Advertisement

Genetics and Biochemistry of RNAi in Drosophila

  • Harsh H. Kavi
  • Harvey Fernandez
  • Weiwu Xie
  • James A. Birchler
Part of the Current Topics in Microbiology and Immunology book series (CT MICROBIOLOGY, volume 320)

Abstract

RNA interference (RNAi) is the technique employing double-stranded RNA to target the destruction of homologous messenger RNAs. It has gained wide usage in genetics. While having the potential for many practical applications, it is a reflection of a much broader spectrum of small RNA-mediated processes in the cell. The RNAi machinery was originally perceived as a defense mechanism against viruses and transposons. While this is certainly true, small RNAs have now been implicated in many other aspects of cell biology. Here we review the current knowledge of the biochemistry of RNAi in Drosophila and the involvement of small RNAs in RNAi, transposon silencing, virus defense, transgene silencing, pairing-sensitive silencing, telomere function, chromatin insulator activity, nucleolar stability, and heterochromatin formation.

The discovery of the role of RNA molecules in the degradation of mRNA transcripts leading to decreased gene expression resulted in a paradigm shift in the field of molecular biology. Transgene silencing was first discovered in plant cells (Matzke et al. 1989; van der Krol et al. 1990; Napoli et al. 1990) and can occur on both the transcriptional and posttranscriptional levels, but both involve short RNA moieties in their mechanism. RNA interference (RNAi) is a type of gene silencing mechanism in which a double-stranded RNA (dsRNA) molecule directs the specific degradation of the corresponding mRNA (target RNA). The technique of RNAi was first discovered in Caenorhabditis elegans in 1994 (Guo and Kemphues 1994). Later the active component was found to be a dsRNA (Fire et al. 1998). In subsequent years, it has been found to occur in diverse eukaryotes such as Drosophila, Schizosaccharomyces pombe, Dictyostelium, Neurospora, plants, mice, humans, and many other organisms (Baulcombe 2004; Hall et al. 2003; Kennerdell and Carthew 2000; Paddison et al. 2002). It is possible that RNAi is a reflection of a much broader spectrum of small RNA functions in the cell as described below.

It is believed that RNAi evolved as a means of protection against viruses and against aberrant transposition by transposable elements in the genome (Kalmykova et al. 2005; Sijen and Plasterk 2003). However recent discoveries of the involvement of small RNAs in many other processes might suggest that these defense mechanisms, while obviously important, might actually be derivative processes rather than evolutionarily basal in origin. The RNAi genes also play an important role in the maintenance of centromeric heterochromatin (Volpe et al. 2002; Pal-Bhadra et al. 2004b) and germline stem cell division (Kennerdell et al. 2002). As a technique, RNAi can also be used as a tool for gene silencing studies and for developing (potentially) therapeutic agents (Jacque et al. 2002).

The trigger for all RNAi-related mechanisms known to date is a dsRNA molecule. This molecule can be introduced artificially or synthesized endogenously, for example, from heterochromatic repeats. The most potent source of artificial dsRNA is a sequence of about 500–700 bp cloned as inverted repeats, which is transcribed to give hairpin-loop dsRNA (Hannon and Conklin 2004). This dsRNA is then cleaved by specialized enzymes and assembled into a multiprotein complex. This results in specific cleavage of the target mRNA by virtue of complementarity between the small RNA (from the trigger) and the target mRNA. A series of genetic, biochemical, and structural studies have identified the different components of the RNAi machinery in Drosophila and also elucidated many mechanistic steps as described below (Fig. 1).

Keywords

siRNA Duplex Guide Strand RNAi Machinery Hybrid Dysgenesis Passenger Strand 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Akhtar A, Becker PB (2000) Activation of transcription through histone H4 acetylation by MOF, an acetyltransferase essential for dosage compensation in Drosophila. Mol Cell 5:367–375.PubMedGoogle Scholar
  2. Amarzguioui M, Holen T, Babaie E, Prydz H (2003) Tolerance for mutations and chemical modifications in a siRNA. Nucleic Acids Res 31:589–595.PubMedGoogle Scholar
  3. Ame JC, Spenlehauer C, de Murcia G (2004) The PARP superfamily. Bioessays 26:882–893.PubMedGoogle Scholar
  4. Aravin AA, Naumova NM, Tulin AV, Vagin VV, Rozovsky YM, Gvozdev VA (2001) Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Curr Biol 11:1017–1027.PubMedGoogle Scholar
  5. Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B, Gaasterland T, Meyer J, Tuschl T (2003) The small RNA profile during Drosophila melanogaster development. Dev Cell 5:337–350.PubMedGoogle Scholar
  6. Bantignies F, Grimaud C, Lavrov S, Gabut M, Cavalli G (2003) Inheritance of Polycomb-dependent chromosomal interactions in Drosophila. Genes Dev 17:2406–2420.PubMedGoogle Scholar
  7. Baulcombe D (2004) RNA silencing in plants. Nature 431:356–363.PubMedGoogle Scholar
  8. Baumberger N, Baulcombe DC (2005) Arabidopsis Argonaute1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs. Proc Natl Acad Sci USA 102:11928–11933.PubMedGoogle Scholar
  9. 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.PubMedGoogle Scholar
  10. Bhadra U, Pal-Bhadra M, Birchler JA (1999) Role of the male specific lethal (msl) genes in modifying the effects of sex chromosomal dosage in Drosophila. Genetics 152:249–268.PubMedGoogle Scholar
  11. Bhadra U, Pal-Bhadra M, Birchler JA (2000) Histone acetylation and gene expression analysis of sex lethal mutants in Drosophila. Genetics 155:753–763.PubMedGoogle Scholar
  12. Bingham PM, Levis R, Rubin GM (1981) Cloning of DNA sequences from the white locus of D. melanogaster by a novel and general method. Cell 25:693–704.PubMedGoogle Scholar
  13. Bingham PM, Kidwell MG, Rubin GM (1982) The molecular basis of P-M hybrid dysgenesis: the role of the P element, a P-strain-specific transposon family. Cell 29:995–1004.PubMedGoogle Scholar
  14. Birchler JA, Pal-Bhadra M, Bhadra U (2003a) Transgene cosuppression in animals. In: Hannon G (ed) RNAi: a guide to gene silencing. Cold Spring Harbor Press, Cold Spring Harbor, pp 23–42.Google Scholar
  15. Birchler JA, Pal-Bhadra M, Bhadra U (2003b) Dosage dependent gene regulation and the compensation of the X chromosome in Drosophila males. Genetica 117:179–190.PubMedGoogle Scholar
  16. Black DM, Jackson MS, Kidwell MG, Dover GA (1987) KP elements repress P-induced hybrid dysgenesis in Drosophila melanogaster. EMBO J 6:4125–4135.PubMedGoogle Scholar
  17. Blumenstiel JP, Hartl DL (2005) Evidence for maternally transmitted small interfering RNA in the repression of transposition in Drosophila virilis. Proc Natl Acad Sci USA 102:15965–15970.PubMedGoogle Scholar
  18. Brennecke J, Aravin AA, Stark A, Dus M, Kellis M, Sachidanandam R, Hannon GJ (2007) Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128:1089–1103.PubMedGoogle Scholar
  19. Bucheton A, Busseau I, Teninges D (2002) I element in Drosophila melanogaster. In: Craig NL, Craigie R, Gellert M, Lambowitz AM (eds) Mobile DNA II. ASM Press, Washington DC, pp 796–812.Google Scholar
  20. 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.PubMedGoogle Scholar
  21. Caudy AA, Ketting RF, Hammond SM, Denli AM, Bathoorn AM, Tops BB, Silva JM, Myers MM, Hannon GJ, Plasterk RH (2003) A micrococcal nuclease homologue in RNAi effector complexes. Nature 425:411–414.PubMedGoogle Scholar
  22. Chaboissier MC, Busseau I, Prosser J, Finnegan DJ, Bucheton A (1990) Identification of a potential RNA intermediate for transposition of the LINE-like element I factor in Drosophila melanogaster. EMBO J 9:3557–3563.PubMedGoogle Scholar
  23. Chaboissier MC, Bucheton A, Finnegan DJ (1998) Copy number control of a transposable element, the I factor, a LINE-like element in Drosophila. Proc Natl Acad Sci USA 95:11781–11785.PubMedGoogle Scholar
  24. Chen Y, Pane A, Schupbach T (2007) Cutoff and aubergine mutations result in retrotransposon upregulation and checkpoint activation in Drosophila. Curr Biol 17:1–6.Google Scholar
  25. Chiu YL, Rana TM (2003) siRNA function in RNAi: a chemical modification analysis. RNA 9:1034–1048.PubMedGoogle Scholar
  26. Ciapponi L, Cenci G, Ducau J, Flores C, Johnson-Schlitz D, Gorski MM, Engels WR, Gatti M (2004) The Drosophila Mre11/Rad50 complex is required to prevent both telomeric fusion and chromosome breakage. Curr Biol 14:1360–1366.PubMedGoogle Scholar
  27. Coller J, Parker R (2004) Eukaryotic mRNA decapping. Annu Rev Biochem 73:861–890.PubMedGoogle Scholar
  28. Cortes A, Huertas D, Fanti L, Pimpinelli S, Marsellach FX, Pina B, Azorin F (1999) DDP1, a single-stranded nucleic acid-binding protein of Drosophila, associates with pericentric heterochromatin and is functionally homologous to the yeast Scp160p, which is involved in the control of cell ploidy. EMBO J 18:3820–3833.PubMedGoogle Scholar
  29. Csink AK, Linsk R, Birchler JA (1994) The Lighten up (Lip) gene of Drosophila melanogaster, a modifier of retroelement expression, position effect variegation and white locus insertion alleles. Genetics 138:153–163.PubMedGoogle Scholar
  30. de Wit E, Greil F, van Steensel B (2005) Genome-wide HP1 binding in Drosophila: developmental plasticity and genomic targeting signals. Genome Res 15:1265–1273.PubMedGoogle Scholar
  31. DeCerbo J, Carmichael GG (2005) Retention and repression: fates of hyperedited RNAs in the nucleus. Curr Opin Cell Biol 17:302–308.PubMedGoogle Scholar
  32. Deng H, Zhang W, Bao X, Martin JN, Girton J, Johansen J, Johansen KM (2005) The JIL-1 kinase regulates the structure of Drosophila polytene chromosomes. Chromosoma 114:173–182.PubMedGoogle Scholar
  33. Deshpande G, Calhoun G, Schedl P (2005) Drosophila argonaute-2 is required early in embryogenesis for the assembly of centric/centromeric heterochromatin, nuclear division, nuclear migration, and germ-cell formation. Genes Dev 19:1680–1685.PubMedGoogle Scholar
  34. Doench JG, Petersen CP, Sharp PA (2003) siRNAs can function as miRNAs. Genes Dev 17:438–442.PubMedGoogle Scholar
  35. Elbashir SM, Lendeckel W, Tuschl T (2001a) RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev 15:188–200.PubMedGoogle Scholar
  36. Elbashir SM, Martinez J, Patkaniowska A, Lendeckel W, Tuschl T (2001b) Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J 20:6877–6888.PubMedGoogle Scholar
  37. 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.PubMedGoogle Scholar
  38. Forstemann K, Tomari Y, Du T, Vagin VV, Denli AM, Bratu DP, Klattenhoff C, Theurkauf WE, Zamore PD (2005) Normal microRNA maturation and germ-line stem cell maintenance requires Loquacious, a double-stranded RNA-binding domain protein. PLoS Biol 3:e236.PubMedGoogle Scholar
  39. Frolov MV, Birchler JA (1998) Mutation in P0, a dual function ribosomal protein/apurinic/apyrimidinic endonuclease, modifies gene expression and position effect variegation in Drosophila. Genetics 150:1487–1495.PubMedGoogle Scholar
  40. Galiana-Arnoux D, Dostert C, Schneemann A, Hoffman JA, Imler JL (2006) Essential function in vivo for Dicer-2 in host defense against RNA viruses in Drosophila. Nat Immunol 7:590–597.PubMedGoogle Scholar
  41. Gazzani S, Lawrenson T, Woodward C, Headon D, Sablowski R (2004) A link between mRNA turnover and RNA interference in Arabidopsis. Science 306:1046–1048.PubMedGoogle Scholar
  42. Girard A, Sachidanandam R, Hannon GJ, Carmell M (2006) A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 442:199–202.PubMedGoogle Scholar
  43. Green CM, Almouzni G (2003) Local action of the chromatin assembly factor CAF-1 at sites of nucleotide excision repair in vivo. EMBO J 22:5163–5174.PubMedGoogle Scholar
  44. Grimaud C, Bantignies F, Pal-Bhadra M, Bhadra U, Cavalli G (2006) RNAi components are required for nuclear clustering of Polycomb Group Response Elements. Cell 124:957–971.PubMedGoogle Scholar
  45. Gunawardane LS, Saito K, Nishida KM, Miyoshi K, Kawamura Y, Nagami T, Siomi H, Siomi MC (2007) A slicer-mediated mechanisms for repeat-associated siRNA 5G end formation in Drosophila. Science 315:1587–1590.PubMedGoogle Scholar
  46. Guo S, Kemphues KJ (1994) par-1, a gene required for establishing polarity in C. elegans embryos, encodes a putative Ser/Thr kinase that is asymmetrically distributed. Cell 81:611–620.Google Scholar
  47. Haley B, Zamore PD (2004) Kinetic analysis of the RNAi enzyme complex. Nat Struct Mol Biol 11:599–606.PubMedGoogle Scholar
  48. Haley KJ, Stuart JR, Raymond JD, Niemi JB, Simmons MJ (2005) Impairment of cytotype regulation of P-element activity in Drosophila melanogaster by mutations in the Su(var) 205 gene. Genetics 171:583–595.PubMedGoogle Scholar
  49. Hall IM, Noma K, Grewal SI (2003) RNA interference machinery regulates chromosome dynamics during mitosis and meiosis in fission yeast. Proc Natl Acad Sci USA 100:193–198.PubMedGoogle Scholar
  50. Hamilton A, Voinnet O, Chappell L, Baulcombe D (2002) Two classes of short interfering RNA in RNA silencing. EMBO J 21:4671–4679.PubMedGoogle Scholar
  51. Han J, Lee Y, Yeom KH, Kim YK, Jin H, Kim VN (2004) The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev 18:3016–3027.PubMedGoogle Scholar
  52. Hannon GJ, Conklin DS (2004) RNA interference by short hairpin RNAs expressed in vertebrate cells. Methods Mol Biol 257:255–266.PubMedGoogle Scholar
  53. Haussecker D, Proudfoot NJ (2005) Dicer-dependent turnover of intergenic transcripts from the human beta-globin gene cluster. Mol Cell Biol 25:9724–9733.PubMedGoogle Scholar
  54. Haynes KA, Caudy AA, Collins L, Elgin SCR (2006) Element 1360 and RNAi components contribute to HP1-dependent silencing of a pericentric reporter. Curr Biol 16:2222–2227.PubMedGoogle Scholar
  55. Huertas D, Cortes A, Casanova J, Azorin F (2004) Drosophila DDP1, a multi-KH-domain protein, contributes to centromeric silencing and chromosome segregation. Curr Biol 14:1611–1620.PubMedGoogle Scholar
  56. Ishizuka A, Siomi MC, Siomi H (2002) A Drosophila fragile X protein interacts with components of RNAi and ribosomal proteins. Genes Dev 16:2497–2508.PubMedGoogle Scholar
  57. Jacque JM, Triques K, Stevenson M (2002) Modulation of HIV-1 replication by RNA interference. Nature 418:435–438.PubMedGoogle Scholar
  58. Jakymiw A, Lian S, Eystathioy T, Li S, Satoh M, Hamel JC, Fritzler MJ, Chan EK (2005) Disruption of GW bodies impairs mammalian RNA interference. Nat Cell Biol 7:1167–1174.Google Scholar
  59. Jensen S, Gassama MP, Heidmann T (1999a) Cosuppression of I transposon activity in Drosophila by I-containing sense and antisense transgenes. Genetics 153:1767–1774.PubMedGoogle Scholar
  60. Jensen S, Gassama MP, Heidmann T (1999b) Taming of transposable elements by homology-dependent gene silencing. Nat Genet 21:209–212.PubMedGoogle Scholar
  61. Jeong Br BR, Wu-Scharf D, Zhang C, Cerutti H (2002) Suppressors of transcriptional transgenic silencing in Chlamydomonas are sensitive to DNA-damaging agents and reactivate transposable elements. Proc Natl Acad Sci USA 99:1076–1081.PubMedGoogle Scholar
  62. Kalmykova AI, Klenov MS, Gvozdev VA (2005) Argonaute protein PIWI controls mobilization of retrotransposons in the Drosophila male germline. Nucleic Acids Res 33:2052–2059.PubMedGoogle Scholar
  63. Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, Patel S, Frise E, Wheeler DA, Lewis SE, Rubin GM, Ashburner M, Celniker SE (2002) The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol 3:RESEARCH0084.PubMedGoogle Scholar
  64. Kanellopoulou C, Muljo SA, Kung AL, Ganesan S, Drapkin R, Jenuwein T, Livingston DM, Rajewsky K (2005) Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev 19:489–501.PubMedGoogle Scholar
  65. Karpen GH, Spradling AC (1992) Analysis of subtelomeric heterochromatin in the Drosophila minichromosome Dp1187 by single P element insertional mutagenesis. Genetics 132:737–753.PubMedGoogle Scholar
  66. Kassis JA, VanSickle EP, Sensabaugh SM (1991) A fragment of engrailed regulatory DNA can mediate transvection of the white gene in Drosophila. Genetics 128:751–761.PubMedGoogle Scholar
  67. Kato H, Goto DB, Martienssen RA, Urano T, Furukawa K, Murakami Y (2005) RNA polymerase II is required for RNAi-dependent heterochromatin assembly. Science 309:467–469.PubMedGoogle Scholar
  68. Kelley RL, Kuroda MI (2003) The Drosophila roX1 RNA gene can overcome silent chromatin by recruiting the male-specific lethal dosage compensation complex. Genetics 164:565–574.PubMedGoogle Scholar
  69. Kelley RL, Meller VH, Gordadze PR, Roman G, Davis RL, Kuroda MI (1999) Epigenetic spreading of the Drosophila dosage compensation complex from roX RNA genes into flanking chromatin. Cell 98:513–522.PubMedGoogle Scholar
  70. Kennerdell JR, Carthew RW (2000) Heritable gene silencing in Drosophila using double-stranded RNA. Nat Biotechnol 18:896–898.PubMedGoogle Scholar
  71. Kennerdell JR, Yamaguchi S, Carthew RW (2002) RNAi is activated during Drosophila oocyte maturation in a manner dependent on aubergine and spindle-E. Genes Dev 16:1884–1889.PubMedGoogle Scholar
  72. Klenov MS, Lavrov SA, Stolyarenko AD, Ryazansky SS, Aravin AA, Tuschl T, Gvozdev VA (2007) Repeat-associated short interfering RNAs are involved in chromatin silencing of retrotransposons in the Drosophila melanogaster germline. Nucleic Acids Res Aug 15 [Epub ahead of print].Google Scholar
  73. Kraynack BA, Baker BF (2005) Small interfering RNAs containing full 2K-O-methylribonucleotide-modified sense strands display Argonaute2/eIF2C2-dependent activity. RNA 12:163–176.PubMedGoogle Scholar
  74. Kruse C, Grunweller A, Willkomm DK, Pfeiffer T, Hartmann RK, Muller PK (1998) tRNA is entrapped in similar, but distinct, nuclear and cytoplasmic ribonucleoprotein complexes, both of which contain vigilin and elongation factor 1 alpha. Biochem J 329:615–621.PubMedGoogle Scholar
  75. Kruse C, Willkomm DK, Grunweller A, Vollbrandt T, Sommer S, Busch S, Pfeiffer T, Brinkmann J, Hartmann RK, Muller PK (2000) Export and transport of tRNA are coupled to a multi-protein complex. Biochem J 346:107–115.PubMedGoogle Scholar
  76. Lee YS, Nakahara K, Pham JW, Kim K, He Z, Sontheimer EJ, Carthew RW (2004) Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 117:69–81.PubMedGoogle Scholar
  77. Lei EP, Corces VG (2006) RNA interference machinery influences the nuclear organization of a chromatin insulator. Nat Genet 38:936–941.PubMedGoogle Scholar
  78. Lemaitre B, Ronsseray S, Coen D (1993) Maternal repression of the P element promoter in the germline of Drosophila melanogaster: a model for the P cytotype. Genetics 135:149–160.PubMedGoogle Scholar
  79. Li AM, Watson A, Fridovich-Keil JL (2003) Scp160p associates with specific mRNAs in yeast. Nucleic Acids Res 31:1830–1837.PubMedGoogle Scholar
  80. Li H, Li WX, Ding SW (2002) Induction and suppression of RNA silencing by an animal virus. Science 296:1319–1321.PubMedGoogle Scholar
  81. Lipardi C, Wei Q, Paterson BM (2001) RNAi as random degradative PCR: siRNA primers convert mRNA into dsRNAs that are degraded to generate new siRNAs. Cell 107:297–307.PubMedGoogle Scholar
  82. 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.PubMedGoogle Scholar
  83. Liu J, Rivas FV, Wohlschlegel J, Yates JR 3rd, Parker R, Hannon GJ (2005a) A role for the P-body component GW182 in microRNA function. Nat Cell Biol 7:1161–1166.Google Scholar
  84. Liu J, Valencia-Sanchez MA, Hannon GJ, Parker R (2005b) MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies. Nat Cell Biol 7:719–723.PubMedGoogle Scholar
  85. Liu LP, Ni JQ, Shi YD, Oakeley EJ, Sun FL (2005) Sex-specific role of Drosophila melanogaster HP1 in regulating chromatin structure and gene transcription. Nat Genet 37:1361–1366.PubMedGoogle Scholar
  86. Liu Q, Rand TA, Kalidas S, Du F, Kim HE, Smith DP, Wang X (2003) R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science 301:1921–1925.PubMedGoogle Scholar
  87. Liu X, Jiang F, Kalidas S, Smith D, Liu Q (2006) Dicer-2 and R2D2 coordinately bind siRNA to promote assembly of the siRISC complexes. RNA 12:1514–1520.PubMedGoogle Scholar
  88. Llave C, Kasschau KD, Rector MA, Carrington JC (2002) Endogenous and silencing-associated small RNAs in plants. Plant Cell 14:1605–1619.PubMedGoogle Scholar
  89. Lozovskaya ER, Scheinker VS, Evgenev MB (1990) A hybrid dysgeneis syndrome in Drosophila virilis. Genetics 126:619–623.PubMedGoogle Scholar
  90. Ma JB, Yuan YR, Meister G, Pei Y, Tuschl T, Patel DJ (2005) Structural basis for 5M-end-specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature 434:666–670.PubMedGoogle Scholar
  91. Malinsky S, Bucheton A, Busseau I (2000) New insights on homology-dependent silencing of I factor activity by transgenes containing ORF1 in Drosophila melanogaster. Genetics 156:1147–1155.PubMedGoogle Scholar
  92. Matranga C, Tomari Y, Shin C, Bartel DP, Zamore PD (2005) Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes. Cell 123:607–620.PubMedGoogle Scholar
  93. Matzke MA, Primig M, Trnovsky J, Matzke AJM (1989) Reversible methylation and inactivation of marker genes in sequentially transformed tobacco plants. EMBO J 8:643–649.PubMedGoogle Scholar
  94. McLean C, Bucheton A, Finnegan DJ (1993) The 5M untranslated region of the I factor, a long interspersed nuclear element-like retrotransposon of Drosophila melanogaster, contains an internal promoter and sequences that regulate expression. Mol Cell Biol 13:1042–1050.PubMedGoogle Scholar
  95. Meister G, Landthaler M, Patkaniowska A, Dorsett Y, Teng G, Tuschl T (2004) Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol Cell 15:185–197.PubMedGoogle Scholar
  96. Mette MF, van der Winden J, Matzke M, Matzke AJ (2002) Short RNAs can identify new candidate transposable element families in Arabidopsis. Plant Physiol 130:6–9.PubMedGoogle Scholar
  97. Miyoshi K, Tsukumo H, Nagami T, Siomi H, Siomi MC (2005) Slicer function of Drosophila Argonautes and its involvement in RISC formation. Genes Dev 19:2837–2848.PubMedGoogle Scholar
  98. Napoli C, Lemieux C, Jorgenson R (1990) Introduction of a chimeric chalcone synthase gene in Petunia results in reversible co-suppression of homologous genes in trans. Plant Cell 2:279–289.PubMedGoogle Scholar
  99. O’Hare K, Driver A, McGrath S, Johnson-Schiltz DM (1992) Distribution and structure of cloned P elements from the Drosophila melanogaster P strain pi2. Genet Res 60:33–41.PubMedGoogle Scholar
  100. Oikemus SR, McGinnis N, Queiroz-Machado J, Tukachinsky H, Takada S, Sunkel CE, Brodsky MH (2004) Drosophila atm/telomere fusion is required for telomeric localization of HP1 and telomere position effect. Genes Dev 18:1850–1861.PubMedGoogle Scholar
  101. Okamura K, Ishizuka A, Siomi H, Siomi MC (2004) Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways. Genes Dev 18:1655–1666.PubMedGoogle Scholar
  102. Paddison PJ, Caudy AA, Hannon GJ (2002) Stable suppression of gene expression by RNAi in mammalian cells. Proc Natl Acad Sci USA 99:1443–1448.PubMedGoogle Scholar
  103. Pal-Bhadra M, Bhadra U, Birchler JA (1997) Cosuppression in Drosophila: gene silencing of Alcohol dehydrogenase by white-Adh transgenes is Polycomb dependent. Cell 90:479–490.PubMedGoogle Scholar
  104. Pal-Bhadra M, Bhadra U, Birchler JA (1999) Cosuppression of nonhomologous transgenes in Drosophila involves mutually related endogenous sequences. Cell 99:35–46.PubMedGoogle Scholar
  105. Pal-Bhadra M, Bhadra U, Birchler JA (2002) RNAi related mechanisms affect both transcriptional and post-transcriptional transgene silencing in Drosophila. Mol Cell 9:315–327.PubMedGoogle Scholar
  106. Pal-Bhadra M, Bhadra U, Birchler JA (2004a) Interrelationship of RNA interference and transcriptional gene silencing in Drosophila. Cold Spring Harb Symp Quant Biol 69:433–438.PubMedGoogle Scholar
  107. Pal-Bhadra M, Leibovitch BA, Gandhi SG, Rao M, Bhadra U, Birchler JA, Elgin SC (2004b) Heterochromatic silencing and HP1 localization in Drosophila are dependent on the RNAi machinery. Science 303:669–672.PubMedGoogle Scholar
  108. Pal-Bhadra M, Bhadra U, Kundu J, Birchler JA (2005) Gene expression analysis of the function of the MSL complex in Drosophila. Genetics 169:2061–2074.Google Scholar
  109. Pane A, Wehr K, Schupbach T (2007) Zucchini and squash encode two putative nucleases required for rasiRNA production in the Drosophila germline. Dev Cell 12:851–862.PubMedGoogle Scholar
  110. Parker JS, Roe SM, Barford D (2005) Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex. Nature 434:663–666.PubMedGoogle Scholar
  111. Peng JC, Karpen GH (2007) H3K9 methylation and RNA interference regulate nucleolar organization and repeated DNA stability. Nat Cell Biol 9:25–35.PubMedGoogle Scholar
  112. Pham JW, Sontheimer EJ (2005) Molecular requirements for RNA-induced silencing complex assembly in the Drosophila RNA interference pathway. J Biol Chem 280:39278–39283.PubMedGoogle Scholar
  113. Pham JW, Pellino JL, Lee YS, Carthew RW, Sontheimer EJ (2004) A Dicer-2-dependent 80s complex cleaves targeted mRNAs during RNAi in Drosophila. Cell 117:83–94.PubMedGoogle Scholar
  114. Picard G (1976) Non-Mendelian female sterility in Drosophila melanogaster: hereditary transmission of I factor. Genetics 83:107–123.PubMedGoogle Scholar
  115. Quivy JP, Roche D, Kirschner D, Tagami H, Nakatani Y, Almouzni G (2004) A CAF-1 dependent pool of HP1 during heterochromatin duplication. EMBO J 23:3516–3526.PubMedGoogle Scholar
  116. Rabinow L, Nguyen-Huynh A, Birchler JA (1991) A trans-acting regulatory gene that inversely affects the expression of the white, brown and scarlet loci in Drosophila melanogaster. Genetics 129:463–480.PubMedGoogle Scholar
  117. Rabinow L, Chiang SL, Birchler JA (1993) Mutations at the Darkener of apricot locus modulate transcript levels of copia and copia-induced mutations in Drosophila melanogaster. Genetics 134:1175–1185.PubMedGoogle Scholar
  118. Reinhart BJ, Bartel DP (2002) Small RNAs correspond to centromere heterochromatic repeats. Science 297:1831.PubMedGoogle Scholar
  119. Reiss D, Josse T, Anxolabehere D, Ronsseray S (2004) Aubergine mutations in Drosophila melanogaster impair P cytotype determination by telomeric P elements inserted in heterochromatin. Mol Genet Genomics 272:336–343.PubMedGoogle Scholar
  120. Rio DC, Laski FA, Rubin GM (1986) Identification and immunochemical analysis of biologically active Drosophila P element transposase. Cell 44:21–32.PubMedGoogle Scholar
  121. Rivas FV, Tolia NH, Song JJ, Aragon JP, Liu J, Hannon GJ, Joshua-Tor L (2005) Purified Argonaute2 and an siRNA form recombinant human RISC. Nat Struct Mol Biol 12:340–349.PubMedGoogle Scholar
  122. Robin S, Chambeyron S, Bucheton A, Busseau I (2003) Gene silencing triggered by non-LTR retrotransposons in the female germline of Drosophila melanogaster. Genetics 164:521–531.PubMedGoogle Scholar
  123. Roche SE, Schiff M, Rio DC (1995) P-element repressor autoregulation involves germ-line transcriptional repression and reduction of third intron splicing. Genes Dev 9:1278–1288.PubMedGoogle Scholar
  124. Ronsseray S, Lehmann M, Anxolabehere D (1991) The maternally inherited regulation of P elements in Drosophila melanogaster can be elicited by two P copies at cytological site 1A on the X chromosome. Genetics 129:501–512.PubMedGoogle Scholar
  125. Ronsseray S, Lehmann M, Nouaud D, Anxolabehere D (1996) The regulatory properties of autonomous subtelomeric P elements are sensitive to a suppressor of variegation in Drosophila melanogaster. Genetics 143:1663–1674.PubMedGoogle Scholar
  126. Ronsseray S, Marin L, Lehmann M, Anxolabehere D (1998) Repression of hybrid dysgenesis in Drosophila melanogaster by combinations of telomeric P-element reporters and naturally occurring P elements. Genetics 149:1857–1866.PubMedGoogle Scholar
  127. Ronsseray S, Josse T, Boivin A, Anxolabehere D (2003) Telomeric transgenes and trans-silencing in Drosophila. Genetica 117:327–335.PubMedGoogle Scholar
  128. Rubin GM, Kidwell MG, Bingham PM (1982) The molecular basis of P-M hybrid dysgenesis: the nature of induced mutations. Cell 29:987–994.PubMedGoogle Scholar
  129. Saito K, Nishida KM, Mori T, Kawamura Y, Miyoshi K, Nagami T, Siomi H, Siomi MC (2006) Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome. Genes Dev 20:2214–2222.PubMedGoogle Scholar
  130. Savitsky M, Kwon D, Georgiev P, Kalmykova A, Gvozdev V (2006) Telomere elongation is under the control of the RNAi-based mechanism in the Drosophila germline. Genes Dev 20:345–354.PubMedGoogle Scholar
  131. Scadden AD (2005) The RISC subunit Tudor-SN binds to hyper-edited double-stranded RNA and promotes its cleavage. Nat Struct Mol Biol 12:489–496.PubMedGoogle Scholar
  132. Scadden AD, Smith CW (2001) RNAi is antagonized by A→I hyper-editing. EMBO Rep 2:1107–1111.PubMedGoogle Scholar
  133. Schramke V, Sheedy DM, Denli AM, Bonila C, Ekwall K, Hannon GJ, Allshire RC (2005) RNA-interference-directed chromatin modification coupled to RNA polymerase II transcription. Nature 435:1275–1279.PubMedGoogle Scholar
  134. Schwarz DS, Hutvagner 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.PubMedGoogle Scholar
  135. Schwarz DS, Tomari Y, Zamore PD (2004) The RNA-induced silencing complex is a Mg2+-dependent endonuclease. Curr Biol 14:787–791.PubMedGoogle Scholar
  136. Sijen T, Plasterk RH (2003) Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi. Nature 426:310–314.PubMedGoogle Scholar
  137. Simmons MJ, Raymond JD, Grimes CD, Belinco C, Haake BC, Jordan M, Lund C, Ojala TA, Papermaster D (1996) Repression of hybrid dysgenesis in Drosophila melanogaster by heat-shock-inducible sense and antisense P-element constructs. Genetics 144:1529–1544.PubMedGoogle Scholar
  138. Simmons MJ, Raymond JD, Niemi JB, Stuart JR, Merriman PJ (2004) The P cytotype in Drosophila melanogaster: a maternally transmitted regulatory state of the germ line associated with telomeric P elements. Genetics 166:243–254.PubMedGoogle Scholar
  139. Siomi MC, Tsukumo H, Ishizuka A, Nagami T, Siomi H (2005) A potential link between transgene silencing and poly(A) tails. RNA 11:1004–1011.PubMedGoogle Scholar
  140. Song K, Jung Y, Jung D, Lee I (2001) Human Ku70 interacts with heterochromatin protein 1alpha. J Biol Chem 276:8321–8327.PubMedGoogle Scholar
  141. Song YH, Mirey G, Betson M, Haber DA, Settleman J (2004) The Drosophila ATM ortholog, dATM, mediates the response to ionizing radiation and to spontaneous DNA damage during development. Curr Biol 14:1354–1359.PubMedGoogle Scholar
  142. Sontheimer EJ (2005) Assembly and function of RNA silencing complexes. Nat Rev Mol Cell Biol 6:127–138.PubMedGoogle Scholar
  143. Sontheimer EJ, Carthew RW (2004) Molecular biology. Argonaute journeys into the heart of RISC. Science 305:1409–1410.PubMedGoogle Scholar
  144. Spierer A, Seum C, Delattre M, Spierer P (2005) Loss of the modifiers of variegation Su(var) 3–7 or HP1 impacts male X polytene chromosome morphology and dosage compensation. J Cell Sci 118:5047–5057.PubMedGoogle Scholar
  145. Stuart JR, Haley KJ, Swedzinski D, Lockner S, Kocian PE, Merriman PJ, Simmons MJ (2002) Telomeric P elements associated with cytotype regulation of the P transposon family in Drosophila melanogaster. Genetics 162:1641–1654.PubMedGoogle Scholar
  146. Sun FL, Haynes K, Simpson CL, Lee SD, Collins L, Wuller J, Eissenberg JC, Elgin SCR (2004) cis-Acting determinants of heterochromatin formation on Drosophila melanogaster chromosome four. Mol Cell Biol 24:8210–8220.PubMedGoogle Scholar
  147. Tahbaz N, Kolb FA, Zhang H, Jaronczyk K, Filipowicz W, Hobman TC (2004) Characterization of the interactions between mammalian PAZ PIWI domain proteins and Dicer. EMBO Rep 5:189–194.PubMedGoogle Scholar
  148. Takeda S, Tadele Z, Hofmann I, Probst AV, Angelis KJ, Kaya H, Araki T, Mengiste T, Mittelsten Scheid O, Shibahara K, Scheel D, Paszkowski J (2004) BRU1, a novel link between responses to DNA damage and epigenetic gene silencing in Arabidopsis. Genes Dev 18:782–793.PubMedGoogle Scholar
  149. Thacker J, Zdzienicka MZ (2004) The XRCC genes: expanding roles in DNA double-strand break repair. DNA Repair (Amst) 3:1081–1090.Google Scholar
  150. Tomari Y, Du T, Haley B, Schwarz DS, Bennett R, Cook HA, Koppetsch BS, Theurkauf WE, Zamore PD (2004a) RISC assembly defects in the Drosophila RNAi mutant armitage. Cell 116:831–841.PubMedGoogle Scholar
  151. Tomari Y, Matranga C, Haley B, Martinez N, Zamore PD (2004b) A protein sensor for siRNA asymmetry. Science 306:1377–1380.PubMedGoogle Scholar
  152. Tonkin LA, Bass BL (2003) Mutations in RNAi rescue aberrant chemotaxis of ADAR mutants. Science 302:1725.PubMedGoogle Scholar
  153. Tonkin LA, Saccomanno L, Morse DP, Brodigan T, Krause M, Bass BL (2002) RNA editing by ADARs is important for normal behavior in Caenorhabditis elegans. EMBO J 21:6025–6035.PubMedGoogle Scholar
  154. Tulin A, Stewart D, Spradling AC (2002) The Drosophila heterochromatic gene encoding poly(ADP-ribose) polymerase (PARP) is required to modulate chromatin structure during development. Genes Dev 16:2108–2119.PubMedGoogle Scholar
  155. Tulin AV, Kogan GL, Filipp D, Balakireva MD, Gvozdev VA (1997) Heterochromatic Stellate gene cluster in Drosophila melanogaster: structure and molecular evolution. Genetics 146:253–262.PubMedGoogle Scholar
  156. Usakin L, Abad J, Vagin VV, de Pablos B, Villasante A, Gvozdov VA (2007) Transcription of the 1.688 satellite DNA family is under the control of RNA interference machinery in Drosophila melanogaster ovaries. Genetics 176:1343–1349.PubMedGoogle Scholar
  157. Uziel T, Lerenthal Y, Moyal L, Andegeko Y, Mittelman L, Shiloh Y (2003) Requirement of the MRN complex for ATM activation by DNA damage. EMBO J 22:5612–5621.PubMedGoogle Scholar
  158. Vagin VV, Klenov MS, Kalmykova AI, Stolyarenko AD, Kotelnikov RN, Gvozdev VA (2004) The RNA interference proteins and vasa locus are involved in the silencing of retrotransposons in the female germline of Drosophila melanogaster. RNA Biol 1:54–58.PubMedGoogle Scholar
  159. Vagin VV, Sigova A, Li C, Seitz H, Gvozdev V, Zamore P (2006) A distinct small RNA pathway silences selfish genetic elements in the germline. Science 313:320–324.PubMedGoogle Scholar
  160. van der Krol AR, Mur LA, Beld M, Mol JNM, Stuitje AR (1990) Flavonoid genes in Petunia: addition of a limited number of gene copies may lead to a suppression of gene expression. Plant Cell 2:291–299.PubMedGoogle Scholar
  161. Verdel A, Jia S, Gerber S, Sugiyama T, Gygi S, Grewal SI, Moazed D (2004) RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303:672–676.PubMedGoogle Scholar
  162. Vermeulen A, Behlen L, Reynolds A, Wolfson A, Marshall WS, Karpilow J, Khvorova A (2005) The contributions of dsRNA structure to Dicer specificity and efficiency. RNA 11:674–682.PubMedGoogle Scholar
  163. Volpe T, Schramke V, Hamilton GL, White SA, Teng G, Martienssen RA, Allshire RC (2003) RNA interference is required for normal centromere function in fission yeast. Chromosome Res 11:137–146.PubMedGoogle Scholar
  164. Volpe TA, Kidner C, Hall IM, Teng G, Grewal SI, Martienssen RA (2002) Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297:1833–1837.PubMedGoogle Scholar
  165. Wang Q, Zhang Z, Blackwell K, Carmichael GG (2005) Vigilins bind to promiscuously A-to-I-edited RNAs and are involved in the formation of heterochromatin. Curr Biol 15:384–391.PubMedGoogle Scholar
  166. Wang XH, Aliyari R, Li WX, Li HW, Kim K, Carthew R, Atkinson P, Ding SW (2006) RNA interference directs innate immunity against viruses in adult Drosophila. Science 312:452–454.PubMedGoogle Scholar
  167. Wang Y, Zhang W, Jin Y, Johansen J, Johansen KM (2001) The JIL-1 tandem kinase mediates histone H3 phosphorylation and is required for maintenance of chromatin structure in Drosophila. Cell 105:433–443.PubMedGoogle Scholar
  168. Williams RW, Rubin GM (2002) Argonaute1 is required for efficient RNA interference in Drosophila embryos. Proc Natl Acad Sci USA 99:6889–6894.PubMedGoogle Scholar
  169. Yang W, Wan, Q, Howell KL, Lee JT, Cho DS, Murray JM, Nishikurg K (2005) ADAR1 RNA deaminase limits short interfering RNA efficacy in mammalian cells. J Biol Chem 280:3946–3953.PubMedGoogle Scholar
  170. Zhang H, Kolb FA, Brondani V, Billy E, Filipowicz W (2002) Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J 21:5875–5885.PubMedGoogle Scholar
  171. Zhang H, Kolb FA, Jaskiewicz L, Westhof E, Filipowicz W (2004) Single processing center models for human Dicer and bacterial RNase III. Cell 118:57–68.PubMedGoogle Scholar
  172. Zhang W, Deng H, Bao X, Lerach S, Girton J, Johansen J, Johansen KM (2006) The JIL-1 histone H3S10 kinase regulates dimethyl H3K9 modifications and heterochromatic spreading in Drosophila. Development 133:229–235.PubMedGoogle Scholar
  173. Zhang Z, Carmichael GG (2001) The fate of dsRNA in the nucleus: a p54nrb-containing complex mediates the nuclear retention of promiscuously A-to-I edited RNAs. Cell 106:465–475.PubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Harsh H. Kavi
  • Harvey Fernandez
  • Weiwu Xie
  • James A. Birchler
    • 1
  1. 1.Division of Biological SciencesUniversity of MissouriColumbiaUSA

Personalised recommendations