Human dicer: Purification, properties, and interaction with PAZ PIWI domain proteins

Methods in Enzymology

Volumn 392, Issue , 2005, Pages 316-336

  Kolb, Fabrice A ^a   Zhang, Haidi ^a   Jaronczyk, Kasia ^a   Tahbaz, Nasser ^a   Hobman, Tom C ^a   Filipowicz, Witold ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

DICER; DOUBLE STRANDED RNA; GLUTATHIONE TRANSFERASE; HYBRID PROTEIN; HYGROMYCIN; MICRORNA; OLIGODEOXYNUCLEOTIDE DERIVATIVE; PROTEINASE K; RECOMBINANT PROTEIN; RIBONUCLEASE; SMALL INTERFERING RNA; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; BACULOVIRUS EXPRESSION SYSTEM; CARBOXY TERMINAL SEQUENCE; CELL LINE; EXPRESSION VECTOR; GEL ELECTROPHORESIS; HUMAN; IMMUNOPRECIPITATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN ISOLATION; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; RNA INTERFERENCE; YEAST;

UNIDENTIFIED BACULOVIRUS;

EID: 11844260705     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(04)92019-8     Document Type: Article

References (57)

1. Bartel D.P. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell. 116:2004;281-297
2. Bartel P.L., Fields S. Analyzing protein-protein interactions using two-hybrid system. Methods Enzymol. 254:1995;241-263
3. Baulcombe D. RNA silencing. Diced defence. Nature. 409:2001;295-296
4. 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
5. Bernstein E., Kim S.Y., Carmell M.A., Murchison E.P., Alcorn H., Li M.Z., Mills A.A., Elledge S.J., Anderson K.V., Hannon G.J. Dicer is essential for mouse development. Nat. Genet. 35:2003;215-217
6. Billy E., Brondani V., Zhang H., Muller U., Filipowicz W. Specific interference with gene expression induced by long, double-stranded RNA in mouse embryonal teratocarcinoma cell lines. Proc. Natl. Acad. Sci. USA. 98:2001;14428-14433
7. Blaszczyk J., Tropea J.E., Bubunenko M., Routzahn K.M., Waugh D.S., Court D.L., Ji X. Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage. Structure (Camb.). 9:2001;1225-1236
8. Caplen N.J., Zheng Z., Falgout B., Morgan R.A. Inhibition of viral gene expression and replication in mosquito cells by dsRNA-triggered RNA interference. Mol. Ther. 6:2002;243-251
9. 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
10. Cavallo R.A., Cox R.T., Moline M.M., Roose J., Polevoy G.A., Clevers H., Peifer M., Bejsovec A. Drosophila Tcf and Groucho interact to repress Wingless signalling activity. Nature. 395:1998;604-608
11. Cerutti L., Mian N., Bateman A. Domains in gene silencing and cell differentiation proteins: The novel PAZ domain and redefinition of the Piwi domain. Trends Biochem. Sci. 25:2000;481-482
12. Cikaluk D.E., Tahbaz N., Hendricks L.C., DiMattia G.E., Hansen D., Pilgrim D., Hobman T.C. GERp95, a membrane-associated protein that belongs to a family of proteins involved in stem cell differentiation. Mol. Biol. Cell. 10:1999;3357-3372
13. Doi N., Zenno S., Ueda R., Ohki-Hamazaki H., Ui-Tei K., Saigo K. Short-interfering-RNA-mediated gene silencing in mammalian cells requires Dicer and eIF2C translation initiation factors. Curr. Biol. 13:2003;41-46
14. Donis-Keller H., Maxam A.M., Gilbert W. Mapping adenines, guanines, and pyrimidines in RNA. Nucleic Acids Res. 4:1977;2527-2538
15. Elbashir S.M., Lendeckel W., Tuschl T. RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev. 15:2001;188-200
16. England T.E., Uhlenbeck O.C. 3′-Terminal labelling of RNA with T4 RNA ligase. Nature. 275:1978;560-561
17. 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
18. Hannon G.J., Zamore P.D. Small RNAs, big biology: Biochemical studies of RNA interference. Hannon G.J. "RNAi: A Guide to Gene Silencing" 2003;87-108 Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
19. Hutvagner G., McLachlan J., Pasquinelli A.E., Balint E., Tuschl T., Zamore P.D. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science. 12:2001;12
20. Ishizuka A., Siomi M.C., Siomi H. A Drosophila fragile X protein interacts with components of RNAi and ribosomal proteins. Genes Dev. 16:2002;2497-2508
21. 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
22. Lai E.C. microRNAs: Runts of the genome assert themselves. Curr. Biol. 13:2003;R925-R936
23. Lee Y., Ahn C., Han J., Choi H., Kim J., Yim J., Lee J., Provost P., Radmark O., Kim S., Kim V.N. The nuclear RNase III Drosha initiates microRNA processing. Nature. 425:2003;415-419
24. 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
25. Lee Y.S., Nakahara K., Pham J.W., Kim K., He Z., Sontheimer E.J., Carthew R.W. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell. 117:2004;69-81
26. Lingel A., Simon B., Izaurralde E., Sattler M. Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain. Nature. 426:2003;465-469
27. Liu Q., Rand T.A., Kalidas S., Du F., Kim H.E., Smith D.P., Wang X. R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science. 301:2003;1921-1925
28. Liu Y., Jiang Y., Qiao D.R., Cao Y. The mechanism and application of posttranscriptional gene silencing. Sheng Wu Gong Cheng Xue Bao. 18:2002;140-143
29. Martens H., Novotny J., Oberstrass J., Steck T.L., Postlethwait P., Nellen W. RNAi in Dictyostelium: The role of RNA-directed RNA polymerases and double-stranded RNase. Mol. Biol. Cell. 13:2002;445-453
30. Matzke M., Aufsatz W., Kanno T., Daxinger L., Papp I., Mette M.F., Matzke A.J. Genetic analysis of RNA-mediated transcriptional gene silencing. Biochim. Biophys. Acta. 1677:2004;129-141
31. McCabe J.B., Berthiaume L.G. Functional roles for fatty acylated amino-terminal domains in subcellular localization. Mol. Biol. Cell. 10:1999;3771-3786
32. Mette M.F., Matzke A.J., Matzke M.A. Resistance of RNA-mediated TGS to HC-Pro, a viral suppressor of PTGS, suggests alternative pathways for dsRNA processing. Curr. Biol. 11:2001;1119-1123
33. Mizushima S., Nagata S. pEF-BOS, a powerful mammalian expression vector. Nucleic Acids Res. 18:1990;5322
34. Morse D.P., Aruscavage P.J., Bass B.L. RNA hairpins in noncoding regions of human brain and Caenorhabditis elegans mRNA are edited by adenosine deaminases that act on RNA. Proc. Natl. Acad. Sci. USA. 99:2002;7906-7911
35. 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
36. Myers J.W., Jones J.T., Meyer T., Ferrell J.E. Jr. Recombinant Dicer efficiently converts large dsRNAs into siRNAs suitable for gene silencing. Nat. Biotechnol. 21:2003;324-328
37. Nicholson A.W. The ribonuclease III superfamily: Forms and functions in RNA, maturation, decay, and gene silencing. Hannon G.J. "RNAi: A Guide to Gene Silencing" 2003;149-174 Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
38. Nykanen A., Haley B., Zamore P.D. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell. 107:2001;309-321
39. Papp I., Mette M.F., Aufsatz W., Daxinger L., Schauer S.E., Ray A., van der Winden J., Matzke M., Matzke A.J. Evidence for nuclear processing of plant micro RNA and short interfering RNA precursors. Plant Physiol. 132:2003;1382-1390
40. Parrish S., Fire A. Distinct roles for RDE-1 and RDE-4 during RNA interference in Caenorhabditis elegans. RNA. 7:2001;1397-1402
41. Pham J.W., Pellino J.L., Lee Y.S., Carthew R.W., Sontheimer E.J. A Dicer-2-dependent 80s complex cleaves targeted mRNAs during RNAi in Drosophila. Cell. 117:2004;83-94
42. Price S.R., Ito N., Oubridge C., Avis J.M., Nagai K. Crystallization of RNA-protein complexes. I. Methods for the large-scale preparation of RNA suitable for crystallographic studies. J. Mol. Biol. 249:1995;398-408
43. 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
44. Sasaki T., Shiohama A., Minoshima S., Shimizu N. Identification of eight members of the Argonaute family in the human genome small star, filled. Genomics. 82:2003;323-330
45. Sharma A.K., Nelson M.C., Brandt J.E., Wessman M., Mahmud N., Weller K.P., Hoffman R. Human CD34(+) stem cells express the hiwi gene, a human homologue of the Drosophila gene piwi. Blood. 97:2001;426-434
46. Song J.J., Liu J., Tolia N.H., Schneiderman J., Smith S.K., Martienssen R.A., Hannon G.J., Joshua-Tor L. The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nat. Struct. Biol. 10:2003;1026-1032
47. 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
48. Tabara H., Yigit E., Siomi H., Mello C.C. The dsRNA binding protein RDE-4 interacts with RDE-1, DCR-1, and a DExH-box helicase to direct RNAi in C. elegans. Cell. 109:2002;861-871
49. Tahbaz N., Carmichael J.B., Hobman T.C. GERp95 belongs to a family of signal-transducing proteins and requires Hsp90 activity for stability and Golgi localization. J. Biol. Chem. 276:2001;43294-43299
50. Tahbaz N., Kolb F.A., Zhang H., Jaronczyk K., Filipowicz W., Hobman T.C. Characterization of the interactions between mammalian PAZ PIWI domain proteins and Dicer. EMBO Rep. 5:2004;189-194
51. Tomari Y., Du T., Haley B., Schwarz D.S., Bennett R., Cook H.A., Koppetsch B.S., Theurkauf W.E., Zamore P.D. RISC assembly defects in the Drosophila RNAi mutant armitage. Cell. 116:2004;831-841
52. Verdel A., Jia S., Gerber S., Sugiyama T., Gygi S., Grewal S.I., Moazed D. RNAi-mediated targeting of heterochromatin by the RITS complex. Science. 303:2004;672-676
53. Wienholds E., Koudijs M.J., van Eeden F.J., Cuppen E., Plasterk R.H. The microRNA-producing enzyme Dicer1 is essential for zebrafish development. Nat. Genet. 35:2003;217-218
54. Yan K.S., Yan S., Farooq A., Han A., Zeng L., Zhou M.M. Structure and conserved RNA binding of the PAZ domain. Nature. 426:2003;468-474
55. Zamore P.D. Ancient pathways programmed by small RNAs. Science. 296:2002;1265-1269
56. 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
57. Zhang H., Kolb F.A., Jaskiewicz L., Westhof E., Filipowicz W. Single processing center models for human Dicer and bacterial RNase III. Cell. 118:2004;57-68