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RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond

Key Points

  • Small RNAs with roles in the nucleus include those that are generated mainly by Dicer proteins and loaded into Argonaute proteins (small interfering RNAs (siRNAs)) and also those that are Dicer-independent (largely generated by the ping-pong cycle) and are loaded into PIWI proteins (PIWI-interacting RNAs (piRNAs)).

  • The subcellular localization where siRNA biogenesis occurs is variable among organisms. However, cytoplasmic Argonaute loading might be conserved.

  • Nuclear RNA interference (RNAi) directs heterochromatic modifications at target loci including methylation of histone H3 at lysine 9 (H3K9; in Schizosaccharomyces pombe) and DNA methylation (in Arabidopsis thaliana). These reduce transcription, facilitating transcriptional gene silencing (TGS).

  • Examples in A. thaliana and S. pombe show that transcription by RNA polymerase is required to produce nascent RNA that is targeted by nuclear RNAi; this process is termed co-transcriptional gene silencing (CTGS).

  • There is evidence in the somatic cells of metazoans that endogenous siRNA pathways are involved in co-transcriptional regulation and heterochromatin formation, suggesting a conserved nuclear role for RNAi.

  • RNAi has a crucial germline role in silencing transposons both post-transcriptionally and transcriptionally.

  • In both metazoans and plants, transposons are revealed for transcription and produce small RNAs that target transposons in the germ cells to maintain silencing through nuclear RNAi.

  • In mammals, piRNAs can direct de novo cytosine methylation in the germ line and have been shown to do so at an imprinted locus. This suggests that nuclear RNAi might have another conserved role in parent-of-origin imprinting.

  • The piRNAs of Caenorhabditis elegans (21U small RNAs) can direct transcriptional silencing by H3K9 methylation in the germ line that is heritable and dependent on nuclear RNAi (NRDE) pathway members.

  • Roles are emerging for small RNAs in DNA repair and genome maintenance, through both the maintenance and regulation of heterochromatic domains (such as centromeres and telomeres) and through direct involvement in DNA repair: for example, at double-strand breaks.

Abstract

A growing number of functions are emerging for RNA interference (RNAi) in the nucleus, in addition to well-characterized roles in post-transcriptional gene silencing in the cytoplasm. Epigenetic modifications directed by small RNAs have been shown to cause transcriptional repression in plants, fungi and animals. Additionally, increasing evidence indicates that RNAi regulates transcription through interaction with transcriptional machinery. Nuclear small RNAs include small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs) and are implicated in nuclear processes such as transposon regulation, heterochromatin formation, developmental gene regulation and genome stability.

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Figure 1: Generalized pathways for the biogenesis of nuclear small RNAs.
Figure 2: Co-transcriptional gene silencing in Schizosaccharomyces pombe.
Figure 3: The RNA-dependent DNA methylation pathway in Arabidopsis thaliana.
Figure 4: RNA-interference-mediated transposon silencing in the germ line.
Figure 5: The 21U small RNA pathway in the Caenorhabditis elegans germ line.

References

  1. 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).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  2. 2

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

    CAS  Article  Google Scholar 

  3. 3

    Kim, V. N., Han, J. & Siomi, M. C. Biogenesis of small RNAs in animals. Nature Rev. Mol. Cell Biol. 10, 126–139 (2009).

    CAS  Article  Google Scholar 

  4. 4

    Colmenares, S. U., Buker, S. M., Bühler, M., Dlakic´, M. & Moazed, D. Coupling of double-stranded RNA synthesis and siRNA generation in fission yeast RNAi. Mol. Cell 27, 449–461 (2007).

    CAS  PubMed  Article  Google Scholar 

  5. 5

    Pak, J. & Fire, A. Distinct populations of primary and secondary effectors during RNAi in C. elegans. Science 315, 241–244 (2007).

    CAS  Article  Google Scholar 

  6. 6

    Lee, H.-C. et al. Diverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi. Mol. Cell 38, 803–814 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  7. 7

    Halic, M. & Moazed, D. Dicer-independent primal RNAs trigger RNAi and heterochromatin formation. Cell 140, 504–516 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  8. 8

    Aoki, K., Moriguchi, H., Yoshioka, T., Okawa, K. & Tabara, H. In vitro analyses of the production and activity of secondary small interfering RNAs in C. elegans. EMBO J. 26, 5007–5019 (2007).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  9. 9

    Kato, H. et al. RNA polymerase II is required for RNAi-dependent heterochromatin assembly. Science 309, 467–469 (2005).

    CAS  PubMed  Article  Google Scholar 

  10. 10

    Emmerth, S. et al. Nuclear retention of fission yeast dicer is a prerequisite for RNAi-mediated heterochromatin assembly. Dev. Cell 18, 102–113 (2010).

    CAS  PubMed  Article  Google Scholar 

  11. 11

    Barraud, P. et al. An extended dsRBD with a novel zinc-binding motif mediates nuclear retention of fission yeast Dicer. EMBO J. 30, 4223–4235 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  12. 12

    Irvine, D. V. et al. Argonaute slicing is required for heterochromatic silencing and spreading. Science 313, 1134–1137 (2006).

    CAS  PubMed  Article  Google Scholar 

  13. 13

    Cernilogar, F. M. et al. Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila. Nature 480, 391–395 (2011). This paper shows that siRNA components AGO2 and DCR2 have a nuclear role, challenging previously held views. It is one of the first examples in metazoans of a role for siRNA in the nucleus, specifically in transcriptional regulation.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  14. 14

    Dalzell, J. J. et al. RNAi effector diversity in nematodes. PLoS Negl. Trop. Dis. 5, e1176 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  15. 15

    Ye, R. et al. Cytoplasmic assembly and selective nuclear import of Arabidopsis ARGONAUTE4/siRNA complexes. Mol. Cell 46, 859–870 (2012).

    CAS  PubMed  Article  Google Scholar 

  16. 16

    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).

    CAS  Article  Google Scholar 

  17. 17

    Guang, S. et al. An argonaute transports siRNAs from the cytoplasm to the nucleus. Science 321, 537–541 (2008).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  18. 18

    Brennecke, J. et al. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128, 1089–1103 (2007). These authors first put forward the ping-pong model of piRNA biogenesis in the D. melanogaster germ line and showed that piRNAs regulate transposon activity.

    CAS  Article  PubMed  Google Scholar 

  19. 19

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

    CAS  Article  Google Scholar 

  20. 20

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

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  21. 21

    Malone, C. D. et al. Specialized piRNA pathways act in germline and somatic tissues of the Drosophila ovary. Cell 137, 522–535 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  22. 22

    Ji, L. & Chen, X. Regulation of small RNA stability: methylation and beyond. Cell Res. 22, 624–636 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  23. 23

    Volpe, T. A. et al. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297, 1833–1837 (2002). This is the first description of nuclear RNAi directing epigenetic modification.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  24. 24

    Motamedi, M. R. et al. Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell 119, 789–802 (2004).

    CAS  PubMed  Article  Google Scholar 

  25. 25

    Verdel, A. RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303, 672–676 (2004).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  26. 26

    Zhang, K., Mosch, K., Fischle, W. & Grewal, S. I. S. Roles of the Clr4 methyltransferase complex in nucleation, spreading and maintenance of heterochromatin. Nature Struct. Mol. Biol. 15, 381–388 (2008).

    CAS  Article  Google Scholar 

  27. 27

    Buker, S. M. et al. Two different Argonaute complexes are required for siRNA generation and heterochromatin assembly in fission yeast. Nature Struct. Mol. Biol. 14, 200–207 (2007).

    CAS  Article  Google Scholar 

  28. 28

    Djupedal, I. et al. RNA Pol II subunit Rpb7 promotes centromeric transcription and RNAi-directed chromatin silencing. Genes Dev. 19, 2301–2306 (2005).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  29. 29

    Kloc, A., Zaratiegui, M., Nora, E. & Martienssen, R. RNA interference guides histone modification during the S phase of chromosomal replication. Curr. Biol. 18, 490–495 (2008).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  30. 30

    Chen, E. S. et al. Cell cycle control of centromeric repeat transcription and heterochromatin assembly. Nature 451, 734–737 (2008).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  31. 31

    Zaratiegui, M. et al. RNAi promotes heterochromatic silencing through replication-coupled release of RNA Pol II. Nature 479, 135–138 (2011). This paper put forward a model that placed co-transcriptional silencing and RNA Pol II release into the context of DNA replication and the inheritance of epigenetic modifications.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  32. 32

    Bühler, M., Verdel, A. & Moazed, D. Tethering RITS to a nascent transcript initiates RNAi- and heterochromatin-dependent gene silencing. Cell 125, 873–886 (2006).

    PubMed  Article  CAS  Google Scholar 

  33. 33

    Zofall, M. et al. Histone H2A.Z cooperates with RNAi and heterochromatin factors to suppress antisense RNAs. Nature 461, 419–422 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  34. 34

    Gullerova, M., Moazed, D. & Proudfoot, N. J. Autoregulation of convergent RNAi genes in fission yeast. Genes Dev. 25, 556–568 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  35. 35

    Gullerova, M. & Proudfoot, N. J. Cohesin complex promotes transcriptional termination between convergent genes in S. pombe. Cell 132, 983–995 (2008).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  36. 36

    Woolcock, K. J., Gaidatzis, D., Punga, T. & Bühler, M. Dicer associates with chromatin to repress genome activity in Schizosaccharomyces pombe. Nature Struct. Mol. Biol. 18, 94–99 (2011).

    CAS  Article  Google Scholar 

  37. 37

    Woolcock, K. J. et al. RNAi keeps Atf1-bound stress response genes in check at nuclear pores. Genes Dev. 26, 683–692 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  38. 38

    Wassenegger, M., Heimes, S., Riedel, L. & Sänger, H.-L. RNA-directed de novo methylation of genomic sequences in plants. Cell 76, 567–576 (1994).

    CAS  Article  Google Scholar 

  39. 39

    Mette, M. F., Aufsatz, W., van der Winden, J., Matzke, M. A. & Matzke, A. J. Transcriptional silencing and promoter methylation triggered by double-stranded RNA. EMBO J. 19, 5194–5201 (2000).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  40. 40

    Aufsatz, W., Mette, M. F., van der Winden, J., Matzke, A. J. M. & Matzke, M. RNA-directed DNA methylation in Arabidopsis. Proc. Natl Acad. Sci. USA 99, 16499–16506 (2002).

    CAS  PubMed  Article  Google Scholar 

  41. 41

    Onodera, Y. et al. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 120, 613–622 (2005).

    CAS  Article  Google Scholar 

  42. 42

    Haag, J. R. & Pikaard, C. S. Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing. Nature Rev. Mol. Cell Biol. 12, 483–492 (2011).

    CAS  Article  Google Scholar 

  43. 43

    Law, J. A., Vashisht, A. A., Wohlschlegel, J. A. & Jacobsen, S. E. SHH1, a homeodomain protein required for DNA methylation, as well as RDR2, RDM4, and chromatin remodeling factors, associate with RNA polymerase IV. PLoS Genet. 7, e1002195 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  44. 44

    Kasschau, K. D. et al. Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol. 5, e57 (2007).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  45. 45

    Zilberman, D., Cao, X. & Jacobsen, S. E. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science 299, 716–719 (2003).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  46. 46

    Wierzbicki, A. T., Ream, T. S., Haag, J. R. & Pikaard, C. S. RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Nature Genet. 41, 630–634 (2009). This is the first identification of co-transcriptional silencing by AGO4 of RNA Pol V transcripts in A. thaliana.

    CAS  Article  Google Scholar 

  47. 47

    Wierzbicki, A. T., Haag, J. R. & Pikaard, C. S. Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell 135, 635–648 (2008).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  48. 48

    El-Shami, M. et al. Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components. Genes Dev. 21, 2539–2544 (2007).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  49. 49

    Rowley, M. J., Avrutsky, M. I., Sifuentes, C. J., Pereira, L. & Wierzbicki, A. T. Independent chromatin binding of ARGONAUTE4 and SPT5L/KTF1 mediates transcriptional gene silencing. PLoS Genet. 7, e1002120 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  50. 50

    He, X.-J. et al. An effector of RNA-directed DNA methylation in Arabidopsis is an ARGONAUTE 4- and RNA-binding protein. Cell 137, 498–508 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  51. 51

    Cao, X. et al. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Curr. Biol. 13, 2212–2217 (2003).

    CAS  Article  Google Scholar 

  52. 52

    Gao, Z. et al. An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature 465, 106–109 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  53. 53

    Henderson, I. R. et al. The de novo cytosine methyltransferase DRM2 requires intact UBA domains and a catalytically mutated paralog DRM3 during RNA-directed DNA methylation in Arabidopsis thaliana. PLoS Genet. 6, e1001182 (2010).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  54. 54

    Pélissier, T., Thalmeir, S., Kempe, D., Sänger, H. L. & Wassenegger, M. Heavy de novo methylation at symmetrical and non-symmetrical sites is a hallmark of RNA-directed DNA methylation. Nucleic Acids Res. 27, 1625–1634 (1999).

    PubMed  PubMed Central  Article  Google Scholar 

  55. 55

    Zheng, X., Zhu, J., Kapoor, A. & Zhu, J.-K. Role of Arabidopsis AGO6 in siRNA accumulation, DNA methylation and transcriptional gene silencing. EMBO J. 26, 1691–1701 (2007).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  56. 56

    Olmedo-Monfil, V. et al. Control of female gamete formation by a small RNA pathway in Arabidopsis. Nature 464, 628–632 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  57. 57

    Zheng, B. et al. Intergenic transcription by RNA polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis. Genes Dev. 23, 2850–2860 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  58. 58

    Johnson, L. M. et al. The SRA methyl-cytosine-binding domain links DNA and histone methylation. Curr. Biol. 17, 379–384 (2007).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  59. 59

    Johnson, L. M., Law, J. A., Khattar, A., Henderson, I. R. & Jacobsen, S. E. SRA-domain proteins required for DRM2-mediated de novo DNA methylation. PLoS Genet. 4, e1000280 (2008).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  60. 60

    Enke, R. A., Dong, Z. & Bender, J. Small RNAs prevent transcription-coupled loss of histone H3 lysine 9 methylation in Arabidopsis thaliana. PLoS Genet. 7, e1002350 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  61. 61

    Liu, F., Bakht, S. & Dean, C. Cotranscriptional role for Arabidopsis DICER-LIKE 4 in transcription termination. Science 335, 1621–1623 (2012).

    CAS  PubMed  Article  Google Scholar 

  62. 62

    Wu, L. et al. DNA methylation mediated by a microRNA pathway. Mol. Cell 38, 465–475 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  63. 63

    Vazquez, F., Blevins, T., Ailhas, J., Boller, T. & Meins, F. Evolution of Arabidopsis MIR genes generates novel microRNA classes. Nucleic Acids Res. 36, 6429–6438 (2008).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  64. 64

    Khraiwesh, B. et al. Transcriptional control of gene expression by microRNAs. Cell 140, 111–122 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  65. 65

    Guang, S. et al. Small regulatory RNAs inhibit RNA polymerase II during the elongation phase of transcription. Nature 465, 1097–1101 (2010). This paper presents one of the early examples in metazoans of the involvement of siRNA and nuclear RNAi in transcriptional regulation.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  66. 66

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

    CAS  PubMed  Article  Google Scholar 

  67. 67

    Gu, S. G. et al. Amplification of siRNA in Caenorhabditis elegans generates a transgenerational sequence-targeted histone H3 lysine 9 methylation footprint. Nature Genet. 44, 157–164 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  68. 68

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

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  69. 69

    Fagegaltier, D. et al. The endogenous siRNA pathway is involved in heterochromatin formation in Drosophila. Proc. Natl Acad. Sci. USA 106, 21258–21263 (2009).

    CAS  PubMed  Article  Google Scholar 

  70. 70

    Deshpande, G. 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 (2005).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  71. 71

    Peng, J. C. & Karpen, G. H. H3K9 methylation and RNA interference regulate nucleolar organization and repeated DNA stability. Nature Cell Biol. 9, 25–35 (2007).

    CAS  PubMed  Article  Google Scholar 

  72. 72

    Kavi, H. H. & Birchler, J. A. Interaction of RNA polymerase II and the small RNA machinery affects heterochromatic silencing in Drosophila. Epigenetics Chromatin 2, 15 (2009).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  73. 73

    Kim, D. H., Villeneuve, L. M., Morris, K. V. & Rossi, J. J. Argonaute-1 directs siRNA-mediated transcriptional gene silencing in human cells. Nature Struct. Mol. Biol. 13, 793–797 (2006).

    CAS  Article  Google Scholar 

  74. 74

    Lippman, Z. et al. Role of transposable elements in heterochromatin and epigenetic control. Nature 430, 471–476 (2004).

    CAS  Article  Google Scholar 

  75. 75

    Slotkin, R. K. et al. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136, 461–472 (2009). This paper shows that small RNAs can move in the A. thaliana malegerm line and can silence transposable elements in pollen. It put forward the idea of revealing transposons in companion cells to enforce silencing in the germ cell.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  76. 76

    Popp, C. et al. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature 463, 1101–1105 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  77. 77

    Calarco, J. P. et al. Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell 151, 194–205 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  78. 78

    Ibarra, C. A. et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science 337, 1360–1364 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  79. 79

    Jullien, P. E., Susaki, D., Yelagandula, R., Higashiyama, T. & Berger, F. DNA methylation dynamics during sexual reproduction in Arabidopsis thaliana. Curr. Biol. 22, 1825–1830 (2012).

    CAS  PubMed  Article  Google Scholar 

  80. 80

    Jullien, P. E. et al. Retinoblastoma and its binding partner MSI1 control imprinting in Arabidopsis. PLoS Biol. 6, e194 (2008).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  81. 81

    Choi, Y. et al. DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis. Cell 110, 33–42 (2002).

    CAS  Article  Google Scholar 

  82. 82

    Hsieh, T.-F. et al. Genome-wide demethylation of Arabidopsis endosperm. Science 324, 1451–1454 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  83. 83

    Martienssen, R. A. Heterochromatin, small RNA and post-fertilization dysgenesis in allopolyploid and interploid hybrids of Arabidopsis. New Phytol. 186, 46–53 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  84. 84

    Wang, S. H. & Elgin, S. C. R. Drosophila PIWI functions downstream of piRNA production mediating a chromatin-based transposon silencing mechanism in female germ line. Proc. Natl Acad. Sci. USA 108, 21164–21169 (2011).

    CAS  PubMed  Article  Google Scholar 

  85. 85

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

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  86. 86

    Klenov, M. S. et al. Separation of stem cell maintenance and transposon silencing functions of PIWI protein. Proc. Natl Acad. Sci. USA 108, 18760–18765 (2011).

    CAS  PubMed  Article  Google Scholar 

  87. 87

    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).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  88. 88

    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).

    CAS  Article  Google Scholar 

  89. 89

    Carmell, M. A. et al. MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Dev. Cell 12, 503–514 (2007).

    CAS  Article  Google Scholar 

  90. 90

    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).

    CAS  PubMed  PubMed Central  Google Scholar 

  91. 91

    Watanabe, T. et al. Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus. Science 332, 848–852 (2011). This work demonstrates that piRNAs can direct de novo DNA methylation in mammals and that piRNAs have a role in parent-of-origin imprinting. It is one of the few examples of nuclear RNAi directing TGS in mammals.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  92. 92

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

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  93. 93

    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).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  94. 94

    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).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  95. 95

    Wang, G. & Reinke, V. A. C. elegans PIWI, PRG-1, regulates 21U-RNAs during spermatogenesis. Curr. Biol. 18, 861–867 (2008).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  96. 96

    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).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  97. 97

    Shirayama, M. et al. piRNAs initiate an epigenetic memory of nonself RNA in the C. elegans germline. Cell 150, 65–77 (2012). This paper presents an in-depth dissection of silencing mediated by the 21U small RNA pathway in the C. elegans germ line. It goes into much more detail than this Review and emphasizes how loci are targeted for silencing.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  98. 98

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

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  99. 99

    Lee, H.-C. et al. C. elegans piRNAs mediate the genome-wide surveillance of germline transcripts. Cell 150, 78–87 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  100. 100

    Maine, E. M. et al. EGO-1, a putative RNA-dependent RNA polymerase, is required for heterochromatin assembly on unpaired dna during C. elegans meiosis. Curr. Biol. 15, 1972–1978 (2005).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  101. 101

    She, X., Xu, X., Fedotov, A., Kelly, W. G. & Maine, E. M. Regulation of heterochromatin assembly on unpaired chromosomes during Caenorhabditis elegans meiosis by components of a small RNA-mediated pathway. PLoS Genet. 5, e1000624 (2009).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  102. 102

    Volpe, T. et al. RNA interference is required for normal centromere function in fission yeast. Chromosome Res. 11, 137–146 (2003).

    CAS  PubMed  Article  Google Scholar 

  103. 103

    Pek, J. W. & Kai, T. A. Role for vasa in regulating mitotic chromosome condensation in Drosophila. Curr. Biol. 21, 39–44 (2011).

    CAS  PubMed  Article  Google Scholar 

  104. 104

    Pek, J. W. & Kai, T. DEAD-box RNA helicase Belle/DDX3 and the RNA interference pathway promote mitotic chromosome segregation. Proc. Natl Acad. Sci. USA 108, 12007–12012 (2011).

    CAS  PubMed  Article  Google Scholar 

  105. 105

    Shpiz, S. & Kalmykova, A. Role of piRNAs in the Drosophila telomere homeostasis. Mob. Genet. Elements 1, 274–278 (2011).

    PubMed  PubMed Central  Article  Google Scholar 

  106. 106

    Savitsky, M. Telomere elongation is under the control of the RNAi-based mechanism in the Drosophila germline. Genes Dev. 20, 345–354 (2006).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  107. 107

    Khurana, J. S., Xu, J., Weng, Z. & Theurkauf, W. E. Distinct functions for the Drosophila piRNA pathway in genome maintenance and telomere protection. PLoS Genet. 6, e1001246 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  108. 108

    Kanoh, J., Sadaie, M., Urano, T. & Ishikawa, F. Telomere binding protein Taz1 establishes Swi6 heterochromatin independently of RNAi at telomeres. Curr. Biol. 15, 1808–1819 (2005).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  109. 109

    Ellermeier, C. et al. RNAi and heterochromatin repress centromeric meiotic recombination. Proc. Natl Acad. Sci. USA 107, 8701–8705 (2010).

    CAS  PubMed  Article  Google Scholar 

  110. 110

    Lee, H.-C. et al. qiRNA is a new type of small interfering RNA induced by DNA damage. Nature 459, 274–277 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  111. 111

    Wei, W. et al. A role for small RNAs in DNA double-strand break repair. Cell 149, 101–112 (2012). This work demonstrates the involvement of 21 nt small RNAs, RdDM members and AGO2 in the repair of DSBs, uncovering a new nuclear RNAi pathway. Importantly, the authors validated their findings in human cells, suggesting a conserved pathway.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  112. 112

    Michalik, K. M., Böttcher, R. & Förstemann, K. A small RNA response at DNA ends in Drosophila. Nucleic Acids Res. 40, 9596–9603 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  113. 113

    Francia, S. et al. Site-specific DICER and DROSHA RNA products control the DNA-damage response. Nature 488, 231–235 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  114. 114

    Taverna, S. D., Coyne, R. S. & Allis, C. D. Methylation of histone h3 at lysine 9 targets programmed DNA elimination in tetrahymena. Cell 110, 701–711 (2002).

    CAS  PubMed  Article  Google Scholar 

  115. 115

    Mochizuki, K., Fine, N. A., Fujisawa, T. & Gorovsky, M. A. Analysis of a PIWI-related gene implicates small RNAs in genome rearrangement in tetrahymena. Cell 110, 689–699 (2002).

    CAS  PubMed  Article  Google Scholar 

  116. 116

    Aronica, L. et al. Study of an RNA helicase implicates small RNA-noncoding RNA interactions in programmed DNA elimination in Tetrahymena. Genes Dev. 22, 2228–2241 (2008).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  117. 117

    Hollick, J. B. Paramutation: a trans-homolog interaction affecting heritable gene regulation. Curr. Opin. Plant Biol. 15, 536–543 (2012).

    CAS  PubMed  Article  Google Scholar 

  118. 118

    Alleman, M. et al. An RNA-dependent RNA polymerase is required for paramutation in maize. Nature 442, 295–298 (2006).

    CAS  PubMed  Article  Google Scholar 

  119. 119

    Hale, C. J., Stonaker, J. L., Gross, S. M. & Hollick, J. B. A novel Snf2 protein maintains trans-generational regulatory states established by paramutation in maize. PLoS Biol. 5, e275 (2007).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  120. 120

    Barbour, J.-E. R. et al. Required to maintain repression2 is a novel protein that facilitates locus-specific paramutation in maize. Plant Cell 24, 1761–1775 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  121. 121

    Brosnan, C. A. et al. Nuclear gene silencing directs reception of long-distance mRNA silencing in Arabidopsis. Proc. Natl Acad. Sci. USA 104, 14741–14746 (2007).

    CAS  PubMed  Article  Google Scholar 

  122. 122

    Melnyk, C. W., Molnar, A., Bassett, A. & Baulcombe, D. C. Mobile 24 nt small RNAs direct transcriptional gene silencing in the root meristems of Arabidopsis thaliana. Curr. Biol. 21, 1678–1683 (2011).

    CAS  PubMed  Article  Google Scholar 

  123. 123

    Molnar, A. et al. Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells. Science 328, 872–875 (2010).

    CAS  PubMed  Article  Google Scholar 

  124. 124

    Dunoyer, P. et al. An endogenous, systemic RNAi pathway in plants. EMBO J. 29, 1699–1712 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  125. 125

    Rechavi, O., Minevich, G. & Hobert, O. Transgenerational inheritance of an acquired small RNA-based antiviral response in C. elegans. Cell 47, 1248–1256 (2011).

    Article  CAS  Google Scholar 

  126. 126

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

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  127. 127

    Lu, J., Zhang, C., Baulcombe, D. C. & Chen, Z. J. Maternal siRNAs as regulators of parental genome imbalance and gene expression in endosperm of Arabidopsis seeds. Proc. Natl Acad. Sci. USA 109, 5529–5534 (2012).

    CAS  PubMed  Article  Google Scholar 

  128. 128

    Mosher, R. A. et al. An atypical epigenetic mechanism affects uniparental expression of Pol IV-dependent siRNAs. PLoS ONE 6, e25756 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

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Acknowledgements

We thank the members of the Martienssen laboratory for discussion. S.E.C. is a Cashin Scholar of the Watson School of Biological Sciences and is supported by a Natural Sciences and Engineering Research Council of Canada Post Graduate Scholarship.

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Correspondence to Robert A. Martienssen.

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Glossary

RNA interference

(RNAi). Silencing at both the post-transcriptional and transcriptional levels that is directed by small RNA molecules.

Post-transcriptional gene silencing

(PTGS). Silencing achieved by the degradation and/or prevention of translation of a transcript targeted by small RNAs.

Transcriptional gene silencing

(TGS). Silencing achieved by the formation of a repressive chromatin environment at a locus targeted by small RNA, making it inaccessible to transcriptional machinery.

Argonaute

The effector proteins of RNA inteference that are composed of three characteristic domains, a PAZ domain and a MID domain, which bind the 3′ and 5′ ends of small interfering RNA respectively, and a PIWI domain, which may possess RNase-H-like slicer activity if the protein is catalytically active.

Co-transcriptional gene silencing

(CTGS). The coupling of repressive epigenetic modification with transcription by an RNA polymerase that produces a nascent RNA molecule targeted by small RNAs.

Pericentromeric regions

Sites of constitutive heterochromatin that flank the central kinetochore-binding region of the centromere and are necessary for proper centromere function.

Histone H3 methylated at lysine 9

(H3K9me). H3K9 can be mono-, di- or tri-methylated. Methylation is catalysed by a histone methyltransferase and is highly enriched in repressive heterochromatin. This mark acts as a binding site for heterochromatin protein 1 (HP1; known as Swi6 in Schizosaccharomyces pombe), the presence of which is the defining feature of heterochromatic loci.

RNA-induced transcriptional silencing complex

(RITSC). The effector of nuclear RNA interference in Schizosaccharomyces pombe. It is composed of an Argonaute protein and other cofactors that may aid in localization to chromatin.

Passenger strand

The antisense small RNA strand in the double-stranded RNA molecule initially loaded by an Argonaute. The passenger strand is released by the catalytic 'slicing' activity of the Argonaute protein (like homologous RNA targets), whereas the guide strand is retained and acts to determine the specificity of the silencing complex.

Position effect variegation

Refers to the variegated expression pattern of a gene that is stochastically inactivated by the spreading of a nearby heterochromatic domain. For example, a pericentromere and an inserted nearby reporter gene.

Cytosine methylation

Covalent modification of a cytosine base catalysed by a DNA methyltransferase that often associates with heterochromatic loci. It can occur in various sequence contexts, including CG, CHG and CHH, which influence establishment and inheritance.

NRDE pathway

In Caenorhabditis elegans, components of the nuclear RNA interference pathway are termed NRDE for 'nuclear RNAi defective' owing to the phenotype of mutants (nrde).

Transposable element

Genetic elements that can move their positions within the genome. The mechanism of transposition varies and defines transposon families.

Companion cells

Cells in the germ line of plants that will not contribute genetically to progeny but are produced by meiosis. These are the vegetative nucleus in the male germ line and the central cell in the female germ line. The central cell is fertilized to produce the endosperm that acts as a supportive tissue to the developing embryo.

Cohesin

Large protein rings that predominantly localize to heterochromatic regions of the genome. They function to keep sister chromatids connected during mitosis, facilitate spindle attachment to chromosomes and are involved in DNA repair through recombination.

Recombination

The joining of similar or identical DNA sequences to produce a novel molecule. Homologous recombination is used as a mechanism to repair damaged DNA in cells; however, at repetitive regions, it can be detrimental by leading to copy number changes of repetitive elements.

Double-strand breaks

(DSBs). A deleterious form of DNA damage that occurs when the covalent bonds of both strands of a double helix are broken at a locus. It can be repaired by homologous recombination or by error-prone non-homologous end joining.

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Castel, S., Martienssen, R. RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond. Nat Rev Genet 14, 100–112 (2013). https://doi.org/10.1038/nrg3355

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