The piRNA Pathway Guards the Germline Genome Against Transposable Elements

Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 886)


Transposable elements (TEs) have the capacity to replicate and insert into new genomic locations. This contributs significantly to evolution of genomes, but can also result in DNA breaks and illegitimate recombination, and therefore poses a significant threat to genomic integrity. Excess damage to the germ cell genome results in sterility. A specific RNA silencing pathway, termed the piRNA pathway operates in germ cells of animals to control TE activity. At the core of the piRNA pathway is a ribonucleoprotein complex consisting of a small RNA, called piRNA, and a protein from the PIWI subfamily of Argonaute nucleases. The piRNA pathway relies on the specificity provided by the piRNA sequence to recognize complementary TE targets, while effector functions are provided by the PIWI protein. PIWI-piRNA complexes silence TEs both at the transcriptional level – by attracting repressive chromatin modifications to genomic targets – and at the posttranscriptional level – by cleaving TE transcripts in the cytoplasm. Impairment of the piRNA pathway leads to overexpression of TEs, significantly compromised genome structure and, invariably, germ cell death and sterility.

The piRNA pathway is best understood in the fruit fly, Drosophila melanogaster, and in mouse. This Chapter gives an overview of current knowledge on piRNA biogenesis, and mechanistic details of both transcriptional and posttranscriptional TE silencing by the piRNA pathway. It further focuses on the importance of post-translational modifications and subcellular localization of the piRNA machinery. Finally, it provides a brief description of analogous pathways in other systems.


piRNA Small RNA Argonautes Piwi proteins TE Transposon Transposable element Tudor domain Transcriptional silencing Posttranscriptional silencing Heterochromatin H3K9me3 DNA methylation Ping-Pong cycle Germ granules Nuage Pole plasm Pi-bodies Intramitochondrial cement 


  1. Al-Mukhtar KA, Webb AC (1971) An ultrastructural study of primordial germ cells, oogonia and early oocytes in Xenopus laevis. J Embryol Exp Morphol 26(2):195–217PubMedGoogle Scholar
  2. Anand A, Kai T (2012) The tudor domain protein kumo is required to assemble the nuage and to generate germline piRNAs in Drosophila. EMBO J 31:870–882Google Scholar
  3. Anne J (2010) Targeting and anchoring Tudor in the pole plasm of the Drosophila oocyte. PLoS One 5(12):e14362. doi: 10.1371/journal.pone.0014362 CrossRefPubMedPubMedCentralGoogle Scholar
  4. Anne J, Mechler BM (2005) Valois, a component of the nuage and pole plasm, is involved in assembly of these structures, and binds to Tudor and the methyltransferase Capsuleen. Development 132(9):2167–2177. doi: 10.1242/dev.01809 CrossRefPubMedGoogle Scholar
  5. Anne J, Ollo R, Ephrussi A, Mechler BM (2007) Arginine methyltransferase Capsuleen is essential for methylation of spliceosomal Sm proteins and germ cell formation in Drosophila. Development 134(1):137–146. doi: 10.1242/dev.02687 CrossRefPubMedGoogle Scholar
  6. Aravin A, Chan D (2011) piRNAs meet mitochondria. Dev Cell 20(3):287–288. doi: 10.1016/j.devcel.2011.03.003 CrossRefPubMedGoogle Scholar
  7. 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: CB 11(13):1017–1027CrossRefPubMedGoogle Scholar
  8. Aravin AA, Klenov MS, Vagin VV, Bantignies F, Cavalli G, Gvozdev VA (2004) Dissection of a natural RNA silencing process in the Drosophila melanogaster germ line. Mol Cell Biol 24(15):6742–6750. doi: 10.1128/MCB.24.15.6742-6750.2004 CrossRefPubMedPubMedCentralGoogle Scholar
  9. Aravin A, Gaidatzis D, Pfeffer S, Lagos-Quintana M, Landgraf P, Iovino N, Morris P, Brownstein MJ, Kuramochi-Miyagawa S, Nakano T, Chien M, Russo JJ, Ju J, Sheridan R, Sander C, Zavolan M, Tuschl T (2006) A novel class of small RNAs bind to MILI protein in mouse testes. Nature 442(7099):203–207, doi: PubMedGoogle Scholar
  10. Aravin AA, Sachidanandam R, Girard A, Fejes-Toth K, Hannon GJ (2007) Developmentally regulated piRNA clusters implicate MILI in transposon control. Science 316(5825):744–747. doi: 10.1126/science.1142612 CrossRefPubMedGoogle Scholar
  11. Aravin A, Sachidanandam R, Bourc’his D, Schaefer C, Pezic D, Toth K, Bestor T, Hannon G (2008) A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol Cell 31(6):785–799. doi: 10.1016/j.molcel.2008.09.003 CrossRefPubMedPubMedCentralGoogle Scholar
  12. Aravin A, van der Heijden G, Castañeda J, Vagin V, Hannon G, Bortvin A (2009) Cytoplasmic compartmentalization of the fetal piRNA pathway in mice. PLoS Genet 5(12):e1000764. doi: 10.1371/journal.pgen.1000764 CrossRefPubMedPubMedCentralGoogle Scholar
  13. Arkov AL, Wang JY, Ramos A, Lehmann R (2006) The role of Tudor domains in germline development and polar granule architecture. Development 133(20):4053–4062. doi: 10.1242/dev.02572 CrossRefPubMedGoogle Scholar
  14. Ashe A, Sapetschnig A, Weick EM, Mitchell J, Bagijn MP, Cording AC, Doebley AL, Goldstein LD, Lehrbach NJ, Le Pen J, Pintacuda G, Sakaguchi A, Sarkies P, Ahmed S, Miska EA (2012) piRNAs can trigger a multigenerational epigenetic memory in the germline of C. elegans. Cell 150(1):88–99. doi: 10.1016/j.cell.2012.06.018 CrossRefPubMedPubMedCentralGoogle Scholar
  15. Bagijn MP, Goldstein LD, Sapetschnig A, Weick EM, Bouasker S, Lehrbach NJ, Simard MJ, Miska EA (2012) Function, targets, and evolution of Caenorhabditis elegans piRNAs. Science 337(6094):574–578. doi: 10.1126/science.1220952 CrossRefPubMedPubMedCentralGoogle Scholar
  16. Bourc’his D, Bestor T (2004) Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431(7004):96–99. doi: 10.1038/nature02886 CrossRefPubMedGoogle Scholar
  17. Bozzetti MP, Massari S, Finelli P, Meggio F, Pinna LA, Boldyreff B, Issinger OG, Palumbo G, Ciriaco C, Bonaccorsi S et al (1995) The Ste locus, a component of the parasitic cry-Ste system of Drosophila melanogaster, encodes a protein that forms crystals in primary spermatocytes and mimics properties of the beta subunit of casein kinase 2. Proc Natl Acad Sci U S A 92(13):6067–6071CrossRefPubMedPubMedCentralGoogle Scholar
  18. Brennecke J, Aravin A, Stark A, Dus M, Kellis M, Sachidanandam R, Hannon G (2007) Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128(6):1089–1103. doi: 10.1016/j.cell.2007.01.043 CrossRefPubMedGoogle Scholar
  19. Carmell M, Xuan Z, Zhang M, Hannon G (2002) The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes Dev 16(21):2733–2742. doi: 10.1101/gad.1026102 CrossRefPubMedGoogle Scholar
  20. Carmell M, Girard A, van de Kant H, Bourc’his D, Bestor T, de Rooij D, Hannon G (2007) MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Dev Cell 12(4):503–514. doi: 10.1016/j.devcel.2007.03.001 CrossRefPubMedGoogle Scholar
  21. Catalanotto C, Azzalin G, Macino G, Cogoni C (2002) Involvement of small RNAs and role of the qde genes in the gene silencing pathway in Neurospora. Genes Dev 16(7):790–795. doi: 10.1101/gad.222402 CrossRefPubMedPubMedCentralGoogle Scholar
  22. Catalanotto C, Pallotta M, ReFalo P, Sachs MS, Vayssie L, Macino G, Cogoni C (2004) Redundancy of the two dicer genes in transgene-induced posttranscriptional gene silencing in Neurospora crassa. Mol Cell Biol 24(6):2536–2545CrossRefPubMedPubMedCentralGoogle Scholar
  23. Cavey M, Hijal S, Zhang X, Suter B (2005) Drosophila valois encodes a divergent WD protein that is required for Vasa localization and Oskar protein accumulation. Development 132:459–468CrossRefPubMedGoogle Scholar
  24. Caterina C, Tony N, Carlo C (2006) Homology effects in Neurospora crassa. FEMS Microbiol Lett 254:182. doi: 10.1111/j.1574-6968.2005.00037.x CrossRefGoogle Scholar
  25. Chalker DL, Yao MC (2001) Nongenic, bidirectional transcription precedes and may promote developmental DNA deletion in Tetrahymena thermophila. Genes Dev 15(10):1287–1298. doi: 10.1101/gad.884601 CrossRefPubMedPubMedCentralGoogle Scholar
  26. Chambeyron S, Popkova A, Payen-Groschêne G, Brun C, Laouini D, Pelisson A, Bucheton A (2008) piRNA-mediated nuclear accumulation of retrotransposon transcripts in the Drosophila female germline. Proc Natl Acad Sci 105(39):14964–14969. doi: 10.1073/pnas.0805943105 CrossRefPubMedPubMedCentralGoogle Scholar
  27. Claycomb JM, Batista PJ, Pang KM, Gu W, Vasale JJ, van Wolfswinkel JC, Chaves DA, Shirayama M, Mitani S, Ketting RF, Conte D Jr, Mello CC (2009) The Argonaute CSR-1 and its 22G-RNA cofactors are required for holocentric chromosome segregation. Cell 139(1):123–134. doi: 10.1016/j.cell.2009.09.014 CrossRefPubMedPubMedCentralGoogle Scholar
  28. Cogoni C, Macino G (1999) Gene silencing in Neurospora crassa requires a protein homologous to RNA-dependent RNA polymerase. Nature 399(6732):166–169. doi: 10.1038/20215 CrossRefPubMedGoogle Scholar
  29. Cook HA, Koppetsch BS, Wu J, Theurkauf WE (2004) The Drosophila SDE3 homolog armitage is required for oskar mRNA silencing and embryonic axis specification. Cell 116:817–829CrossRefPubMedGoogle Scholar
  30. Cox D, Chao A, Baker J, Chang L, Qiao D, Lin H (1998) A novel class of evolutionarily conserved genes defined by piwi are essential for stem cell self-renewal. Genes Dev 12(23):3715–3727. doi: 10.1101/gad.12.23.3715 CrossRefPubMedPubMedCentralGoogle Scholar
  31. Czech B, Preall J, McGinn J, Hannon G (2013) A transcriptome-wide RNAi screen in the Drosophila ovary reveals factors of the germline piRNA pathway. Mol Cell 50(5):749–761. doi: 10.1016/j.molcel.2013.04.007 CrossRefPubMedPubMedCentralGoogle Scholar
  32. Duharcourt S, Butler A, Meyer E (1995) Epigenetic self-regulation of developmental excision of an internal eliminated sequence on Paramecium tetraurelia. Genes Dev 9(16):2065–2077CrossRefPubMedGoogle Scholar
  33. Duharcourt S, Keller AM, Meyer E (1998) Homology-dependent maternal inhibition of developmental excision of internal eliminated sequences in Paramecium tetraurelia. Mol Cell Biol 18(12):7075–7085CrossRefPubMedPubMedCentralGoogle Scholar
  34. Eddy EM (1974) Fine structural observations on the form and distribution of nuage in germ cells of the rat. Anat Rec 178(4):731–757. doi: 10.1002/ar.1091780406 CrossRefPubMedGoogle Scholar
  35. Eddy EM, Ito S (1971) Fine structural and radioautographic observations on dense perinuclear cytoplasmic material in tadpole oocytes. J Cell Biol 49(1):90–108CrossRefPubMedPubMedCentralGoogle Scholar
  36. Findley SD, Tamanaha M, Clegg NJ, Ruohola-Baker H (2003) Maelstrom, a Drosophila spindle-class gene, encodes a protein that colocalizes with Vasa and RDE1/AGO1 homolog, Aubergine, in nuage. Development 130:859–871CrossRefPubMedGoogle Scholar
  37. Gillespie DE, Berg CA (1995) Homeless is required for RNA localization in Drosophila oogenesis and encodes a new member of the DE-H family of RNA-dependent ATPases. Genes Dev 9:2495–2508CrossRefPubMedGoogle Scholar
  38. Girard A, Sachidanandam R, Hannon G, Carmell M (2006) A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 442(7099):199–202. doi: 10.1038/nature04917 PubMedGoogle Scholar
  39. Grivna S, Beyret E, Wang Z, Lin H (2006) A novel class of small RNAs in mouse spermatogenic cells. Genes Dev 20(13):1709–1714. doi: 10.1101/gad.1434406 CrossRefPubMedPubMedCentralGoogle Scholar
  40. Handler D, Olivieri D, Novatchkova M, Gruber FS, Meixner K, Mechtler K, Stark A, Sachidanandam R, Brennecke J (2011) A systematic analysis of Drosophila TUDOR domain-containing proteins identifies Vreteno and the Tdrd12 family as essential primary piRNA pathway factors. EMBO J 30(19):3977–3993. doi: 10.1038/emboj.2011.308 CrossRefPubMedPubMedCentralGoogle Scholar
  41. Handler D, Meixner K, Pizka M, Lauss K, Schmied C, Gruber F, Brennecke J (2013) The genetic makeup of the Drosophila piRNA pathway. Mol Cell 50(5):762–777. doi: 10.1016/j.molcel.2013.04.031 CrossRefPubMedPubMedCentralGoogle Scholar
  42. Hathaway DS, Selman GG (1961) Certain aspects of cell lineage and morphogenesis studied in embryos of Drosophila melanogaster with an ultra-violet micro-beam. J Embryol Exp Morphol 9:310–325PubMedGoogle Scholar
  43. Hay B, Ackerman L, Barbel S, Jan LY, Jan YN (1988) Identification of a component of Drosophila polar granules. Development 103(4):625–640PubMedGoogle Scholar
  44. Hegner RW (1911) The germ cell determinants in the eggs of chrysomelid beetles. Science 33(837):71–72. doi: 10.1126/science.33.837.71 CrossRefPubMedGoogle Scholar
  45. Hegner RW (1912) The history of the germ cells in the paedogenetic larva of Miastor. Science 36(917):124–126. doi: 10.1126/science.36.917.124 CrossRefPubMedGoogle Scholar
  46. Harris AN, Macdonald PM (2001) Aubergine encodes a Drosophila polar granule component required for pole cell formation and related to eIF2C. Development 128:2823–2832PubMedGoogle Scholar
  47. Houwing S, Kamminga L, Berezikov E, Cronembold D, Girard A, van den Elst H, Filippov D, Blaser H, Raz E, Moens C, Plasterk R, Hannon G, Draper B, Ketting R (2007) A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish. Cell 129(1):69–82. doi: 10.1016/j.cell.2007.03.026 CrossRefPubMedGoogle Scholar
  48. Huang H-Y, Houwing S, Kaaij L, Meppelink A, Redl S, Gauci S, Vos H, Draper B, Moens C, Burgering B, Ladurner P, Krijgsveld J, Berezikov E, Ketting R (2011a) Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. EMBO J 30(16):3298–3308. doi: 10.1038/emboj.2011.228 CrossRefPubMedPubMedCentralGoogle Scholar
  49. Huang H, Gao Q, Peng X, Choi S-Y, Sarma K, Ren H, Morris A, Frohman M (2011b) piRNA-associated germline nuage formation and spermatogenesis require MitoPLD profusogenic mitochondrial-surface lipid signaling. Dev Cell 20(3):376–387. doi: 10.1016/j.devcel.2011.01.004 CrossRefPubMedPubMedCentralGoogle Scholar
  50. Ipsaro J, Haase A, Knott S, Joshua-Tor L, Hannon G (2012) The structural biochemistry of Zucchini implicates it as a nuclease in piRNA biogenesis. Nature 491(7423):279–283. doi: 10.1038/nature11502 CrossRefPubMedPubMedCentralGoogle Scholar
  51. Jahn CL, Klobutcher LA (2002) Genome remodeling in ciliated protozoa. Annu Rev Microbiol 56:489–520. doi: 10.1146/annurev.micro.56.012302.160916 CrossRefPubMedGoogle Scholar
  52. 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(5733):467–469. doi: 10.1126/science.1114955 CrossRefPubMedGoogle Scholar
  53. Kawaoka S, Izumi N, Katsuma S, Tomari Y (2011) 3′ end formation of PIWI-interacting RNAs in vitro. Mol Cell 43(6):1015–1022. doi: 10.1016/j.molcel.2011.07.02 CrossRefPubMedGoogle Scholar
  54. Kawaoka S, Hara K, Shoji K, Kobayashi M, Shimada T, Sugano S, Tomari Y, Suzuki Y, Katsuma S (2013) The comprehensive epigenome map of piRNA clusters. Nucleic Acids Res 41(3):1581–1590. doi: 10.1093/nar/gks1275 CrossRefPubMedGoogle Scholar
  55. Kibanov MV, Egorova KS, Ryazansky SS, Sokolova OA, Kotov AA, Olenkina OM, Stolyarenko AD, Gvozdev VA, Olenina LV (2011) A novel organelle, the piNG-body, in the nuage of Drosophila male germ cells is associated with piRNA-mediated gene silencing. Mol Biol Cell 22(18):3410–3419. doi: 10.1091/mbc.E11-02-0168 CrossRefPubMedPubMedCentralGoogle Scholar
  56. Kirino Y, Kim N, de Planell-Saguer M, Khandros E, Chiorean S, Klein P, Rigoutsos I, Jongens T, Mourelatos Z (2009) Arginine methylation of Piwi proteins catalysed by dPRMT5 is required for Ago3 and Aub stability. Nat Cell Biol 11(5):652–658. doi: 10.1038/ncb1872 CrossRefPubMedPubMedCentralGoogle Scholar
  57. Kirino Y, Vourekas A, Sayed N, de Lima Alves F, Thomson T, Lasko P, Rappsilber J, Jongens TA, Mourelatos Z (2010a) Arginine methylation of Aubergine mediates Tudor binding and germ plasm localization. RNA 16(1):70–78. doi: 10.1261/rna.1869710 CrossRefPubMedPubMedCentralGoogle Scholar
  58. Kirino Y, Vourekas A, Kim N, de Lima Alves F, Rappsilber J, Klein PS, Jongens TA, Mourelatos Z (2010b) Arginine methylation of vasa protein is conserved across phyla. J Biol Chem 285(11):8148–8154. doi: 10.1074/jbc.M109.089821 CrossRefPubMedPubMedCentralGoogle Scholar
  59. Klattenhoff C, Xi H, Li C, Lee S, Xu J, Khurana JS, Zhang F, Schultz N, Koppetsch BS, Nowosielska A, Seitz H, Zamore PD, Weng Z, Theurkauf WE (2009) The Drosophila HP1 homolog Rhino is required for transposon silencing and piRNA production by dual-strand clusters. Cell 138(6):1137–1149. doi: 10.1016/j.cell.2009.07.014 CrossRefPubMedPubMedCentralGoogle Scholar
  60. Klenov M, Lavrov S, Stolyarenko A, Ryazansky S, Aravin A, Tuschl T, Gvozdev V (2007) Repeat-associated siRNAs cause chromatin silencing of retrotransposons in the Drosophila melanogaster germline. Nucleic Acids Res 35(16):5430–5438. doi: 10.1093/nar/gkm576 CrossRefPubMedPubMedCentralGoogle Scholar
  61. Klenov MS, Sokolova OA, Yakushev EY, Stolyarenko AD, Mikhaleva EA, Lavrov SA, Gvozdev VA (2011) Separation of stem cell maintenance and transposon silencing functions of Piwi protein. Proc Natl Acad Sci U S A 108(46):18760–18765. doi: 10.1073/pnas.1106676108 CrossRefPubMedPubMedCentralGoogle Scholar
  62. Kugler JM, Lasko P (2009) Localization, anchoring and translational control of oskar, gurken, bicoid and nanos mRNA during Drosophila oogenesis. Fly 3(1):15–28CrossRefPubMedGoogle Scholar
  63. Kuramochi-Miyagawa S, Kimura T, Yomogida K, Kuroiwa A, Tadokoro Y, Fujita Y, Sato M, Matsuda Y, Nakano T (2001) Two mouse piwi-related genes: miwi and mili. Mech Dev 108(1–2):121–133. doi: 10.1016/S0925-4773(01)00499-3 CrossRefPubMedGoogle Scholar
  64. Kuramochi-Miyagawa S, Kimura T, Ijiri T, Isobe T, Asada N, Fujita Y, Ikawa M, Iwai N, Okabe M, Deng W, Lin H, Matsuda Y, Nakano T (2004) Mili, a mammalian member of piwi family gene, is essential for spermatogenesis. Development 131(4):839–849. doi: 10.1242/dev.00973 CrossRefPubMedGoogle Scholar
  65. Kuramochi-Miyagawa S, Watanabe T, Gotoh K, Totoki Y, Toyoda A, Ikawa M, Asada N, Kojima K, Yamaguchi Y, Ijiri T, Hata K, Li E, Matsuda Y, Kimura T, Okabe M, Sakaki Y, Sasaki H, Nakano T (2008) DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes. Genes Dev 22(7):908–917. doi: 10.1101/gad.1640708 CrossRefPubMedPubMedCentralGoogle Scholar
  66. Kuramochi-Miyagawa S, Watanabe T, Gotoh K, Takamatsu K, Chuma S, Kojima-Kita K, Shiromoto Y, Asada N, Toyoda A, Fujiyama A, Totoki Y, Shibata T, Kimura T, Nakatsuji N, Noce T, Sasaki H, Nakano T (2010) MVH in piRNA processing and gene silencing of retrotransposons. Genes Dev 24(9):887–892. doi: 10.1101/gad.1902110 CrossRefPubMedPubMedCentralGoogle Scholar
  67. Lau N, Seto A, Kim J, Kuramochi-Miyagawa S, Nakano T, Bartel D, Kingston R (2006) Characterization of the piRNA complex from rat testes. Science (New York, NY) 313(5785):363–367. doi: 10.1126/science.1130164 CrossRefGoogle Scholar
  68. Le Thomas A, Rogers A, Webster A, Marinov G, Liao S, Perkins E, Hur J, Aravin A, Tóth K (2013) Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state. Genes Dev 27(4):390–399. doi: 10.1101/gad.209841.112 CrossRefPubMedPubMedCentralGoogle Scholar
  69. Lee DW, Pratt RJ, McLaughlin M, Aramayo R (2003) An argonaute-like protein is required for meiotic silencing. Genetics 164(2):821–828PubMedPubMedCentralGoogle Scholar
  70. Lee HC, Gu W, Shirayama M, Youngman E, Conte D Jr, Mello CC (2012) C. elegans piRNAs mediate the genome-wide surveillance of germline transcripts. Cell 150(1):78–87. doi: 10.1016/j.cell.2012.06.016 CrossRefPubMedPubMedCentralGoogle Scholar
  71. Li C, Vagin VV, Lee S, Xu J, Ma S, Xi H, Seitz H, Horwich MD, Syrzycka M, Honda BM, Kittler EL, Zapp ML, Klattenhoff C, Schulz N, Theurkauf WE, Weng Z, Zamore PD (2009) Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell 137(3):509–521. doi: 10.1016/j.cell.2009.04.027 CrossRefPubMedPubMedCentralGoogle Scholar
  72. Li X, Roy C, Dong X, Bolcun-Filas E, Wang J, Han B, Xu J, Moore M, Schimenti J, Weng Z, Zamore P (2013) An ancient transcription factor initiates the burst of piRNA production during early meiosis in mouse testes. Mol Cell 50(1):67–81. doi: 10.1016/j.molcel.2013.02.016 CrossRefPubMedPubMedCentralGoogle Scholar
  73. Liang L, Diehl-Jones W, Lasko P (1994) Localization of vasa protein to the Drosophila pole plasm is independent of its RNA-binding and helicase activities. Development 120(5):1201–1211PubMedGoogle Scholar
  74. Lim AK, Kai T (2007) Unique germ-line organelle, nuage, functions to repress selfish genetic elements in Drosophila melanogaster. Proc Natl Acad Sci U S A 104(16):6714–6719. doi: 10.1073/pnas.0701920104 CrossRefPubMedPubMedCentralGoogle Scholar
  75. Lin H, Spradling A (1997) A novel group of pumilio mutations affects the asymmetric division of germline stem cells in the Drosophila ovary. Development 124(12):2463–2476PubMedGoogle Scholar
  76. Liu Y, Mochizuki K, Gorovsky MA (2004) Histone H3 lysine 9 methylation is required for DNA elimination in developing macronuclei in Tetrahymena. Proc Natl Acad Sci U S A 101(6):1679–1684. doi: 10.1073/pnas.0305421101 CrossRefPubMedPubMedCentralGoogle Scholar
  77. Liu K, Chen C, Guo Y, Lam R, Bian C, Xu C, Zhao D, Jin J, MacKenzie F, Pawson T, Min J (2010a) Structural basis for recognition of arginine methylated Piwi proteins by the extended Tudor domain. Proc Natl Acad Sci U S A 107(43):18398–18403. doi: 10.1073/pnas.1013106107 CrossRefPubMedPubMedCentralGoogle Scholar
  78. Liu H, Wang JY, Huang Y, Li Z, Gong W, Lehmann R, Xu RM (2010b) Structural basis for methylarginine-dependent recognition of Aubergine by Tudor. Genes Dev 24(17):1876–1881. doi: 10.1101/gad.1956010 CrossRefPubMedPubMedCentralGoogle Scholar
  79. Liu L, Qi H, Wang J, Lin H (2011) PAPI, a novel TUDOR-domain protein, complexes with AGO3, ME31B and TRAL in the nuage to silence transposition. Development 138(9):1863–1873. doi: 10.1242/dev.059287 CrossRefPubMedPubMedCentralGoogle Scholar
  80. Luteijn MJ, van Bergeijk P, Kaaij LJ, Almeida MV, Roovers EF, Berezikov E, Ketting RF (2012) Extremely stable Piwi-induced gene silencing in Caenorhabditis elegans. EMBO J 31(16):3422–3430. doi: 10.1038/emboj.2012.213 CrossRefPubMedPubMedCentralGoogle Scholar
  81. Ma L, Buchold G, Greenbaum M, Roy A, Burns K, Zhu H, Han D, Harris R, Coarfa C, Gunaratne P, Yan W, Matzuk M (2009) GASZ is essential for male meiosis and suppression of retrotransposon expression in the male germline. PLoS Genet 5(9):e1000635. doi: 10.1371/journal.pgen.1000635 CrossRefPubMedPubMedCentralGoogle Scholar
  82. Mahowald AP (1968) Polar granules of Drosophila. II. Ultrastructural changes during early embryogenesis. J Exp Zool 167(2):237–261. doi: 10.1002/jez.1401670211 CrossRefPubMedGoogle Scholar
  83. Malone CD, Anderson AM, Motl JA, Rexer CH, Chalker DL (2005) Germ line transcripts are processed by a Dicer-like protein that is essential for developmentally programmed genome rearrangements of Tetrahymena thermophila. Mol Cell Biol 25(20):9151–9164. doi: 10.1128/MCB.25.20.9151-9164.2005 CrossRefPubMedPubMedCentralGoogle Scholar
  84. Malone CD, Brennecke J, Dus M, Stark A, McCombie WR, Sachidanandam R, Hannon GJ (2009) Specialized piRNA pathways act in germline and somatic tissues of the Drosophila ovary. Cell 137(3):522–535. doi: 10.1016/j.cell.2009.03.040 CrossRefPubMedPubMedCentralGoogle Scholar
  85. Mathioudakis N, Palencia A, Kadlec J, Round A, Tripsianes K, Sattler M, Pillai R, Cusack S (2012) The multiple Tudor domain-containing protein TDRD1 is a molecular scaffold for mouse Piwi proteins and piRNA biogenesis factors. RNA (New York, NY) 18(11):2056–2072. doi: 10.1261/rna.034181.112 CrossRefGoogle Scholar
  86. Matzke M, Aufsatz W, Kanno T, Daxinger L, Papp I, Mette MF, Matzke AJ (2004) Genetic analysis of RNA-mediated transcriptional gene silencing. Biochim Biophys Acta 1677(1–3):129–141. doi: 10.1016/j.bbaexp.2003.10.015, S0167478103002859 [pii]CrossRefPubMedGoogle Scholar
  87. Megosh HB, Cox DN, Campbell C, Lin H (2006) The role of PIWI and the miRNA machinery in Drosophila germline determination. Curr Biol: CB 16(19):1884–1894. doi: 10.1016/j.cub.2006.08.051 CrossRefPubMedGoogle Scholar
  88. Meikar O, Da Ros M, Korhonen H, Kotaja N (2011) Chromatoid body and small RNAs in male germ cells. Reproduction (Cambridge, England) 142(2):195–209. doi: 10.1530/REP-11-0057 CrossRefGoogle Scholar
  89. Mette MF, Aufsatz W, van der Winden J, Matzke MA, Matzke AJ (2000) Transcriptional silencing and promoter methylation triggered by double-stranded RNA. EMBO J 19(19):5194–5201. doi: 10.1093/emboj/19.19.5194 CrossRefPubMedPubMedCentralGoogle Scholar
  90. Mochizuki K, Gorovsky M (2004a) Small RNAs in genome rearrangement in Tetrahymena. Curr Opin Genet Dev 14(2):181–187. doi: 10.1016/j.gde.2004.01.004 CrossRefPubMedGoogle Scholar
  91. Mochizuki K, Gorovsky MA (2004b) Conjugation-specific small RNAs in Tetrahymena have predicted properties of scan (scn) RNAs involved in genome rearrangement. Genes Dev 18(17):2068–2073. doi: 10.1101/gad.1219904 CrossRefPubMedPubMedCentralGoogle Scholar
  92. Mochizuki K, Gorovsky MA (2005) A Dicer-like protein in Tetrahymena has distinct functions in genome rearrangement, chromosome segregation, and meiotic prophase. Genes Dev 19(1):77–89. doi: 10.1101/gad.1265105 CrossRefPubMedPubMedCentralGoogle Scholar
  93. Mochizuki K, Fine NA, Fujisawa T, Gorovsky MA (2002) Analysis of a piwi-related gene implicates small RNAs in genome rearrangement in tetrahymena. Cell 110(6):689–699CrossRefPubMedGoogle Scholar
  94. Muerdter F, Guzzardo P, Gillis J, Luo Y, Yu Y, Chen C, Fekete R, Hannon G (2013) A genome-wide RNAi screen draws a genetic framework for transposon control and primary piRNA biogenesis in Drosophila. Mol Cell 50(5):736–748. doi: 10.1016/j.molcel.2013.04.006 CrossRefPubMedPubMedCentralGoogle Scholar
  95. Nishida K, Okada T, Kawamura T, Mituyama T, Kawamura Y, Inagaki S, Huang H, Chen D, Kodama T, Siomi H, Siomi M (2009) Functional involvement of Tudor and dPRMT5 in the piRNA processing pathway in Drosophila germlines. EMBO J 28(24):3820–3831. doi: 10.1038/emboj.2009.365 CrossRefPubMedPubMedCentralGoogle Scholar
  96. Nishida KM et al (2015) Respective functions of two distinct Siwi complexes assembled during PIWI-interacting RNA biogenesis in Bombyx germ cells. Cell Rep 10(2):193–203CrossRefPubMedGoogle Scholar
  97. Nishimasu H, Ishizu H, Saito K, Fukuhara S, Kamatani M, Bonnefond L, Matsumoto N, Nishizawa T, Nakanaga K, Aoki J, Ishitani R, Siomi H, Siomi M, Nureki O (2012) Structure and function of Zucchini endoribonuclease in piRNA biogenesis. Nature 491(7423):284–287. doi: 10.1038/nature11509 CrossRefPubMedGoogle Scholar
  98. Okada M, Kleinman IA, Schneiderman HA (1974) Restoration of fertility in sterilized Drosophila eggs by transplantation of polar cytoplasm. Dev Biol 37(1):43–54CrossRefPubMedGoogle Scholar
  99. Olivieri D, Sykora MM, Sachidanandam R, Mechtler K, Brennecke J (2010) An in vivo RNAi assay identifies major genetic and cellular requirements for primary piRNA biogenesis in Drosophila. EMBO J 29:3301–3317CrossRefPubMedPubMedCentralGoogle Scholar
  100. Pane A, Jiang P, Zhao DY, Singh M, Schupbach T (2011) The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline. EMBO J 30(22):4601–4615. doi: 10.1038/emboj.2011.334 CrossRefPubMedPubMedCentralGoogle Scholar
  101. Patil VS, Kai T (2010) Repression of retroelements in Drosophila germline via piRNA pathway by the Tudor domain protein Tejas. Curr Biol 20:724–730CrossRefPubMedGoogle Scholar
  102. Pek JW, Lim AK, Kai T (2009) Drosophila maelstrom ensures proper germline stem cell lineage differentiation by repressing microRNA-7. Dev Cell 17:417–424CrossRefPubMedGoogle Scholar
  103. Ponting CP (1997) Tudor domains in proteins that interact with RNA. Trends Biochem Sci 22(2):51–52CrossRefPubMedGoogle Scholar
  104. Preall JB, Czech B, Guzzardo PM, Muerdter F, Hannon GJ (2012) Shutdown is a component of the Drosophila piRNA biogenesis machinery. RNA 18:1446–1457CrossRefPubMedPubMedCentralGoogle Scholar
  105. Rangan P, Malone CD, Navarro C, Newbold SP, Hayes PS, Sachidanandam R, Hannon GJ, Lehmann R (2011) piRNA production requires heterochromatin formation in Drosophila. Curr Biol: CB 21(16):1373–1379. doi: 10.1016/j.cub.2011.06.057 CrossRefPubMedPubMedCentralGoogle Scholar
  106. Reyes-Turcu FE, Grewal SI (2012) Different means, same end-heterochromatin formation by RNAi and RNAi-independent RNA processing factors in fission yeast. Curr Opin Genet Dev 22(2):156–163. doi: 10.1016/j.gde.2011.12.004 CrossRefPubMedPubMedCentralGoogle Scholar
  107. Ro S, Park C, Song R, Nguyen D, Jin J, Sanders K, McCarrey J, Yan W (2007) Cloning and expression profiling of testis-expressed piRNA-like RNAs. RNA (New York, NY) 13(10):1693–1702. doi: 10.1261/rna.640307 CrossRefGoogle Scholar
  108. Romano N, Macino G (1992) Quelling: transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences. Mol Microbiol 6(22):3343–3353CrossRefPubMedGoogle Scholar
  109. Rozhkov N, Hammell M, Hannon G (2013) Multiple roles for Piwi in silencing Drosophila transposons. Genes Dev 27(4):400–412. doi: 10.1101/gad.209767.112 CrossRefPubMedPubMedCentralGoogle Scholar
  110. Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP (2006) Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127(6):1193–1207. doi: 10.1016/j.cell.2006.10.040 CrossRefPubMedGoogle Scholar
  111. Saito K, Sakaguchi Y, Suzuki T, Siomi H, Siomi MC (2007) Pimet, the Drosophila homolog of HEN1, mediates 2′-O-methylation of Piwi- interacting RNAs at their 3′ ends. Genes Dev 21:1603–1608CrossRefPubMedPubMedCentralGoogle Scholar
  112. Saito K, Inagaki S, Mituyama T, Kawamura Y, Ono Y, Sakota E, Kotani H, Asai K, Siomi H, Siomi MC (2009a) A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila. Nature 461(7268):1296–1299, doi: CrossRefPubMedGoogle Scholar
  113. Saito K, Inagaki S, Mituyama T, Kawamura Y, Ono Y, Sakota E, Kotani H, Asai K, Siomi H, Siomi MC (2009b) A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila. Nature 461(7268):1296–1299. doi: 10.1038/nature08501 CrossRefPubMedGoogle Scholar
  114. Sato K, Nishida KM, Shibuya A, Siomi MC, Siomi H (2011) Maelstrom coordinates microtubule organization during Drosophila oogenesis through interaction with components of the MTOC. Genes Dev 25:2361–2373CrossRefPubMedPubMedCentralGoogle Scholar
  115. Schmidt A, Palumbo G, Bozzetti M, Tritto P, Pimpinelli S, Schäfer U (1999) Genetic and molecular characterization of sting, a gene involved in crystal formation and meiotic drive in the male germ line of Drosophila melanogaster. Genetics 151(2):749–760PubMedPubMedCentralGoogle Scholar
  116. Shirayama M, Seth M, Lee HC, Gu W, Ishidate T, Conte D Jr, Mello CC (2012) piRNAs initiate an epigenetic memory of nonself RNA in the C. elegans germline. Cell 150(1):65–77. doi: 10.1016/j.cell.2012.06.015 CrossRefPubMedPubMedCentralGoogle Scholar
  117. Shiu PK, Raju NB, Zickler D, Metzenberg RL (2001) Meiotic silencing by unpaired DNA. Cell 107(7):905–916CrossRefPubMedGoogle Scholar
  118. Shoji M, Tanaka T, Hosokawa M, Reuter M, Stark A, Kato Y, Kondoh G, Okawa K, Chujo T, Suzuki T, Hata K, Martin SL, Noce T, Kuramochi-Miyagawa S, Nakano T, Sasaki H, Pillai RS, Nakatsuji N, Chuma S (2009) The TDRD9-MIWI2 complex is essential for piRNA-mediated retrotransposon silencing in the mouse male germline. Dev Cell 17(6):775–787, doi: CrossRefPubMedGoogle Scholar
  119. Shpiz S, Kwon D, Rozovsky Y, Kalmykova A (2009) rasiRNA pathway controls antisense expression of Drosophila telomeric retrotransposons in the nucleus. Nucleic Acids Res 37(1):268–278. doi: 10.1093/nar/gkn960 CrossRefPubMedGoogle Scholar
  120. Shpiz S, Olovnikov I, Sergeeva A, Lavrov S, Abramov Y, Savitsky M, Kalmykova A (2011) Mechanism of the piRNA-mediated silencing of Drosophila telomeric retrotransposons. Nucleic Acids Res 39(20):8703–8711. doi: 10.1093/nar/gkr552 CrossRefPubMedPubMedCentralGoogle Scholar
  121. Sienski G, Dönertas D, Brennecke J (2012) Transcriptional silencing of transposons by Piwi and maelstrom and its impact on chromatin state and gene expression. Cell 151(5):964–980. doi: 10.1016/j.cell.2012.10.040 CrossRefPubMedPubMedCentralGoogle Scholar
  122. Siomi M, Sato K, Pezic D, Aravin A (2011) PIWI-interacting small RNAs: the vanguard of genome defence. Nat Rev Mol Cell Biol 12(4):246–258. doi: 10.1038/nrm3089 CrossRefPubMedGoogle Scholar
  123. Slotkin R, Martienssen R (2007) Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 8(4):272–285. doi: 10.1038/nrg2072 CrossRefPubMedGoogle Scholar
  124. Slotkin RK, Vaughn M, Borges F, Tanurdzic M, Becker JD, Feijo JA, Martienssen RA (2009) Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136(3):461–472. doi: 10.1016/j.cell.2008.12.038 CrossRefPubMedPubMedCentralGoogle Scholar
  125. Song SU, Kurkulos M, Boeke JD, Corces VG (1997) Infection of the germ line by retroviral particles produced in the follicle cells: a possible mechanism for the mobilization of the gypsy retroelement of Drosophila. Development 124(14):2789–2798PubMedGoogle Scholar
  126. Song J-J, Smith S, Hannon G, Joshua-Tor L (2004) Crystal structure of Argonaute and its implications for RISC slicer activity. Science (New York, NY) 305(5689):1434–1437. doi: 10.1126/science.1102514 CrossRefGoogle Scholar
  127. Soper S, van der Heijden G, Hardiman T, Goodheart M, Martin S, de Boer P, Bortvin A (2008) Mouse maelstrom, a component of nuage, is essential for spermatogenesis and transposon repression in meiosis. Dev Cell 15(2):285–297. doi: 10.1016/j.devcel.2008.05.015 CrossRefPubMedPubMedCentralGoogle Scholar
  128. Stapleton W, Das S, McKee BD (2001) A role of the Drosophila homeless gene in repression of Stellate in male meiosis. Chromosoma 110(3):228–240CrossRefPubMedGoogle Scholar
  129. Szakmary A, Reedy M, Qi H, Lin H (2009) The Yb protein defines a novel organelle and regulates male germline stem cell self-renewal in Drosophila melanogaster. J Cell Biol 185:613. doi: 10.1083/jcb.200903034 CrossRefPubMedPubMedCentralGoogle Scholar
  130. Thomson T, Lasko P (2004) Drosophila tudor is essential for polar granule assembly and pole cell specification, but not for posterior patterning. Genesis 40(3):164–170. doi: 10.1002/gene.20079 CrossRefPubMedGoogle Scholar
  131. Vagin VV, Sigova A, Li C, Seitz H, Gvozdev V, Zamore PD (2006) A distinct small RNA pathway silences selfish genetic elements in the germline. Science 313(5785):320–324. doi: 10.1126/science.1129333 CrossRefPubMedGoogle Scholar
  132. Vagin V, Wohlschlegel J, Qu J, Jonsson Z, Huang X, Chuma S, Girard A, Sachidanandam R, Hannon G, Aravin A (2009) Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members. Genes Dev 23(15):1749–1762. doi: 10.1101/gad.1814809 CrossRefPubMedPubMedCentralGoogle Scholar
  133. Vagin VV, Yu Y, Jankowska A, Luo Y, Wasik KA, Malone CD, Harrison E, Rosebrock A, Wakimoto BT, Fagegaltier D et al (2013) Minotaur is critical for primary piRNA biogenesis. RNA 19:1064–1077CrossRefPubMedPubMedCentralGoogle Scholar
  134. Voigt F, Reuter M, Kasaruho A, Schulz E, Pillai R, Barabas O (2012) Crystal structure of the primary piRNA biogenesis factor Zucchini reveals similarity to the bacterial PLD endonuclease Nuc. RNA (New York, NY) 18(12):2128–2134. doi: 10.1261/rna.034967.112 CrossRefGoogle Scholar
  135. Volpe AM, Horowitz H, Grafer CM, Jackson SM, Berg CA (2001) Drosophila rhino encodes a female specific chromo-domain protein that affects chromosome structure and egg polarity. Genetics 159:1117–1134PubMedPubMedCentralGoogle Scholar
  136. Xiol J et al (2014) RNA clamping by Vasa assembles a piRNA amplifier complex on transposon transcripts. Cell 157(7):1698–1711CrossRefPubMedGoogle Scholar
  137. Wang Y, Juranek S, Li H, Sheng G, Tuschl T, Patel D (2008) Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex. Nature 456(7224):921–926. doi: 10.1038/nature07666 CrossRefPubMedPubMedCentralGoogle Scholar
  138. Watanabe T, Tomizawa S-i, Mitsuya K, Totoki Y, Yamamoto Y, Kuramochi-Miyagawa S, Iida N, Hoki Y, Murphy P, Toyoda A, Gotoh K, Hiura H, Arima T, Fujiyama A, Sado T, Shibata T, Nakano T, Lin H, Ichiyanagi K, Soloway P, Sasaki H (2011a) Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus. Science (New York, NY) 332(6031):848–852. doi: 10.1126/science.1203919 CrossRefGoogle Scholar
  139. Watanabe T, Chuma S, Yamamoto Y, Kuramochi-Miyagawa S, Totoki Y, Toyoda A, Hoki Y, Fujiyama A, Shibata T, Sado T, Noce T, Nakano T, Nakatsuji N, Lin H, Sasaki H (2011b) MITOPLD is a mitochondrial protein essential for nuage formation and piRNA biogenesis in the mouse germline. Dev Cell 20(3):364–375. doi: 10.1016/j.devcel.2011.01.005 CrossRefPubMedPubMedCentralGoogle Scholar
  140. Webster A et al (2015) Aub and Ago3 are recruited to nuage through two mechanisms to form a ping-pong complex assembled by Krimper. Mol Cell 59(4):564–575CrossRefPubMedPubMedCentralGoogle Scholar
  141. Yao MC, Chao JL (2005) RNA-guided DNA deletion in Tetrahymena: an RNAi-based mechanism for programmed genome rearrangements. Annu Rev Genet 39:537–559. doi: 10.1146/annurev.genet.39.073003.095906 CrossRefPubMedGoogle Scholar
  142. Zamparini AL, Davis MY, Malone CD, Vieira E, Zavadil J, Sachidanandam R, Hannon GJ, Lehmann R (2011) Vreteno, a gonad-specific protein, is essential for germline development and primary piRNA biogenesis in Drosophila. Development 138:4039–4050CrossRefPubMedPubMedCentralGoogle Scholar
  143. Zhang K, Mosch K, Fischle W, Grewal SI (2008) Roles of the Clr4 methyltransferase complex in nucleation, spreading and maintenance of heterochromatin. Nat Struct Mol Biol 15(4):381–388. doi: 10.1038/nsmb.1406 CrossRefPubMedGoogle Scholar
  144. Zhang Z, Xu J, Koppetsch BS, Wang J, Tipping C, Ma S, Weng Z, Theurkauf WE, Zamore PD (2011) Heterotypic piRNA Ping-Pong requires qin, a protein with both E3 ligase and Tudor domains. Mol Cell 44(4):572–584. doi: 10.1016/j.molcel.2011.10.011 CrossRefPubMedPubMedCentralGoogle Scholar
  145. Zhang F, Wang J, Xu J, Zhang Z, Koppetsch BS, Schultz N, Vreven T, Meignin C, Davis I, Zamore PD, Weng Z, Theurkauf WE (2012) UAP56 couples piRNA clusters to the perinuclear transposon silencing machinery. Cell 151(4):871–884. doi: 10.1016/j.cell.2012.09.040 CrossRefPubMedPubMedCentralGoogle Scholar
  146. Zofall M, Grewal SI (2006) Swi6/HP1 recruits a JmjC domain protein to facilitate transcription of heterochromatic repeats. Mol Cell 2(5):681. doi: 10.1016/j.molcel.2006.05.010 CrossRefGoogle Scholar

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© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  1. 1.Division of Biology and BioengineeringCalifornia Institute of TechnologyPasadenaUSA

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