal thymic organ cultures. Curr. Opin. Immu-nol. 6, 293–297.
Hare, K. J., Jenkinson, E. J., and Anderson, G. (1999) In vitro models of T cell develop-ment. Semin. Immunol. 11, 3–12.
Schmitt, T. M., de Pooter, R. F., Gronski, M. A., Cho, S. K., Ohashi, P. S., and Zuniga-Pflucker, J. C. (2004) Induction of T cell development and establishment of T cell compe-tence from embryonic stem cells differentiated in vitro. Nat. Immunol. 5, 410–417.
Chen, C. Z., Li, L., Li, M., and Lodish, H. F. (2003) The endoglin (positive) sca-1(posi-tive) rhodamine(low) phenotype defines a near-homogeneous population of long-term repopulating hematopoietic stem cells. Immunity 19, 525–533.
Chen, C. Z., Li, M., de Graaf, D., et al. (2002) Identification of endoglin as a functional marker that defines long-term repopulating hematopoietic stem cells. Proc. Natl. Acad. Sci. USA 99, 15,468–15,473.
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Min, H., Chen, CZ. (2006). Methods for Analyzing MicroRNA Expression and Function During Hematopoietic Lineage Differentiation. In: Ying, SY. (eds) MicroRNA Protocols. Methods in Molecular Biology™, vol 342. Humana Press. https://doi.org/10.1385/1-59745-123-1:209
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DOI: https://doi.org/10.1385/1-59745-123-1:209
Publisher Name: Humana Press
Print ISBN: 978-1-58829-581-1
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