ATP modulates siRNA interactions with an endogenous human Dicer complex

RNA

Volumn 11, Issue 11, 2005, Pages 1719-1724

  Pellino, Janice L ^a   Jaskiewicz, Lukasz ^b   Filipowicz, Witold ^b   Sontheimer, Erik J ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

^b FRIEDRICH MIESCHER INSTITUTE FOR BIOMEDICAL RESEARCH   (Switzerland)

Author keywords

Dicer; RNA interference (RNAi); RNA induced silencing complex (RISC); Short interfering RNA (siRNA)

Indexed keywords

ADENOSINE TRIPHOSPHATE; DOUBLE STRANDED RNA; ENZYME DICER; GLYCEROL; RECOMBINANT PROTEIN; RIBONUCLEASE; SMALL INTERFERING RNA; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; COMPLEX FORMATION; CONTROLLED STUDY; CROSS LINKING; GEL ELECTROPHORESIS; HUMAN; HUMAN CELL; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN LOCALIZATION; PROTEIN PURIFICATION; PROTEIN RNA BINDING; RNA STRUCTURE; SEDIMENTATION;

ADENOSINE TRIPHOSPHATE; CROSS-LINKING REAGENTS; DEAD-BOX RNA HELICASES; ENDORIBONUCLEASES; HELA CELLS; HUMANS; KIDNEY; RNA HELICASES; RNA INTERFERENCE; RNA, SMALL INTERFERING;

EID: 27144469457     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2102805     Document Type: Article

References (35)

1. Bernstein, E., Caudy, A.A., Hammond, S.M., and Hannon, G.J. 2001. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409: 363-366.
2. Billy, E., Brondani, V., Zhang, H., Muller, U., and Filipowicz, W. 2001. Specific interference with gene expression induced by long, double-stranded RNA in mouse embryonal teratocarcinoma cell lines. Proc. Natl. Acad. Sci. 98: 14428-14433.
3. Carmell, M.A. and Hannon, G.J. 2004. RNase III enzymes and the initiation of gene silencing. Nat. Struct. Mol. Biol. 11: 214-218.
4. Chendrimada, T.P., Gregory, R.I., Kumaraswamy, E., Norman, J., Cooch, N., Nishikura, K., and Shiekhattar, R. 2005. TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 436: 740-744.
5. Dignam, J.D., Lebovitz, R.M., and Roeder, R.G. 1983. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 11: 1475-1489.
6. Doi, N., Zenno, S., Ueda, R., Ohki-Hamazaki, H., Ui-Tei, K., and Saigo, K. 2003. Short-interfering-RNA-mediated gene silencing in mammalian cells requires Dicer and eIF2C translation initiation factors. Curr. Biol. 13: 41-46.
7. Filipowicz, W. 2005. RNAi: The nuts and bolts of the RISC Machine. Cell 122: 17-20.
8. Fire, A., Xu, S., Montgomery, M.K., Kostas, S.A., Driver, S.E., and Mello, C.C. 1998. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806-811.
9. Haase, A., Jaskiewicz, L., Zhang, H., Laine, S., Sack, R., Gatignol, A., and Filipowicz, W. 2005. TRBP, a regulator of cellular PKR and HIV-1 virus expression, interacts with Dicer and functions in RNA silencing. EMBO Rep. http://www.nature.com/embor/journal/vaop/ ncurrent/full/7400509.html#abstract
10. Kanellopoulou, C., Muljo, S.A., Kung, A.L., Ganesan, S., Drapkin, R., Jenuwein, T., Livingston, D.M., and Rajewsky, K. 2005. Dicerdeficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes & Dev. 19: 489-501.
11. Khvorova, A., Reynolds, A., and Jayasena, S.D. 2003. Functional siRNAs and miRNAs exhibit strand bias. Cell 115: 209-216.
12. Kim, D.H., Behlke, M.A., Rose, S.D., Chang, M.S., Choi, S., and Rossi, J.J. 2005. Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy. Nat. Biotechnol. 23: 222-226.
13. Lee, Y.S., Nakahara, K., Pham, J.W., Kim, K., He, Z., Sontheimer, E.J., and Carthew, R.W. 2004. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 117: 69-81.
14. Liu, Q., Rand, T.A., Kalidas, S., Du, F., Kim, H.E., Smith, D.P., and Wang, X. 2003. R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science 301: 1921-1925.
15. Liu, J., Carmell, M.A., Rivas, F.V., Marsden, C.G., Thomson, J.M., Song, J.J., Hammond, S.M., Joshua-Tor, L., and Hannon, G.J. 2004. Argonaute2 is the catalytic engine of mammalian RNAi. Science 305: 1437-1441.
16. Martinez, J., Patkaniowska, A., Urlaub, H., Luhrmann, R., and Tuschl, T. 2002. Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell 110: 563-574.
17. Meister, G. and Tuschl, T. 2004. Mechanisms of gene silencing by double-stranded RNA. Nature 431: 343-349.
18. Meister, G., Landthaler, M., Patkaniowska, A., Dorsett, Y., Teng, G., and Tuschl, T. 2004. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol. Cell 15: 185-197.
19. Nykänen, A., Haley, B., and Zamore, P.D. 2001. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 107: 309-321.
20. Pham, J.W., Pellino, J.L., Lee, Y.S., Carthew, R.W., and Sontheimer, E.J. 2004. A Dicer-2-dependent 80S complex cleaves targeted mRNAs during RNAi in Drosophila. Cell 117: 83-94.
21. Provost, P., Dishart, D., Doucet, J., Frendewey, D., Samuelsson, B., and Radmark, O. 2002. Ribonuclease activity and RNA binding of recombinant human Dicer. EMBO J. 21: 5864-5874.
22. Reynolds, A., Leake, D., Boese, Q., Scaringe, S., Marshall, W.S., and Khvorova, A. 2004. Rational siRNA design for RNA interference. Nat. Biotechnol. 22: 326-330.
23. Rivas, F.V., Tolia, N.H., Song, J.J., Aragon, J.P., Liu, J., Hannon, G.J., and Joshua-Tor, L. 2005. Purified Argonaute2 and an siRNA form recombinant human RISC. Nat. Struct. Mol. Biol. 12: 340-349.
24. Rose, S.D., Kim, D.H., Amarzguioui, M., Heidel, J.D., Collingwood, M.A., Davis, M.E., Rossi, J.J., and Behlke, M.A. 2005. Functional polarity is introduced by Dicer processing of short substrate RNAs. Nucleic Acids Res. 33: 4140-4156.
25. Schwarz, D.S., Hutvagner, G., Du, T., Xu, Z., Aronin, N., and Zamore, P.D. 2003. Asymmetry in the assembly of the RNAi enzyme complex. Cell 115: 199-208.
26. Siolas, D., Lerner, C., Burchard, J., Ge, W., Linsley, P.S., Paddison, P.J., Hannon, G.J., and Cleary, M.A. 2005. Synthetic shRNAs as potent RNAi triggers. Nat. Biotechnol. 23: 227-231.
27. Song, J.J., Smith, S.K., Hannon, G.J., and Joshua-Tor, L. 2004. Crystal structure of Argonaute and its implications for RISC slicer activity. Science 305: 1434-1437.
28. Sontheimer, E.J. 2005. Assembly and function of RNA silencing complexes. Nat. Rev. Mol. Cell. Biol. 6: 127-138.
29. Stark, H., Dube, P., Luhrmann, R., and Kastner, B. 2001. Arrangement of RNA and proteins in the spliceosomal U1 small nuclear ribonucleoprotein particle. Nature 409: 539-542.
30. Tomari, Y. and Zamore, P.D. 2005. Perspective: Machines for RNAi. Genes & Dev. 19: 517-529.
31. Tomari, Y., Du, T., Haley, B., Schwarz, D.S., Bennett, R., Cook, H.A., Koppetsch, B.S., Theurkauf, W.E.,and Zamore, P.D. 2004a. RISCassembly defects in the Drosophila RNAimutant armitage. Cell 116: 831-841.
32. Tomari, Y., Matranga, C., Haley, B., Martinez, N., and Zamore, P.D. 2004b. A protein sensor for siRNA asymmetry. Science 306: 1377-1380.
33. Yuan, Y.-R., Pei, Y., Ma, J.-B., Kuryavyi, V., Zhadina, M., Meister, G., Chen, H.-Y., Dauter, Z., Tuschl, T., and Patel, D.J. 2005. Crystal structure of A. aeolicus Argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage. Mol. Cell 19: 405-419.
34. Zhang, H., Kolb, F.A., Brondani, V., Billy, E., and Filipowicz, W. 2002. Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J. 21: 5875-5885.
35. Zhang, H., Kolb, F.A., Jaskiewicz, L., Westhof, E., and Filipowicz, W. 2004. Single processing center models for human Dicer and bacterial RNase III. Cell 118: 57-68.