In vitro analyses of the production and activity of secondary small interfering RNAs in C. elegans

EMBO Journal

Volumn 26, Issue 24, 2007, Pages 5007-5019

  Aoki, Kazuma ^a   Moriguchi, Hiromi ^a   Yoshioka, Tomoko ^a   Okawa, Katsuya ^a   Tabara, Hiroaki ^a,b  

^a KYOTO UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

Argonaute; RdRP; RNAi; siRNA

Indexed keywords

MESSENGER RNA; RNA POLYMERASE; SMALL INTERFERING RNA;

ARTICLE; CAENORHABDITIS ELEGANS; CELL FREE SYSTEM; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME SYNTHESIS; IN VITRO STUDY; NONHUMAN; PRIORITY JOURNAL; PROTEIN TARGETING;

ANIMALS; ANIMALS, GENETICALLY MODIFIED; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; CELL-FREE SYSTEM; DEAD-BOX RNA HELICASES; ENDORIBONUCLEASES; EUKARYOTIC INITIATION FACTOR-2; GENE EXPRESSION REGULATION; MULTIPROTEIN COMPLEXES; RECOMBINANT FUSION PROTEINS; RNA INTERFERENCE; RNA REPLICASE; RNA, HELMINTH; RNA, MESSENGER; RNA, SMALL INTERFERING; RNA-BINDING PROTEINS; TRANSGENES;

CAENORHABDITIS ELEGANS;

EID: 37149049127     PISSN: 02614189     EISSN: 14602075     Source Type: Journal    
DOI: 10.1038/sj.emboj.7601910     Document Type: Article

References (36)

1. 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
2. Chen CC, Simard MJ, Tabara H, Brownell DR, McCollough JA, Mello CC (2005) A member of the polymerase β nucleotidyltransferase superfamily is required for RNA interference in C. elegans. Curr Biol 15: 378-383
3. Cogoni C, Macino G (1999) Gene silencing in Neurospora crassa requires a protein homologous to RNA-dependent RNA polymerase. Nature 399: 166-169
4. Colmenares SU, Buker SM, Buhler M, Dlakic M, Moazed D (2007) Coupling of double-stranded RNA synthesis and siRNA generation in fission yeast RNAi. Mol Cell 27: 449-461
5. 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
6. Duchaine TF, Wohlschlegel JA, Kennedy S, Bei Y, Conte Jr D, Pang K, Brownell DR, Harding S, Mitani S, Ruvkun G, Yates III JR, Mello CC (2006) Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways. Cell 124: 343-354
7. Elbashir SM, Lendeckel W, Tuschl T (2001) RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev 15: 188-200
8. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806-811
9. Grishok A, Pasquinelli AE, Conte D, Li N, Parrish S, Ha I, Baillie DL, Fire A, Ruvkun G, Mello CC (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
10. Hamilton AJ, Baulcombe DC (1999) A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286: 950-952
11. Hammond SM, Bernstein E, Beach D, Hannon GJ (2000) An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404: 293-296
12. 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
13. 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
14. Lee SR, Collins K (2007) Physical and functional coupling of RNA-dependent RNA polymerase and Dicer in the biogenesis of endogenous siRNAs. Nat Struct Mol Biol 14: 604-610
15. Liu J, Carmell MA, Rivas FV, Marsden CG, Thomson JM, Song JJ, Hammond SM, Joshua-Tor L, Hannon GJ (2004) Argonaute2 is the catalytic engine of mammalian RNAi. Science 305: 1437-1441
16. Makeyev EV, Bamford DH (2002) Cellular RNA-dependent RNA polymerase involved in posttranscriptional gene silencing has two distinct activity modes. Mol Cell 10: 1417-1427
17. Martinez J, Patkaniowska A, Urlaub H, Luhrmann R, Tuschl T (2002) Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell 110: 563-574
18. Mello CC, Conte Jr D (2004) Revealing the world of RNA interference. Nature 431: 338-342
19. Motamedi MR, Verdel A, Colmenares SU, Gerber SA, Gygi SP, Moazed D (2004) Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell 119: 789-802
20. Mourrain P, Beclin C, Elmayan T, Feuerbach F, Godon C, Morel JB, Jouette D, Lacombe AM, Nikic S, Picault N, Remoue K, Sanial M, Vo TA, Vaucheret H (2000) Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell 101: 533-542
21. Nykanen A, Haley B, Zamore PD (2001) ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 107: 309-321
22. Pak J, Fire A (2007) Distinct populations of primary and secondary effectors during RNAi in C. elegans. Science 315: 241-244
23. Parker GS, Eckert DM, Bass BL (2006) RDE-4 preferentially binds long dsRNA and its dimerization is necessary for cleavage of dsRNA to siRNA. RNA 12: 807-818
24. Qi Y, Denli AM, Hannon GJ (2005) Biochemical specialization within Arabidopsis RNA silencing in plants. Mol Cell 19: 421-428
25. Salgado PS, Koivunen MR, Makeyev EV, Bamford DH, Stuart DI, Grimes JM (2006) The structure of an RNAi polymerase links RNA silencing and transcription. PLoS Biol 4: e434
26. Schiebel W, Pelissier T, Riedel L, Thalmeir S, Schiebel R, Kempe D, Lottspeich F, Sanger HL, Wassenegger M (1998) Isolation of an RNA-directed RNA polymerase-specific cDNA clone from tomato. Plant Cell 10: 2087-2101
27. 2+-dependent endonuclease. Curr Biol 14: 787-791
28. Sijen T, Fleenor J, Simmer F, Thijssen KL, Parrish S, Timmons L, Plasterk RH, Fire A (2001) On the role of RNA amplification in dsRNA-triggered gene silencing. Cell 107: 465-476
29. Sijen T, Steiner FA, Thijssen KL, Plasterk RH (2007) Secondary siRNAs result from unprimed RNA synthesis and form a distinct class. Science 315: 244-247
30. Smardon A, Spoerke JM, Stacey SC, Klein ME, Mackin N, Maine EM (2000) EGO-1 is related to RNA-directed RNA polymerase and functions in germ-line development and RNA interference in C. elegans. Curr Biol 10: 169-178
31. Tabara H, Sarkissian M, Kelly WG, Fleenor J, Grishok A, Timmons L, Fire A, Mello CC (1999) The rde-1 gene, RNA interference, and transposon silencing in C. elegans. Cell 99: 123-132
32. 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
33. Tang G, Reinhart BJ, Bartel DP, Zamore PD (2003) A biochemical framework for RNA silencing in plants. Genes Dev 17: 49-63
34. 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
35. Yigit E, Batista PJ, Bei Y, Pang KM, Chen CC, Tolia NH, Joshua-Tor L, Mitani S, Simard MJ, Mello CC (2006) Analysis of the C. elegans Argonaute family reveals that distinct Argonautes act sequentially during RNAi. Cell 127: 747-757
36. 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