Gene expression regulators - MicroRNAs

Chinese Science Bulletin

Volumn 50, Issue 13, 2005, Pages 1281-1292

  Chen, Fang ^a,b   Yin, James Q ^a  

^a INSTITUTE OF BIOPHYSICS   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

Bioinformatics; Gene regulation; miRNA; RNAi

Indexed keywords

EID: 33748852455     PISSN: 10016538     EISSN: 18619541     Source Type: Journal    
DOI: 10.1360/982005-573     Document Type: Review

References (94)

1. David, P. B., microRNAs: Genomics, biogenesis, mechanism, and function, Cell, 2004, 116: 281-297.
2. 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, 1993, 75: 843-854.
3. Reinhart, B. J., Slack, F. J., Basson, M. et al., The 21 nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature, 2000, 403: 901-906.
4. Yin, J. Q., Wang, Y., siRNA-mediated gene regulation system: Now and the future, Int. J. Mol. Med., 2002, 10: 355-365.
5. Tan, F. L., Yin, J. Q., Application of RNAi to cancer research and therapy, Front Biosci., 2005, 10: 1946-1960.
6. Yin, J. Q., Jiang, L., miRNA-directed gene intertalk, Chin. Acad. Forum (in Chinese), 2004, 11(20): 1-4.
7. Lee, Y., Kim, M., Han, J. et al., microRNA genes are transcribed by RNA polymerase II, EMBO J., 2004, 23(20): 4051-4060.
8. Rodriguez, A., Griffiths-Jones, S., Ashurst, J. L. et al., Identification of mammalian microRNA host genes and transcription units, Genome Res., 2004,14(10A): 1902-1910.
9. Lee, Y., Ahn, C., Han, J. et al., The nuclear RNase III Drosha initiates microRNA processing, Nature, 2003, 425: 415-419.
10. Elsebet, L., Stephan, G., Angelo, C. et al., Nuclear Export of MicroRNA Precursors, Science, 2004, 303: 95-98.
11. Yi, R., Qin, Y., Macara, I. G. et al., Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs, Genes Dev., 2003, 17: 3011-3016.
12. Kim, V. N., microRNA precursors in motion: exportin-5 mediates their nuclear export, Trends Cell Biol., 2004, 14(4): 156-159.
13. Zeng, Y., Cullen, B. R., Structural requirements for pre-microRNA binding and nuclear export by Exportin 5, Nucleic Acids Res., 2004, 32(16): 4776-4785.
14. Zhang, H., Kolb, F. A., Jaskiewicz, L. et al., Single processing center models for human Dicer and bacterial RNase III, Cell, 2004, 118: 57-68.
15. Hutvágner, G., Zamore, P. D., A microRNA in a multiple-turnover RNAi enzyme complex, Science, 2002, 297: 2056-2060.
16. Zeng, Y., Yi, R., Cullen, B. R., microRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms, Proc. Natl. Acad. Sci. USA., 2003, 100: 9779-9784.
17. Doench, J. G., Peterson, C. P., Sharp, P. A., siRNAs can function as miRNAs, Genes Dev., 2003, 17: 438-442.
18. Bracht, J., Hunter, S., Eachus, R. et al., Trans-splicing and polyadenylation of let-7 microRNA primary transcripts, RNA, 2004, 10(10): 1586-1594.
19. Denli, A. M., Tops, B. B., Plasterk, R. H. et al., Processing of primary microRNAs by the Microprocessor complex, Nature, 2004, 432: 231-235.
20. Gregory, R. I., Yan, K., Amuthan, G. et al., The microprocessor complex mediates the genesis of microRNAs, Nature, 2004, 432: 235-240.
21. Han, J., Lee, Y., Yeom, K. H. et al., The Drosha-DGCR8 complex in primary microRNA processing, Genes Dev., 2004, 18: 3016-3027.
22. Landthaler, M., Yalcin, A., Tuschl, T., The human DiGeorge syndrome critical region gene 8 and its D. melanogaster homolog are required for miRNA biogenesis, Curr. Biol., 2004, 14: 2162-2167.
23. Lee, Y. S., Nakahara, K., Pham, J. W. et al., Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways, Cell, 2004, 117(1): 69-81.
24. Okamura, K., Ishizuka, A., Siomi, H. et al., Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways, Genes Dev., 2004, 18(14): 1655-1666.
25. Hutvagner, G., Mclachlan, J., Pasquinelli, A. E. et al., A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA, Science, 2001, 293: 834-838.
26. Mansfield, J. H., Harfe, B. D., Nissen, R. et al., microRNA-responsive 'sensor' transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression, Nat. Genet., 2004, 36(10): 1079-1083.
27. Yekta, S., Shin, I. H., Bartel, D. P., microRNA-directed cleavage of HOXB8 mRNA, Science, 2004, 304(5670): 594-596.
28. Lagos-Quintana, M., Rauhut, R., Lendeckel, W. et al., Identification of novel genes coding for small expressed RNAs, Science, 2001, 294: 853-858.
29. Lau, N. C., Lim, L. P., Weinstein, E. G. et al., An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans, Science, 2001, 294: 858-862.
30. Lee, R. C., Ambros, V., An extensive class of small RNAs in Caenorhabditis elegans, Science, 2001, 294: 862-864.
31. Lagos-Quintana, M., Rauhut, R., Yalcin, A. et al., Identification of tissue-specific microRNAs from mouse, Curr. Biol., 2002, 12: 735-739.
32. Lagos-Quintana, M., Rauhut, R., Meyer, J. et al., New microRNAs from mouse and human, RNA, 2003, 9: 175-179.
33. Lim, L. P., Glasner, M. E., Yekta, S. et al., Vertebrate microRNA genes, Science, 2003, 299: 1540.
34. Lim, L. P., Lau, N. C., Weinstein, E. G. et al., The microRNAs of Caenorhabdilis elegans. Genes Dev., 2003, 17: 991-1008.
35. Ambros, V., Lee, R. C., Identification of microRNAs and other tiny noncoding RNAs by cDNA cloning, Methods Mol. Biol., 2004, 265: 131-158.
36. Aravin, A. A., Lagos-Quintana, M., Yalcin, A. et al., The small RNA profile during Drosophila melanogaster development, Dev. Cell, 2003, 5: 337-350.
37. Mourelatos, Z., Dostie, J., Paushkin, S. et al., miRNPs: A novel class of ribonucleoproteins containing numerous microRNAs, Genes Dev., 2002, 16: 720-728.
38. Houbaviy, H. B., Murray, M. F., Sharp, P. A., Embryonic stem cell-specific microRNAs, Dev. Cell, 2003, 5: 351-358.
39. Dostie, J., Mourelatos, Z., Yang, M., et al., Numerous microRNPs in neuronal cells containing novel microRNAs, RNA, 2003, 9: 180-186.
40. Kim, J., Krichevsky, A., Grad, Y. et al., Identification of many microRNAs that copurify with polyribosomes in mammalian neurons, Proc. Natl. Acad. Sci. USA, 2004, 101: 360-365.
41. Michael, M. Z., O'Connor, S. M., van Holst Pellekaan, N. G. et al., Reduced accumulation of specific microRNAs in colorectal neoplasia, Mol. Cancer Res., 2003, 1: 82-91.
42. Ambros, V., Lee, R. C., Lavanway, A. et al., microRNAs and other tiny endogenous RNAs in C. elegans, Curr. Biol., 2003, 13: 807-818.
43. Wang, J. F., Zhou, H., Chen, Y. Q. et al., Identification of 20 microRNAs from Oryza sativa, Nucleic Acids Res., 2004, 32(5): 1688-1695.
44. Pfeffer, S., Zavolan, M., Grasser, F. A. et al., Identification of virus-encoded microRNAs, Science, 2004, 304(5671): 734-736.
45. Pfeffer, S., Sewer, A., Lagos-Quintana, M. et al., Identification of microRNAs of the herpesvirus family, Nat. methods, 2005, 2: 269-276.
46. Suh, M. R., Lee, Y., Kim, J. Y. et al., Human embryonic stem cells express a unique set of microRNAs, Dev. Biol., 2004, 270(2): 488-498.
47. Seitz, H., Royo, H., Bortolin, M. L. et al., A large imprinted microRNA gene cluster at the mouse Dlk1-Gtl2 domain, Genome Res., 2004, 14(9): 1741-1748.
48. Kasashima, K., Nakamura, Y., Kozu, T., Altered expression profiles of microRNAs during TPA-induced differentiation of HL-60 cells, Biochem. Biophys. Res. Commun., 2004, 322(2): 403-410.
49. Sempere, L. F., Freemantle, S., Pitha-Rowe, I. et al., Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation, Genome Biol., 2004, 5(3): R13.
50. Allawi, H. T., Dahlberg, J. E., Olson, S. et al., Quantitation of microRNAs using a modified Invader assay, RNA, 2004, 10(7): 1153-1161.
51. Liu, C. G., Calin, G. A., Meloon, B. et al., An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues, Proc. Natl. Acad. Sci. USA, 2004, 101(26): 9740-9744.
52. Esau, C., Kang, X., Peralta, E. et al., microRNA-143 regulates adipocyte differentiation, J. Biol. Chem., 2004, 279(50): 52361-52365.
53. Calin, G. A., Liu, C. G., Sevignani, C. et al., microRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias, Proc. Natl. Acad. Sci. USA, 2004, 101(32): 11755-11760.
54. Miska, E. A., Alvarez-Saavedra, E., Townsend, M. et al., Microarray analysis of microRNA expression in the developing mammalian brain, Genome Biol., 2004, 5(9): R68.
55. Nelson, P. T., Baldwin, D. A., Scearce, L. M. et al., Microarray-based, high-throughput gene expression profiling of microRNAs, Nat. methods, 2004, 1: 155-161.
56. Chen, X., A microRNA as a Translational Repressor of APETALA2 in Arabidopsis Flower Development, Science, 2004, 303: 2022-2025.
57. Juarez, M. T., Kui, J. S., Thomas, J. et al., microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity. Nature, 2004, 428(6978): 84-88.
58. 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., 2003, 259(2): 364-379.
59. Ohler, U., Yekta, S., Lim, L. P. et al., Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification, RNA, 2004, 10(9): 1309-1322.
60. Lai, E. C., Tomancak, P., Williams, R. W. et al., Computational identification of Drosophila microRNA genes. Genome Biol., 2003, 4: R42.
61. Legendre, M., Lambert, A., Gautheret, D., Profile-based detection of microRNA precursors in animal genomes, Bioinformatics, 2005, 21(7): 841-845.
62. Berezikov, E., Guryev, V., van de Belt, J. et al., Phylogenetic shadowing and computational identification of human microRNA genes, Cell, 2005, 120(1): 21-24.
63. Hofacker, I. L., Vienna RNA secondary structure server. Nucleic Acids Res., 2003, 31: 3429-3431.
64. Ambros, V., Bartel, B., Bartel, D. P. et al., A uniform system for microRNA annotation, RNA, 2003, 9: 277-279.
65. Griffiths-Jones, S., The microRNA registry, Nucleic Acids Res., 2004, 32: D109-D111.
66. Bartel, D. P., Chen, C. Z., Micromanagers of gene expression: The potentially widespread influence of metazoan microRNAs, Nat. Rev. Genet., 2004, 5(5): 396-400.
67. He, L., Hannon, G. J., MicroRNAs: Small RNAs with a big role in gene regulation, Nat. Rev. Genet., 2004, 5(7): 522-531.
68. Hipfner, D. R., Weigmann, K., Cohen, S. M., The bantam gene regulates Drosophila growth, Genetics, 2002, 161: 1527-1537.
69. Brennecke, J., Hipfner, D. R., Stark, A. et al., bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila, Cell, 2003, 113: 25-36.
70. Xu, P., Vernooy, S. Y., Guo, M. et al., The Drosophila microRNA mir-14 suppresses cell death and is required for normal fat metabolism, Curr. Biol., 2003, 13: 790-795.
71. Johnston, R. J., Hobert, O., A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans, Nature, 2003, 426: 845-849.
72. Chang, S., Johnston, R. J., Frokjaer-Jensen, C. et al., microRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode, Nature, 2004, 430(7001): 785-789.
73. Chen, C. Z., Li, L., Lodish, H. F. et al., microRNAs modulate hematopoietic lineage differentiation. Science, 2004, 303: 83-86.
74. Matthew, N. P., Eliasson, L., Krutzfeldt, J. et al., A pancreatic islet-specific microRNA regulates insulin secretion, Nature, 2004, 432: 226-230.
75. Giraldez, A. J., Cinalli, R. M., Glasner, M. E. et al., microRNAs Regulate Brain Morphogenesis in Zebrafish, Science, 2005, 308: 833-838
76. Stark, A., Brennecke, J., Russell, R. B. et al., Identification of Drosophila microRNA targets, PLOS Biol., 2003, 1: e60.
77. Enright, A. J., John, B., Gaul, U. et al., microRNA targets in Drosophila, Genome Biol., 2003, 5: R1.
78. John, B., Enright, A. J., Aravin, A. et al., Human microRNA Targets, PLoS Biol., 2004, 2(11): e363.
79. Lewis, B. P., Shih, I., Jones-Rhoades, M. W. et al., Prediction of mammalian microRNA targets, Cell, 2003, 115: 787-798.
80. Lewis, B. P., Burge, C. B., Bartel, D. P., Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets, Cell, 2005, 120(1): 15-20.
81. Kiriakidou, M., Nelson, P. T., Kouranov, A. et al., A combined computational-experimental approach predicts human microRNA targets, Genes Dev., 2004, 18(10): 1165-1178.
82. Rehmsmeier, M., Steffen, P., Hochsmann, M. et al., Fast and effective prediction of microRNA/target duplexes, RNA, 2004, 10(10): 1507-1517.
83. Krek, A., Grun, D., Poy, M. N. et al., Combinatorial microRNA target predictions, Nat. Genet., 2005, 37: 495-500.
84. Kuersten, S., Goodwin, E. B., The power of the 3' UTR: translational control and development, Nat. Rev. Genet., 2003, 4: 626-663.
85. Xie, X., Lu, J:, Kulbokas, E. J. et al., Systematic discovery of regulatory motifs in human promoters and 3′UTRs by comparison of several mammals, Nature, 2005, 434: 338-345.
86. Lai, E. C., microRNAs are complementary to 3′UTR motifs that mediate negative post-transcriptional regulation, Nat. Genet., 2002, 30: 363-364.
87. Lingel, A., Simon, B., Izaurralde, E. et al., Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain, Nature, 2003, 426: 465-469.
88. Song, J. J., Liu, J., Tolia, N. H. et al., The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes, Nat. Struct. Biol., 2003, 10: 1026-1032.
89. Yan, K. S., Yan, S., Farooq, A. et al., Structure and conserved RNA binding of the PAZ domain, Nature, 2003, 426: 468-474.
90. Lim, L. P., Lau, N. C., Garrett-Engele, P. et al., Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs, Nature, 2005, 433: 769-773.
91. Ambros, V., The functions of animal microRNAs, Nature, 2004, 431(7006): 350-355.
92. Takamizawa, J., Konishi, H., Yanagisawa, K. et al., Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival, Cancer Res., 2004, 64(11): 3753-3756.
93. Tang, N., Zhang, B. Q., Yan, G. et al., RNA interference-mediated inhibition of Hepatitis B Virus replication, Chinese Science Bulletin, 2004, 49(14): 1470-1475.
94. Xu, Y., Zhu, C. G., Jin, Y. F. et al., Inhibition of BmNPV replication in Bombyx mori cell by dsRNA triggered RNA interference, Chinese Science Bulletin, 2004, 49(12): 1261-1266.