MicroRNAs: small RNAs with a big role in gene regulation (original) (raw)

References

1. del Solar, G. & Espinosa, M. Plasmid copy number control: an ever-growing story. Mol. Microbiol. 37, 492–500 (2000).
   CAS PubMed Google Scholar
2. Mlynarczyk, S. K. & Panning, B. X inactivation: Tsix and Xist as yin and yang. Curr. Biol. 10, R899–R903 (2000).
   CAS PubMed Google Scholar
3. Ambros, V. MicroRNA pathways in flies and worms: growth, death, fat, stress, and timing. Cell 113, 673–676 (2003).
   CAS PubMed Google Scholar
4. Bartel, D. P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281–297 (2004).
   Article CAS PubMed Google Scholar
5. Lai, E. C. microRNAs: runts of the genome assert themselves. Curr. Biol. 13, R925–R936 (2003).
   CAS PubMed Google Scholar
6. Pasquinelli, A. E. & Ruvkun, G. Control of developmental timing by micrornas and their targets. Annu. Rev. Cell Dev. Biol. 18, 495–513 (2002).
   CAS PubMed Google Scholar
7. McManus, M. T. MicroRNAs and cancer. Semin. Cancer Biol. 13, 253–258 (2003).
   CAS PubMed Google Scholar
8. Carrington, J. C. & Ambros, V. Role of microRNAs in plant and animal development. Science 301, 336–338 (2003).
   CAS PubMed Google Scholar
9. Johnston, R. J. & Hobert, O. A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature 426, 845–849 (2003).
   Article CAS PubMed Google Scholar
10. Chalfie, M., Horvitz, H. R. & Sulston, J. E. Mutations that lead to reiterations in the cell lineages of C. elegans. Cell 24, 59–69 (1981).
    CAS PubMed Google Scholar
11. Ambros, V. A hierarchy of regulatory genes controls a larva-to-adult developmental switch in C. elegans. Cell 57, 49–57 (1989).
    CAS PubMed Google Scholar
12. Ambros, V. & Horvitz, H. R. Heterochronic mutants of the nematode Caenorhabditis elegans. Science 226, 409–416 (1984).
    CAS PubMed Google Scholar
13. 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). Described the identification of the first microRNA, lin-4 , and reported the sequence complementarity between lin-4 and the 3′ UTR of the lin-14 mRNA.
    CAS PubMed Google Scholar
14. Wightman, B., Burglin, T. R., Gatto, J., Arasu, P. & Ruvkun, G. Negative regulatory sequences in the lin-14 3'-untranslated region are necessary to generate a temporal switch during Caenorhabditis elegans development. Genes Dev. 5, 1813–1824 (1991).
    CAS PubMed Google Scholar
15. Ruvkun, G. & Giusto, J. The Caenorhabditis elegans heterochronic gene lin-14 encodes a nuclear protein that forms a temporal developmental switch. Nature 338, 313–319 (1989).
    CAS PubMed Google Scholar
16. Olsen, P. H. & Ambros, V. 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, 671–680 (1999).
    CAS PubMed Google Scholar
17. Ha, I., Wightman, B. & Ruvkun, G. A bulged lin-4/lin-14 RNA duplex is sufficient for Caenorhabditis elegans lin-14 temporal gradient formation. Genes Dev. 10, 3041–3050 (1996).
    CAS PubMed Google Scholar
18. 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). Described the translational repression of LIN-14 by lin-4 during temporal regulation of larval development. This was the first functional characterization of a microRNA.
    CAS PubMed Google Scholar
19. Moss, E. G., Lee, R. C. & Ambros, V. The cold shock domain protein LIN-28 controls developmental timing in C. elegans and is regulated by the lin-4 RNA. Cell 88, 637–646 (1997).
    CAS PubMed Google Scholar
20. Reinhart, B. J. et al. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403, 901–906 (2000).
    Article CAS PubMed Google Scholar
21. Lin, S. Y. et al. The C. elegans hunchback homolog, hbl-1, controls temporal patterning and is a probable microRNA target. Dev. Cell 4, 639–650 (2003).
    CAS PubMed Google Scholar
22. Abrahante, J. E. et al. The _Caenorhabditis elegans hunchback_-like gene lin-57/hbl-1 controls developmental time and is regulated by microRNAs. Dev. Cell 4, 625–637 (2003).
    CAS PubMed Google Scholar
23. Slack, F. J. et al. 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, 659–669 (2000).
    Article CAS PubMed Google Scholar
24. Vella, M. C., Choi, E. Y., Lin, S. Y., Reinert, K. & Slack, F. J. The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3′ UTR. Genes Dev. 18, 132–137 (2004).
    CAS PubMed PubMed Central Google Scholar
25. Lagos-Quintana, M. et al. Identification of tissue-specific microRNAs from mouse. Curr. Biol. 12, 735–739 (2002).
    Article CAS PubMed Google Scholar
26. Sempere, L. F. 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. 5, R13 (2004).
    PubMed PubMed Central Google Scholar
27. Pasquinelli, A. E. et al. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408, 86–89 (2000).
    CAS PubMed Google Scholar
28. Lee, Y. et al. The nuclear RNase III Drosha initiates microRNA processing. Nature 425, 415–419 (2003). Described the identification of Drosha and characterizes its function in processing pri-miRNA into pre-miRNA.
    CAS PubMed Google Scholar
29. Lee, Y., Jeon, K., Lee, J. T., Kim, S. & Kim, V. N. MicroRNA maturation: stepwise processing and subcellular localization. EMBO J. 21, 4663–4670 (2002).
    CAS PubMed PubMed Central Google Scholar
30. Hannon, G. J. RNA interference. Nature 418, 244–251 (2002).
    CAS PubMed Google Scholar
31. Elbashir, S. M. et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494–498 (2001).
    CAS PubMed Google Scholar
32. Elbashir, S. M., Lendeckel, W. & Tuschl, T. RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev. 15, 188–200 (2001).
    CAS PubMed PubMed Central Google Scholar
33. Zamore, P. D., Tuschl, T., Sharp, P. A. & Bartel, D. P. RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101, 25–33 (2000).
    CAS PubMed Google Scholar
34. Baulcombe, D. Viruses and gene silencing in plants. Arch. Virol. 15 (Suppl.), 189–201 (1999).
    CAS Google Scholar
35. Aufsatz, W., Mette, M. F., van der Winden, J., Matzke, A. J. & Matzke, M. RNA-directed DNA methylation in Arabidopsis. Proc. Natl Acad. Sci. USA 99 (Suppl 4), 16499–16506 (2002).
    CAS PubMed PubMed Central Google Scholar
36. Mette, M. F., Aufsatz, W., van der Winden, J., Matzke, M. A. & Matzke, A. J. Transcriptional silencing and promoter methylation triggered by double-stranded RNA. EMBO J. 19, 5194–5201 (2000).
    CAS PubMed PubMed Central Google Scholar
37. Grewal, S. I. & Moazed, D. Heterochromatin and epigenetic control of gene expression. Science 301, 798–802 (2003).
    CAS PubMed Google Scholar
38. Volpe, T. A. et al. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297, 1833–1837 (2002).
    CAS PubMed Google Scholar
39. Ketting, R. F., Haverkamp, T. H., van Luenen, H. G. & Plasterk, R. H. Mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner syndrome helicase and RNaseD. Cell 99, 133–141 (1999).
    CAS PubMed Google Scholar
40. Tabara, H. et al. The rde-1 gene, RNA interference, and transposon silencing in C. elegans. Cell 99, 123–132 (1999).
    CAS PubMed Google Scholar
41. Chen, X. A MicroRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303, 2022–2025 (2004).
    CAS PubMed Google Scholar
42. Llave, C., Xie, Z., Kasschau, K. D. & Carrington, J. C. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297, 2053–2056 (2002).
    CAS PubMed Google Scholar
43. Rhoades, M. W. et al. Prediction of plant microRNA targets. Cell 110, 513–520 (2002). The first bioinfomatic effort to predict microRNA targets on the basis of sequence complementarity between plant miRNAs and their putative targets. It has guided functional studies of several miRNAs.
    CAS PubMed Google Scholar
44. Yekta, S., Shih, I. H. & Bartel, D. P. MicroRNA-directed cleavage of HOXB8 mRNA. Science 304, 594–596 (2004).
    CAS PubMed Google Scholar
45. Doench, J. G., Petersen, C. P. & Sharp, P. A. siRNAs can function as miRNAs. Genes Dev. 17, 438–442 (2003).
    CAS PubMed PubMed Central Google Scholar
46. Bernstein, E., Caudy, A. A., Hammond, S. M. & Hannon, G. J. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409, 363–366 (2001). Described the identification of Dicer and characterized its function in processing long dsRNAs into small interfering RNAs.
    CAS PubMed Google Scholar
47. Hutvagner, G. et al. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293, 834–838 (2001).
    CAS PubMed Google Scholar
48. Hammond, S. M., Boettcher, S., Caudy, A. A., Kobayashi, R. & Hannon, G. J. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 293, 1146–1150 (2001). Described the purification of the RISC, and the identification of Argonaute 2 as a key component.
    CAS PubMed Google Scholar
49. Caudy, A. A., Myers, M., Hannon, G. J. & Hammond, S. M. Fragile X-related protein and VIG associate with the RNA interference machinery. Genes Dev. 16, 2491–2496 (2002).
    CAS PubMed PubMed Central Google Scholar
50. Mourelatos, Z. et al. miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev. 16, 720–728 (2002).
    CAS PubMed PubMed Central Google Scholar
51. Dostie, J., Mourelatos, Z., Yang, M., Sharma, A. & Dreyfuss, G. Numerous microRNPs in neuronal cells containing novel microRNAs. RNA 9, 180–186 (2003).
    CAS PubMed PubMed Central Google Scholar
52. Lagos-Quintana, M., Rauhut, R., Meyer, J., Borkhardt, A. & Tuschl, T. New microRNAs from mouse and human. RNA 9, 175–179 (2003).
    CAS PubMed PubMed Central Google Scholar
53. Zeng, Y. & Cullen, B. R. Sequence requirements for micro RNA processing and function in human cells. RNA 9, 112–123 (2003).
    CAS PubMed PubMed Central Google Scholar
54. Lund, E., Guttinger, S., Calado, A., Dahlberg, J. E. & Kutay, U. Nuclear export of microRNA precursors. Science 303, 95–98 (2004).
    CAS PubMed Google Scholar
55. Grishok, A. et al. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106, 23–34 (2001).
    CAS PubMed Google Scholar
56. Ketting, R. F. et al. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev. 15, 2654–2659 (2001).
    CAS PubMed PubMed Central Google Scholar
57. Lingel, A., Simon, B., Izaurralde, E. & Sattler, M. Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain. Nature 426, 465–469 (2003).
    CAS PubMed Google Scholar
58. Song, J. J. et al. The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nature Struct. Biol. 10, 1026–1032 (2003).
    CAS PubMed Google Scholar
59. Yan, K. S. et al. Structure and conserved RNA binding of the PAZ domain. Nature 426, 468–474 (2003).
    PubMed Google Scholar
60. Carmell, M. A. & Hannon, G. J. RNase III enzymes and the initiation of gene silencing. Nature Struct. Mol. Biol. 11, 214–218 (2004).
    CAS Google Scholar
61. Blaszczyk, J. et al. Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage. Structure (Camb). 9, 1225–1236 (2001).
    CAS Google Scholar
62. Papp, I. et al. Evidence for nuclear processing of plant micro RNA and short interfering RNA precursors. Plant Physiol. 132, 1382–1390 (2003).
    CAS PubMed PubMed Central Google Scholar
63. Park, W., Li, J., Song, R., Messing, J. & Chen, X. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr. Biol. 12, 1484–1495 (2002).
    CAS PubMed PubMed Central Google Scholar
64. Timmons, L. The long and short of siRNAs. Mol. Cell 10, 435–437 (2002).
    CAS PubMed Google Scholar
65. Schauer, S. E., Jacobsen, S. E., Meinke, D. W. & Ray, A. DICER-LIKE1: blind men and elephants in Arabidopsis development. Trends Plant Sci. 7, 487–491 (2002).
    CAS PubMed Google Scholar
66. Pham, J. W., Pellino, J. L., Lee, Y. S., Carthew, R. W. & Sontheimer, E. J. A Dicer-2-dependent 80S complex cleaves targeted mRNAs during RNAi in Drosophila. Cell 117, 83–94 (2004).
    CAS PubMed Google Scholar
67. Lee, Y. S. et al. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 117, 69–81 (2004).
    CAS PubMed Google Scholar
68. Jin, P. et al. Biochemical and genetic interaction between the fragile X mental retardation protein and the microRNA pathway. Nature Neurosci. 7, 113–117 (2004).
    CAS PubMed Google Scholar
69. Liu, Q. et al. R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science 301, 1921–1925 (2003).
    CAS PubMed Google Scholar
70. Pellino, J. L. & Sontheimer, E. J. R2D2 leads the silencing trigger to mRNA's death star. Cell 115, 132–133 (2003).
    CAS PubMed Google Scholar
71. Schwarz, D. S. et al. Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199–208 (2003).
    CAS PubMed Google Scholar
72. Khvorova, A., Reynolds, A. & Jayasena, S. D. Functional siRNAs and miRNAs exhibit strand bias. Cell 115, 209–216 (2003). This paper, together with reference 71, characterized the regulatory mechanism of the asymmetric assembly of siRNA/miRNA into the RISC complex.
    CAS PubMed Google Scholar
73. 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).
    CAS PubMed Google Scholar
74. Hake, S. MicroRNAs: a role in plant development. Curr. Biol. 13, R851–R852 (2003).
    CAS PubMed Google Scholar
75. Carmell, M. A., Xuan, Z., Zhang, M. Q. & Hannon, G. J. The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes Dev. 16, 2733–2742 (2002).
    CAS PubMed Google Scholar
76. Caudy, A. A. et al. A micrococcal nuclease homologue in RNAi effector complexes. Nature 425, 411–414 (2003).
    CAS PubMed Google Scholar
77. 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).
    CAS PubMed Google Scholar
78. Lagos-Quintana, M., Rauhut, R., Lendeckel, W. & Tuschl, T. Identification of novel genes coding for small expressed RNAs. Science 294, 853–858 (2001).
    CAS PubMed Google Scholar
79. Lee, R. C. & Ambros, V. An extensive class of small RNAs in Caenorhabditis elegans. Science 294, 862–864 (2001). This paper, together with references 77 and 78, was among the first cloning efforts to identify large numbers of miRNAs from worm, fly and mammals.
    CAS PubMed Google Scholar
80. Kim, J. et al. Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc. Natl Acad. Sci. USA 101, 360–365 (2004).
    CAS PubMed Google Scholar
81. Griffiths-Jones, S. The microRNA Registry. Nucleic Acids Res. 32 (Database issue), D109–D111 (2004).
    CAS PubMed PubMed Central Google Scholar
82. Reinhart, B. J., Weinstein, E. G., Rhoades, M. W., Bartel, B. & Bartel, D. P. MicroRNAs in plants. Genes Dev. 16, 1616–1626 (2002).
    CAS PubMed PubMed Central Google Scholar
83. Lim, L. P., Glasner, M. E., Yekta, S., Burge, C. B. & Bartel, D. P. Vertebrate microRNA genes. Science 299, 1540 (2003).
    CAS PubMed Google Scholar
84. Lim, L. P. et al. The microRNAs of Caenorhabditis elegans. Genes Dev. 17, 991–1008 (2003).
    CAS PubMed PubMed Central Google Scholar
85. Sempere, L. F., Sokol, N. S., Dubrovsky, E. B., Berger, E. M. & Ambros, V. Temporal regulation of microRNA expression in Drosophila melanogaster mediated by hormonal signals and broad-complex gene activity. Dev. Biol. 259, 9–18 (2003).
    CAS PubMed Google Scholar
86. Houbaviy, H. B., Murray, M. F. & Sharp, P. A. Embryonic stem cell-specific microRNAs. Dev. Cell 5, 351–358 (2003).
    CAS PubMed Google Scholar
87. Aravin, A. A. et al. The small RNA profile during Drosophila melanogaster development. Dev. Cell 5, 337–350 (2003).
    CAS PubMed Google Scholar
88. Metzler, M., Wilda, M., Busch, K., Viehmann, S. & Borkhardt, A. High expression of precursor microRNA-155/BIC RNA in children with Burkitt lymphoma. Genes Chromosomes Cancer 39, 167–169 (2004).
    CAS PubMed Google Scholar
89. 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).
    CAS PubMed PubMed Central Google Scholar
90. Krichevsky, A. M., King, K. S., Donahue, C. P., Khrapko, K. & Kosik, K. S. A microRNA array reveals extensive regulation of microRNAs during brain development. RNA 9, 1274–1281 (2003).
    CAS PubMed PubMed Central Google Scholar
91. Knight, S. W. & Bass, B. L. A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science 293, 2269–2271 (2001).
    CAS PubMed PubMed Central Google Scholar
92. Wienholds, E., Koudijs, M. J., van Eeden, F. J., Cuppen, E. & Plasterk, R. H. The microRNA-producing enzyme Dicer1 is essential for zebrafish development. Nature Genet. 35, 217–218 (2003).
    CAS PubMed Google Scholar
93. Bernstein, E. et al. Dicer is essential for mouse development. Nature Genet. 35, 215–217 (2003).
    CAS PubMed Google Scholar
94. Moussian, B., Schoof, H., Haecker, A., Jurgens, G. & Laux, T. Role of the ZWILLE gene in the regulation of central shoot meristem cell fate during Arabidopsis embryogenesis. EMBO J. 17, 1799–1809 (1998).
    CAS PubMed PubMed Central Google Scholar
95. Cox, D. N. et al. A novel class of evolutionarily conserved genes defined by piwi are essential for stem cell self-renewal. Genes Dev. 12, 3715–3727 (1998).
    CAS PubMed PubMed Central Google Scholar
96. Hipfner, D. R., Weigmann, K. & Cohen, S. M. The Bantam gene regulates Drosophila growth. Genetics 161, 1527–1537 (2002).
    CAS PubMed PubMed Central Google Scholar
97. 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).
    CAS PubMed Google Scholar
98. Palatnik, J. F. et al. Control of leaf morphogenesis by microRNAs. Nature 425, 257–263 (2003).
    CAS PubMed Google Scholar
99. Chen, C. Z., Li, L., Lodish, H. F. & Bartel, D. P. MicroRNAs modulate hematopoietic lineage differentiation. Science 303, 83–86 (2004).
    CAS PubMed Google Scholar
100. 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).
     CAS PubMed Google Scholar
101. Stark, A., Brennecke, J., Russell, R. B. & Cohen, S. M. Identification of Drosophila microRNA targets. PLoS Biol. 1, E60 (2003).
     PubMed PubMed Central Google Scholar
102. 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).
     CAS PubMed PubMed Central Google Scholar
103. Michael, M. Z., O'Connor, S. M., 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).
     CAS PubMed Google Scholar
104. Tang, G., Reinhart, B. J., Bartel, D. P. & Zamore, P. D. A biochemical framework for RNA silencing in plants. Genes Dev. 17, 49–63 (2003).
     CAS PubMed PubMed Central Google Scholar
105. Emery, J. F. et al. Radial patterning of Arabidopsis shoots by class III HD-ZIP and KANADI genes. Curr. Biol. 13, 1768–1774 (2003).
     CAS PubMed Google Scholar
106. Juarez, M. T., Kui, J. S., Thomas, J., Heller, B. A. & Timmermans, M. C. microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity. Nature 428, 84–88 (2004).
     CAS PubMed Google Scholar

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