Processing of pre-microRNAs by the Dicer-1-Loquacious complex in drosophila cells

PLoS Biology

Volumn 3, Issue 7, 2005, Pages 1202-1212

  Saito, Kuniaki ^a   Ishizuka, Akira ^a   Siomi, Haruhiko ^a   Siomi, Mikiko C ^a  

^a UNIVERSITY OF TOKUSHIMA   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; DROSOPHILA PROTEIN; LOQUACIOUS PROTEIN, DROSOPHILA; RIBONUCLEASE III; RNA BINDING PROTEIN;

ANIMAL CELL; ANTIBODY AFFINITY; ARTICLE; BIOGENESIS; CONTROLLED STUDY; DROSOPHILA; GENE EXPRESSION REGULATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; RNA BINDING; RNA PURIFICATION; RNA STRUCTURE; AMINO ACID SEQUENCE; ANIMAL; DROSOPHILA MELANOGASTER; METABOLISM; MOLECULAR GENETICS; PROTEIN ANALYSIS; SEQUENCE ALIGNMENT;

AMINO ACID SEQUENCE; ANIMALS; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; MICRORNAS; MOLECULAR SEQUENCE DATA; PROTEIN INTERACTION MAPPING; RIBONUCLEASE III; RNA-BINDING PROTEINS; SEQUENCE ALIGNMENT;

EID: 22744454230     PISSN: 15449173     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.0030235     Document Type: Article

References (82)

1. Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854.
2. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, et al. (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403: 901-906.
3. Llave C, Xie Z, Kasschau KD, Carrington JC (2002) Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297: 2053-2056.
4. Brennecke J, Hipfner DR, Stark A, Russell RB, Cohen SM (2003) bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 113: 25-36.
5. Palatnik JF, Allen E, Wu X, Schommer C, Schwab R, et al. (2003) Control of leaf morphogenesis by microRNAs. Nature 425: 257-263.
6. Xu P, Vernooy SY, Guo M, Hay BA (2003) The Drosophila microRNA Mir-14 suppresses cell death and is required for normal fat metabolism. Curr Biol 13: 790-795.
7. Johnston RJ, Hobert O (2003) A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature 426: 845-849.
8. Chen CZ, Li L, Lodish HF, Bartel DP (2004) MicroRNAs modulate hematopoietic lineage differentiation. Science 303: 83-86.
9. Yekta S, Shih IH, Bartel DP (2004) MicroRNA-directed cleavage of HOXB8 mRNA. Science 304: 594-596.
10. Carrington JC, Ambros V (2003) Role of microRNAs in plant and animal development. Science 301: 336-338.
11. Bartel DP (2004) MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
12. Baulcombe D (2004) RNA silencing in plants. Nature 431: 356-363.
13. Meister G, Tuschl T (2004) Mechanisms of gene silencing by double-stranded RNA. Nature 431: 343-349.
14. Sontheimer EJ (2005) Assembly and function of RNA silencing complexes. Nat Rev Mol Cell Biol 6: 127-138.
15. Tomari Y, Zamore PD (2005) Perspective: Machines for RNAi. Genes Dev 19: 517-529.
16. Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, et al. (2000) Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408: 86-89.
17. Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001) Identification of novel genes coding for small expressed RNAs. Science 294: 853-858.
18. Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T (2002) Identification of tissue-specific microRNAs from mouse. Curr Biol 12: 735-739.
19. Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T (2003) New microRNAs from mouse and human. RNA 9: 175-179.
20. Lau NC, Lim LP, Weinstein EG, Bartel DP (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294: 858-862.
21. Lee RC, Ambros V (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294: 862-864.
22. Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, et al. (2002) miRNPs: A novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev 16: 720-728.
23. Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP (2002) MicroRNAs in plants. Genes Dev 16: 1616-1626.
24. Ambros V, Lee RC, Lavanway A, Williams PT, Jewell D (2003) MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr Biol 13: 807-818.
25. Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, et al. (2003) The small RNA profile during Drosophila melanogaster development. Dev Cell 5: 337-350.
26. Dostie J, Mourelatos Z, Yang M, Sharma A, Dreyfuss G (2003) Numerous microRNPs in neuronal cells containing novel microRNAs. RNA 9: 180-186.
27. Grad Y, Aach J, Hayes GD, Reinhart BJ, Church GM, et al. (2003) Computational and experimental identification of C. elegans microRNAs. Mol Cell 11: 1253-1263.
28. Houbaviy HB, Murray MF, Sharp PA (2003) Embryonic stem cell-specific MicroRNAs. Dev Cell 5: 351-358.
29. Lai EC, Tomancak P, Williams RW, Rubin GM (2003) Computational identification of Drosophila microRNA genes. Genome Biol 4: R42.
30. Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, et al. (2003) The microRNAs of Caenorhabditis elegans. Genes Dev 17: 991-1008.
31. Berezikov E, Guryev V, van de Belt J, Wienholds E, Plasterk RHA, et al. (2005) Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120: 21-24.
32. John B, Enright AJ, Aravin A, Tuschl T, Sander C, et al. (2004) Human microRNAs targets. PLoS Biol 2: e363.
33. Brennecke J, Stark A, Russell RB, Cohen SM (2005) Principles of microRNA-target recognition. PLoS Biol 3: e85.
34. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, et al. (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433: 769-773.
35. Lee Y, Kim M, Han J, Yeom KH, Lee S, et al. (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J 23: 4051-4060.
36. Lee Y, Jeon K, Lee JT, Kim S, Kim VN (2002) MicroRNA maturation: Stepwise processing and subcellular localization. EMBO J 21: 4663-4670.
37. Lee Y, Ahn C, Han J, Choi H, Kim J, et al. (2003) The nuclear RNase III Drosha initiates microRNA processing. Nature 425: 415-419.
38. Basyuk E, Suavet F, Doglio A, Bordonne R, Bertrand E (2003) Human let-7 stem-loop precursors harbor features of RNase III cleavage products. Nucleic Acids Res 31: 6593-6597.
39. Yi R, Qin Y, Macara IG, Cullen BR (2003) Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev 17: 3011-3016.
40. Bohnsack MT, Czaplinski K, Gorlich D (2004) Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of premiRNAs. RNA 10: 185-191.
41. Lund E, Guttinger S, Calado A, Dahlberg JE, Kutay U (2004) Nuclear export of microRNA precursors. Science 303: 95-98.
42. Hutvagner G, McLachlan J, Pasquinelli AE, Balint E, Tuschl T, et al. (2001) A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293: 834-838.
43. Grishok A, Pasquinelli AE, Conte D, Li N, Parrish S, et al. (2001) Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106: 23-34.
44. Ketting RF, Fischer SE, Bernstein E, Sijen T, Hannon GJ, et al. (2001) Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev 15: 2654-2659.
45. Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, et al. (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115: 199-208.
46. Hutvagner G, Zamore PD (2002) A microRNA in a multiple-turnover RNAi enzyme complex. Science 297: 2056-2060.
47. Olsen PH, Ambros V (1999) 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.
48. Tomari Y, Zamore PD (2005) MicroRNA biogenesis: Drosha can't cut it without a partner. Curr Biol 15: R61-64.
49. Denli AM, Tops BB, Plasterk RH, Ketting RF, Hannon GJ (2004) Processing of primary microRNAs by the Microprocessor complex. Nature 432: 231-235.
50. Gregory RI, Yan KP, Amuthan G, Chendrimada T, Doratotaj B, et al. (2004) The Microprocessor complex mediates the genesis of microRNAs. Nature 432: 235-240.
51. Han J, Lee Y, Yeom KH, Kim YK, Jin H, et al. (2005) The Drosh-DGCR8 complex in primary microRNA processing. Genes Dev 18: 3016-3027.
52. Landthaler M, Yalcin A, Tuschl T (2004) The human DiGeorge syndrome critical region gene 8 and its D. melanogaster homolog are required for miRNA biogenesis. Curr Biol 15: 2162-2167.
53. Papp I, Mette MF, Aufsatz W, Daxinger L, Schauer SE, et al. (2003) Evidence for nuclear processing of plant micro RNA and short interfering RNA precursors. Plant Physiol 132: 1382-1390.
54. Kurihara Y, Watanabe Y (2004) Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc Natl Acad Sci U S A 101: 12753-12758.
55. Vazquez F, Gasciolli V, Crete P, Vaucheret H (2004) The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing. Curr Biol 14: 346-351.
56. Han MH, Goud S, Song L, Fedoroff N (2004) The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proc Natl Acad Sci U S A 101: 1093-1098.
57. Bernstein E, Caudy AA, Hammond SM, Hannon GJ (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409: 363-366.
58. Lee YS, Nakahara K, Pham JW, Kim K, He Z, et al. (2004) Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 117: 69-81.
59. Liu Q, Rand TA, Kalidas S, Du F, Kim HE, et al. (2003) R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science 301: 1921-1925.
60. Okamura K, Ishizuka A, Siomi H, Siomi MC (2004) Distinct roles for Argonaute proteins in small RNA-directed cleavage pathways. Genes Dev 18: 1655-1666.
61. Boutros M, Kiger AA, Armknecht S, Kerr K, Hild M, et al. (2004) Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science 303: 832-835.
62. Lasko P (2000) The Drosophila melanogaster genome: Translation factors and RNA binding proteins. J Cell Biol 150: F51-F56.
63. Tabara H, Yigit E, Siomi H, Mello CC (2002) 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: 861-871.
64. Schwarz DS, Tomari Y, Zamore PD (2004) The RNA-induced silencing complex is a Mg2+-dependent endonuclease. Curr Biol 14: 787-791.
65. Nicholson AW (2003) The ribonuclease III superfamily: Forms and functions in RNA, maturation, decay, and gene silencing. In: Hannon GJeditor. RNAi: A guide to gene silencing. Cold Spring Harbor Laboratory Press, Plainview (New York): pp. 149-174.
66. Tomari Y, Matranga C, Haley B, Martinez N, Zamore PD (2004) A protein sensor for siRNA asymmetry. Science 306: 1377-1380.
67. Peters GA, Hartmann R, Qin J, Sen GC (2001) Modular structure of PACT: Distinct domains for binding and activating PKR. Mol Cell Biol 21: 1908-1920.
68. Zhang H, Kolb F, Jaskiewicz L, Westhof E, Filipowicz W (2004) Single processing center models for human Dicer and bacterial RNase III. Cell 118: 57-68.
69. Patel RC, Sen GC (1998) PACT, a protein activator for the interferon-induced protein kinase, PKR. EMBO J 17: 4379-4390.
70. Gatignol A, Buckler-White A, Berkhout B, Jeang KT (1991) Characterization of a human TAR RNA-binding protein that activates the HIV-1 LTR. Science 251: 1597-1600.
71. Fierro-Monti I, Mathews MB (2000) Proteins binding to duplexed RNA: One motif, multiple functions. Trends Biochem Sci 25: 241-246.
72. Kaempfer R (2003) RNA sensors: Novel regulators of gene expression. EMBO Rep 4: 1043-1047.
73. Saunders LR, Barber GN (2003) The dsRNA binding protein family: Critical roles, diverse cellular functions. FASEB J 17: 961-983.
74. Park H, Davies MV, Langland JO, Chang HW, Nam YS, et al. (1994) TAR RNA-binding protein is an inhibitor of the interferon-induced protein kinase PKR. Proc Natl Acad Sci U S A 91: 4713-4717.
75. Clemens JC, Worby CA, Simonson-Leff N, Muda M, Maehama T, et al. (2000) Use of double-stranded RNA interference in Drosophila cell lines to dissect signal transduction pathways. Proc Natl Acad Sci U S A 97: 6499-6503.
76. Kataoka Y, Takeichi M, Uemura T (2001) Developmental roles and molecular characterization of a Drosophila homologue of Arabidopsis Argonaute1, the founder of a novel gene superfamily. Genes Cells 6: 313-325.
77. Eckmann CR, Jantsch MF (1997) Xlrbpa, a double-stranded RNA-binding protein associated with ribosomes and heterogeneous nuclear RNPs. J Cell Biol 138: 239-253.
78. Hammond SM, Boettcher S, Caudy AA, Kobayashi R, Hannon GJ (2001) Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 293: 1146-1150.
79. Ishizuka A, Siomi MC, Siomi H (2002) A Drosophila fragile X protein interacts with components of RNAi and ribosomal proteins. Genes Dev 16: 2497-2508.
80. Djikeng A, Shi H, Tschudi C, Shen S, Ullu E (2003) An siRNA ribonucleoprotein is found associated with polyribosomes in Trypanosoma brucei. RNA 9: 802-808.
81. Kim J, Krichevsky A, Grad Y, Hayes GD, Kosik KS, et al. (2004) Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc Natl Acad Sci U S A 101: 360-365.
82. Pham JW, Pellino JL, Lee YS, Carthew RW, Sontheimer EJ (2004) A Dicer-2-dependent 80s complex cleaves targeted mRNAs during RNAi in Drosophila. Cell 117: 83-94.