MicroRNA function in animal development

FEBS Letters

Volumn 579, Issue 26, 2005, Pages 5911-5922

  Wienholds, Erno ^a   Plasterk, Ronald H A ^a  

^a HUBRECHT INSTITUTE   (Netherlands)

Author keywords

Development; Differentiation; Disease; MicroRNA; Vertebrate

Indexed keywords

MESSENGER RNA; MICRORNA;

APOPTOSIS; BASE PAIRING; BIOGENESIS; DEVELOPMENT; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; HUMAN; HUMAN GENOME; NONHUMAN; PREDICTION; PRIORITY JOURNAL; SHORT SURVEY; SIGNAL TRANSDUCTION; VERTEBRATE;

ANIMALS; APOPTOSIS; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; CELL DIFFERENTIATION; CLONING, MOLECULAR; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENOME, HUMAN; HUMANS; MEMBRANE PROTEINS; MICRORNAS; MODELS, BIOLOGICAL; NEOPLASMS; PHYLOGENY; RECEPTORS, NOTCH; REPRESSOR PROTEINS; RNA; SIGNAL TRANSDUCTION; ZEBRAFISH;

ANIMALIA; VERTEBRATA;

EID: 26944495173     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2005.07.070     Document Type: Short Survey

References (146)

1. 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
2. B. Wightman, T.R. Burglin, J. Gatto, P. Arasu, and G. Ruvkun Negative regulatory sequences in the lin-14 3′-untranslated region are necessary to generate a temporal switch during Caenorhabditis elegans development Genes Dev. 5 1991 1813 1824
3. 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
4. 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
5. A.E. Pasquinelli, B.J. Reinhart, F. Slack, M.Q. Martindale, M.I. Kuroda, B. Maller, D.C. Hayward, E.E. Ball, B. Degnan, P. Muller, J. Spring, A. Srinivasan, M. Fishman, J. Finnerty, J. Corbo, M. Levine, P. Leahy, E. Davidson, and G. Ruvkun Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA Nature 408 2000 86 89
6. 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
7. M. Lagos-Quintana, R. Rauhut, W. Lendeckel, and T. Tuschl Identification of novel genes coding for small expressed RNAs Science 294 2001 853 858
8. R.C. Lee, and V. Ambros An extensive class of small RNAs in Caenorhabditis elegans Science 294 2001 862 864
9. 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
10. 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
11. 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
12. X. Chen microRNA biogenesis and function in plants FEBS Lett. 579 2005 5923 5931
13. S. Griffiths-Jones The microRNA Registry Nucleic Acids Res. 32 Database issue 2004 D109 D111
14. V. Ambros, B. Bartel, D.P. Bartel, C.B. Burge, J.C. Carrington, X. Chen, G. Dreyfuss, S.R. Eddy, S. Griffiths-Jones, M. Marshall, M. Matzke, G. Ruvkun, and T. Tuschl A uniform system for microRNA annotation RNA 9 2003 277 279
15. R.J. Johnston, and O. Hobert A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans Nature 426 2003 845 849
16. 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
17. 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
18. E.C. Lai microRNAs: runts of the genome assert themselves Curr. Biol. 13 2003 R925 R936
19. A. Aravin, and T. Tuschl Identification and characterization of small RNAs involved in RNA silencing FEBS Lett. 579 2005 5830 5840
20. V. Ambros, R.C. Lee, A. Lavanway, P.T. Williams, and D. Jewell MicroRNAs and other tiny endogenous RNAs in C. elegans Curr. Biol. 13 2003 807 818
21. A.A. Aravin, M. Lagos-Quintana, A. Yalcin, M. Zavolan, D. Marks, B. Snyder, T. Gaasterland, J. Meyer, and T. Tuschl The small RNA profile during Drosophila melanogaster development Dev. Cell 5 2003 337 350
22. M. Lagos-Quintana, R. Rauhut, J. Meyer, A. Borkhardt, and T. Tuschl New microRNAs from mouse and human RNA 9 2003 175 179
23. 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
24. J. Kim, A. Krichevsky, Y. Grad, G.D. Hayes, K.S. Kosik, G.M. Church, and G. Ruvkun Identification of many microRNAs that copurify with polyribosomes in mammalian neurons Proc. Natl. Acad. Sci. USA 101 2004 360 365
25. Z. Mourelatos, J. Dostie, S. Paushkin, A. Sharma, B. Charroux, L. Abel, J. Rappsilber, M. Mann, and G. Dreyfuss miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs Genes Dev. 16 2002 720 728
26. 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
27. H.B. Houbaviy, M.F. Murray, and P.A. Sharp Embryonic stem cell-specific microRNAs Dev. Cell 5 2003 351 358
28. M.R. Suh, Y. Lee, J.Y. Kim, S.K. Kim, S.H. Moon, J.Y. Lee, K.Y. Cha, H.M. Chung, H.S. Yoon, S.Y. Moon, V.N. Kim, and K.S. Kim Human embryonic stem cells express a unique set of microRNAs Dev. Biol. 270 2004 488 498
29. T. Watanabe, A. Takeda, K. Mise, T. Okuno, T. Suzuki, N. Minami, and H. Imai Stage-specific expression of microRNAs during Xenopus development FEBS Lett. 579 2005 318 324
30. L.P. Lim, M.E. Glasner, S. Yekta, C.B. Burge, and D.P. Bartel Vertebrate microRNA genes Science 299 2003 1540
31. P.Y. Chen, H. Manninga, K. Slanchev, M. Chien, J.J. Russo, J. Ju, R. Sheridan, B. John, D.S. Marks, D. Gaidatzis, C. Sander, M. Zavolan, and T. Tuschl The developmental miRNA profiles of zebrafish as determined by small RNA cloning Genes Dev. 19 2005 1288 1293
32. S. Pfeffer, A. Sewer, M. Lagos-Quintana, R. Sheridan, C. Sander, F.A. Grasser, L.F. van Dyk, C.K. Ho, S. Shuman, M. Chien, J.J. Russo, J. Ju, G. Randall, B.D. Lindenbach, C.M. Rice, V. Simon, D.D. Ho, M. Zavolan, and T. Tuschl Identification of microRNAs of the herpesvirus family Nat. Methods 2 2005 269 276
33. S. Pfeffer, M. Zavolan, F.A. Grasser, M. Chien, J.J. Russo, J. Ju, B. John, A.J. Enright, D. Marks, C. Sander, and T. Tuschl Identification of virus-encoded microRNAs Science 304 2004 734 736
34. L.P. Lim, N.C. Lau, E.G. Weinstein, A. Abdelhakim, S. Yekta, M.W. Rhoades, C.B. Burge, and D.P. Bartel The microRNAs of Caenorhabditis elegans Genes Dev. 17 2003 991 1008
35. E.C. Lai, P. Tomancak, R.W. Williams, and G.M. Rubin Computational identification of Drosophila microRNA genes Genome Biol. 4 2003 R42
36. U. Ohler, S. Yekta, L.P. Lim, D.P. Bartel, and C.B. Burge Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification RNA 10 2004 1309 1322
37. Y. Grad, J. Aach, G.D. Hayes, B.J. Reinhart, G.M. Church, G. Ruvkun, and J. Kim Computational and experimental identification of C. elegans microRNAs Mol. Cell 11 2003 1253 1263
38. I. Bentwich Prediction and validation of microRNAs and their targets FEBS Lett. 579 2005 5904 5910
39. I. Bentwich, A. Avniel, Y. Karov, R. Aharonov, S. Gilad, O. Barad, A. Barzilai, P. Einat, U. Einav, E. Meiri, E. Sharon, Y. Spector, and Z. Bentwich Identification of hundreds of conserved and nonconserved human microRNAs Nat. Genet. 37 2005 766 770
40. A. Rodriguez, S. Griffiths-Jones, J.L. Ashurst, and A. Bradley Identification of mammalian microRNA host genes and transcription units Genome Res. 14 2004 1902 1910
41. S. Baskerville, and D.P. Bartel Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes RNA 11 2005 241 247
42. E. Wienholds, W.P. Kloosterman, E. Miska, E. Alvarez-Saavedra, E. Berezikov, E. de Bruijn, H.R. Horvitz, S. Kauppinen, and R.H. Plasterk MicroRNA expression in zebrafish embryonic development Science 309 2005 310 311
43. G.A. Calin, C. Sevignani, C.D. Dumitru, T. Hyslop, E. Noch, S. Yendamuri, M. Shimizu, S. Rattan, F. Bullrich, M. Negrini, and C.M. Croce Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers Proc. Natl. Acad. Sci. USA 101 2004 2999 3004
44. L.F. Sempere, N.S. Sokol, E.B. Dubrovsky, E.M. Berger, and V. Ambros Temporal regulation of microRNA expression in Drosophila melanogaster mediated by hormonal signals and broad-complex gene activity Dev. Biol. 259 2003 9 18
45. S.M. Johnson, S.Y. Lin, and F.J. Slack 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 2003 364 379
46. M.N. Poy, L. Eliasson, J. Krutzfeldt, S. Kuwajima, X. Ma, P.E. Macdonald, S. Pfeffer, T. Tuschl, N. Rajewsky, P. Rorsman, and M. Stoffel A pancreatic islet-specific microRNA regulates insulin secretion Nature 432 2004 226 230
47. C.Z. Chen, L. Li, H.F. Lodish, and D.P. Bartel MicroRNAs modulate hematopoietic lineage differentiation Science 303 2004 83 86
48. L.F. Sempere, S. Freemantle, I. Pitha-Rowe, E. Moss, E. Dmitrovsky, and V. Ambros Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation Genome Biol. 5 2004 R13
49. T. Babak, W. Zhang, Q. Morris, B.J. Blencowe, and T.R. Hughes Probing microRNAs with microarrays: tissue specificity and functional inference RNA 10 2004 1813 1819
50. O. Barad, E. Meiri, A. Avniel, R. Aharonov, A. Barzilai, I. Bentwich, U. Einav, S. Gilad, P. Hurban, Y. Karov, E.K. Lobenhofer, E. Sharon, Y.M. Shiboleth, M. Shtutman, Z. Bentwich, and P. Einat MicroRNA expression detected by oligonucleotide microarrays: system establishment and expression profiling in human tissues Genome Res. 14 2004 2486 2494
51. 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 1 7
52. A.M. Krichevsky, K.S. King, C.P. Donahue, K. Khrapko, and K.S. Kosik A microRNA array reveals extensive regulation of microRNAs during brain development RNA 9 2003 1274 1281
53. Y. Lee, M. Kim, J. Han, K.H. Yeom, S. Lee, S.H. Baek, and V.N. Kim MicroRNA genes are transcribed by RNA polymerase II EMBO J. 23 2004 4051 4060
54. X. Cai, C.H. Hagedorn, and B.R. Cullen Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs RNA 10 2004 1957 1966
55. Y. Lee, K. Jeon, J.T. Lee, S. Kim, and V.N. Kim MicroRNA maturation: stepwise processing and subcellular localization EMBO J. 21 2002 4663 4670
56. Y. Lee, C. Ahn, J. Han, H. Choi, J. Kim, J. Yim, J. Lee, P. Provost, O. Radmark, S. Kim, and V.N. Kim The nuclear RNase III Drosha initiates microRNA processing Nature 425 2003 415 419
57. 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
58. 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
59. 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
60. 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
61. E. Lund, S. Guttinger, A. Calado, J.E. Dahlberg, and U. Kutay Nuclear export of microRNA precursors Science 303 2004 95 98
62. R. Yi, Y. Qin, I.G. Macara, and B.R. Cullen Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs Genes Dev. 17 2003 3011 3016
63. M.T. Bohnsack, K. Czaplinski, and D. Gorlich Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs RNA 10 2004 185 191
64. G. Hutvagner, J. McLachlan, A.E. Pasquinelli, E. Balint, T. Tuschl, and P.D. Zamore A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA Science 293 2001 834 838
65. 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
66. R.F. Ketting, S.E. Fischer, E. Bernstein, T. Sijen, G.J. Hannon, and R.H. Plasterk Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans Genes Dev. 15 2001 2654 2659
67. P.D. Zamore, T. Tuschl, P.A. Sharp, and D.P. Bartel RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals Cell 101 2000 25 33
68. E. Bernstein, A.A. Caudy, S.M. Hammond, and G.J. Hannon Role for a bidentate ribonuclease in the initiation step of RNA interference Nature 409 2001 363 366
69. S.M. Elbashir, W. Lendeckel, and T. Tuschl RNA interference is mediated by 21- and 22-nucleotide RNAs Genes Dev. 15 2001 188 200
70. S.M. Hammond Dicing and slicing. The core machinery of the RNA interference pathway FEBS Lett. 579 2005 5822 5829
71. H. Tabara, E. Yigit, H. Siomi, and C.C. Mello The dsRNA binding protein RDE-4 interacts with RDE-1, DCR-1, and a DExH-box helicase to direct RNAi in C. elegans Cell 109 2002 861 871
72. T.P. Chendrimada, R.I. Gregory, E. Kumaraswamy, J. Norman, N. Cooch, K. Nishikura, and R. Shiekhattar TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing Nature 2005
73. K. Forstemann, Y. Tomari, T. Du, V.V. Vagin, A.M. Denli, D.P. Bratu, C. Klattenhoff, W.E. Theurkauf, and P.D. Zamore Normal microRNA maturation and germ-line stem cell maintenance requires loquacious, a double-stranded RNA-binding domain protein PLoS Biol. 3 2005 e236
74. K. Saito, A. Ishizuka, H. Siomi, and M.C. Siomi Processing of pre-microRNAs by the Dicer-1-Loquacious complex in drosophila cells PLoS Biol. 3 2005 e235
75. F. Jiang, X. Ye, X. Liu, L. Fincher, D. McKearin, and Q. Liu Dicer-1 and R3D1-L catalyze microRNA maturation in Drosophila Genes Dev. 19 2005 1674 1679
76. A. Khvorova, A. Reynolds, and S.D. Jayasena Functional siRNAs and miRNAs exhibit strand bias Cell 115 2003 209 216
77. D.S. Schwarz, G. Hutvagner, T. Du, Z. Xu, N. Aronin, and P.D. Zamore Asymmetry in the assembly of the RNAi enzyme complex Cell 115 2003 199 208
78. G. Hutvagner Small RNA asymmetry in RNAi: Function in RISC assembly and gene regulation FEBS Lett. 579 2005 5850 5857
79. G. Hutvagner, and P.D. Zamore A microRNA in a multiple-turnover RNAi enzyme complex Science 297 2002 2056 2060
80. S.M. Hammond, E. Bernstein, D. Beach, and G.J. Hannon An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells Nature 404 2000 293 296
81. J.G. Doench, C.P. Petersen, and P.A. Sharp siRNAs can function as miRNAs Genes Dev. 17 2003 438 442
82. Y. Zeng, R. Yi, and B.R. Cullen MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms Proc. Natl. Acad. Sci. USA 100 2003 9779 9784
83. S. Saxena, Z.O. Jonsson, and A. Dutta Small RNAs with imperfect match to endogenous mRNA repress translation. Implications for off-target activity of small inhibitory RNA in mammalian cells J. Biol. Chem. 278 2003 44312 44319
84. Y. Zeng, E.J. Wagner, and B.R. Cullen Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells Mol. Cell 9 2002 1327 1333
85. P.H. Olsen, and V. Ambros The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation Dev. Biol. 216 1999 671 680
86. K. Seggerson, L. Tang, and E.G. Moss Two genetic circuits repress the Caenorhabditis elegans heterochronic gene lin-28 after translation initiation Dev. Biol. 243 2002 215 225
87. G.L. Sen, and H.M. Blau Argonaute 2/RISC resides in sites of mammalian mRNA decay known as cytoplasmic bodies Nat. Cell. Biol. 7 2005 633 636
88. J. Liu, M.A. Valencia-Sanchez, G.J. Hannon, and R. Parker MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies Nat. Cell. Biol. 7 2005 719 723
89. J.H. Mansfield, B.D. Harfe, R. Nissen, J. Obenauer, J. Srineel, A. Chaudhuri, R. Farzan-Kashani, M. Zuker, A.E. Pasquinelli, G. Ruvkun, P.A. Sharp, C.J. Tabin, and M.T. McManus MicroRNA-responsive 'sensor' transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression Nat. Genet. 36 2004 1079 1083
90. S. Yekta, I.H. Shih, and D.P. Bartel MicroRNA-directed cleavage of HOXB8 mRNA Science 304 2004 594 596
91. S.M. Hammond, S. Boettcher, A.A. Caudy, R. Kobayashi, and G.J. Hannon Argonaute2, a link between genetic and biochemical analyses of RNAi Science 293 2001 1146 1150
92. G. Meister, M. Landthaler, A. Patkaniowska, Y. Dorsett, G. Teng, and T. Tuschl Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs Mol. Cell 15 2004 185 197
93. J. Liu, M.A. Carmell, F.V. Rivas, C.G. Marsden, J.M. Thomson, J.J. Song, S.M. Hammond, L. Joshua-Tor, and G.J. Hannon Argonaute2 is the catalytic engine of mammalian RNAi Science 305 2004 1437 1441
94. K. Okamura, A. Ishizuka, H. Siomi, and M.C. Siomi Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways Genes Dev. 18 2004 1655 1666
95. G. Meister, M. Landthaler, Y. Dorsett, and T. Tuschl Sequence-specific inhibition of microRNA- and siRNA-induced RNA silencing RNA 10 2004 544 550
96. G. Hutvagner, M.J. Simard, C.C. Mello, and P.D. Zamore Sequence-Specific Inhibition of Small RNA Function PLoS Biol. 2 2004 E98
97. 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
98. Y.S. Lee, H.K. Kim, S. Chung, K.S. Kim, and A. Dutta Depletion of human micro-RNA miR-125b reveals that it is critical for the proliferation of differentiated cells but not for the down-regulation of putative targets during differentiation J. Biol. Chem. 280 2005 16635 16641
99. E.C. Lai Predicting and validating microRNA targets Genome Biol. 5 2004 115
100. J. Brennecke, A. Stark, R.B. Russell, and S.M. Cohen Principles of microRNA-target recognition PLoS Biol. 3 2005 e85
101. B. John, A.J. Enright, A. Aravin, T. Tuschl, C. Sander, and D.S. Marks Human microRNA targets PLoS Biol. 2 2004 e363
102. A. Krek, D. Grun, M.N. Poy, R. Wolf, L. Rosenberg, E.J. Epstein, P. MacMenamin, I. da Piedade, K.C. Gunsalus, M. Stoffel, and N. Rajewsky Combinatorial microRNA target predictions Nat. Genet. 37 2005 495 500
103. J.G. Doench, and P.A. Sharp Specificity of microRNA target selection in translational repression Genes Dev. 18 2004 504 511
104. M.C. Vella, E.Y. Choi, S.Y. Lin, K. Reinert, and F.J. Slack The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3′ UTR Genes Dev. 18 2004 132 137
105. W.P. Kloosterman, E. Wienholds, R.F. Ketting, and R.H. Plasterk Substrate requirements for let-7 function in the developing zebrafish embryo Nucleic Acids Res. 32 2004 6284 6291
106. 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
107. 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
108. 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
109. 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
110. 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
111. 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
112. 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
113. A. Stark, J. Brennecke, R.B. Russell, and S.M. Cohen Identification of Drosophila microRNA targets PLOS Biol. 1 2003 1 13
114. A. Boutla, C. Delidakis, and M. Tabler Developmental defects by antisense-mediated inactivation of micro-RNAs 2 and 13 in Drosophila and the identification of putative target genes Nucleic Acids Res. 31 2003 4973 4980
115. 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
116. E.C. Lai Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation Nat. Genet. 30 2002 363 364
117. C. Kanellopoulou, S.A. Muljo, A.L. Kung, S. Ganesan, R. Drapkin, T. Jenuwein, D.M. Livingston, and K. Rajewsky Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing Genes Dev. 19 2005 489 501
118. 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
119. 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
120. 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
121. 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
122. Y. Zhao, E. Samal, and D. Srivastava Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis Nature 436 2005 214 220
123. C. Esau, X. Kang, E. Peralta, E. Hanson, E.G. Marcusson, L.V. Ravichandran, Y. Sun, S. Koo, R.J. Perera, R. Jain, N.M. Dean, S.M. Freier, C.F. Bennett, B. Lollo, and R. Griffey MicroRNA-143 regulates adipocyte differentiation J. Biol. Chem. 279 2004 52361 52365
124. 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
125. H. Seitz, N. Youngson, S.P. Lin, S. Dalbert, M. Paulsen, J.P. Bachellerie, A.C. Ferguson-Smith, and J. Cavaille Imprinted microRNA genes transcribed antisense to a reciprocally imprinted retrotransposon-like gene Nat. Genet. 34 2003 261 262
126. H. Seitz, H. Royo, M.L. Bortolin, S.P. Lin, A.C. Ferguson-Smith, and J. Cavaille A large imprinted microRNA gene cluster at the mouse Dlk1-Gtl2 domain Genome Res. 14 2004 1741 1748
127. J. Chang, E. Nicolas, D. Marks, C. Sander, A. Lerro, M.A. Buendia, C. Xu, W.S. Mason, T. Moloshok, R. Bort, K.S. Zaret, and J.M. Taylor miR-122, a mammalian liver-specific microRNA, is processed from hcr mRNA and may downregulate the high affinity cationic amino acid transporter CAT-1 RNA Biol. 1 2004 106 113
128. Z. Yu, T. Raabe, and N.B. Hecht MicroRNA122a reduces expression of the post-transcriptionally regulated germ cell transition protein 2 (Tnp2) messenger RNA (mRNA) by mRNA cleavage Biol. Reprod. 2005
129. A.M. Cheng, M.W. Byrom, J. Shelton, and L.P. Ford Antisense inhibition of human miRNAs and indications for an involvement of miRNA in cell growth and apoptosis Nucleic Acids Res. 33 2005 1290 1297
130. 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
131. J. Lu, G. Getz, E.A. Miska, E. Alvarez-Saavedra, J. Lamb, D. Peck, A. Sweet-Cordero, B.L. Ebert, R.H. Mak, A.A. Ferrando, J.R. Downing, T. Jacks, H.R. Horvitz, and T.R. Golub MicroRNA expression profiles classify human cancers Nature 435 2005 834 838
132. L.P. Lim, N.C. Lau, P. Garrett-Engele, A. Grimson, J.M. Schelter, J. Castle, D.P. Bartel, P.S. Linsley, and J.M. Johnson Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs Nature 433 2005 769 773
133. D.P. Bartel, and C.Z. Chen Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs Nat. Rev. Genet. 5 2004 396 400
134. D.P. Bartel MicroRNAs: genomics, biogenesis, mechanism, and function Cell 116 2004 281 297
135. P. Jin, D.C. Zarnescu, S. Ceman, M. Nakamoto, J. Mowrey, T.A. Jongens, D.L. Nelson, K. Moses, and S.T. Warren Biochemical and genetic interaction between the fragile X mental retardation protein and the microRNA pathway Nat. Neurosci. 7 2004 113 117
136. Y. Karube, H. Tanaka, H. Osada, S. Tomida, Y. Tatematsu, K. Yanagisawa, Y. Yatabe, J. Takamizawa, S. Miyoshi, T. Mitsudomi, and T. Takahashi Reduced expression of Dicer associated with poor prognosis in lung cancer patients Cancer Sci. 96 2005 111 115
137. G.A. Calin, C.D. Dumitru, M. Shimizu, R. Bichi, S. Zupo, E. Noch, H. Aldler, S. Rattan, M. Keating, K. Rai, L. Rassenti, T. Kipps, M. Negrini, F. Bullrich, and C.M. Croce Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia Proc. Natl. Acad. Sci. USA 99 2002 15524 15529
138. M.Z. Michael, O.C. SM, N.G. van Holst Pellekaan, G.P. Young, and R.J. James Reduced accumulation of specific microRNAs in colorectal neoplasia Mol. Cancer Res. 1 2003 882 891
139. M. Metzler, M. Wilda, K. Busch, S. Viehmann, and A. Borkhardt High expression of precursor microRNA-155/BIC RNA in children with Burkitt lymphoma Genes Chromosomes Cancer 39 2004 167 169
140. P.S. Eis, W. Tam, L. Sun, A. Chadburn, Z. Li, M.F. Gomez, E. Lund, and J.E. Dahlberg Accumulation of miR-155 and BIC RNA in human B cell lymphomas Proc. Natl. Acad. Sci. USA 2005
141. J. Takamizawa, H. Konishi, K. Yanagisawa, S. Tomida, H. Osada, H. Endoh, T. Harano, Y. Yatabe, M. Nagino, Y. Nimura, T. Mitsudomi, and T. Takahashi Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival Cancer Res. 64 2004 3753 3756
142. L. He, J.M. Thomson, M.T. Hemann, E. Hernando-Monge, D. Mu, S. Goodson, S. Powers, C. Cordon-Cardo, S.W. Lowe, G.J. Hannon, and S.M. Hammond A microRNA polycistron as a potential human oncogene Nature 435 2005 828 833
143. 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
144. X. Cai, S. Lu, Z. Zhang, C.M. Gonzalez, B. Damania, and B.R. Cullen Kaposi's sarcoma-associated herpesvirus expresses an array of viral microRNAs in latently infected cells Proc. Natl. Acad. Sci. USA 102 2005 5570 5575
145. C.S. Sullivan, A.T. Grundhoff, S. Tevethia, J.M. Pipas, and D. Ganem SV40-encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells Nature 435 2005 682 686
146. S. Omoto, M. Ito, Y. Tsutsumi, Y. Ichikawa, H. Okuyama, E.A. Brisibe, N.K. Saksena, and Y.R. Fujii HIV-1 nef suppression by virally encoded microRNA Retrovirology 1 2004 44