How microRNAs control cell division, differentiation and death

Current Opinion in Genetics and Development

Volumn 15, Issue 5 SPEC. ISS., 2005, Pages 563-568

  Miska, Eric A ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; SMALL INTERFERING RNA;

APOPTOSIS; CARCINOGENESIS; CELL DEATH; CELL DIFFERENTIATION; CELL DIVISION; CELL PROLIFERATION; GENE EXPRESSION; GENE TARGETING; HUMAN; INVERTEBRATE; MORPHOGENESIS; NERVE CELL DIFFERENTIATION; NONHUMAN; ORGANOGENESIS; POSTTRANSCRIPTIONAL GENE SILENCING; PRIORITY JOURNAL; REVIEW; RNA INTERFERENCE; RNA TRANSLATION; TISSUE GROWTH; VERTEBRATE; VIRUS INFECTION;

ANIMALIA; DANIO RERIO; INVERTEBRATA;

EID: 24344494340     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gde.2005.08.005     Document Type: Review

References (74)

1. V. Ambros, and H.R. Horvitz Heterochronic mutants of the nematode Caenorhabditis elegans Science 226 1984 409 416
2. M. Chalfie, H.R. Horvitz, and J.E. Sulston Mutations that lead to reiterations in the cell lineages of C. elegans Cell 24 1981 59 69
3. H.R. Horvitz, and J.E. Sulston Isolation and genetic characterization of cell-lineage mutants of the nematode Caenorhabditis elegans Genetics 96 1980 435 454
4. R.C. Lee, R.L. Feinbaum, and V. Ambros The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 Cell 75 1993 843 854
5. B. Wightman, I. Ha, and G. Ruvkun Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans Cell 75 1993 855 862
6. B.J. Reinhart, F.J. Slack, M. Basson, A.E. Pasquinelli, J.C. Bettinger, A.E. Rougvie, H.R. Horvitz, and G. Ruvkun The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans Nature 403 2000 901 906
7. A.E. Pasquinelli, B.J. Reinhart, F. Slack, M.Q. Martindale, M.I. Kuroda, B. Maller, D.C. Hayward, E.E. Ball, B. Degnan, and P. Muller Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA Nature 408 2000 86 89
8. R.C. Lee, and V. Ambros An extensive class of small RNAs in Caenorhabditis elegans Science 294 2001 862 864
9. M. Lagos-Quintana, R. Rauhut, W. Lendeckel, and T. Tuschl Identification of novel genes coding for small expressed RNAs Science 294 2001 853 858
10. N.C. Lau, L.P. Lim, E.G. Weinstein, and D.P. Bartel An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans Science 294 2001 858 862
11. B.J. Reinhart, E.G. Weinstein, M.W. Rhoades, B. Bartel, and D.P. Bartel MicroRNAs in plants Genes Dev 16 2002 1616 1626
12. C. Llave, K.D. Kasschau, M.A. Rector, and J.C. Carrington Endogenous and silencing-associated small RNAs in plants Plant Cell 14 2002 1605 1619
13. E. Berezikov, V. Guryev, J. van de Belt, E. Wienholds, R.H. Plasterk, and E. Cuppen Phylogenetic shadowing and computational identification of human microRNA genes Cell 120 2005 21 24
14. C.A. Kidner, and R.A. Martienssen The developmental role of microRNA in plants Curr Opin Plant Biol 8 2005 38 44
15. S. Baskerville, and D.P. Bartel Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes RNA 11 2005 241 247
16. Zilberman D, Henikoff S: Epigenetic inheritance in Arabidopsis: selective silence. Curr Opin Genet Dev 15: in press.
17. B.R. Cullen Transcription and processing of human microRNA precursors Mol Cell 16 2004 861 865
18. Y. Lee, C. Ahn, J. Han, H. Choi, J. Kim, J. Yim, J. Lee, P. Provost, O. Radmark, and S. Kim The nuclear RNase III Drosha initiates microRNA processing Nature 425 2003 415 419
19. A.M. Denli, B.B. Tops, R.H. Plasterk, R.F. Ketting, and G.J. Hannon Processing of primary microRNAs by the microprocessor complex Nature 432 2004 231 235
20. R.I. Gregory, K.P. Yan, G. Amuthan, T. Chendrimada, B. Doratotaj, N. Cooch, and R. Shiekhattar The microprocessor complex mediates the genesis of microRNAs Nature 432 2004 235 240
21. J. Han, Y. Lee, K.H. Yeom, Y.K. Kim, H. Jin, and V.N. Kim The Drosha-DGCR8 complex in primary microRNA processing Genes Dev 18 2004 3016 3027
22. M. Landthaler, A. Yalcin, and T. Tuschl The human DiGeorge syndrome critical region gene 8 and its D. melanogaster homolog are required for miRNA biogenesis Curr Biol 14 2004 2162 2167
23. E. Lund, S. Guttinger, A. Calado, J.E. Dahlberg, and U. Kutay Nuclear export of microRNA precursors Science 303 2003 95 98
24. J.W. Pham, and E.J. Sontheimer The making of an siRNA Mol Cell 15 2004 163 164
25. D.P. Bartel MicroRNAs: genomics, biogenesis, mechanism, and function Cell 116 2004 281 297
26. Y. Tomari, and P.D. Zamore MicroRNA biogenesis: drosha can't cut it without a partner Curr Biol 15 2005 R61 R64
27. Pasquinelli AE, Hunter S, Bracht J: MicroRNAs: a developing story. Curr Opin Genet Dev 15:200-205.
28. S. Yekta, I.H. Shih, and D.P. Bartel MicroRNA-directed cleavage of HOXB8 mRNA Science 304 2004 594 596 The authors describe how a mammalian microRNA, miR-196, can direct the cleavage of the HOXB8 mRNA.
29. J.H. Mansfield, B.D. Harfe, R. Nissen, J. Obenauer, J. Srineel, A. Chaudhuri, R. Farzan-Kashani, M. Zuker, A.E. Pasquinelli, and G. Ruvkun MicroRNA-responsive 'sensor' transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression Nat Genet 36 2004 1079 1083
30. Q. Jing, S. Huang, S. Guth, T. Zarubin, A. Motoyama, J. Chen, F. Di Padova, S.C. Lin, H. Gram, and J. Han Involvement of microRNA in AU-rich element-mediated mRNA instability Cell 120 2005 623 634 Here, the authors describe a possible new role for microRNAs in the control of AU-rich element-mediated mRNA decay, implicating miR-16.
31. D. Baulcombe RNA silencing in plants Nature 431 2004 356 363
32. E.G. Moss, R.C. Lee, and V. Ambros The cold shock domain protein LIN-28 controls developmental timing in C. elegans and is regulated by the lin-4 RNA Cell 88 1997 637 646
33. F.J. Slack, M. Basson, Z. Liu, V. Ambros, H.R. Horvitz, and G. Ruvkun The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor Mol Cell 5 2000 659 669
34. J.E. Abrahante, A.L. Daul, M. Li, M.L. Volk, J.M. Tennessen, E.A. Miller, and A.E. Rougvie The Caenorhabditis elegans hunchback-like gene lin-57/hbl-1 controls developmental time and is regulated by microRNAs Dev Cell 4 2003 625 637
35. S.Y. Lin, S.M. Johnson, M. Abraham, M.C. Vella, A. Pasquinelli, C. Gamberi, E. Gottlieb, and F.J. Slack The C. elegans hunchback homolog, hbl-1, controls temporal patterning and is a probable microRNA target Dev Cell 4 2003 639 650
36. H. Grosshans, T. Johnson, K.L. Reinert, M. Gerstein, and F.J. Slack The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans Dev Cell 8 2005 321 330 The authors identify at least two new direct let-7 target mRNAs, including the transcription factors genes daf-12 and pha-4.
37. S.M. Johnson, H. Grosshans, J. Shingara, M. Byrom, R. Jarvis, A. Cheng, E. Labourier, K.L. Reinert, D. Brown, and F.J. Slack RAS is regulated by the let-7 microRNA family Cell 120 2005 635 647
38. R.J. Johnston, and O. Hobert A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans Nature 426 2003 845 849
39. S. Chang, R.J. Johnston Jr., C. Frokjaer-Jensen, S. Lockery, and O. Hobert MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode Nature 430 2004 785 789
40. J. Brennecke, D.R. Hipfner, A. Stark, R.B. Russell, and S.M. Cohen bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila Cell 113 2003 25 36
41. P. Xu, S.Y. Vernooy, M. Guo, and B.A. Hay The Drosophila microRNA mir-14 suppresses cell death and is required for normal fat metabolism Curr Biol 13 2003 790 795
42. E.C. Lai Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation Nat Genet 30 2002 363 364
43. A. Stark, J. Brennecke, R.B. Russell, and S.M. Cohen Identification of Drosophila microRNA targets PLoS Biol 1 2003 e60
44. J. Brennecke, A. Stark, R.B. Russell, and S.M. Cohen Principles of microRNA-target recognition PLoS Biol 3 2005 e85
45. E.C. Lai, B. Tam, and G.M. Rubin Pervasive regulation of Drosophila Notch target genes by GY-box-, Brd-box-, and K-box-class microRNAs Genes Dev 19 2005 1067 1080
46. A.J. Giraldez, R.M. Cinalli, M.E. Glasner, A.J. Enright, J.M. Thomson, S. Baskerville, S.M. Hammond, D.P. Bartel, and A.F. Schier MicroRNAs regulate brain morphogenesis in zebrafish Science 308 2005 833 838 The authors' analysis of a maternal and zygotic Dicer-mutant zebrafish points to important roles for microRNAs in gastrulation and the development of brain, heart and somites. This study points toward a direct role for members of the miR-430 family of microRNAs in brain development.
47. C.Z. Chen, L. Li, H.F. Lodish, and D.P. Bartel MicroRNAs modulate hematopoietic lineage differentiation Science 303 2004 83 86
48. M.N. Poy, L. Eliasson, J. Krutzfeldt, S. Kuwajima, X. Ma, P.E. Macdonald, S. Pfeffer, T. Tuschl, N. Rajewsky, and P. Rorsman A pancreatic islet-specific microRNA regulates insulin secretion Nature 432 2004 226 230
49. C.H. Lecellier, P. Dunoyer, K. Arar, J. Lehmann-Che, S. Eyquem, C. Himber, A. Saib, and O. Voinnet A cellular microRNA mediates antiviral defense in human cells Science 308 2005 557 560
50. L. He, J.M. Thomson, M.T. Hemann, E. Hernando-Monge, D. Mu, S. Goodson, S. Powers, C. Cordon-Cardo, S.W. Lowe, and G.J. Hannon A microRNA polycistron as a potential human oncogene Nature 435 2005 828 833 Using a mouse c-Myc co-cooperativity model, the authors demonstrate the first functional link between a cluster of microRNAs and cancer.
51. G.A. Calin, C.D. Dumitru, M. Shimizu, R. Bichi, S. Zupo, E. Noch, H. Aldler, S. Rattan, M. Keating, and K. Rai Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukaemia Proc Natl Acad Sci USA 99 2002 15524 15529
52. G.A. Calin, C.G. Liu, C. Sevignani, M. Ferracin, N. Felli, C.D. Dumitru, M. Shimizu, A. Cimmino, S. Zupo, and M. Dono MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias Proc Natl Acad Sci USA 101 2004 11755 11760
53. J. Lu, G. Getz, E.A. Miska, E. Alvarez-Saavedra, J. Lamb, D. Peck, A. Sweet-Cordero, B.L. Ebert, R.H. Mak, and A.A. Ferrando MicroRNA expression profiles classify human cancers Nature 435 2005 834 838 Many microRNAs may be regulated in primary human tumours, suggesting a role in human cancer.
54. G.A. Calin, C. Sevignani, C.D. Dumitru, T. Hyslop, E. Noch, S. Yendamuri, M. Shimizu, S. Rattan, F. Bullrich, and M. Negrini Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers Proc Natl Acad Sci USA 101 2004 2999 3004
55. M.T. McManus MicroRNAs and cancer Semin Cancer Biol 13 2003 253 258
56. K.A. O'Donnell, E.A. Wentzel, K.I. Zeller, C.V. Dang, and J.T. Mendell c-Myc-regulated microRNAs modulate E2F1 expression Nature 435 2005 839 843 The authors provide the first demonstration of a transcription factor directly regulating a microRNA primary transcript.
57. S. Pfeffer, A. Sewer, M. Lagos-Quintana, R. Sheridan, C. Sander, F.A. Grasser, L.F. van Dyk, C.K. Ho, S. Shuman, and M. Chien Identification of microRNAs of the herpesvirus family Nat Methods 2 2005 269 276
58. S. Pfeffer, M. Zavolan, F.A. Grasser, M. Chien, J.J. Russo, J. Ju, B. John, A.J. Enright, D. Marks, and C. Sander Identification of virus-encoded microRNAs Science 304 2004 734 736 The authors identify microRNAs that are encoded by the Epstein-Barr virus, a member of the herpesvirus family. This suggests a role for microRNA in viral infection.
59. S.W. Knight, and B.L. Bass A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans Science 293 2001 2269 2271
60. A. Grishok, A.E. Pasquinelli, D. Conte, N. Li, S. Parrish, I. Ha, D.L. Baillie, A. Fire, G. Ruvkun, and C.C. Mello Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing Cell 106 2001 23 34
61. E. Wienholds, M.J. Koudijs, F.J. van Eeden, E. Cuppen, and R.H. Plasterk The microRNA-producing enzyme Dicer1 is essential for zebrafish development Nat Genet 35 2003 217 218
62. E. Bernstein, S.Y. Kim, M.A. Carmell, E.P. Murchison, H. Alcorn, M.Z. Li, A.A. Mills, S.J. Elledge, K.V. Anderson, and G.J. Hannon Dicer is essential for mouse development Nat Genet 35 2003 215 217
63. B.S. Cobb, T.B. Nesterova, E. Thompson, A. Hertweck, E. O'Connor, J. Godwin, C.B. Wilson, N. Brockdorff, A.G. Fisher, and S.T. Smale T cell lineage choice and differentiation in the absence of the RNase III enzyme Dicer J Exp Med 201 2005 1367 1373
64. T. Fukagawa, M. Nogami, M. Yoshikawa, M. Ikeno, T. Okazaki, Y. Takami, T. Nakayama, and M. Oshimura Dicer is essential for formation of the heterochromatin structure in vertebrate cells Nat Cell Biol 6 2004 784 791
65. M. Kiriakidou, P.T. Nelson, A. Kouranov, P. Fitziev, C. Bouyioukos, Z. Mourelatos, and A. Hatzigeorgiou A combined computational-experimental approach predicts human microRNA targets Genes Dev 18 2004 1165 1178
66. N. Rajewsky, and N.D. Socci Computational identification of microRNA targets Dev Biol 267 2004 529 535
67. B. John, A.J. Enright, A. Aravin, T. Tuschl, C. Sander, and D.S. Marks Human microRNA targets PLoS Biol 2 2004 e363
68. B.P. Lewis, C.B. Burge, and D.P. Bartel Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets Cell 120 2005 15 20
69. B.P. Lewis, I.H. Shih, M.W. Jones-Rhoades, D.P. Bartel, and C.B. Burge Prediction of mammalian microRNA targets Cell 115 2003 787 798
70. X. Xie, J. Lu, E.J. Kulbokas, T.R. Golub, V. Mootha, K. Lindblad-Toh, E.S. Lander, and M. Kellis Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals Nature 434 2005 338 345 The authors take a complementary approach to the search for microRNA targets. They perform a systematic screen for motifs in 3′UTRs of human genes that are conserved in mammals and identify many sequences with complementarity to microRNAs.
71. M. Lagos-Quintana, R. Rauhut, A. Yalcin, J. Meyer, W. Lendeckel, and T. Tuschl Identification of tissue-specific microRNAs from mouse Curr Biol 12 2002 735 739
72. E.A. Miska, E. Alvarez-Saavedra, M. Townsend, A. Yoshii, N. Sestan, P. Rakic, M. Constantine-Paton, and H.R. Horvitz Microarray analysis of microRNA expression in the developing mammalian brain Genome Biol 5 2004 R68
73. J.M. Thomson, J. Parker, C.M. Perou, and S.M. Hammond A custom microarray platform for analysis of microRNA gene expression Nat Methods 1 2004 47 53
74. E. Wienholds, W.P. Kloosterman, E.A. Miska, E. Alvarez-Saavedra, E. Berezikov, E. de Bruijn, H.R. Horvitz, S. Kauppinen, and Plasterk RHA MicroRNA expression in zebrafish embryonic development Science 309 2005 310 311 Here, the first robust microRNA in situ technology is demonstrated on zebrafish embryos. This technique offers unprecedented spatial resolution of microRNA expression and has the potential to revolutionize the identification of microRNA function.