Coupling of Double-Stranded RNA Synthesis and siRNA Generation in Fission Yeast RNAi

Molecular Cell

Volumn 27, Issue 3, 2007, Pages 449-461

  Colmenares, Serafin U ^a   Buker, Shane M ^a   Buhler, Marc ^a   Dlakić, Mensur ^b   Moazed, Danesh ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

^b MONTANA STATE UNIVERSITY   (United States)

Author keywords

DNA; RNA

Indexed keywords

DICER; DOUBLE STRANDED RNA; HELICASE; PROTEIN DCR1; RNA DIRECTED RNA POLYMERASE; SMALL INTERFERING RNA; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CENTROMERE; FISSION YEAST; GENE SILENCING; HETEROCHROMATIN; NONHUMAN; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; RNA INTERFERENCE; RNA SYNTHESIS; RNA TRANSCRIPTION; SACCHAROMYCES; YEAST;

ADENOSINE TRIPHOSPHATASES; ADENOSINE TRIPHOSPHATE; AMINO ACID SEQUENCE; CENTROMERE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMOSOME SEGREGATION; HETEROCHROMATIN; MOLECULAR SEQUENCE DATA; MUTATION; PROTEIN CONFORMATION; RNA INTERFERENCE; RNA REPLICASE; RNA, DOUBLE-STRANDED; RNA, SMALL INTERFERING; SCHIZOSACCHAROMYCES; SCHIZOSACCHAROMYCES POMBE PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID;

SCHIZOSACCHAROMYCETACEAE;

EID: 34547211819     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2007.07.007     Document Type: Article

References (55)

1. Allshire R.C., Javerzat J.P., Redhead N.J., and Cranston G. Position effect variegation at fission yeast centromeres. Cell 76 (1994) 157-169
2. Bernstein E., Caudy A.A., Hammond S.M., and Hannon G.J. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409 (2001) 363-366
3. Buhler M., Verdel A., and Moazed D. Tethering RITS to a nascent transcript initiates RNAi- and heterochromatin-dependent gene silencing. Cell 125 (2006) 873-886
4. Buhler M., Haas W., Gygi S.P., and Moazed D. RNAi-dependent and -independent RNA turnover mechanisms contribute to heterochromatic gene silencing. Cell 129 (2007) 707-721
5. Buker S.M., Iida T., Buhler M., Villen J., Gygi S.P., Nakayama J., and Moazed D. Two different Argonaute complexes are required for siRNA generation and heterochromatin assembly in fission yeast. Nat. Struct. Mol. Biol. 14 (2007) 200-207
6. Cam H., Sugiyama T., Chen E.S., Chen X., Fitzgerald P., and Grewal S.I. Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome. Nat. Genet. 37 (2005) 809-819
7. Catalanotto C., Pallotta M., ReFalo P., Sachs M.S., Vayssie L., Macino G., and Cogoni C. Redundancy of the two dicer genes in transgene-induced posttranscriptional gene silencing in Neurospora crassa. Mol. Cell. Biol. 24 (2004) 2536-2545
8. Chendrimada T.P., Gregory R.I., Kumaraswamy E., Norman J., Cooch N., Nishikura K., and Shiekhattar R. TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 436 (2005) 740-744
9. Doench J.G., Petersen C.P., and Sharp P.A. siRNAs can function as miRNAs. Genes Dev. 17 (2003) 438-442
10. Duchaine T.F., Wohlschlegel J.A., Kennedy S., Bei Y., Conte Jr. D., Pang K., Brownell D.R., Harding S., Mitani S., Ruvkun G., et al. Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways. Cell 124 (2006) 343-354
11. Eisenberg D., Luthy R., and Bowie J.U. VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol. 277 (1997) 396-404
12. Fire A., Xu S., Montgomery M.K., Kostas S.A., Driver S.E., and Mello C.C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391 (1998) 806-811
13. Forstemann K., Tomari Y., Du T., Vagin V.V., Denli A.M., Bratu D.P., Klattenhoff C., Theurkauf W.E., and Zamore P.D. Normal microRNA maturation and germ-line stem cell maintenance requires Loquacious, a double-stranded RNA-binding domain protein. PLoS Biol. 3 (2005) e236 10.1371/journal.pbio.0030236
14. Gan J., Tropea J.E., Austin B.P., Court D.L., Waugh D.S., and Ji X. Structural insight into the mechanism of double-stranded RNA processing by ribonuclease III. Cell 124 (2006) 355-366
15. Golden T.A., Schauer S.E., Lang J.D., Pien S., Mushegian A.R., Grossniklaus U., Meinke D.W., and 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
16. Gregory R.I., Chendrimada T.P., Cooch N., and Shiekhattar R. Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell 123 (2005) 631-640
17. Haase A.D., Jaskiewicz L., Zhang H., Laine S., Sack R., Gatignol A., and Filipowicz W. TRBP, a regulator of cellular PKR and HIV-1 virus expression, interacts with Dicer and functions in RNA silencing. EMBO Rep. 6 (2005) 961-967
18. Hamilton A.J., and Baulcombe D.C. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286 (1999) 950-952
19. Hammond S.M., Bernstein E., Beach D., and Hannon G.J. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404 (2000) 293-296
20. Hammond S.M., Boettcher S., Caudy A.A., Kobayashi R., and Hannon G.J. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 293 (2001) 1146-1150
21. Hiraguri A., Itoh R., Kondo N., Nomura Y., Aizawa D., Murai Y., Koiwa H., Seki M., Shinozaki K., and Fukuhara T. Specific interactions between Dicer-like proteins and HYL1/DRB-family dsRNA-binding proteins in Arabidopsis thaliana. Plant Mol. Biol. 57 (2005) 173-188
22. Hutvagner G., McLachlan J., Pasquinelli A.E., Balint E., Tuschl T., and Zamore P.D. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293 (2001) 834-838
23. Irvine D.V., Zaratiegui M., Tolia N.H., Goto D.B., Chitwood D.H., Vaughn M.W., Joshua-Tor L., and Martienssen R.A. Argonaute slicing is required for heterochromatic silencing and spreading. Science 313 (2006) 1134-1137
24. Jacobsen S.E., Running M.P., and Meyerowitz E.M. Disruption of an RNA helicase/RNAse III gene in Arabidopsis causes unregulated cell division in floral meristems. Development 126 (1999) 5231-5243
25. Jiang F., Ye X., Liu X., Fincher L., McKearin D., and Liu Q. Dicer-1 and R3D1-L catalyze microRNA maturation in Drosophila. Genes Dev. 19 (2005) 1674-1679
26. Kadotani N., Nakayashiki H., Tosa Y., and Mayama S. One of the two Dicer-like proteins in the filamentous fungi Magnaporthe oryzae genome is responsible for hairpin RNA-triggered RNA silencing and related small interfering RNA accumulation. J. Biol. Chem. 279 (2004) 44467-44474
27. Ketting R.F., Fischer S.E., Bernstein E., Sijen T., Hannon G.J., and 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
28. Knight S.W., and Bass B.L. A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science 293 (2001) 2269-2271
29. Lee S.R., and Collins K. Two classes of endogenous small RNAs in Tetrahymena thermophila. Genes Dev. 20 (2006) 28-33
30. Lee Y.S., Nakahara K., Pham J.W., Kim K., He Z., Sontheimer E.J., and Carthew R.W. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 117 (2004) 69-81
31. Lee R.C., Hammell C.M., and Ambros V. Interacting endogenous and exogenous RNAi pathways in Caenorhabditis elegans. RNA 12 (2006) 589-597
32. Lee Y., Hur I., Park S.Y., Kim Y.K., Suh M.R., and Kim V.N. The role of PACT in the RNA silencing pathway. EMBO J. 25 (2006) 522-532
33. Liu Q., Rand T.A., Kalidas S., Du F., Kim H.E., Smith D.P., and Wang X. R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science 301 (2003) 1921-1925
34. Liu X., Jiang F., Kalidas S., Smith D., and Liu Q. Dicer-2 and R2D2 coordinately bind siRNA to promote assembly of the siRISC complexes. RNA 12 (2006) 1514-1520
35. Macrae I.J., Zhou K., Li F., Repic A., Brooks A.N., Cande W.Z., Adams P.D., and Doudna J.A. Structural basis for double-stranded RNA processing by Dicer. Science 311 (2006) 195-198
36. Martinez J., Patkaniowska A., Urlaub H., Luhrmann R., and Tuschl T. Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell 110 (2002) 563-574
37. Mochizuki K., and Gorovsky M.A. A Dicer-like protein in Tetrahymena has distinct functions in genome rearrangement, chromosome segregation, and meiotic prophase. Genes Dev. 19 (2005) 77-89
38. Motamedi M.R., Verdel A., Colmenares S.U., Gerber S.A., Gygi S.P., and Moazed D. Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell 119 (2004) 789-802
39. Nykanen A., Haley B., and Zamore P.D. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 107 (2001) 309-321
40. Partridge J.F., Scott K.S., Bannister A.J., Kouzarides T., and Allshire R.C. cis-acting DNA from fission yeast centromeres mediates histone H3 methylation and recruitment of silencing factors and cohesin to an ectopic site. Curr. Biol. 12 (2002) 1652-1660
41. Pause A., and Sonenberg N. Mutational analysis of a DEAD box RNA helicase: the mammalian translation initiation factor eIF-4A. EMBO J. 11 (1992) 2643-2654
42. Provost P., Dishart D., Doucet J., Frendewey D., Samuelsson B., and Radmark O. Ribonuclease activity and RNA binding of recombinant human Dicer. EMBO J. 21 (2002) 5864-5874
43. Provost P., Silverstein R.A., Dishart D., Walfridsson J., Djupedal I., Kniola B., Wright A., Samuelsson B., Radmark O., and Ekwall K. Dicer is required for chromosome segregation and gene silencing in fission yeast cells. Proc. Natl. Acad. Sci. USA 99 (2002) 16648-16653
44. Reinhart B.J., and Bartel D.P. Small RNAs correspond to centromere heterochromatic repeats. Science 297 (2002) 1831
45. Sijen T., Fleenor J., Simmer F., Thijssen K.L., Parrish S., Timmons L., Plasterk R.H., and Fire A. On the role of RNA amplification in dsRNA-triggered gene silencing. Cell 107 (2001) 465-476
46. Tabara H., Yigit E., Siomi H., and 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
47. Tahbaz N., Kolb F.A., Zhang H., Jaronczyk K., Filipowicz W., and Hobman T.C. Characterization of the interactions between mammalian PAZ PIWI domain proteins and Dicer. EMBO Rep. 5 (2004) 189-194
48. Tomari Y., Matranga C., Haley B., Martinez N., and Zamore P.D. A protein sensor for siRNA asymmetry. Science 306 (2004) 1377-1380
49. Verdel A., Jia S., Gerber S., Sugiyama T., Gygi S., Grewal S.I., and Moazed D. RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303 (2004) 672-676
50. Volpe T.A., Kidner C., Hall I.M., Teng G., Grewal S.I., and Martienssen R.A. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297 (2002) 1833-1837
51. Yoshikawa M., Peragine A., Park M.Y., and Poethig R.S. A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev. 19 (2005) 2164-2175
52. Zamore P.D., Tuschl T., Sharp P.A., and 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
53. Zeng Y., Wagner E.J., and Cullen B.R. Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells. Mol. Cell 9 (2002) 1327-1333
54. Zhang H., Kolb F.A., Brondani V., Billy E., and Filipowicz W. Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J. 21 (2002) 5875-5885
55. Zhang H., Kolb F.A., Jaskiewicz L., Westhof E., and Filipowicz W. Single processing center models for human Dicer and bacterial RNase III. Cell 118 (2004) 57-68