Maternal Depletion of Piwi, a Component of the RNAi System, Impacts Heterochromatin Formation in

English version České info

A persistent question in epigenetics is how heterochromatin is targeted for assembly at specific domains, and how that chromatin state is faithfully transmitted. Stable heterochromatin is necessary to silence transposable elements (TEs) and maintain genome integrity. Both the RNAi system and heterochromatin components HP1 (Swi6) and H3K9me2/3 are required for initial establishment of heterochromatin structures in S. pombe. Here we utilize both loss of function alleles and the newly developed Drosophila melanogaster transgenic shRNA lines to deplete proteins of interest at specific development stages to dissect their roles in heterochromatin assembly in early zygotes and in maintenance of the silencing chromatin state during development. Using reporters subject to Position Effect Variegation (PEV), we find that depletion of key proteins in the early embryo can lead to loss of silencing assayed at adult stages. The piRNA component Piwi is required in the early embryo for reporter silencing in non-gonadal somatic cells, but knock-down during larval stages has no impact. This implies that Piwi is involved in targeting HP1a when heterochromatin is established at the late blastoderm stage and possibly also during embryogenesis, but that the silent chromatin state created is transmitted through cell division independent of the piRNA system. In contrast, heterochromatin structural protein HP1a is required for both initial heterochromatin assembly and the following mitotic inheritance. HP1a profiles in piwi mutant animals confirm that Piwi depletion leads to decreased HP1a levels in pericentric heterochromatin, particularly in TEs. The results suggest that the major role of the piRNA system in assembly of heterochromatin in non-gonadal somatic cells occurs in the early embryo during heterochromatin formation, and further demonstrate that failure of heterochromatin formation in the early embryo impacts the phenotype of the adult.

Vyšlo v časopise: Maternal Depletion of Piwi, a Component of the RNAi System, Impacts Heterochromatin Formation in. PLoS Genet 9(9): e32767. doi:10.1371/journal.pgen.1003780
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003780

Souhrn

Zdroje

1. HeitzE (1928) Das Heterochromatin der Moose. I Jahrb Wiss Botanik 69: 762–818.

2. SunFL, CuaycongMH, ElginSCR (2001) Long-range nucleosome ordering is associated with gene silencing in Drosophila melanogaster pericentric heterochromatin. Mol Cell Biol 21: 2867–2879.

3. HuisingaKL, Brower-TolandB, ElginSC (2006) The contradictory definitions of heterochromatin: transcription and silencing. Chromosoma 115: 110–122.

4. FilionGJ, van BemmelJG, BraunschweigU, TalhoutW, KindJ, et al. (2010) Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell 143: 212–224.

5. KharchenkoPV, AlekseyenkoAA, SchwartzYB, MinodaA, RiddleNC, et al. (2011) Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 471: 480–485.

6. ErnstJ, KheradpourP, MikkelsenTS, ShoreshN, WardLD, et al. (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473: 43–49.

7. HassaPO, HottigerMO (2005) An epigenetic code for DNA damage repair pathways? Biochem Cell Biol 83: 270–285.

8. GreenbergRA (2011) Histone tails: Directing the chromatin response to DNA damage. Febs Lett 585: 2883–2890.

9. PengJC, KarpenGH (2008) Epigenetic regulation of heterochromatic DNA stability. Curr Opin Genet Dev 18: 204–211.

10. TingDT, LipsonD, PaulS, BranniganBW, AkhavanfardS, et al. (2011) Aberrant overexpression of satellite repeats in pancreatic and other epithelial cancers. Science 331: 593–596.

11. CamHP, SugiyamaT, ChenES, ChenX, FitzGeraldPC, et al. (2005) Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome. Nat Genet 37: 809–819.

12. GrewalSIS, JiaST (2007) Heterochromatin revisited. Nat Rev Genet 8: 35–46.

13. LippmanZ, MartienssenR (2004) The role of RNA interference in heterochromatic silencing. Nature 431: 364–370.

14. ChanSWL, HendersonIR, JacobsenSE (2005) Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet 6: 351–360.

15. MatzkeM, KannoT, HuettelB, DaxingerL, MatzkeAJM (2007) Targets of RNA-directed DNA methylation. Curr Opin Plant Biol 10: 512–519.

16. MochizukiK, GorovskyMA (2004) Small RNAs in genome rearrangement in Tetrahymena. Curr Opin Genet Dev 14: 181–187.

17. MorrisKV, ChanSWL, JacobsenSE, LooneyDJ (2004) Small interfering RNA-induced transcriptional gene silencing in human cells. Science 305: 1289–1292.

18. TingAH, SchuebelKE, HermanJG, BaylinSB (2005) Short double-stranded RNA induces transcriptional gene silencing in human cancer cells in the absence of DNA methylation. Nat Genet 37: 906–910.

19. SentmanatMF, ElginSC (2012) Ectopic assembly of heterochromatin in Drosophila melanogaster triggered by transposable elements. Proc Natl Acad Sci U S A 109: 14104–14109.

20. WangSH, ElginSC (2011) Drosophila Piwi functions downstream of piRNA production mediating a chromatin-based transposon silencing mechanism in female germ line. Proc Natl Acad Sci U S A 108: 21164–21169.

21. SienskiG, DönertasD, BrenneckeJ (2012) Transcriptional silencing of transposons by Piwi and Maelstrom and its impact on chromatin state and gene expression. Cell 151: 964–980.

22. BonasioR, TuS, ReinbergD (2010) Molecular signals of epigenetic states. Science 330: 612–616.

23. KlenovMS, SokolovaOA, YakushevEY, StolyarenkoAD, MikhalevaEA, et al. (2011) Separation of stem cell maintenance and transposon silencing functions of Piwi protein. Proc Natl Acad Sci U S A 108: 18760–18765.

24. MoazedD (2011) Mechanisms for the inheritance of chromatin states. Cell 146: 510–518.

25. WheelerBS, RudermanBT, WillardHF, ScottKC (2012) Uncoupling of genomic and epigenetic signals in the maintenance and inheritance of heterochromatin domains in fission yeast. Genetics 190: 549–557.

26. ShirayamaM, SethM, LeeHC, GuWF, IshidateT, et al. (2012) piRNAs initiate an epigenetic memory of nonself RNA in the C. elegans germline. Cell 150: 65–77.

27. AsheA, SapetschnigA, WeickEM, MitchellJ, BagijnMP, et al. (2012) piRNAs can trigger a multigenerational epigenetic memory in the germline of C. elegans. Cell 150: 88–99.

28. GattiM, PimpinelliS (1992) Functional elements in Drosophila melanogaster heterochromatin. Annu Rev Genet 26: 239–275.

29. MullerH (1930) Types of visible variations induced by X-rays in Drosophila. J Genet 22: 299–334.

30. WallrathLL, ElginSC (1995) Position effect variegation in Drosophila is associated with an altered chromatin structure. Genes Dev 9: 1263–1277.

31. RudolphT, YonezawaM, LeinS, HeidrichK, KubicekS, et al. (2007) Heterochromatin formation in Drosophila is initiated through active removal of H3K4 methylation by the LSD1 homolog SU(VAR)3-3. Mol Cell 26: 103–115.

32. VogelMJ, PagieL, TalhoutW, NieuwlandM, KerkhovenRM, et al. (2009) High-resolution mapping of heterochromatin redistribution in a Drosophila position-effect variegation model. Epigenetics Chromatin 2: 1.

33. SchottaG, EbertA, KraussV, FischerA, HoffmannJ, et al. (2002) Central role of Drosophila SU(VAR)3-9 in histone H3-K9 methylation and heterochromatic gene silencing. EMBO J 21: 1121–1131.

34. FodorBD, ShukeirN, ReuterG, JenuweinT (2010) Mammalian Su(var) genes in chromatin control. Annu Rev Cell Dev Biol 26: 471–501.

35. EissenbergJC, ElginSC (2000) The HP1 protein family: getting a grip on chromatin. Curr Opin Genet Dev 10: 204–210.

36. MartinC, ZhangY (2005) The diverse functions of histone lysine methylation. Nat Rev Mol Cell Biol 6: 838–849.

37. Foe VE, Odell GM, Edgar BA (1993) Mitosis and morphogenesis in the Drosophila embryo: Point and counterpoint. In: M Bate and A Martinez-Arias eds. The Development of Drosophila, vol 1. New York: Cold Spring Harbor Laboratory Press. pp.149–300.

38. LuBY, MaJY, EissenbergJC (1998) Developmental regulation of heterochromatin-mediated gene silencing in Drosophila. Development 125: 2223–2234.

39. EissenbergJC, JamesTC, FosterhartnettDM, HartnettT, NganV, et al. (1990) Mutation in a heterochromatin-specific chromosomal protein is associated with suppression of position-effect variegation in Drosophila melanogaster. Proc Natl Acad Sci U S A 87: 9923–9927.

40. GraveleyBR, BrooksAN, CarlsonJW, DuffMO, LandolinJM, et al. (2011) The developmental transcriptome of Drosophila melanogaster. Nature 471: 473–479.

41. LuBY, BishopCP, EissenbergJC (1996) Developmental timing and tissue specificity of heterochromatin-mediated silencing. EMBO J 15: 1323–1332.

42. AkkoucheA, GrentzingerT, FabletM, ArmeniseC, BurletN, et al. (2013) Maternally deposited germline piRNAs silence the tirant retrotransposon in somatic cells. EMBO Rep 14: 458–464.

43. HaaseAD, FenoglioS, MuerdterF, GuzzardoPM, CzechB, et al. (2010) Probing the initiation and effector phases of the somatic piRNA pathway in Drosophila. Genes Dev 24: 2499–2504.

44. DufourtJ, BrassetE, DessetS, PouchinP, VauryC (2011) Polycomb group-dependent, heterochromatin protein 1-independent, chromatin structures silence retrotransposons in somatic tissues outside ovaries. DNA Res 18: 451–461.

45. BrenneckeJ, MaloneCD, AravinAA, SachidanandamR, StarkA, et al. (2008) An epigenetic role for maternally inherited piRNAs in transposon silencing. Science 322: 1387–1392.

46. RougetC, PapinC, BoureuxA, MeunierAC, FrancoB, et al. (2010) Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo. Nature 467: 1128–1132.

47. TraceyWD, NingXQ, KlinglerM, KramerSG, GergenJP (2000) Quantitative analysis of gene function in the Drosophila embryo. Genetics 154: 273–284.

48. NiJQ, ZhouR, CzechB, LiuLP, HolderbaumL, et al. (2011) A genome-scale shRNA resource for transgenic RNAi in Drosophila. Nat Methods 8: 405–407.

49. StallerMV, YanD, RandklevS, BragdonMD, WunderlichZB, et al. (2013) Depleting gene activities in early Drosophila embryos with the “maternal-Gal4-shRNA” system. Genetics 193: 51–61.

50. LeeT, LuoL (1999) Mosaic analysis with a repressible cell marker for studies of gene function in neuronal morphogenesis. Neuron 22: 451–461.

51. KlenovMS, LavrovSA, StolyarenkoAD, RyazanskySS, AravinAA, et al. (2007) Repeat-associated siRNAs cause chromatin silencing of retrotransposons in the Drosophila melanogaster germline. Nucleic Acids Res 35: 5430–5438.

52. QuiringR, WalldorfU, KloterU, GehringWJ (1994) Homology of the eyeless gene of Drosophila to the small eye gene in mice and aniridia in humans. Science 265: 785–789.

53. SchneidermanJI, GoldsteinS, AhmadK (2010) Perturbation analysis of heterochromatin-mediated gene silencing and somatic inheritance. PLoS Genet 6: e1001095.

54. Brower-TolandB, RiddleNC, JiangHM, HuisingaKL, ElginSCR (2009) Multiple SET methyltransferases are required to maintain normal heterochromatin domains in the genome of Drosophila melanogaster. Genetics 181: 1303–1319.

55. TzengTY, LeeCH, ChanLW, ShenCKJ (2007) Epigenetic regulation of the Drosophila chromosome 4 by the histone H3K9 methyltransferase dSETDB1. Proc Natl Acad Sci U S A 104: 12691–12696.

56. SeumC, ReoE, PengHZ, RauscherFJ, SpiererP, et al. (2007) Drosophila SETDB1 is required for chromosome 4 silencing. PLoS Genet 3: 709–719.

57. RiddleNC, JungYL, GuT, AlekseyenkoAA, AskerD, et al. (2012) Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain. PLoS Genet 8: e1002954.

58. BrenneckeJ, AravinAA, StarkA, DusM, KellisM, et al. (2007) Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128: 1089–1103.

59. MoshkovichN, LeiEP (2010) HP1 recruitment in the absence of Argonaute proteins in Drosophila. PLoS Genet 6: e1000880.

60. YinH, LinH (2007) An epigenetic activation role of Piwi and a Piwi-associated piRNA in Drosophila melanogaster. Nature 450: 304–308.

61. HuangXA, YinH, SweeneyS, RahaD, SnyderM, et al. (2013) A major epigenetic programming mechanism guided by piRNAs. Dev Cell 24: 502–516.

62. Pal-BhadraM, LeibovitchBA, GandhiSG, ChikkaMR, BhadraU, et al. (2004) Heterochromatic silencing and HP1 localization in Drosophila are dependent on the RNAi machinery. Science 303: 669–672.

63. ChintapalliVR, WangJ, DowJAT (2007) Using FlyAtlas to identify better Drosophila melanogaster models of human disease. Nat Genet 39: 715–720.

64. AravinAA, Lagos-QuintanaM, YalcinA, ZavolanM, MarksD, et al. (2003) The small RNA profile during Drosophila melanogaster development. Dev Cell 5: 337–350.

65. RanganP, MaloneCD, NavarroC, NewboldSP, HayesPS, et al. (2011) piRNA production requires heterochromatin formation in Drosophila. Curr Biol 21: 1373–1379.

66. EissenbergJC, ReuterG (2009) Cellular mechanism for targeting heterochromatin formation in Drosophila. Int Rev Cel Mol Bio 273: 1–47.

67. AulnerN, MonodC, MandicourtG, JullienD, CuvierO, et al. (2002) The AT-hook protein D1 is essential for Drosophila melanogaster development and is implicated in position-effect variegation. Mol Cell Biol 22: 1218–1232.

68. BlattesR, MonodC, SusbielleG, CuvierO, WuJH, et al. (2006) Displacement of D1, HP1 and topoisomerase II from satellite heterochromatin by a specific polyamide. EMBO J 25: 2397–2408.

69. ShafferCD, WullerJM, ElginSC (1994) Raising large quantities of Drosophila for biochemical experiments. Methods Cell Biol 44: 99–108.

70. SunFL, HaynesK, SimpsonCL, LeeSD, CollinsL, et al. (2004) cis-Acting determinants of heterochromatin formation on Drosophila melanogaster chromosome four. Mol Cell Biol 24: 8210–8220.

71. GonczyP, ViswanathanS, DiNardoS (1992) Probing spermatogenesis in Drosophila with P-element enhancer detectors. Development 114: 89–98.

72. LivakKJ, SchmittgenTD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25: 402–408.

73. JamesTC, EissenbergJC, CraigC, DietrichV, HobsonA, et al. (1989) Distribution patterns of HP1, a heterochromatin-associated nonhistone chromosomal protein of Drosophila. Eur J Cell Biol 50: 170–180.

74. SaitoK, NishidaKM, MoriT, KawamuraY, MiyoshiK, et al. (2006) Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome. Genes Dev 20: 2214–2222.

75. MillerKG, FieldCM, AlbertsBM (1989) Actin-binding proteins from Drosophila embryos: a complex network of interacting proteins detected by F-actin affinity chromatography. J Cell Biol 109: 2963–2975.

76. StephensGE, SlawsonEE, CraigCA, ElginSC (2005) Interaction of heterochromatin protein 2 with HP1 defines a novel HP1-binding domain. Biochemistry 44: 13394–13403.

77. CoxDN, ChaoA, BakerJ, ChangL, QiaoD, et al. (1998) A novel class of evolutionarily conserved genes defined by piwi are essential for stem cell self-renewal. Genes Dev 12: 3715–3727.

78. RiddleNC, MinodaA, KharchenkoPV, AlekseyenkoAA, SchwartzYB, et al. (2011) Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Res 21: 147–163.