Strategies to determine the biological function of micrornas

Nature Genetics

Volumn 38, Issue 6S, 2006, Pages S14-

  Krützfeldt, Jan ^a   Poy, Matthew N ^a   Stoffel, Markus ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; TRANSCRIPTION FACTOR;

3' UNTRANSLATED REGION; ALGORITHM; CAENORHABDITIS ELEGANS; CELL DIFFERENTIATION; CELL GROWTH; CELL METABOLISM; DROSOPHILA MELANOGASTER; GENE EXPRESSION REGULATION; GENE SILENCING; GENE TARGETING; GENOME; IN VITRO STUDY; IN VIVO STUDY; NONHUMAN; PRIORITY JOURNAL; REVIEW; RNA ANALYSIS; RNA INTERFERENCE; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION;

ANIMALS; GENE EXPRESSION PROFILING; GENE SILENCING; HUMANS; MICRORNAS; OLIGONUCLEOTIDES, ANTISENSE;

EID: 84984765629     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng1799     Document Type: Article

References (64)

1. Lagos-Quintana, M., Rauhut, R., Lendeckel, W. & Tuschl, T. Identification of novel genes coding for small expressed RNAs. Science 294, 853–858 (2001).
2. Lau, N.C., Lim, L.P., Weinstein, E.G. & Bartel, D.P. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294, 858–862 (2001).
3. Lee, R.C. & Ambros, V. An extensive class of small RNAs in Caenorhabditis elegans. Science 294, 862–864 (2001).
4. Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B. & Bartel, D.P. MicroRNAs in plants. Genes Dev. 16, 1616–1626 (2002).
5. Bentwich, I. et al. Identification of hundreds of conserved and nonconserved human microRNAs. Nat. Genet. 37, 766–770 (2005).
6. Berezikov, E. et al. Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120, 21–24 (2005).
7. Lee, Y. et al. MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 23, 4051–4060 (2004).
8. Bartel, D.P. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116, 281–297 (2004).
9. Kim, V.N. MicroRNA biogenesis: Coordinated cropping and dicing. Nat. Rev. Mol. Cell Biol. 6, 376–385 (2005).
10. Lee, R.C., Feinbaum, R.L. & Ambros, V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843–854 (1993).
11. 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 75, 855–862 (1993).
12. Brennecke, J., Hipfner, D.R., Stark, A., Russell, R.B. & Cohen, S.M. bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 113, 25–36 (2003).
13. Xu, P., Vernooy, S.Y., Guo, M. & Hay, B.A. The Drosophila microRNA Mir-14 suppresses cell death and is required for normal fat metabolism. Curr. Biol. 13, 790–795 (2003).
14. Giraldez, A.J. et al. MicroRNAs regulate brain morphogenesis in zebrafish. Science 308, 833–838 (2005).
15. Lagos-Quintana, M. et al. Identification of tissue-specific microRNAs from mouse. Curr. Biol. 12, 735–739 (2002).
16. Ambros, V. & Lee, R.C. Identification of microRNAs and other tiny noncoding RNAs by cDNA cloning. Methods Mol. Biol. 265, 131–158 (2004).
17. Berezikov, E., Cuppen, E. & Plasterk, R.H.A. Approaches to miRNA discovery. Nat. Genet. 38, S2–S7 (2006).
18. Baskerville, S. & Bartel, D.P. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11, 241–247 (2005).
19. Barad, O. et al. MicroRNA expression detected by oligonucleotide microarrays: System establishment and expression profiling in human tissues. Genome Res. 14, 2486–2494 (2004).
20. Nelson, P.T. et al. Microarray-based, high-throughput gene expression profiling of microRNAs. Nat. Methods 1, 155–161 (2004).
21. Thomson, J.M., Parker, J., Perou, C.M. & Hammond, S.M. A custom microarray platform for analysis of microRNA gene expression. Nat. Methods 1, 47–53 (2004).
22. Chen, J.F. et al. The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nat. Genet. 38, 228–233 (2006).
23. Zhao, Y., Samal, E. & Srivastava, D. Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 436, 214–220 (2005).
24. Esau, C. et al. MicroRNA-143 regulates adipocyte differentiation. J. Biol. Chem. 279, 52361–52365 (2004).
25. Calin, G.A. et al. 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 (2002).
26. Michael, M.Z., SM, O.C., van Holst Pellekaan, N.G., Young, G.P. & James, R.J. Reduced accumulation of specific microRNAs in colorectal neoplasia. Mol. Cancer Res. 1, 882–891 (2003).
27. Johnson, S.M. et al. RAS is regulated by the let-7 microRNA family. Cell 120, 635–647 (2005).
28. Takamizawa, J. et al. Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival. Cancer Res. 64, 3753–3756 (2004).
29. Eis, P.S. et al. Accumulation of miR-155 and BIC RNA in human B cell lymphomas. Proc. Natl. Acad. Sci. USA 102, 3627–3632 (2005).
30. He, L. et al. A microRNA polycistron as a potential human oncogene. Nature 435, 828–833 (2005).
31. Calin, G.A. et al. Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc. Natl. Acad. Sci. USA 101, 2999–3004 (2004).
32. Lu, J. et al. MicroRNA expression profiles classify human cancers. Nature 435, 834–838 (2005).
33. Johnson, S.M., Lin, S.Y. & Slack, F.J. The time of appearance of the C. elegans let-7 microRNA is transcriptionally controlled utilizing a temporal regulatory element in its promoter. Dev. Biol. 259, 364–379 (2003).
34. Mansfield, J.H. et al. MicroRNA-responsive ‘sensor’ transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression. Nat. Genet. 36, 1079–1083 (2004).
35. Kloosterman, W.P., Wienholds, E., de Bruijn, E., Kauppinen, S. & Plasterk, R.H. In situ detection of miRNAs in animal embryos using LNA-modified oligonucleotide probes. Nat. Methods 3, 27–29 (2006).
36. John, B. et al. Human MicroRNA targets. PLoS Biol. 2, 1862–1879 (2004).
37. Kiriakidou, M. et al. A combined computational-experimental approach predicts human microRNA targets. Genes Dev. 18, 1165–1178 (2004).
38. Krek, A. et al. Combinatorial microRNA target predictions. Nat. Genet. 37, 495–500 (2005).
39. Rajewsky, N. microRNA target predictions in animals. Nat. Genet. 38, S8–S13 (2006).
40. Lewis, B.P., Shih, I.H., Jones-Rhoades, M.W., Bartel, D.P. & Burge, C.B. Prediction of mammalian microRNA targets. Cell 115, 787–798 (2003).
41. Krutzfeldt, J. et al. Silencing of microRNAs in vivo with ‘antagomirs’. Nature 438, 685–689 (2005).
42. Farh, K.K. et al. The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science 310, 1817–1821 (2005).
43. Poy, M.N. et al. A pancreatic islet-specific microRNA regulates insulin secretion. Nature 432, 226–230 (2004).
44. Schratt, G.M. et al. A brain-specific microRNA regulates dendritic spine development. Nature 439, 283–289 (2006).
45. Lim, L.P. et al. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433, 769–773 (2005).
46. Chen, C.Z., Li, L., Lodish, H.F. & Bartel, D.P. MicroRNAs modulate hematopoietic lineage differentiation. Science 303, 83–86 (2004).
47. Hayashita, Y. et al. A polycistronic microRNA cluster, miR-17–92, is overexpressed in human lung cancers and enhances cell proliferation. Cancer Res. 65, 9628–9632 (2005).
48. Kanellopoulou, C. et al. Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev. 19, 489–501 (2005).
49. Harfe, B.D., McManus, M.T., Mansfield, J.H., Hornstein, E. & Tabin, C.J. The RNaseIII enzyme Dicer is required for morphogenesis but not patterning of the vertebrate limb. Proc. Natl. Acad. Sci. USA 102, 10898–10903 (2005).
50. Harris, K.S., Zhang, Z., McManus, M.T., Harfe, B.D. & Sun, X. Dicer function is essential for lung epithelium morphogenesis. Proc. Natl. Acad. Sci. USA 103, 2208–2213 (2006).
51. Ying, S.Y. & Lin, S.L. MicroRNA: Fine-tunes the function of genes in zebrafish. Biochem. Biophys. Res. Commun. 335, 1–4 (2005).
52. Meister, G., Landthaler, M., Dorsett, Y. & Tuschl, T. Sequence-specific inhibition of microRNA- and siRNA-induced RNA silencing. RNA 10, 544–550 (2004).
53. Hutvagner, G., Simard, M.J., Mello, C.C. & Zamore, P.D. Sequence-specific inhibition of small RNA function. PLoS Biol. 2, E98 (2004).
54. Leaman, D. et al. Antisense-mediated depletion reveals essential and specific functions of microRNAs in Drosophila development. Cell 121, 1097–1108 (2005).
55. Esau, C. et al. miR-122 regulation of lipid metabolism revealed by in vivo antisense targeting. Cell Metab. 3, 87–98 (2006).
56. Bagga, S. et al. Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 122, 553–563 (2005).
57. Soutschek, J. et al. Therapeutic silencing of an endogenous gene by systemic administration of modified siRNAs. Nature 432, 173–178 (2004).
58. Fazi, F. et al. A minicircuitry comprised of microRNA-223 and transcription factors NFI-A and C/EBPalpha regulates human granulopoiesis. Cell 123, 819–831 (2005).
59. O’Donnell, K.A., Wentzel, E.A., Zeller, K.I., Dang, C.V. & Mendell, J.T. c-Myc-regulated microRNAs modulate E2F1 expression. Nature 435, 839–843 (2005).
60. Vo, N. et al. A cAMP-response element binding protein-induced microRNA regulates neuronal morphogenesis. Proc. Natl. Acad. Sci. USA 102, 16426–16431 (2005).
61. Conaco, C., Otto, S., Han, J.J. & Mandel, G. Reciprocal actions of REST and a microRNA promote neuronal identity. Proc. Natl. Acad. Sci. USA 103, 2422–2427 (2006).
62. Liu, J. et al. A role for the P-body component GW182 in microRNA function. Nat. Cell Biol. 7, 1161–1166 (2005).
63. Liu, J., Valencia-Sanchez, M.A., Hannon, G.J. & Parker, R. MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies. Nat. Cell Biol. 7, 719–723 (2005).
64. Yang, W. et al. Modulation of microRNA processing and expression through RNA editing by ADAR deaminases. Nat. Struct. Mol. Biol. 13, 13–21 (2006).