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Profiling of regulatory microRNA transcriptomes in various biological processes: a review

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Abstract

A class of small, non-coding ribonucleic acids, termed microRNA (miRNA), has recently emerged as a new key player in the cellular control of gene expression. By either blocking translation or inducing target mRNA degradation, miRNA not only participates in regular biological processes within cells and tissues but is also involved in pathological processes. Many human malignancies have been linked to specific miRNA expression patterns, raising hopes for new approaches to therapy. While such human disease-related mechanisms have been widely discussed and frequently reviewed, miRNA’s general significance in animals has been less in editorial focus, despite its obvious role in basic physiological processes, e.g. neurosensory maturation, development of fertility, and hibernation. Using selected examples, this review highlights our current knowledge of miRNA’s potential and its promise as a new tool for gene regulation.

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References

  • Agami R, 2010. miRNAs, RNA binding proteins and cancer. Eur J Clin Invest 40: 370–374.

    Article  CAS  PubMed  Google Scholar 

  • Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, et al. 2003. A uniform system for microRNA annotation. RNA 9: 277–279.

    Article  CAS  PubMed  Google Scholar 

  • Ambros V, Chen X, 2007. The regulation of genes and genomes by small RNAs. Development 134: 1635–1641.

    Article  CAS  PubMed  Google Scholar 

  • Armisen J, Gilchrist MJ, Wilczynska A, Standart N, Miska EA, 2009. Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrateXenopus tropicalis. Genome Res 19: 1766–1775.

    Article  CAS  PubMed  Google Scholar 

  • Backes C, Meese E, Lenhof H-P, Keller A, 2010. A dictionary on microRNAs and their putative target pathways. Nucl Acids Res doi: 10.1093/nar/gkq167.

  • Bartel, DP, 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281–297.

    Article  CAS  PubMed  Google Scholar 

  • Baskerville S, Bartel DP, 2005. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11: 241–247.

    Article  CAS  PubMed  Google Scholar 

  • Bates DJ, Li N, Liang R, Sarojini H, An J, Masternak MM, et al. 2010. MicroRNA regulation in Ames dwarf mouse liver may contribute to delayed aging. Aging Cell 9: 1–18.

    Article  CAS  PubMed  Google Scholar 

  • Calin GA, Dumitru CD, Shimizu M, Bichi R, Zupo S, Noch E, et al. 2002. Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci USA 99: 15524–15529.

    Article  CAS  PubMed  Google Scholar 

  • Castro F, Sharbati S, Rodriguez-Alvarez LL, Cox JF, Hultschig C, Einspanier R, 2010. MiRNA expression profiling of elongated cloned and in vitro-fertilized bovine embryos. Theriogenelogy 73: 71–85.

    Article  CAS  Google Scholar 

  • Chen CZ, Li L, Lodish HF, Bartel DP, 2004. MicroRNAs modulate hematopoietic lineage differentiation. Science 303: 83–86.

    Article  CAS  PubMed  Google Scholar 

  • Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, at al. 2005. The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes Dev 19: 1288–1293.

    Article  CAS  PubMed  Google Scholar 

  • DeGuire V, Caron M, Scott N, Menard C, Gaumont-Leclerc M-F, Chartrand P, et al. 2010. Designing small multiple-target artificial RNAs. Nucl Acids Res doi:10.1093/nar/gkq354.

  • Di Leva G, Croce CM, 2010. Roles of small RNAs in tumor formation. Trends Mol Med 16: 257–267.

    Article  PubMed  CAS  Google Scholar 

  • Friedländer MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S, et al. 2008. Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 26: 407–415.

    Article  PubMed  CAS  Google Scholar 

  • Friedman LM, Dror AA, Mor E, Tenne T, Toren G, Satoh T, et al. 2009. MicroRNAs are essential for development and function of inner ear hair cells in vertebrates. Proc Natl Acad Sci USA 106: 7915–7920.

    Article  CAS  PubMed  Google Scholar 

  • Garzon R, Liu S, Fabbri M, Liu Z, Heaphy CEA, Callegari E, et al. 2009. MicroRNA-29b induces global DNA hypomethylation and tumor suppressor gene reexpression in acute myeloid leukemia by targeting directly DNMT3A and 3B and indirectly DNMT1. Blood 113: 6411–6418. Hoffman AE, Zheng T, Yi C, Leaderer D, Weidhaas J,

    Article  CAS  PubMed  Google Scholar 

  • Slack F, et al. 2009. microRNA miR-196a-2 and breast cancer: a genetic and epigenetic association study and functional analysis. Cancer Res 69: 5970–5977.

    Article  PubMed  CAS  Google Scholar 

  • Hsu S-D, Chu C-H, Tsou A-P, Chen S-J, Chen H-C, Hsu P, et al. 2008. miRNAMap 2.0: genomic maps of miRNAs in metazoan genomes. Nucl Acids Res 36: D165-D169.

    Article  CAS  PubMed  Google Scholar 

  • Huang Z, Huang D, Ni S, Peng Z, Sheng W, Du X, 2010. Plasma microRNAs are promising novel biomarkers for early detection of colorectal cancer. Int J Cancer 127: 118–126.

    CAS  PubMed  Google Scholar 

  • Hwang JH, Voortman J, Giovannetti E, Steinberg SM, Leon LG, Kim YT, et al. 2010. Identification of microRNA-21 as a biomarker for chemoresistance and clinical outcome following adjuvant therapy in resectable pancreatic cancer. PLoS One 5: e10630.

    Article  CAS  Google Scholar 

  • Jiang X, Tsitsiou E, Herrick S, Lindsay MA, 2010. miRNAs and the regulation of fibrosis. FEBS 277: 2015–2021.

    Article  CAS  Google Scholar 

  • Kanwar JR, Mahidhara G, Kanwar RK, 2010. miRNA in human cancer and chromic inflammatory diseases. Front Biosci 2: 1113–1126.

    Google Scholar 

  • Keller A, Leidinger P, Borries A, Wendschlag A, Wucherpfennig F, Scheffler M, et al. 2009. miRNAs in lung cancer — studying complex fingerprints in patient’s blood cells by microarray experiments. BMC Cancer 9: 353.

    Article  PubMed  CAS  Google Scholar 

  • Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T, 2002. Identification of tissue-specific microRNAs from mouse. Curr Biol 12: 735–739.

    Article  CAS  PubMed  Google Scholar 

  • Lai EC, Tomancak P, Williams RW, Rubin GM, 2003. Computational identification ofDrosophila microRNA genes. Genome Biol 4: R42.

    Article  Google Scholar 

  • Lau NC, Lim LP, Weinstein EG, Bartel DP, 2001. An abundant class of tiny RNAs with probable regulatory roles inCaenorhabditis elegans. Science 294: 858–862.

    Article  CAS  PubMed  Google Scholar 

  • Lee RC, Ambros V, 2001. An extensive class of small RNAs inCaenorhabditis elegans. Science 294: 862–864.

    Article  CAS  PubMed  Google Scholar 

  • Lee RC, Feinbaum RL, Ambros V, 1993. TheC. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843–854.

    Article  CAS  PubMed  Google Scholar 

  • Li L, Chen X-P, Li Y-J, 2010. miRNA-146a and human disease. Scan J Immunol 71: 227–231.

    Article  CAS  Google Scholar 

  • Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP, 2003a. Vertebrate microRNA genes. Science 299: 1540.

    Article  CAS  PubMed  Google Scholar 

  • Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, et al. 2003b. The microRNAs ofCaenorhabditis elegans. Genes Dev 17: 991–1008.

    Article  CAS  PubMed  Google Scholar 

  • LiuY,HuW,WangH,LuM,ShaoC,MenzelC,et al.2010. Genomic analysis of miRNAs in an extreme mammalian hibernator, the Arctic ground squirrel. Physiol Genomics doi:10.1152/physiolgenomics.00054.

  • Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, Green PJ, 2005. Elucidation of the small RNA component of the transcriptome. Science 309: 1567–1569.

    Article  CAS  PubMed  Google Scholar 

  • Lu S, Sun YH, Shi R, Clark C, Li L, Chiang VL, 2005. Novel and mechanical stress-responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell 17: 2186 -2203.

    Article  CAS  PubMed  Google Scholar 

  • Lubka M, Müller M, Baus-Lonèar M, Hinz M, Blaschke K, Hoffmann W, et al. 2008. Lack of cytoprotective trefoil peptide 3 results in hearing impairment and accelerated presbyacusis. Cell Physiol Biochem 21: 437–444.

    Article  CAS  PubMed  Google Scholar 

  • Ma J, Dong C, Ji C, 2010. MicroRNA and drug resistance. Cancer Gene Ther 17: 523–531.

    Article  CAS  PubMed  Google Scholar 

  • Mavrakis KJ, Wendel HG, 2010. TargetScreen: an unbiased approach to identify functionally important microRNA targets. Cell Cycle 9: 2080–2084.

    Article  CAS  Google Scholar 

  • Michalak P, Malone JH, 2008. Testis-derived miRNA profiles of African clawed frogs (Xenopus) and their sterile hybrids. Genomics 91: 158–164.

    Article  CAS  PubMed  Google Scholar 

  • Mishra PJ, Bertino JR, 2009. MicroRNA polymorphisms: the future of pharmacogenomics, molecular epidemiology and individualized medicine. Pharmacogenomics 10: 399–416.

    Article  CAS  PubMed  Google Scholar 

  • Miska EA, Alvarez-Saavedra E, Townsend M, Yoshii A, Sestan N, Rakic P, et al. 2004. Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biol. 5: R68-R68.

    Article  PubMed  Google Scholar 

  • Pan W, Zhu S, Yuan M, Cui H, Wang L, Luo X, et al. 2010. MicroRNA-148a Contribute to DNA hypomethylation in lupus CD4+ T cells by directly and indirectly targeting DNA methyltransferase 1. J Immunol 184: 6773–6781.

    Article  CAS  PubMed  Google Scholar 

  • Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, et al. 2000. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408: 86–89.

    Article  CAS  PubMed  Google Scholar 

  • Ruvkun G, Wightman B, Ha I, 2004. The 20 years it took to recognize the importance of tiny RNAs. Cell 23: S116: S93–S96.

    Google Scholar 

  • Ryan BM, Robles AI, Harris CC, 2010. Genetic variation in miRNA networks: implications for cancer research. Nat Rev Cancer 10: 389–402.

    Article  CAS  PubMed  Google Scholar 

  • Sethupathy P, Corda B, Hatzigeorgiou AG, 2006. TarBase: a comprehensive database of experimentally supported animal miRNA targets. RNA 12: 192–197.

    Article  CAS  PubMed  Google Scholar 

  • Shah AA, Leidinger P, Blin N, Meese E, 2010. miRNA: Small molecules as potential novel biomarkers in cancer. Curr Med Chem (in press).

  • Sharbati S, Friedländer MR, Sharbati J, Hoeke L, Chen W, Keller A, et al. 2010. Deciphering the porcine intestinal microRNA transcriptome. BMC Genomics. 11: 275. Slaby O, Lakomy R, Fadrus P, Hrstka R, Kren L,

    Article  PubMed  CAS  Google Scholar 

  • Lzicarova E, et al. 2010. MicroRNA-181 family predicts response to concomitant chemoradiotherapy with temozolomide in glioblastoma patients. Neoplasma 57: 264–269.

    Article  PubMed  CAS  Google Scholar 

  • Vaz C, Ahmad HM, Sharma P, Gupta R, Kumar L, Kulshreshtha R, et al. 2010. Analysis of miRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood. BMC Genomics 11: 288.

    Article  PubMed  CAS  Google Scholar 

  • Waldman, S.A. and Terzic, A, 2009. Application of microRNA in cancer: Exploring the advantages of miRNA. Clinical and Translational Science 2: 248–249.

    Article  CAS  PubMed  Google Scholar 

  • Wang W-C, Lin F-M, Chang W-C, Lin K-Y, Huang HD, Lin NS, 2009. miREXpress: analyzing high-throughput sequencing data for profiling miRNA expression. BMC Bioinformatics 10: 328.

    Article  PubMed  CAS  Google Scholar 

  • Wang X, Zhang J, Li F, Gu J, He T, Zhang X, Li Y, 2005. MicroRNA identification based on sequence and structure alignment. Bioinformatics 21: 3610–3614.

    Article  CAS  PubMed  Google Scholar 

  • Weston MD, Pierce ML, Rocha-Sanchez S, Beisel KW, Soukup GA, 2006. MiRNA gene expression in the mouse inner ear. Brain Res 1111: 95–104.

    Article  CAS  PubMed  Google Scholar 

  • Wienholds E, Kloosterman WP, Miska E, Alvarez-Saavedra E, Berezikov E, de Bruijn E, et al. 2005. MicroRNA expression in zebrafish embryonic development. Science 309: 310–311.

    Article  CAS  PubMed  Google Scholar 

  • Wightman B, Ha I, 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  CAS  PubMed  Google Scholar 

  • Yan N, Ma K, Ma J, Chen W, Wang Y, Cao G, et al. 2010. Profiling microRNAs differentially expressed in rabbit retina. Adv Exp Med Biol 664: 203–209.

    Article  CAS  PubMed  Google Scholar 

  • Zhang L, Hammell M, Kudlow BA, Ambros V, Han M, 2009. Systematic analysis of dynamic miRNA-target interactions during C.elegans development. Development 136: 3043–3055.

    Article  CAS  PubMed  Google Scholar 

  • Zhu E, Zhao F, Xu G, Hou H, Zhou L, Li X, et al. 2010. mirTools: miRNA profiling and discovery based on high-throughput sequencing. Nucl Acids Res doi:10.1093/nar/gkq393.

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Authors and Affiliations

  1. Division of Molecular Genetics, Institute of Human Genetics, University of Tübingen, Wilhelmstr. 27, 72074, Tübingen, Germany

    A. A. Shah & N. Blin

  2. Institute of Human Genetics, University of Saarland, Homburg, Germany

    E. Meese

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  1. A. A. Shah
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  2. E. Meese
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  3. N. Blin
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Correspondence to N. Blin.

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Shah, A.A., Meese, E. & Blin, N. Profiling of regulatory microRNA transcriptomes in various biological processes: a review. J Appl Genet 51, 501–507 (2010). https://doi.org/10.1007/BF03208880

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