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PIWI-interacting RNAs: from generation to transgenerational epigenetics

Nature Reviews Genetics volume 14, pages 523–534 (2013)Cite this article

Subjects

Key Points

  • PIWI-interacting RNAs (piRNAs) are made from dedicated precursor transcripts that are transcribed from specialized loci.

  • piRNA biogenesis from their precursors involves at least three different steps: first, the 5′ end is created by an endonuclease; second, the piRNA intermediate is loaded into a PIWI protein; and third, the 3′ end is trimmed and modified.

  • Target selection by PIWI–piRNA complexes may depend on perfect or near perfect base-pairing interactions — for example, as occurs in Drosophila melanogaster and mice — or on interactions involving substantial mismatches, as occurs in Caenorhabditis elegans.

  • PIWI proteins can trigger changes to the chromatin of their target loci. The exact mechanisms are thus far still not clear but bear similarities to the RNAi-heterochromatin pathway of fission yeast.

  • The heterochromatin changes imposed by PIWI proteins can be inherited stably across generations. In some cases, maintenance of this silencing can occur in absence of further PIWI pathway activity.

  • Changes to the chromatin structure of PIWI targets may convert such targets into piRNA-producing loci. In such cases, transcripts from these targets are efficiently routed into piRNA biogenesis pathways.

Abstract

Small-RNA-guided gene regulation is a recurring theme in biology. Animal germ cells are characterized by an intriguing small-RNA-mediated gene-silencing mechanism known as the PIWI pathway. For a long time, both the biogenesis of PIWI-interacting RNAs (piRNAs) as well as their mode of gene silencing has remained elusive. A recent body of work is shedding more light on both aspects and implicates PIWI in the establishment of transgenerational epigenetic states. In fact, the epigenetic states imposed by PIWI on targets may actually drive piRNA production itself. These findings start to couple small RNA biogenesis with small-RNA-mediated epigenetics.

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Figure 1: Transcription and selection of piRNA precursors.
Figure 2: Primary and secondary piRNA biogenesis.
Figure 3: Effects of PIWI pathways on chromatin.
Figure 4: Transgenerational inheritance of PIWI-induced heterochromatin.
Figure 5: Conversion of a Piwi target locus into a piRNA-producing locus.

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References

  1. Cox, D. N. et al. A novel class of evolutionarily conserved genes defined by PIWI are essential for stem cell self-renewal. Genes Dev. 12, 3715–3727 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Deng, W. & Lin, H. Miwi, a murine homolog of Piwi, encodes a cytoplasmic protein essential for spermatogenesis. Dev. Cell 2, 819–830 (2002).

    Article  CAS  PubMed  Google Scholar 

  3. Ghildiyal, M. & Zamore, P. D. Small silencing RNAs: an expanding universe. Nature Rev. Genet. 10, 94–108 (2009).

    Article  CAS  PubMed  Google Scholar 

  4. Song, J. J. Crystal structure of argonaute and its implications for RISC slicer activity. Science 305, 1434–1437 (2004).

    Article  CAS  PubMed  Google Scholar 

  5. Tolia, N. H. & Joshua-Tor, L. Slicer and the Argonautes. Nature Chem. Biol. 3, 36–43 (2007).

    Article  CAS  Google Scholar 

  6. Wang, Y. et al. Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes. Nature 461, 754–761 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Schirle, N. T. & MacRae, I. J. The crystal structure of human Argonaute2. Science 336, 1037–1040 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Elkayam, E. et al. The structure of human argonaute-2 in complex with miR-20a. Cell 150, 100–110 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Wang, Y. et al. Structure of an Argonaute silencing complex with a seed-containing guide DNA and target RNA duplex. Nature 456, 921–926 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. van Wolfswinkel, J. C. & Ketting, R. F. The role of small non-coding RNAs in genome stability and chromatin organization. J. Cell Sci. 123, 1825–1839 (2010).

    Article  CAS  PubMed  Google Scholar 

  11. Czech, B. & Hannon, G. J. Small RNA sorting: matchmaking for Argonautes. Nature Rev. Genet. 12, 19–31 (2010).

    Article  CAS  PubMed  Google Scholar 

  12. Siomi, H. & Siomi, M. C. On the road to reading the RNA-interference code. Nature 457, 396–404 (2009).

    Article  CAS  PubMed  Google Scholar 

  13. Jinek, M. & Doudna, J. A. A three-dimensional view of the molecular machinery of RNA interference. Nature 457, 405–412 (2009).

    Article  CAS  PubMed  Google Scholar 

  14. Rana, T. M. Illuminating the silence: understanding the structure and function of small RNAs. Nature Rev. Mol. Cell Biol. 8, 23–36 (2007).

    Article  CAS  Google Scholar 

  15. Malone, C. D. & Hannon, G. J. Small RNAs as guardians of the genome. Cell 136, 656–668 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Kazazian, H. H. Mobile elements: drivers of genome evolution. Science 303, 1626–1632 (2004).

    Article  CAS  PubMed  Google Scholar 

  17. Rouget, C. et al. Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo. Nature 467, 1128–1132 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Castel, S. E. & Martienssen, R. A. RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond. Nature Rev. Genet. 14, 100–112 (2013).

    Article  CAS  PubMed  Google Scholar 

  19. Robine, N. et al. A broadly conserved pathway generates 3′UTR-directed primary piRNAs. Curr. Biol. 19, 2066–2076 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Seto, A. G., Kingston, R. E. & Lau, N. C. The coming of age for PIWI proteins. Mol. Cell 26, 603–609 (2007).

    Article  CAS  PubMed  Google Scholar 

  21. Rajasethupathy, P. et al. A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity. Cell 149, 693–707 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Houwing, S. et al. A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in zebrafish. Cell 129, 69–82 (2007).

    Article  CAS  Google Scholar 

  23. Vagin, V. V. A. Distinct small RNA pathway silences selfish genetic elements in the germline. Science 313, 320–324 (2006).

    Article  CAS  PubMed  Google Scholar 

  24. Brennecke, J. et al. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128, 1089–1103 (2007).

    Article  CAS  PubMed  Google Scholar 

  25. Li, X. Z. et al. An ancient transcription factor initiates the burst of piRNA production during early meiosis in mouse testes. Mol. Cell 50, 67–81 (2013). This paper describes the first transcription factor that initiates the transcription of pachytene piRNA precursors and genes involved in piRNA biogenesis, thereby creating a feed-forward loop to boost piRNA abundance.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Al-Muktar, K. A. K. & Webb, A. C. An ultrastructural study of primordial germ cells, oogonia and early oocytes in Xenopus laevis. J. Embryol. Exp. Morphol. 26, 195–217 (1971).

    Google Scholar 

  27. Ketting, R. F. The many faces of RNAi. Dev. Cell 20, 148–161 (2011).

    Article  CAS  PubMed  Google Scholar 

  28. Aravin, A. A., Sachidanandam, R., Girard, A., Fejes-Toth, K. & Hannon, G. J. Developmentally regulated piRNA clusters implicate MILI in transposon control. Science 316, 744–747 (2007).

    Article  CAS  PubMed  Google Scholar 

  29. Gunawardane, L. S. et al. A slicer-mediated mechanism for repeat-associated siRNA 5′ end formation in Drosophila. Science 315, 1587–1590 (2007).

    Article  CAS  PubMed  Google Scholar 

  30. Li, C. et al. Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell 137, 509–521 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Grentzinger, T. et al. piRNA-mediated transgenerational inheritance of an acquired trait. Genome Res. 22, 1877–1888 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Brennecke, J. et al. An epigenetic role for maternally inherited piRNAs in transposon silencing. Science 322, 1387–1392 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Klattenhoff, C. & Theurkauf, W. Biogenesis and germline functions of piRNAs. Development 135, 3–9 (2007).

    Article  CAS  PubMed  Google Scholar 

  34. Siomi, M. C., Sato, K., Pezic, D. & Aravin, A. A. PIWI-interacting small RNAs: the vanguard of genome defence. Nature Rev. Mol. Cell Biol. 12, 246–258 (2011).

    Article  CAS  Google Scholar 

  35. Grivna, S. T., Pyhtila, B. & Lin, H. MIWI associates with translational machinery and PIWI-interacting RNAs (piRNAs) in regulating spermatogenesis. Proc. Natl Acad. Sci. USA 103, 13415–13420 (2006).

    Article  CAS  PubMed  Google Scholar 

  36. Molnar, A., Melnyk, C. & Baulcombe, D. C. Silencing signals in plants: a long journey for small RNAs. Genome Biol. 12, 215 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. hler, M. B. U. & Gasser, S. M. Silent chromatin at the middle and ends: lessons from yeasts. EMBO J. 28, 2149–2161 (2009).

    Article  CAS  Google Scholar 

  38. Grewal, S. I. RNAi-dependent formation of heterochromatin and its diverse functions. Curr. Opin. Genet. Dev. 20, 134–141 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Das, P. P. et al. Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline. Mol. Cell 31, 79–90 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Batista, P. J. et al. PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans. Mol. Cell 31, 67–78 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Billi, A. C. et al. A conserved upstream motif orchestrates autonomous, germline-enriched expression of Caenorhabditis elegans piRNAs. PLoS Genet. 9, e1003392 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Ruby, J. G. et al. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127, 1193–1207 (2006).

    Article  CAS  PubMed  Google Scholar 

  43. Cecere, G., Zheng, G. X. Y., Mansisidor, A. R., Klymko, K. E. & Grishok, A. Promoters recognized by forkhead proteins exist for individual 21U-RNAs. Mol. Cell 47, 734–745 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Gu, W. et al. CapSeq and CIP-TAP identify Pol II start sites and reveal capped small RNAs as C. elegans piRNA precursors. Cell 151, 1488–1500 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Brannan, K. et al. mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription. Mol. Cell 46, 311–324 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Aravin, A. et al. A novel class of small RNAs bind to MILI protein in mouse testes. Nature 442, 203–207 (2006).

    Article  CAS  PubMed  Google Scholar 

  47. Aravin, A. A., Hannon, G. J. & Brennecke, J. The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science 318, 761–764 (2007).

    Article  CAS  PubMed  Google Scholar 

  48. Lau, N. C. et al. Characterization of the piRNA complex from rat testes. Science 313, 363–367 (2006).

    Article  CAS  PubMed  Google Scholar 

  49. Girard, A., Sachidanandam, R., Hannon, G. J. & Carmell, M. A. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 442, 199–202 (2006).

    Article  PubMed  Google Scholar 

  50. Klattenhoff, C. et al. The Drosophila HP1 homolog rhino is required for transposon silencing and piRNA production by dual-strand clusters. Cell 138, 1137–1149 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Grewal, S. I. S. & Jia, S. Heterochromatin revisited. Nature Rev. Genet. 8, 35–46 (2007).

    Article  CAS  PubMed  Google Scholar 

  52. Keller, C. et al. HP1(Swi6) mediates the recognition and destruction of heterochromatic RNA transcripts. Mol. Cell 47, 215–227 (2012). This work shows the RNA-binding activity of SWI6 is required for silencing but leaves heterochromatin formation intact.

    Article  CAS  PubMed  Google Scholar 

  53. Zhang, F. et al. UAP56 couples piRNA clusters to the perinuclear transposon silencing machinery. Cell 151, 871–884 (2012). This paper describes the roles of nuclear UAP56 and perinuclear Vasa proteins in forming a piRNA-processing compartment that spans the nuclear envelope and is essential for piRNA production and transposon silencing.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Pane, A. Wehr, K. & Schüpbach, T. Zucchini and squash encode two putative nucleases required for rasiRNA production in the Drosophila germline. Dev. Cell 12, 851–862 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Huang, H. et al. piRNA-associated germline nuage formation and spermatogenesis require MitoPLD profusogenic mitochondrial-surface lipid signaling. Dev. Cell 20, 376–387 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Watanabe, T. et al. MITOPLD is a mitochondrial protein essential for nuage formation and piRNA biogenesis in the mouse germline. Dev. Cell 20, 364–375 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Saito, K. et al. Roles for the Yb body components Armitage and Yb in primary piRNA biogenesis in Drosophila. Genes Dev. 24, 2493–2498 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Choi, S.-Y. et al. A common lipid links Mfn-mediated mitochondrial fusion and SNARE-regulated exocytosis. Nature Cell Biol. 8, 1255–1262 (2006).

    Article  CAS  PubMed  Google Scholar 

  59. Voigt, F. et al. Crystal structure of the primary piRNA biogenesis factor Zucchini reveals similarity to the bacterial PLD endonuclease Nuc. RNA 18, 2128–2134 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Nishimasu, H. et al. Structure and function of Zucchini endoribonuclease in piRNA biogenesis. Nature 491, 284–287 (2012).

    Article  CAS  PubMed  Google Scholar 

  61. Ipsaro, J. J., Haase, A. D., Knott, S. R., Joshua-Tor, L. & Hannon, G. J. The structural biochemistry of Zucchini implicates it as a nuclease in piRNA biogenesis. Nature 491, 279–283 (2012). References 59, 60 and 61 show crystal structures of Zuc, showing that it has a nuclease domain and possesses single-stranded nuclease activity. These studies provide proof that Zuc is a nucleasethat probably acts to specify piRNA 5′ ends.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Mi, S. et al. Sorting of small RNAs into Arabidopsis Argonaute complexes is directed by the 5′ terminal nucleotide. Cell 133, 116–127 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Kawaoka, S., Izumi, N., Katsuma, S. & Tomari, Y. 3′ end formation of PIWI-interacting RNAs in vitro. Mol. Cell 43, 1015–1022 (2011).

    Article  CAS  PubMed  Google Scholar 

  64. Iwasaki, S. et al. Hsc70/Hsp90 chaperone machinery mediates ATP-dependent RISC loading of small RNA duplexes. Mol. Cell 39, 292–299 (2010).

    Article  CAS  PubMed  Google Scholar 

  65. Johnston, M., Geoffroy, M.-C., Sobala, A., Hay, R. & Hutvagner, G. HSP90 protein stabilizes unloaded Argonaute complexes and microscopic P-bodies in human cells. Mol. Biol. Cell 21, 1462–1469 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Miyoshi, T., Takeuchi, A., Siomi, H. & Siomi, M. C. A direct role for Hsp90 in pre-RISC formation in Drosophila. Nature Struct. Mol. Biol. 17, 1024–1026 (2010).

    Article  CAS  Google Scholar 

  67. Iki, T., Yoshikawa, M., Meshi, T. & Ishikawa, M. Cyclophilin 40 facilitates HSP90-mediated RISC assembly in plants. EMBO J. 31, 267–278 (2012).

    Article  CAS  PubMed  Google Scholar 

  68. Gangaraju, V. K. et al. Drosophila Piwi functions in Hsp90-mediated suppression of phenotypic variation. Nature Genet. 43, 153–158 (2010).

    Article  CAS  PubMed  Google Scholar 

  69. Olivieri, D., Senti, K.-A., Subramanian, S., Sachidanandam, R. & Brennecke, J. The cochaperone shutdown defines a group of biogenesis factors essential for all piRNA populations in Drosophila. Mol. Cell 47, 954–969 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Specchia, V. et al. Hsp90 prevents phenotypic variation by suppressing the mutagenic activity of transposons. Nature 463, 662–665 (2010).

    Article  CAS  PubMed  Google Scholar 

  71. Vagin, V. V. et al. Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members. Genes Dev. 23, 1749–1762 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Xiol, J. et al. A role for Fkbp6 and the chaperone machinery in piRNA amplification and transposon silencing. Mol. Cell 47, 970–979 (2012).

    Article  CAS  PubMed  Google Scholar 

  73. Kamminga, L. M. et al. Hen1 is required for oocyte development and piRNA stability in zebrafish. EMBO J. 29, 3688–3700 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Saito, K. et al. Pimet, the Drosophila homolog of HEN1, mediates 2′-O-methylation of Piwi-interacting RNAs at their 3′ ends. Genes Dev. 21, 1603–1608 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Horwich, M. D. et al. The Drosophila RNA methyltransferase, DmHen1, modifies germline piRNAs and single-stranded siRNAs in RISC. Curr. Biol. 17, 1265–1272 (2007).

    Article  CAS  PubMed  Google Scholar 

  76. Yu, B. Methylation as a crucial step in plant microRNA biogenesis. Science 307, 932–935 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Kurth, H. M. & Mochizuki, K. 2′-O-methylation stabilizes Piwi-associated small RNAs and ensures DNA elimination in Tetrahymena. RNA 15, 675–685 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Ameres, S. L. et al. Target RNA-directed trimming and tailing of small silencing RNAs. Science 328, 1534–1539 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Ameres, S. L., Hung, J.-H., Xu, J., Weng, Z. & Zamore, P. D. Target RNA-directed tailing and trimming purifies the sorting of endo-siRNAs between the two Drosophila Argonaute proteins. RNA 17, 54–63 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Vourekas, A. et al. Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis. Nature Struct. Mol. Biol. 19, 773–781 (2012).

    Article  CAS  Google Scholar 

  81. Bagijn, M. P. et al. Function, targets, and evolution of Caenorhabditis elegans piRNAs. Science 337, 574–578 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Lee, H.-C. et al. C. elegans piRNAs mediate the genome-wide surveillance of germline Transcripts. Cell 150, 78–87 (2012). References 81 and 82 show that the C. elegans -specific PIWI protein PRG-1 binds its targets by imperfectly base pairing and silences independently of its endonuclease activity. Instead, it recruits a downstream small RNA pathway that generates endogenous siRNAs (endo-siRNAs) to induce silencing.

    Article  CAS  PubMed  Google Scholar 

  83. Reuter, M. et al. Miwi catalysis is required for piRNA amplification-independent LINE1 transposon silencing. Nature 480, 264–267 (2011).

    Article  CAS  PubMed  Google Scholar 

  84. Huang, X. A. et al. A major epigenetic programming mechanism guided by piRNAs. Dev. Cell 24, 502–516 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Cox, D. N., Chao, A. & Lin, H. piwi encodes a nucleoplasmic factor whose activity modulates the number and division rate of germline stem cells. Development 127, 503–514 (2000).

    CAS  PubMed  Google Scholar 

  86. Aravin, A. A. et al. A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol. Cell 31, 785–799 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Houwing, S., Berezikov, E. & Ketting, R. F. Zili is required for germ cell differentiation and meiosis in zebrafish. EMBO J. 27, 2702–2711 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Qi, H. et al. The Yb body a major site for Piwi-associated RNA biogenesis and a gateway for Piwi expression and transport to the nucleus in somatic cells. J. Biol. Chem. 286, 3789–3797 (2011).

    Article  CAS  PubMed  Google Scholar 

  89. Olivieri, D., Sykora, M. M., Sachidanandam, R., Mechtler, K. & Brennecke, J. An in vivo RNAi assay identifies major genetic and cellular requirements for primary piRNA biogenesis in Drosophila. EMBO J. 29, 3301–3317 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Kuramochi-Miyagawa, S. et al. MVH in piRNA processing and gene silencing of retrotransposons. Genes Dev. 24, 887–892 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Luteijn, M. J. et al. Extremely stable Piwi-induced gene silencing in Caenorhabditis elegans. EMBO J. 31, 3422–3430 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Ashe, A. et al. piRNAs can trigger a multigenerational epigenetic memory in the germline of C. elegans. Cell 150, 88–99 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Shirayama, M. et al. piRNAs initiate an epigenetic memory of nonself RNA in the C. elegans germline. Cell 150, 65–77 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Buckley, B. A. et al. A nuclear Argonaute promotes multigenerational epigenetic inheritance and germline immortality. Nature 489, 447–451 (2012). References 91, 92, 93 and 94 show a role for PRG-1 in inducing stably inherited silenced state by recruiting a nuclear RNAi machinery that triggers heterochromatin formation. Reference 94 demonstrates the nuclear activity of WAGO-9 in RNAi-induced transgenerational silencing and reveals a role in germline mortality.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Burton, N. O., Burkhart, K. B. & Kennedy, S. Nuclear RNAi maintains heritable gene silencing in Caenorhabditis elegans. Proc. Natl Acad. Sci. 108, 19683–19688 (2011).

    Article  PubMed  Google Scholar 

  96. Burkhart, K. B. et al. A pre-mRNA-associating factor links endogenous siRNAs to chromatin regulation. PLoS Genet. 7, e1002249 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Kuramochi-Miyagawa, S. et al. Mili, a mammalian member of Piwi family gene, is essential for spermatogenesis. Development 131, 839–849 (2004).

    Article  CAS  PubMed  Google Scholar 

  98. Morgan, H. D., Santos, F., Green, K., Dean, W. & Reik, W. Epigenetic reprogramming in mammals. Hum. Mol. Genet. 14 (Suppl. 1), R47–R58 (2005).

    Article  CAS  PubMed  Google Scholar 

  99. Claycomb, J. M. et al. The Argonaute CSR-1 and its 22G-RNA cofactors are required for holocentric chromosome segregation. Cell 139, 123–134 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Wolfswinkel, J. C. V. et al. CDE-1 affects chromosome segregation through uridylation of CSR-1-bound siRNAs. Cell 139, 135–148 (2009).

    Article  CAS  PubMed  Google Scholar 

  101. Fang, W., Wang, X., Bracht, J. R., Nowacki, M. & Landweber, L. F. Piwi-interacting RNAs protect DNA against loss during oxytricha genome rearrangement. Cell 151, 1243–1255 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Yin, H. & Lin, H. An epigenetic activation role of Piwi and a Piwi-associated piRNA in Drosophila melanogaster. Nature 450, 304–308 (2007).

    Article  CAS  PubMed  Google Scholar 

  103. Brower-Toland, B. et al. Drosophila PIWI associates with chromatin and interacts directly with HP1a. Genes Dev. 21, 2300–2311 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Rozhkov, N. V., Hammell, M. & Hannon, G. J. Multiple roles for Piwi in silencing Drosophila transposons. Genes Dev. 27, 400–412 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Sienski, G., Donertas, D. & Brennecke, J. Transcriptional silencing of transposons by Piwi and maelstrom and its impact on chromatin state and gene expression. Cell 151, 964–980 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Le Thomas, A. et al. Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state. Genes Dev. 27, 390–399 (2013). References 104, 105 and 106, along with reference 82, show that D. melanogaster Piwi is required to establish heterochromatic H3K9me3 marks on transposons and their genomic surroundings. Reference 105 also shows that the high-mobility group (HMG) protein Mael is essential for transposon silencing but not for heterochromatin formation.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Darricarrère, N., Liu, N., Watanabe, T. & Lin, H. Function of Piwi, a nuclear Piwi/Argonaute protein, is independent of its slicer activity. Proc. Natl Acad. Sci. 110, 1297–1302 (2013).

    Article  PubMed  Google Scholar 

  108. Aravin, A. A. et al. Cytoplasmic compartmentalization of the fetal piRNA pathway in mice. PLoS Genet. 5, e1000764 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. de Vanssay, A. et al. Paramutation in Drosophila linked to emergence of a piRNA-producing locus. Nature 490, 112–115 (2012). This work shows that piRNA targets can be converted into piRNA-producing loci, resulting in genetic behavior that closely mirrors that of paramutation.

    Article  CAS  PubMed  Google Scholar 

  110. Erhard, K. F. Jr & Hollick, J. B. Paramutation: a process for acquiring trans-generational regulatory states. Curr. Opin. Plant Biol. 14, 210–216 (2011).

    Article  CAS  PubMed  Google Scholar 

  111. Pilu, R. Paramutation: just a curiosity or fine tuning of gene expression in the next generation? Curr. Genom. 12, 298–306 (2011).

    Article  CAS  Google Scholar 

  112. Muerdter, F. et al. A genome-wide RNAi screen draws a genetic framework for transposon control and primary piRNA biogenesis in Drosophila. Mol. Cell. http://dx.doi.org/10.1016/j.molcel.2013.04.006 (2013).

  113. Czech, B., Preall, J. B., McGinn, J. & Hannon, G. J. A transcriptome-wide RNAi screen in the Drosophila ovary reveals factors of the germline piRNA pathway. Mol. Cell http://dx.doi.org/10.1016/j.molcel.2013.04.007 (2013).

  114. Handler, D. et al. The genetic makeup of the Drosophila piRNA pathway. Mol. Cell http://dx.doi.org/10.1016/j.molcel.2013.04.031 (2013).

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Acknowledgements

The authors thank members of their laboratory for helpful discussions. This work is supported by grants from the European Research Council (ERC; StG 202819), the Netherlands Organization for Scientific Research (NWO; ECHO 700.57.006 and Vici 724.011.001) and the Boehringer Ingelheim Stiftung. The authors apologize to those colleagues whose work could not be cited owing to space restrictions.

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Authors and Affiliations

  1. Hubrecht Institute-KNAW and University Medical Centre Utrecht, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands

    Maartje J. Luteijn & René F. Ketting

  2. Institute for Molecular Biology, Ackermannweg 4, Mainz, D-55128, Germany

    René F. Ketting

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  1. Maartje J. Luteijn
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  2. René F. Ketting
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Correspondence to René F. Ketting.

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Glossary

21U RNAs

Short RNA molecules found in Caenorhabditis elegans that are characterized by a length of mostly 21 nt and a uracil at their 5′ end. 21U RNAs are bound by the Piwi proteins PRG-1 and PRG-2.

Pachytene

The third stage of meiotic prophase. Homologous chromosomes are tightly held together by the synaptonemal complex, and homologous recombination ('crossing over') begins.

RNA-induced transcriptional silencing complex

(RITS complex). An RNA interference (RNAi) effector complex required for heterochromatin assembly in fission yeast. It targets centromeric transcripts to induce both histone H3 at lysine 9 (H3K9) methylation and small interfering RNA amplification.

22G RNAs

Short RNA molecules in Caenorhabditis elegans made by RNA-dependent RNA polymerase (RdRP) activity on an RNA template. 22G RNAs are characterized by a triphosphate group at their 5′ end and a strong preference for a G at their 5′ end. They are bound by Argonaute proteins.

RNA-dependent RNA polymerases

(RdRP). RNA polymerases that use single-stranded RNA as a template to synthesize double-stranded RNA.

RNA-induced epigenetic silencing

(RNAe). A form of epigenetic silencing that can be induced by various forms of RNA interference (RNAi)-related pathways, resulting in trimethylation of histone H3 at lysine 9 (H3K9) residues at the silenced locus. The silencing is maintained through both mitosis and meiosis and can last for tens of generations.

Paramutation

The interaction between two alleles through which the epigenetic state of one allele can be imposed on the other allele.

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Luteijn, M., Ketting, R. PIWI-interacting RNAs: from generation to transgenerational epigenetics. Nat Rev Genet 14, 523–534 (2013). https://doi.org/10.1038/nrg3495

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