Abstract
MicroRNAs (miRNAs) are single-strand nonprotein coding RAN with 18 to 25-nucleotides long. With complementary sequence to target messenger RNA (mRNA), miRNA regulates mRNA degradation and protein translation. miRNAs have been identified in various organisms ranging from virus to human. Increasing evidence indicates that mammalian gene regulation has multiple layers and the availability of mRNA is not the sole regulation mechanism. The evolutionally conserved miRNA may be a primary regulation mechanism of gene expression. Its role in directing embryo development and stem cell differentiation should not be underestimated.
Due to the small size of miRNA, identifying it with experimental approach (e.g., direct cloning) is difficult. The cell type and developmental-specific expression of miRNA make the experimental approach even more difficult. Consequently, bioinformatics approaches have been developed to identify novel miRNA. In human miRNA study, many studies search for the mostly complete human genomic sequence. Here, we report a rapid bioinformatics approach to mine miRNA from gene specific introns. Intronic miRNA may directly regulate the expression of its target genes during development. The reported bioinformatics approach not only identifies the potential miRNA, but also provides the intron location of these miRNA like sequence. This information is critical for studying the gene–gene interaction via miRNA, and facilitates the study of miRNA in gene expression regulation.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Bartel DP, Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297
Elgar G, Vavouri T, Elgar G, Vavouri T (2008) Tuning in to the signals: noncoding sequence conservation in vertebrate genomes. Trends Genet 24:344–352
Smalheiser NR, Torvik VI, Smalheiser NR, Torvik VI (2005) Mammalian microRNAs derived from genomic repeats. Trends Genet 21:322–326
Brennecke J, Hipfner DR, Stark A et al (2003) bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 113:25–36
Poy MN, Eliasson L, Krutzfeldt J et al (2004) A pancreatic islet-specific microRNA regulates insulin secretion. Nature 432:226–230
Chen CZ, Li L, Lodish HF et al (2004) MicroRNAs modulate hematopoietic lineage differentiation. Science 303:83–86
Trang P, Weidhaas JB, Slack FJ, Trang P, Weidhaas JB, Slack FJ (2008) MicroRNAs as potential cancer therapeutics. Oncogene 27(suppl 2):S52–S57
Li C, Feng Y, Coukos G et al (2009) Therapeutic microRNA strategies in human cancer. AAPS J 11:747–757
Schratt G, Schratt G (2009) microRNAs at the synapse. Nat Rev Neurosci 10:842–849
Meister G, Tuschl T, Meister G, Tuschl T (2004) Mechanisms of gene silencing by double-stranded RNA. Nature 431:343–349
Baulcombe D, Baulcombe D (2004) RNA silencing in plants. Nature 431:356–363
Mello CC, Conte D Jr, Mello CC, Conte D Jr (2004) Revealing the world of RNA interference. Nature 431:338–342
Bonci D, Coppola V, Musumeci M et al (2008) The miR-15a-miR-16-1 cluster controls prostate cancer by targeting multiple oncogenic activities. Nat Med 14:1271–1277
Klein U, Lia M, Crespo M et al (2010) The DLEU2/miR-15a/16-1 cluster controls B cell proliferation and its deletion leads to chronic lymphocytic leukemia. Cancer Cell 17:28–40
Mendell JT, Mendell JT (2008) miRiad roles for the miR-17-92 cluster in development and disease. Cell 133:217–222
Selcuklu SD, Donoghue MT, Spillane C, Selcuklu SD, Donoghue MTA, Spillane C (2009) miR-21 as a key regulator of oncogenic processes. Biochem Soc Trans 37:918–925
Tam W, Dahlberg JE, Tam W, Dahlberg JE (2006) miR-155/BIC as an oncogenic microRNA. Genes Chromosomes Cancer 45:211–212
Hermeking H, Hermeking H (2010) The miR-34 family in cancer and apoptosis. Cell Death Differ 17:193–199
Takahashi K, Tanabe K, Ohnuki M et al (2007) Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131:861–872
Suh MR, Lee Y, Kim JY et al (2004) Human embryonic stem cells express a unique set of microRNAs. Dev Biol 270:488–498
Card DA, Hebbar PB, Li L et al (2008) Oct4/Sox2-regulated miR-302 targets cyclin D1 in human embryonic stem cells. Mol Cell Biol 28:6426–6438
Anokye-Danso F, Trivedi CM, Juhr D et al (2011) Highly efficient miRNA-mediated reprogramming of mouse and human somatic cells to pluripotency. Cell Stem Cell 8:376–388
Lin SL, Chang DC, Chang-Lin S et al (2008) Mir-302 reprograms human skin cancer cells into a pluripotent ES-cell-like state. RNA 14:2115–2124
Liao B, Bao X, Liu L et al (2011) MicroRNA cluster 302–367 enhances somatic cell reprogramming by accelerating a mesenchymal-to-epithelial transition. J Biol Chem 286: 17359–17364
Ambros V, Bartel B, Bartel DP et al (2003) A uniform system for microRNA annotation. RNA 9:277–279
Lee Y, Ahn C, Han J et al (2003) The nuclear RNase III Drosha initiates microRNA processing. Nature 425:415–419
Xue C, Li F, He T et al (2005) Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinformatics 6:310
Smith SM, Murray DW (2012) An overview of microRNA methods: expression profiling and target identification. Methods in Molecular Biology 823:119–138
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Kuo, CH., Goldberg, M.D., Lin, SL., Ying, SY., Zhong, J.F. (2013). Identify Intronic MicroRNA with Bioinformatics. In: Ying, SY. (eds) MicroRNA Protocols. Methods in Molecular Biology, vol 936. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-083-0_6
Download citation
DOI: https://doi.org/10.1007/978-1-62703-083-0_6
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-082-3
Online ISBN: 978-1-62703-083-0
eBook Packages: Springer Protocols