Exceptional stories of microRNAs

Experimental Biology and Medicine

Volumn 238, Issue 4, 2013, Pages 339-343

  Lee, Heon Jin ^a  

^a Kyungpook National University   (South Korea)

Author keywords

Ago; Dicer; Drosha; miRNA; siRNA

Indexed keywords

GENOMIC DNA; MICRORNA; MICRORNA 29B; RNA POLYMERASE II; SMALL NUCLEOLAR RNA;

3' UNTRANSLATED REGION; ALGORITHM; APOPTOSIS; BIOGENESIS; CYTOPLASM; EUKARYOTIC CELL; GENE EXPRESSION; HUMAN; KNOCKOUT MOUSE; NONHUMAN; PROTEIN SYNTHESIS; REGULATOR GENE; REVIEW; RNA PROCESSING; VIRUS CELL TRANSFORMATION;

AGO; DICER; DROSHA; MIRNA; SIRNA;

3' UNTRANSLATED REGIONS; ANIMALS; GENE EXPRESSION REGULATION; HUMANS; INTRONS; MICRORNAS; RIBONUCLEASE III; RIBONUCLEASES; RNA INTERFERENCE;

EID: 84880449626     PISSN: 15353702     EISSN: 15353699     Source Type: Journal    
DOI: 10.1258/ebm.2012.012251     Document Type: Review

References (56)

1. Mattick JS, Makunin IV. Small regulatory RNAs in mammals. Hum Mol Genet 2005;14:R121-32.
2. Eckstein F. Small non-coding RNAs as magic bullets. Trends Biochem Sci 2005;30:445-52.
3. Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN. MicroRNA genes are transcribed by RNA polymerase II. EMBO J 2004;23:4051-60.
4. Tomari Y, Zamore PD. MicroRNA biogenesis: drosha can't cut it without a partner. Curr Biol 2005;15:R61-4.
5. Cullen BR. Transcription and processing of human microRNA precursors. Mol Cell 2004;16:861-5.
6. Ouellet DL, Perron MP, Gobeil LA, Plante P, Provost P. MicroRNAs in gene regulation: when the smallest governs it all. J Biomed Biotechnol 2006;2006:69616.
7. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004;116:281-97.
8. Lee R, Feinbaum R, Ambros V. A short history of a short RNA. Cell 2004;116:S89-92, 1 p following S6.
9. Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993;75:843-54.
10. Wightman B, Ha I, Ruvkun G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 1993;75:855-62.
11. Zamore PD, Haley B. Ribo-gnome: the big world of small RNAs. Science 2005;309:1519-24.
12. Lee HJ, Palkovits M, Young WS III. miR-7b, a microRNA up-regulated in the hypothalamus after chronic hyperosmolar stimulation, inhibits Fos translation. Proc Natl Acad Sci USA 2006;103:15669-74.
13. Lee I, Ajay SS, Yook JI, Kim HS, Hong SH, Kim NH, Dhanasekaran SM, Chinnaiyan AM, Athey BD. New class of microRNA targets containing simultaneous 5′-UTR and 3′-UTR interaction sites. Genome Res 2009;19:1175-83.
14. Place RF, Li LC, Pookot D, Noonan EJ, Dahiya R. MicroRNA-373 induces expression of genes with complementary promoter sequences. Proc Natl Acad Sci USA 2008;105:1608-13.
15. Qin W, Shi Y, Zhao B, Yao C, Jin L, Ma J, Jin Y. miR-24 regulates apoptosis by targeting the open reading frame (ORF) region of FAF1 in cancer cells. PLoS ONE 2010;5:e9429.
16. Tay Y, Zhang J, Thomson AM, Lim B, Rigoutsos I. MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature 2008;455:1124-8.
17. Forman JJ, Legesse-Miller A, Coller HA. A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence. Proc Natl Acad Sci USA 2008;105:14879-84.
18. Medema RH. Optimizing RNA interference for application in mammalian cells. Biochem J 2004;380:593-603.
19. Li LC, Okino ST, Zhao H, Pookot D, Place RF, Urakami S, Enokida H, Dahiya R. Small dsRNAs induce transcriptional activation in human cells. Proc Natl Acad Sci USA 2006;103:17337-42.
20. Huang V, Qin Y, Wang J, Wang X, Place RF, Lin G, Lue TF, Li LC. RNAa is conserved in mammalian cells. PLoS ONE 2010;5:e8848.
21. Hwang HW, Wentzel EA, Mendell JT. A hexanucleotide element directs microRNA nuclear import. Science 2007;315:97-100.
22. McCarthy JJ. MicroRNA-206: the skeletal muscle-specific myomiR. Biochim Biophys Acta 2008;1779:682-91.
23. Politz JC, Hogan EM, Pederson T. MicroRNAs with a nucleolar location. RNA 2009;15:1705-15.
24. Ender C, Krek A, Friedlander MR, Beitzinger M, Weinmann L, Chen W, Pfeffer S, Rajewsky N, Meister G. A human snoRNA with microRNA-like functions. Mol Cell 2008;32:519-28.
25. Lung B, Zemann A, Madej MJ, Schuelke M, Techritz S, Ruf S, Bock R, Huttenhofer A. Identification of small non-coding RNAs from mitochondria and chloroplasts. Nucleic Acids Res 2006; 34:3842-52.
26. Kren BT, Wong PY, Sarver A, Zhang X, Zeng Y, Steer CJ. MicroRNAs identified in highly purified liver-derived mitochondria may play a role in apoptosis. RNA Biol 2009;6:65-72.
27. Park NJ, Zhou H, Elashoff D, Henson BS, Kastratovic DA, Abemayor E, Wong DT. Salivary microRNA: discovery, characterization, and clinical utility for oral cancer detection. Clin Cancer Res 2009;15:5473-7.
28. Mitchell PS, Parkin RK, Kroh EM, Fritz BR, Wyman SK, Pogosova-Agadjanyan EL, Peterson A, Noteboom J, O'Briant KC, Allen A, Lin DW, Urban N, Drescher CW, Knudsen BS, Stirewalt DL, Gentleman R, Vessella RL, Nelson PS, Martin DB, Tewari M. Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci USA 2008;105:10513-8.
29. Kosaka N, Iguchi H, Yoshioka Y, Takeshita F, Matsuki Y, Ochiya T. Secretory mechanisms and intercellular transfer of microRNAs in living cells. J Biol Chem 2010;285:17442-52.
30. Zhang Y, Liu D, Chen X, Li J, Li L, Bian Z, Sun F, Lu J, Yin Y, Cai X, Sun Q, Wang K, Ba Y, Wang Q, Wang D, Yang J, Liu P, Xu T, Yan Q, Zhang J, Zen K, Zhang CY. Secreted monocytic miR-150 enhances targeted endothelial cell migration. Mol Cell 2010;39:133-44.
31. Chong MM, Zhang G, Cheloufi S, Neubert TA, Hannon GJ, Littman DR. Canonical and alternate functions of the microRNA biogenesis machinery. Genes Dev 2010;24:1951-60.
32. Yang JS, Lai EC. Alternative miRNA biogenesis pathways and the interpretation of core miRNA pathway mutants. Mol Cell 2011;43:892-903.
33. Bernstein E, Kim SY, Carmell MA, Murchison EP, Alcorn H, Li MZ, Mills AA, Elledge SJ, Anderson KV, Hannon GJ. Dicer is essential for mouse development. Nat Genet 2003;35:215-7.
34. Chen JF, Murchison EP, Tang R, Callis TE, Tatsuguchi M, Deng Z, Rojas M, Hammond SM, Schneider MD, Selzman CH, Meissner G, Patterson C, Hannon GJ, Wang DZ. Targeted deletion of Dicer in the heart leads to dilated cardiomyopathy and heart failure. Proc Natl Acad Sci USA 2008;105:2111-6.
35. Cuellar TL, Davis TH, Nelson PT, Loeb GB, Harfe BD, Ullian E, McManus MT. Dicer loss in striatal neurons produces behavioral and neuroanatomical phenotypes in the absence of neurodegeneration. Proc Natl Acad Sci USA 2008;105:5614-9.
36. Cifuentes D, Xue H, Taylor DW, Patnode H, Mishima Y, Cheloufi S, Ma E, Mane S, Hannon GJ, Lawson ND, Wolfe SA, Giraldez AJ. A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity. Science 2010;328:1694-8.
37. Cheloufi S, Dos Santos CO, Chong MM, Hannon GJ. A dicerindependent miRNA biogenesis pathway that requires Ago catalysis. Nature 2010;465:584-9.
38. Ruby JG, Jan CH, Bartel DP. Intronic microRNA precursors that bypass Drosha processing. Nature 2007;448:83-6.
39. Kim VN, Nam JW. Genomics of microRNA. Trends Genet 2006;22:165-73.
40. Lin SL, Kim H, Ying SY. Intron-mediated RNA interference and microRNA (miRNA). Front Biosci 2008;13:2216-30.
41. Baskerville S, Bartel DP. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 2005;11:241-7.
42. Osokine I, Hsu R, Loeb GB, McManus MT. Unintentional miRNA ablation is a risk factor in gene knockout studies: a short report. PLoS Genet 2008;4:e34.
43. Valor LM, Grant SG. Clustered gene expression changes flank targeted gene loci in knockout mice. PLoS ONE 2007;2:e1303.
44. Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A. Identification of mammalian microRNA host genes and transcription units. Genome Res 2004;14:1902-10.
45. Ro S, Park C, Sanders KM, McCarrey JR, Yan W. Cloning and expression profiling of testis-expressed microRNAs. Dev Biol 2007;311:592-602.
46. Drinnenberg IA, Weinberg DE, Xie KT, Mower JP, Wolfe KH, Fink GR, Bartel DP. RNAi in budding yeast. Science 2009;326:544-50.
47. Livny J, Waldor MK. Identification of small RNAs in diverse bacterial species. Curr Opin Microbiol 2007;10:96-101.
48. Waters LS, Storz G. Regulatory RNAs in bacteria. Cell 2009;136:615-28.
49. Gottesman S. Micros for microbes: non-coding regulatory RNAs in bacteria. Trends Genet 2005;21:399-404.
50. Stougaard P, Molin S, Nordstrom K. RNAs involved in copy-number control and incompatibility of plasmid R1. Proc Natl Acad Sci USA 1981;78:6008-12.
51. Tomizawa J, Itoh T, Selzer G, Som T. Inhibition of ColE1 RNA primer formation by a plasmid-specified small RNA. Proc Natl Acad Sci USA 1981;78:1421-5.
52. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M, Matzke M, Ruvkun G, Tuschl T. A uniform system for microRNA annotation. RNA 2003;9:277-9.
53. Lee HJ, Hong SH. Analysis of microRNA-size, small RNAs in Streptococcus mutans by deep sequencing. FEMS Microbiol Lett 2012;326:131-6.
54. Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 2011; 39:D152-7.
55. Cullen BR. Viruses and microRNAs: RISCy interactions with serious consequences. Genes Dev 2011;25:1881-94.
56. Grundhoff A, Sullivan CS. Virus-encoded microRNAs. Virology 2011;411:325-43.