Sequence-specific inhibition of small RNA function

PLoS Biology

Volumn 2, Issue 4, 2004, Pages

  Hutvágner, György ^a   Simard, Martin J ^a   Mello, Craig C ^a   Zamore, Phillip D ^a  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HELMINTH PROTEIN; MESSENGER RNA; MICRORNA; OLIGONUCLEOTIDE; PROTEIN ALG 1; PROTEIN ALG 2; PROTEIN S 100; SMALL INTERFERING RNA; UNCLASSIFIED DRUG;

ANIMAL EXPERIMENT; ARTICLE; CAENORHABDITIS ELEGANS; CELL LYSATE; CONTROLLED STUDY; DROSOPHILA; EXTRACT; GENE FUNCTION; HELA CELL; HUMAN; HUMAN CELL; HUMAN CELL CULTURE; NONHUMAN; NUCLEOTIDE SEQUENCE; RNA CLEAVAGE; RNA SEQUENCE; RNA SPLICING; ANIMAL; BIOTINYLATION; CHEMISTRY; GENE SILENCING; GENETIC PROCEDURES; GENETIC TRANSFECTION; METABOLISM; MOLECULAR GENETICS; NORTHERN BLOTTING; PHENOTYPE; RNA INTERFERENCE; TRANSGENIC ANIMAL;

ANIMALIA; CAENORHABDITIS; CAENORHABDITIS ELEGANS; VERMES;

ANIMALS; ANIMALS, GENETICALLY MODIFIED; BIOTINYLATION; BLOTTING, NORTHERN; CAENORHABDITIS ELEGANS; DROSOPHILA; GENE SILENCING; GENETIC TECHNIQUES; HELA CELLS; HUMANS; MICRORNAS; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDES; PHENOTYPE; RNA INTERFERENCE; RNA, MESSENGER; RNA, SMALL INTERFERING; TRANSFECTION;

EID: 19344378192     PISSN: 15449173     EISSN: None     Source Type: Journal    
DOI: 10.1371/journal.pbio.0020098     Document Type: Article

References (81)

1. 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. Find this article online
2. 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. Find this article online
3. 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. Find this article online
4. Boutla A, Delidakis C, Tabler M (2003) 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: 4973-4980. Find this article online
5. Brennecke J, Cohen S (2003) Towards a complete description of the microRNA complement of animal genomes. Genome Biol 4: 228. Find this article online
6. 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. Find this article online
7. Caplen NJ, Fleenor J, Fire A, Morgan RA (2000) dsRNA-mediated gene silencing in cultured Drosophila cells: A tissue culture model for the analysis of RNA interference. Gene 252: 95-105. Find this article online
8. Caplen NJ, Parrish S, Imani F, Fire A, Morgan RA (2001) Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems. Proc Natl Acad Sci U S A 98: 9742-9747. Find this article online
9. Carthew RW (2001) Gene silencing by double-stranded RNA. Curr Opin Cell Biol 13: 244-248. Find this article online
10. Catalanotto C, Azzalin G, Macino G, Cogoni C (2000) Transcription: Gene silencing in worms and fungi. Nature 404: 245. Find this article online
11. Catalanotto C, Azzalin G, Macino G, Cogoni C (2002) Involvement of small RNAs and role of the qde genes in the gene silencing pathway in Neurospora. Genes Dev 16: 790-795. Find this article online
12. Caudy AA, Myers M, Hannon GJ, Hammond SM (2002) Fragile X-related protein and VIG associate with the RNA interference machinery. Genes Dev 16: 2491-2496. Find this article online
13. Cogoni C, Macino G (1997) Isolation of quelling-defective (qde) mutants impaired in posttranscriptional transgene-induced gene silencing in Neurospora crassa. Proc Natl Acad Sci U S A 94: 10233-10238. Find this article online
14. Cogoni C, Macino G (1999a) Gene silencing in Neurospora crassa requires a protein homologous to RNA-dependent RNA polymerase. Nature 399: 166-169. Find this article online
15. Cogoni C, Macino G (1999b) Posttranscriptional gene silencing in Neurospora by a RecQ DNA helicase. Science 286: 2342-2344. Find this article online
16. Conte D, Mello CC (2003) RNA interference in Caenorhabditis elegans. In: Asubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, et al., editors. Current protocols in molecular biology New York: John Wiley and Sons. pp26.23.1-26.23.20.
17. Dalmay T, Hamilton A, Rudd S, Angell S, Baulcombe DC (2000) An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell 101: 543-553. Find this article online
18. Dalmay T, Horsefield R, Braunstein TH, Baulcombe DC (2001) SDE3 encodes an RNA helicase required for post-transcriptional gene silencing in Arabidopsis. EMBO J 20: 2069-2078. Find this article online
19. Doench JG, Petersen CP, Sharp PA (2003) siRNAs can function as miRNAs. Genes Dev 17: 438-442. Find this article online
20. Dostie J, Mourelatos Z, Yang M, Sharma A, Dreyfuss G (2003) Numerous microRNPs in neuronal cells containing novel microRNAs. RNA 9: 180-186. Find this article online
21. Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, et al. (2001a) Duplexes of 21-nucleotide RNAs mediate RNA interference in mammalian cell culture. Nature 411: 494-498. Find this article online
22. Elbashir SM, Lendeckel W, Tuschl T (2001b) RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev 15: 188-200. Find this article online
23. Elbashir SM, Martinez J, Patkaniowska A, Lendeckel W, Tuschl T (2001c) Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J 20: 6877-6888. Find this article online
24. Enright A, John B, Gaul U, Tuschl T, Sander C, et al. (2003) MicroRNA targets in Drosophila. Genome Biol 5: R1. Find this article online
25. Fagard M, Boutet S, Morel J-B, Bellini C, Vaucheret H (2000) AGO1, QDE-2, and RDE-1 are related proteins required for post-transcriptional gene silencing in plants, quelling in fungi, and RNA interference in animals. Proc Natl Acad Sci U S A 97: 11650-11654. Find this article online
26. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, et al. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806-811. Find this article online
27. Grishok A, Mello CC (2002) RNAi (Nematodes: Caenorhabditis elegans). Adv Genet 46: 339-360. Find this article online
28. Grishok A, Tabara H, Mello C (2000) Genetic requirements for inheritance of RNAi in C. elegans. Science 287: 2494-2497. Find this article online
29. 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. Find this article online
30. Ha I, Wightman B, Ruvkun G (1996) A bulged lin-4/lin-14 RNA duplex is sufficient for Caenorhabditis elegans lin-14 temporal gradient formation. Genes Dev 10: 3041-3050. Find this article online
31. Haley B, Tang G, Zamore PD (2003) In vitro analysis of RNA interference in Drosophila melanogaster. Methods 30: 330-336. Find this article online
32. Hammond SM, Boettcher S, Caudy AA, Kobayashi R, Hannon GJ (2001a) Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 293: 1146-1150. Find this article online
33. Hammond SM, Caudy AA, Hannon GJ (2001b) Post-transcriptional gene silencing by double-stranded RNA. Nat Rev Genet 2: 110-119. Find this article online
34. Hutvágner G, Zamore PD (2002) A microRNA in a multiple-turnover RNAi enzyme complex. Science 297: 2056-2060. Find this article online
35. Hutvágner G, McLachlan J, Pasquinelli AE, Balint É, 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. Find this article online
36. Inoue H, Hayase Y, Imura A, Iwai S, Miura K, et al. (1987) Synthesis and hybridization studies on two complementary nona(2′-O-methyl) ribonucleotides. Nucleic Acids Res 15: 6131-6148. Find this article online
37. Ketting RF, Plasterk RH (2000) A genetic link between co-suppression and RNA interference in C. elegans. Nature 404: 296-298. Find this article online
38. Ketting RF, Haverkamp TH, van Luenen HG, Plasterk RH (1999) 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. Find this article online
39. 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. Find this article online
40. Khvorova A, Reynolds A, Jayasena SD (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115: 209-216. Find this article online
41. Knight SW, Bass BL (2001) A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science 293: 2269-2271. Find this article online
42. Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001) Identification of novel genes coding for small expressed RNAs. Science 294: 853-858. Find this article online
43. Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, et al. (2002) Identification of tissue-specific microRNAs from mouse. Curr Biol 12: 735-739. Find this article online
44. 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. Find this article online
45. Lee RC, Ambros V (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294: 862-864. Find this article online
46. 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. Find this article online
47. Lewis B, Shih I, Jones-Rhoades M, Bartel D, Burge C (2003) Prediction of mammalian microRNA targets. Cell 115: 787-798. Find this article online
48. Liang XH, Liu Q, Michaeli S (2003) Small nucleolar RNA interference induced by antisense or double-stranded RNA in trypanosomatids. Proc Natl Acad Sci U S A 100: 7521-7526. Find this article online
49. Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, et al. (2003) The microRNAs of Caenorhabditis elegans. Genes Dev 17: 991-1008. Find this article online
50. 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. Find this article online
51. Martinez J, Patkaniowska A, Urlaub H, Lührmann R, Tuschl T (2002) Single-stranded antisense siRNA guide target RNA cleavage in RNAi. Cell 110: 563-574. Find this article online
52. Moss EG, Lee RC, Ambros V (1997) 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. Find this article online
53. Mourelatos Z, Dostie J, Paushkin S, Sharma AK, Charroux B, et al. (2002) miRNPs: A novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev 16: 720-728. Find this article online
54. Mourrain P, Beclin C, Elmayan T, Feuerbach F, Godon C, et al. (2000) Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell 101: 533-542. Find this article online
55. Nykänen A, Haley B, Zamore PD (2001) ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 107: 309-321. Find this article online
56. 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. Find this article online
57. Persengiev SP, Zhu X, Green MR (2003) Nonspecific, concentration- dependent stimulation and repression of mammalian gene expression by small interfering RNAs (siRNAs). RNA 10: 12-18. Find this article online
58. 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. Find this article online
59. Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP (2002) MicroRNAs in plants. Genes Dev 16: 1616-1626. Find this article online
60. Saxena S, Jonsson ZO, Dutta A (2003) Small RNAs with imperfect match to endogenous mRNA repress translation: Implications for off-target activity of siRNA in mammalian cells. J Biol Chem 278: 44312-44319. Find this article online
61. Schwarz DS, Hutvágner G, Haley B, Zamore PD (2002) Evidence that siRNAs function as guides, not primers, in the Drosophila and human RNAi pathways. Mol Cell 10: 537-548. Find this article online
62. Schwarz DS, Hutvágner G, Du T, Xu Z, Aronin N, et al. (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115: 199-208. Find this article online
63. Seggerson K, Tang L, Moss EG (2002) Two genetic circuits repress the Caenorhabditis elegans heterochronic gene lin-28 after translation initiation. Dev Biol 243: 215-225. Find this article online
64. Semizarov D, Frost L, Sarthy A, Kroeger P, Halbert DN, et al. (2003) Specificity of short interfering RNA determined through gene expression signatures. Proc Natl Acad Sci U S A 100: 6347-6352. Find this article online
65. Slack FJ, Basson M, Liu Z, Ambros V, Horvitz HR, et al. (2000) 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. Find this article online
66. Sledz CA, Holko M, de Veer MJ, Silverman RH, Williams BR (2003) Activation of the interferon system by short-interfering RNAs. Nat Cell Biol 5: 834-839. Find this article online
67. Stark A, Brennecke J, Russell RB, Cohen SM (2003) Identification of Drosophila microRNA targets. PLoS Biol 1: e6010.1371/journal.pbio.0000060. Find this article online
68. Tabara H, Sarkissian M, Kelly WG, Fleenor J, Grishok A, et al. (1999) The rde-1 gene, RNA interference, and transposon silencing in C. elegans. Cell 99: 123-132. Find this article online
69. 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. Find this article online
70. Tang G, Reinhart BJ, Bartel DP, Zamore PD (2003) A biochemical framework for RNA silencing in plants. Genes Dev 17: 49-63. Find this article online
71. Tijsterman M, Ketting RF, Okihara KL, Sijen T, Plasterk RH (2002a) RNA helicase MUT-14-dependent gene silencing triggered in C. elegans by short antisense RNAs. Science 295: 694-697. Find this article online
72. Tijsterman M, Okihara KL, Thijssen K, Plasterk RH (2002b) PPW-1, a PAZ/PIWI protein required for efficient germline RNAi, is defective in a natural isolate of C. elegans. Curr Biol 12: 1535-1540. Find this article online
73. Tuschl T, Zamore PD, Lehmann R, Bartel DP, Sharp PA (1999) Targeted mRNA degradation by double-stranded RNA in vitro. Genes Dev 13: 3191-3197. Find this article online
74. Vella MC, Choi EY, Lin SY, Reinert K, Slack FJ (2004) The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3′UTR. Genes Dev 18: 132-137. Find this article online
75. Wightman B, Ha I, Ruvkun G (1993) Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75: 855-862. Find this article online
76. Wu-Scharf D, Jeong B, Zhang C, Cerutti H (2000) Transgene and transposon silencing in Chlamydomonas reinhardtii by a DEAH-box RNA helicase. Science 290: 1159-1163. Find this article online
77. 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. Find this article online
78. Zamore PD, Tuschl T, Sharp PA, Bartel DP (2000) RNAi: Double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101: 25-33. Find this article online
79. Zeng Y, Cullen BR (2003) Sequence requirements for micro RNA processing and function in human cells. RNA 9: 112-123. Find this article online
80. Zeng Y, Wagner EJ, Cullen BR (2002) Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells. Mol Cell 9: 1327-1333. Find this article online
81. Zeng Y, Yi R, Cullen BR (2003) MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms. Proc Natl Acad Sci U S A 100: 9779-9784. Find this article online