Abstract
The microRNAs (or miRNAs) are small noncoding RNAs (21—25 nt) that are processed from large hairpin RNA precursors and are believed to be involved in a wide range of developmental and cellular processes, by either repressing translation or triggering mRNA interference (RNA interference). Over 200 of distinct genes encoding miRNAs have been identified through either computer-assisted approaches or complementary deoxyribonucleic acid cloning strategies in many organisms including worm, plants, flies, mouse, and human. Recently, a microarray based robust method to profile miRNAs expression in organs cell lines and tissues in mammalians were developed (1). Using this method, we have identified a group of miRNAs preferentially expressed in human primary adipocytes and knocking down one such miRNA (miRNA 143) reverses the differentiation process (2). Groups of kidney specific miRNAs share evolutionary conserved phylogenetic foot print Ets1 in the upstream of the miRNA, possibly important for kidney physiological maintenance were reported. A detail protocol of the method are discussed to develop miRNA profile for global gene expression in tissues, organs, and cell lines in eukaryotes.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Yingqing, S., Seongjoon, K., Neill, W., et al. (2004) Development of a microarray to detect human and mouse microRNAs and characterization of expression in human organs. Nucleic Acid Res. 32, E188.
Esau, C., Kang, X., Peralta, E., et al. (2004) MicroRNA-143 regulates adipocyte differentiation. MicroRNA-143 regulates adipocyte differentiation. J. Biol. Chem. 10, 52,361–52,365.
Ambros, V. (2003) MicroRNA pathways in flies and worms: growth, death, fat, stress, and timing. Cell 113, 673–676.
Bartel, B. and Bartel, D. P. (2003) MicroRNAs: at the root of plant development? Plant Physiol. 132, 709–717.
Palatnik, J. F., Allen, E., Wu, X., et al. (2003) Control of leaf morphogenesis by microRNAs. Nature 425, 257–263.
Bartel, D. P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281–297.
Pasquinelli, A. E., Reinhart, B. J., Slack, F., et al. (2000) Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408, 86–89.
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.
Reinhart, B. J., Weinstein, E. G., Rhoades, M. W., Bartel, B., and Bartel, D. P. (2002) MicroRNAs in plants. Genes Dev. 16, 1616–1626.
Lim, L. P., Glasner, M. E., Yekta, S., Burge, C. B., and Bartel, D. P. (2003) Vertebrate microRNA genes. Science 299, 1540.
Lim, L. P., Lau, N. C., Weinstein, E. G., et al. (2003) The microRNAs of Caenorhabditis elegans. Genes Dev. 17, 991–1008.
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.
Grad, Y., Aach, J., Hayes, G. D., et al. (2003) Computational and experimental identification 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.
Lee, R. C. and Ambros, V. (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294, 862–864.
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.
Lagos-Quintana, M., Rauhut, R., Meyer, J., Borkhardt, A., and Tuschl, T. (2003) New microRNAs from mouse and human. RNA 9, 175–179.
Mourelatos, Z., Dostie, J., Paushkin, S., et al. (2002) miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev. 16, 720–728.
Dostie, J., Mourelatos, Z., Yang, M., Sharma, A., and Dreyfuss, G. (2003) Numerous microRNPs in neuronal cells containing novel microRNAs. RNA 9, 180–186.
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.
Lai, E. C., Tomancak, P., Williams, R. W., and Rubin, G. M. (2003) Computational identification of Drosophila microRNA genes. Genome Biol. 4, R42.
Calin, G. A., Sevignani, C., Dumitru, C. D., et al. (2004) Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc. Natl. Acad. Sci. USA 101, 2999–3004.
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.
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.
Calin, G. A., Liu, C. G., Sevignani, C., et al. (2004) MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. Proc. Natl. Acad. Sci. USA 101, 11,755–11,760.
Babak, T., Zhang, W., Morris, Q., Blencowe, B. J., and Hughes, T. R. (2004) Probing microRNAs with microarrays: tissue specificity and functional inference. RNA 10, 1813–1819.
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.
Thomson, J. M., Parker, J., Perou, C. M., and Hammond, S. M. (2004) A custom microarray platform for analysis of microRNA gene expression. Nat. Methods 1, 47–53.
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 2, 155–161.
Esquela-Kerscher, A. and Slack, F. J. (2004) The age of high-throughput microRNA profiling. Nat. Methods 2, 106–107.
Rosner, B. (2000) Fundamentals of Biostatistics. Duxbury, New York.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Humana Press Inc., Totowa, NJ
About this protocol
Cite this protocol
Perera, R.J. (2007). A Microarray-Based Method to Profile Global microRNA Expression in Human and Mouse. In: Rampal, J.B. (eds) Microarrays. Methods in Molecular Biology, vol 382. Humana Press. https://doi.org/10.1007/978-1-59745-304-2_9
Download citation
DOI: https://doi.org/10.1007/978-1-59745-304-2_9
Publisher Name: Humana Press
Print ISBN: 978-1-58829-944-4
Online ISBN: 978-1-59745-304-2
eBook Packages: Springer Protocols