The small RNA profile during Drosophila melanogaster development

Developmental Cell

Volumn 5, Issue 2, 2003, Pages 337-350

  Aravin, Alexei A ^a   Lagos Quintana, Mariana ^b   Yalcin, Abdullah ^c   Zavolan, Mihaela ^b   Marks, Debora ^d   Snyder, Ben ^b   Gaasterland, Terry ^b   Meyer, Jutta ^b   Tuschl, Thomas ^b  

^a INSTITUTE OF MOLECULAR GENETICS   (Russian Federation)

^b ROCKEFELLER UNIVERSITY   (United States)

^c MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

^d Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICROSATELLITE DNA; MITOCHONDRIAL RNA; RIBONUCLEASE III; RIBOSOME RNA; RNA; SATELLITE DNA; SMALL NUCLEAR RNA; SMALL NUCLEOLAR RNA; TRANSFER RNA;

ANIMAL CELL; CHROMATIN STRUCTURE; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; EMBRYO; HETEROCHROMATIN; INSECT DEVELOPMENT; ISOLATION PROCEDURE; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; REGULATORY MECHANISM; REVIEW; RNA ANALYSIS; RNA CLEAVAGE; RNA SEQUENCE; TESTIS; TRANSPOSON;

ANIMALIA; DROSOPHILA MELANOGASTER; INSECTA; MELANOGASTER; TRANSPOSONS;

EID: 0041941514     PISSN: 15345807     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1534-5807(03)00228-4     Document Type: Article

References (103)

1. Abrahante J.E. Daul A.L. Li M. Volk M.L. Tennessen J.M. Miller E.A. Rougvie A.E. The Caenorhabditis elegans hunchback-like gene lin-57/hbl-1 controls developmental time and is regulated by microRNAs Dev. Cell 4 2003 625-637
2. Ambros V. Bartel B. Bartel D.P. Burge C.B. Carrington J.C. Chen X. Dreyfuss G. Eddy S.R. Griffiths-Jones S. Marshall M. et al. A uniform system for microRNA annotation RNA 9 2003 277-279
3. Ambros V. Lee R.C. Lavanway A. Williams P.T. Jewell D. MicroRNAs and Other Tiny Endogenous RNAs in C. elegans Curr. Biol. 13 2003 807-818
4. Aravin A.A. Naumova N.M. Tulin A.V. Vagin V.V. Rozovsky Y.M. Gvozdev V.A. Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline Curr. Biol. 11 2001 1017-1027
5. Bashirullah A. Pasquinelli A.E. Kiger A.A. Perrimon N. Ruvkun G. Thummel C.S. Coordinate regulation of small temporal RNAs at the onset of Drosophila metamorphosis Dev. Biol. 259 2003 1-8
6. Bender M. New lethal loci in the 42AB region of the Drosophila melanogaster 2nd chromosome Drosoph. Inf. Serv. 77 1996 143
7. 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 2001 363-366
8. Bomsztyk K. Van Seuningen I. Suzuki H. Denisenko O. Ostrowski J. Diverse molecular interactions of the hnRNP K protein FEBS Lett. 403 1997 113-115
9. 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 2003 25-36
10. Caplen N.J. Parrish S. Imani F. Fire A. Morgan R.A. Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems Proc. Natl. Acad. Sci. USA 98 2001 9742-9747
11. 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 2002 2733-2742
12. Chomczynski P. Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction Anal. Biochem. 162 1987 156-159
13. Dejgaard K. Leffers H. Rasmussen H.H. Madsen P. Kruse T.A. Gesser B. Nielsen H. Celis J.E. Identification, molecular cloning, expression and chromosome mapping of a family of transformation upregulated hnRNP-K proteins derived by alternative splicing J. Mol. Biol. 236 1994 33-48
14. Denli A.M. Hannon G.J. Rnai: an ever-growing puzzle Trends Biochem. Sci. 28 2003 196-201
15. Djikeng A. Shi H. Tschudi C. Ullu E. RNA interference in Trypanosoma brucei: cloning of small interfering RNAs provides evidence for retroposon-derived 24-26-nucleotide RNAs RNA 7 2001 1522-1530
16. Doench J.G. Petersen C.P. Sharp P.A. siRNAs can function as miRNAs Genes Dev. 17 2003 438-442
17. Dostie J. Mourelatos Z. Yang M. Sharma A. Dreyfuss G. Numerous microRNPs in neuronal cells containing novel microRNAs RNA 9 2003 180-186
18. Dynlacht B.D. Brook A. Dembski M. Yenush L. Dyson N. DNA-binding and trans-activation properties of Drosophila E2F and DP proteins Proc. Natl. Acad. Sci. USA 91 1994 6359-6363
19. Elbashir S.M. Harborth J. Lendeckel W. Yalcin A. Weber K. Tuschl T. Duplexes of 21-nucleotide RNAs mediate RNA interference in mammalian cell culture Nature 411 2001 494-498
20. Elbashir S.M. Lendeckel W. Tuschl T. RNA interference is mediated by 21 and 22 nt RNAs Genes Dev. 15 2001 188-200
21. Finnegan E.J. Margis R. Waterhouse P.M. Posttranscriptional gene silencing is not compromised in the Arabidopsis CARPEL FACTORY (DICER-LIKE1) mutant, a homolog of Dicer-1 from Drosophila Curr. Biol. 13 2003 236-240
22. Fogarty P. Campbell S.D. Abu-Shumays R. Phalle B.S. Yu K.R. Uy G.L. Goldberg M.L. Sullivan W. The Drosophila grapes gene is related to checkpoint gene chk1/rad27 and is required for late syncytial division fidelity Curr. Biol. 7 1997 418-426
23. Golden T.A. Schauer S.E. Lang J.D. Pien S. Mushegian A.R. Grossniklaus U. Meinke D.W. Ray A. SHORT INTEGUMENTS1/SUSPENSOR1/CARPEL FACTORY, a Dicer homolog, is a maternal effect gene required for embryo development in Arabidopsis Plant Physiol. 130 2002 808-822
24. Grad Y. Aach J. Hayes G.D. Reinhart B.J. Church G.M. Ruvkun G. Kim J. Computational and experimental identification of C. elegans microRNAs Mol. Cell 11 2003 1253-1263
25. Grishok A. Mello C.C. RNAi (Nematodes: Caenorhabditis elegans) Adv. Genet. 46 2002 339-360
26. Grishok A. Pasquinelli A.E. Conte D. Li N. Parrish S. Ha I. Baillie D.L. Fire A. Ruvkun G. Mello C.C. 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
27. Hall I.M. Shankaranarayana G.D. Noma K. Ayoub N. Cohen A. Grewal S.I. Establishment and maintenance of a heterochromatin domain Science 297 2002 2232-2237
28. Hamilton A. Voinnet O. Chappell L. Baulcombe D. Two classes of short interfering RNA in RNA silencing EMBO J. 21 2002 4671-4679
29. Hammond S.M. Bernstein E. Beach D. Hannon G.J. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells Nature 404 2000 293-296
30. 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 2001 1146-1150
31. Hoskins, R.A., Smith, C.D., Carlson, J.W., Carvalho, A.B., Halpern, A., Kaminker, J.S., Kennedy, C., Mungall, C.J., Sullivan, B.A., Sutton, G.G., et al. (2002). Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. Genome Biol. 3, RESEARCH0085.1-0085.16.
32. Hutvágner G. McLachlan J. Bálint É. Tuschl T. Zamore P.D. A cellular function for the RNA interference enzyme Dicer in small temporal RNA maturation Science 93 2001 834-838
33. Hutvágner G. Zamore P.D. A microRNA in a multiple-turnover RNAi enzyme complex Science 297 2002 2056-2060
34. Johnson K.N. Christian P.D. The novel genome organization of the insect picorna-like virus Drosophila C virus suggests this virus belongs to a previously undescribed virus family J. Gen. Virol. 79 1998 191-203
35. Kaminker, J.S., Bergman, C.M., Kronmiller, B., Carlson, J., Svirskas, R., Patel, S., Frise, E., Wheeler, D.A., Lewis, S.E., Rubin, G.M., et al. (2002). The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol. 3, RESEARCH0084.1-0084.20.
36. Kennerdell J.R. Yamaguchi S. Carthew R.W. RNAi is activated during Drosophila oocyte maturation in a manner dependent on aubergine and spindle-E Genes Dev. 16 2002 1884-1889
37. Ketting R.F. Fischer S.E. Bernstein E. Sijen T. Hannon G.J. Plasterk R.H. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans Genes Dev. 15 2001 2654-2659
38. 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 1999 133-141
39. Kogan G.L. Tulin A.V. Aravin A.A. Abramov Y.A. Kalmykova A.I. Maisonhaute C. Gvozdev V.A. The GATEretrotransposon in Drosophila melanogaster: mobility in heterochromatin and aspects of its expression in germline tissues Mol. Genet. Genomics 269 2003 234-242
40. Lagos-Quintana M. Rauhut R. Lendeckel W. Tuschl T. Identification of novel genes coding for small expressed RNAs Science 294 2001 853-858
41. Lagos-Quintana M. Rauhut R. Meyer J. Borkhardt A. Tuschl T. New microRNAs from mouse and human RNA 9 2003 175-179
42. Lagos-Quintana M. Rauhut R. Yalcin A. Meyer J. Lendeckel W. Tuschl T. Identification of tissue-specific microRNAs from mouse Curr. Biol. 12 2002 735-739
43. Lai E.C. Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation Nat. Genet. 30 2002 363-364
44. 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 2001 858-862
45. Lee R.C. Ambros V. An extensive class of small RNAs in Caenorhabditis elegans Science 294 2001 862-864
46. 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 1993 843-854
47. Lee Y. Jeon K. Lee J.T. Kim S. Kim V.N. MicroRNA maturation: stepwise processing and subcellular localization EMBO J. 21 2002 4663-4670
48. Li H. Li W.X. Ding S.W. Induction and suppression of RNA silencing by an animal virus Science 296 2002 1319-1321
49. Lim L.P. Glasner M.E. Yekta S. Burge C.B. Bartel D.P. Vertebrate microRNA genes Science 299 2003-1540
50. Lim L.P. Lau N.C. Weinstein E.G. Abdelhakim A. Yekta S. Rhoades M.W. Burge C.B. Bartel D.P. The microRNAs of Caenorhabditis elegans Genes Dev. 17 2003 991-1008
51. Lin S.Y. Johnson S.M. Abraham M. Vella M.C. Pasquinelli A. Gamberi C. Gottlieb E. Slack F.J. The C. elegans hunchback homolog, hbl-1, controls temporal patterning and is a probable microRNA target Dev. Cell 4 2003 639-650
52. Livak K.J. Organization and mapping of a sequence on the Drosophila melanogaster X and Y chromosomes that is transcribed during spermatogenesis Genetics 107 1984 611-634
53. Livak K.J. Detailed structure of the Drosophila melanogaster stellate genes and their transcripts Genetics 124 1990 303-316
54. Llave C. Kasschau K.D. Rector M.A. Carrington J.C. Endogenous and silencing-associated small RNAs in plants Plant Cell 14 2002 1605-1619
55. 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 2002 2053-2056
56. Lohe A.R. Hilliker A.J. Roberts P.A. Mapping simple repeated DNA sequences in heterochromatin of Drosophila melanogaster Genetics 134 1993 1149-1174
57. Mallory A.C. Reinhart B.J. Bartel D. Vance V.B. Bowman L.H. A viral suppressor of RNA silencing differentially regulates the accumulation of short interfering RNAs and micro-RNAs in tobacco Proc. Natl. Acad. Sci. USA 99 2002 15228-15233
58. Martinez J. Patkaniowska A. Urlaub H. Lührmann R. Tuschl T. Single-stranded antisense siRNAs guide target RNA cleavage in RNAi Cell 110 2002 563-574
59. Mattick J.S. Gagen M.J. The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms Mol. Biol. Evol. 18 2001 1611-1630
60. Merino E. Balbas P. Puente J.L. Bolivar F. Antisense overlapping open reading frames in genes from bacteria to humans Nucleic Acids Res. 22 1994 1903-1908
61. Mette M.F. van der Winden J. Matzke M. Matzke A.J. Short RNAs can identify new candidate transposable element families in Arabidopsis Plant Physiol. 130 2002 6-9
62. Mochizuki K. Fine N.A. Fujisawa T. Gorovsky M.A. Analysis of a piwi-related gene implicates small RNAs in genome rearrangement in tetrahymena Cell 110 2002 689-699
63. Moss E.G. MicroRNAs: hidden in the genome Curr. Biol. 12 2002 R138-R140
64. Mourelatos Z. Dostie J. Paushkin S. Sharma A. Charroux B. Abel L. Rappsilber J. Mann M. Dreyfuss G. miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs Genes Dev. 16 2002 720-728
65. Nykänen A. Haley B. Zamore P.D. ATP requirements and small interfering RNA structure in the RNA interference pathway Cell 107 2001 309-321
66. 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 1999 671-680
67. Pal-Bhadra M. Bhadra U. Birchler J.A. RNAi related mechanism affect both transcriptional and posttranscriptional transgene silencing in Drosophila Mol. Cell 9 2002 315-327
68. Palumbo G. Bonaccorsi S. Robbins L.G. Pimpinelli S. Genetic analysis of Stellate elements of Drosophila melanogaster Genetics 138 1994 1181-1197
69. Park, W., Li, J., Song, R., Messing, J., and Chen, X. (2002). CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr. Biol. 12.
70. Pasquinelli A.E. Reinhart B.J. Slack F. Martindale M.Q. Kuroda M.I. Maller B. Hayward D.C. Ball E.D. Degnan B. Müller P. et al. Conservation of the sequence of let-7 heterochronic regulatory RNA Nature 408 2000 86-89
71. Pasquinelli A.E. Ruvkun G. Control and developmental timing by microRNAs and their targets Annu. Rev. Cell Dev. Biol. 18 2002 495-513
72. Pfeffer S. Lagos-Quintana M. Tuschl T. Cloning of small RNA molecules. In Ausubel F.M. Brent R. Kingston R.E. Moore D.D. Seidmann J.G. Smith J.A. Struhl K. (Eds.), Current Protocols in Molecular Biology 2003 26 Wiley and Sons New York 24.21-26.24.16.
73. Plasterk R.H. RNA silencing: the genome's immune system Science 296 2002 1263-1265
74. Provost P. Dishart D. Doucet J. Frendewey D. Samuelsson B. Radmark O. Ribonuclease activity and RNA binding of recombinant human Dicer EMBO J. 21 2002 5864-5874
75. Reinhart B.J. Bartel D.P. Small RNAs correspond to centromere heterochromatic repeats Science 297 2002 1831
76. Reinhart B.J. Slack F.J. Basson M. Pasquinelli A.E. Bettinger J.C. Rougvie A.E. Horvitz H.R. Ruvkun G. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans Nature 403 2000 901-906
77. Reinhart B.J. Weinstein E.G. Rhoades M.W. Bartel B. Bartel D.P. MicroRNAs in plants Genes Dev. 16 2002 1616-1626
78. Rhoades M. Reinhart B. Lim L. Burge C. Bartel B. Bartel D. Prediction of plant microRNA targets Cell 110 2002 513
79. Roignant J.Y. Carre C. Mugat B. Szymczak D. Lepesant J.A. Antoniewski C. Absence of transitive and systemic pathways allows cell-specific and isoform-specific RNAi in Drosophila RNA 9 2003 299-308
80. Schauer S.E. Jacobsen S.E. Meinke D.W. Ray A. DICER-LIKE1: blind men and elephants in arabidopsis development Trends Plant Sci. 7 2002 487-491
81. Schmidt A. Palumbo G. Bozzetti M.P. Tritto P. Pimpinelli S. Schafer U. Genetic and molecular characterization of sting, a gene involved in crystal formation and meiotic drive in the male germ line of Drosophila melanogaster Genetics 151 1999 749-760
82. Seggerson K. Tang L. Moss E.G. Two genetic circuits repress the Caenorhabditis elegans heterochronic gene lin-28 after translation initiation Dev. Biol. 243 2002 215-225
83. 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 2003 9-18
84. Shendure, J., and Church, G.M. (2002). Computational discovery of sense-antisense transcription in the human and mouse genomes. Genome Biol. 3, RESEARCH0044.1-0044.14.
85. Stapleton W. Das S. McKee B.D. A role of the Drosophila homeless gene in repression of Stellate in male meiosis Chromosoma 110 2001 228-240
86. Tabara H. Sarkissian M. Kelly W.G. Fleenor J. Grishok A. Timmons L. Fire A. Mello C.C. The rde-1 gene, RNA interference, and transposon silencing in C. elegans Cell 99 1999 123-132
87. Tang G. Reinhart B.J. Bartel D.P. Zamore P.D. A biochemical framework for RNA silencing in plants Genes Dev. 17 2003 49-63
88. Tautz D. Hancock J.M. Webb D.A. Tautz C. Dover G.A. Complete sequences of the rRNA genes of Drosophila melanogaster Mol. Biol. Evol. 5 1988 366-376
89. Taverna S.D. Coyne R.S. Allis C.D. Methylation of histone h3 at lysine 9 targets programmed DNA elimination in tetrahymena Cell 110 2002 701-711
90. Voinnet O. RNA silencing: small RNAs as ubiquitous regulators of gene expression Curr. Opin. Plant Biol. 5 2002 444-451
91. Volpe T.A. Kidner C. Hall I.M. Teng G. Grewal S.I. Martienssen R.A. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi Science 297 2002 1833-1837
92. Wassenegger M. Gene silencing-based disease resistance Transgenic Res. 11 2002 639-653
93. Waterhouse P.M. Wang M.B. Lough T. Gene silencing as an adaptive defence against viruses Nature 411 2001 834-842
94. 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 1993 855-862
95. Williams R.W. Rubin G.M. ARGONAUTE1 is required for efficient RNA interference in Drosophila embryos Proc. Natl. Acad. Sci. USA 99 2002 6889-6894
96. Wu-Scharf D. Jeong B. Zhang C. Cerutti H. Transgene and transposon silencing in Chlamydomonas reinhardtii by a DEAH-Box RNA helicase Science 290 2000 1159-1163
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 2003 790-795
98. Yelin R. Dahary D. Sorek R. Levanon E.Y. Goldstein O. Shoshan A. Diber A. Biton S. Tamir Y. Khosravi R. et al. Widespread occurrence of antisense transcription in the human genome Nat. Biotechnol. 21 2003 379-386
99. Yuan G. Klambt C. Bachellerie J.P. Brosius J. Hüttenhofer A. RNomics in Drosophila melanogaster: identification of 66 candidates for novel non-messenger RNAs Nucleic Acids Res. 31 2003 2495-2507
100. Zamore P.D. Ancient pathways programmed by small RNAs Science 296 2002 1265-1269
101. 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 2000 25-33
102. Zhang H. Kolb F.A. Brondani V. Billy E. Filipowicz W. Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP EMBO J. 21 2002 5875-5885
103. Zilberman D. Cao X. Jacobsen S.E. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation Science 299 2003 716-719