Arabidopsis hda6 regulates locus-directed heterochromatin silencing in cooperation with met1

PLoS Genetics

Volumn 7, Issue 4, 2011, Pages

  To, Taiko Kim ^a,b   Kim, Jong Myong ^a   Matsui, Akihiro ^a   Kurihara, Yukio ^a   Morosawa, Taeko ^a   Ishida, Junko ^a   Tanaka, Maho ^a   Endo, Takaho ^c   Kakutani, Tetsuji ^d   Toyoda, Tetsuro ^c   Kimura, Hiroshi ^e   Yokoyama, Shigeyuki ^b   Shinozaki, Kazuo ^a   Seki, Motoaki ^a,f  

^a RIKEN   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c RIKEN YOKOHAMA INSTITUTE   (Japan)

^d NATIONAL INSTITUTE OF GENETICS   (Japan)

^e OSAKA UNIVERSITY   (Japan)

^f YOKOHAMA CITY UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA METHYLTRANSFERASE 1; HISTONE DEACETYLASE 6; HISTONE H3; HISTONE H4; SMALL INTERFERING RNA; ARABIDOPSIS PROTEIN; DNA (CYTOSINE 5) METHYLTRANSFERASE; HDA6 PROTEIN, ARABIDOPSIS; HISTONE DEACETYLASE; MET1 PROTEIN, ARABIDOPSIS;

ACETYLATION; ARABIDOPSIS; ARTICLE; CHROMATIN STRUCTURE; CONTROLLED STUDY; DNA METHYLATION; ENZYME BINDING; ENZYME DEFICIENCY; EPIGENETICS; GENE EXPRESSION; GENE LOCUS; GENE SEQUENCE; GENE SILENCING; HETEROCHROMATIN; MUTANT; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GROWTH; GENE EXPRESSION REGULATION; GENETIC EPIGENESIS; GENETICS; METABOLISM; PROTEIN BINDING;

ARABIDOPSIS; EUKARYOTA;

ACETYLATION; ARABIDOPSIS; ARABIDOPSIS PROTEINS; DNA (CYTOSINE-5-)-METHYLTRANSFERASE; DNA METHYLATION; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION, PLANT; GENE SILENCING; GENETIC LOCI; HETEROCHROMATIN; HISTONE DEACETYLASES; PROTEIN BINDING;

EID: 79955591951     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1002055     Document Type: Article

References (63)

1. Henderson IR, Jacobsen SE, (2007) Epigenetic inheritance in plants. Nature 447: 418-424.
2. Ho L, Crabtree GR, (2010) Chromatin remodelling during development. Nature 463: 474-484.
3. Slotkin RK, Martienssen R, (2007) Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 8: 272-285.
4. Cedar H, Bergman Y, (2009) Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet 10: 295-304.
5. Okano M, Bell DW, Haber DA, Li E, (1999) DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99: 247-257.
6. Peters AH, O'Carroll D, Scherthan H, Mechtler K, Sauer S, et al. (2001) Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability. Cell 107: 323-337.
7. Lagger G, O'Carroll D, Rembold M, Khier H, Tischler J, et al. (2002) Essential function of histone deacetylase 1 in proliferation control and CDK inhibitor repression. EMBO J 21: 2672-2681.
8. Montgomery RL, Davis CA, Potthoff MJ, Haberland M, Fielitz J, et al. (2007) Histone deacetylases 1 and 2 redundantly regulate cardiac morphogenesis, growth, and contractility. Genes Dev 21: 1790-1802.
9. Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, et al. (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126: 1189-1201.
10. Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S, (2006) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 39: 61-69.
11. Turck F, Roudier F, Farrona S, Martin-Magniette ML, Guillaume E, et al. (2007) Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27. PLoS Genet 3: e86 doi:10.1371/journal.pgen.0030086.
12. Zhang X, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, et al. (2007) Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol 5: e129 doi:10.1371/journal.pbio.0050129.
13. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, et al. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133: 523-536.
14. Millar CB, Grunstein M, (2006) Genome-wide patterns of histone modifications in yeast. Nat Rev Mol Cell Biol 7: 657-666.
15. Yang XJ, Seto E, (2008) The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men. Nat Rev Mol Cell Biol 9: 206-218.
16. Minucci S, Pelicci PG, (2006) Histone deacetylase inhibitors and the promise of epigenetic (and more) treatments for cancer. Nat Rev Cancer 6: 38-51.
17. Kazantsev AG, Thompson LM, (2008) Therapeutic application of histone deacetylase inhibitors for central nervous system disorders. Nat Rev Drug Discovery 7: 854-868.
18. Matzke MA, Birchler JA, (2005) RNAi-mediated pathways in the nucleus. Nat Rev Genet 6: 24-35.
19. Finnegan EJ, Dennis ES, (1993) Isolation and identification by sequence homology of a putative cytosine methyltransferase from Arabidopsis thaliana. Nucleic Acids Res 21: 2383-2388.
20. Vongs A, Kakutani T, Martienssen RA, Richards EJ, (1993) Arabidopsis thaliana DNA methylation mutants. Science 260: 1926-1928.
21. Saze H, Mittelsten Scheid O, Paszkowski J, (2003) Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nat Genet 34: 65-69.
22. Aufsatz W, Mette MF, Matzke AJ, Matzke M, (2004) The role of MET1 in RNA-directed de novo and maintenance methylation of CG dinucleotides. Plant Mol Biol 54: 793-804.
23. Jackson JP, Lindroth AM, Cao X, Jacobsen SE, (2002) Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416: 556-560.
24. Jasencakova Z, Soppe WJ, Meister A, Gernand D, Turner BM, et al. (2003) Histone modifications in Arabidopsis- high methylation of H3 lysine 9 is dispensable for constitutive heterochromatin. Plant J 33: 471-480.
25. Johnson LM, Cao X, Jacobsen SE, (2002) Interplay between Two Epigenetic Marks: DNA Methylation and Histone H3 Lysine 9 Methylation. Curr Biol 12: 1360-1367.
26. Lindroth AM, Shultism D, Jasencakova Z, Fuchs J, Johnson L, et al. (2004) Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J 23: 4286-4296.
27. Aufsatz W, Mette MF, van der Winden J, Matzke M, Matzke AJ, (2002) HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double-stranded RNA. EMBO J 21: 6832-6841.
28. Probst AV, Fagard M, Proux F, Mourrain P, Boutet S, et al. (2004) Arabidopsis histone deacetylase HDA6 is required for maintenance of transcriptional gene silencing and determines nuclear organization of rDNA repeats. Plant Cell 16: 1021-1034.
29. May BP, Lippman ZB, Fang Y, Spector DL, Martienssen RA, (2005) Differential regulation of strand-specific transcripts from Arabidopsis centromeric satellite repeats. PLoS Genet 1: e79 doi:10.1371/journal.pgen.0010079.
30. Earley KW, Pontvianne F, Wierzbicki AT, Blevins T, Tucker S, et al. (2010) Mechanisms of HDA6-mediated rRNA gene silencing: suppression of intergenic Pol II transcription and differential effects on maintenance versus siRNA-directed cytosine methylation. Genes Dev 24: 1119-1132.
31. Pandey R, Muller A, Napoli CA, Selinger DA, Pikaard CS, et al. (2002) Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Res 30: 5036-5055.
32. Furner IJ, Sheikh MA, Collett CE, (1998) Gene silencing and homology-dependent gene silencing in Arabidopsis: genetic modifiers and DNA methylation. Genetics 149: 651-662.
33. Murfett J, Wang XJ, Hagen G, Guilfoyle TJ, (2001) Identification of Arabidopsis histone deacetylase HDA6 mutants that affect transgene expression. Plant Cell 13: 1047-1061.
34. Earley K, Lawrence RJ, Pontes O, Reuther R, Enciso AJ, et al. (2006) Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale gene silencing in nucleolar dominance. Genes Dev 20: 1283-1293.
35. Vaillant I, Tutois S, Cuvillier C, Schubert I, Tourmente S, (2007) Regulation of Arabidopsis thaliana 5S rRNA genes. Plant Cell Physiol 48: 745-752.
36. Lippman Z, May B, Yordan C, Singer T, Martienssen R, (2003) Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS Biol 1: e67 doi:10.1371/journal.pcbi.0010067.
37. Rangwala SH, Richards EJ, (2007) Differential epigenetic regulation within an Arabidopsis retroposon family. Genetics 176: 151-160.
38. Elmayan T, Proux F, Vaucheret H, (2005) Arabidopsis RPA2: A Genetic Link among Transcriptional Gene Silencing, DNA Repair, and DNA Replication. Curr Biol 15: 1919-1925.
39. Toyoda T, Shinozaki K, (2005) Tiling array-driven elucidation of transcriptional structures based on maximum-likelihood and Markov models. Plant J 43: 611-621.
40. Buisine N, Quesneville H, Colot V, (2008) Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets. Genomics 91: 467-475.
41. Aufsatz W, Stoiber T, Rakic B, Naumann K, (2007) Arabidopsis histone deacetylase 6: a green link to RNA silencing. Oncogene 26: 5477-5488.
42. Kasschau KD, Fahlgren N, Chapman EJ, Sullivan CM, Cumbie JS, et al. (2007) Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol 5: e57 doi:10.1371/journal.pbio.0050057.
43. Kurihara Y, Matsui A, Kawashima M, Kaminuma E, Ishida J, et al. (2008) Identification of the candidate genes regulated by RNA-directed DNA methylation in Arabidopsis. Biochem Biophys Res Commun 376: 553-557.
44. Fuchs J, Demidov D, Houben A, Schubert I, (2006) Chromosomal histone modification patterns-from conservation to diversity. Trends Plant Sci 11: 199-208.
45. Huettel B, Kanno T, Daxinger L, Aufsatz W, Matzke AJ, et al. (2006) Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis. EMBO J 25: 2828-2836.
46. Zhang Y, Reinberg D, (2001) Transcription regulation by histone methylation: interplay between different covalent modifications of the core histone tails. Genes Dev 15: 2343-2360.
47. Suka N, Suka Y, Carmen AA, Wu J, Grunstein M, (2001) Highly specific antibodies determine histone acetylation site usage in yeast heterochromatin and euchromatin. Mol Cell 8: 473-479.
48. Mathieu O, Reinders J, Caikovski M, Smathajitt C, Paszkowski J, (2007) Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation. Cell 130: 851-862.
49. Mirouze M, Reinders J, Bucher E, Nishimura T, Schneeberger K, et al. (2009) Selective epigenetic control of retrotransposition in Arabidopsis. Nature 461: 427-430.
50. Teixeira FK, Heredia F, Sarazin A, Roudier F, Boccara M, et al. (2009) A role for RNAi in the selective correction of DNA methylation defects. Science 323: 1600-1604.
51. Slotkin RK, Vaughn M, Borges F, Tanurdzić M, Becker JD, et al. (2009) Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136: 461-472.
52. Robertson KD, Ait-Si-Ali S, Yokochi T, Wade PA, Jones PL, et al. (2000) DNMT1 forms a complex with Rb, E2F1 and HDAC1 and represses transcription from E2F-responsive promoters. Nat Genet 25: 338-342.
53. Rountree MR, Bachman KE, Baylin SB, (2000) DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci. Nat Genet 25: 269-277.
54. Bai S, Ghoshal K, Datta J, Majumder S, Yoon SO, et al. (2005) DNA methyltransferase 3b regulates nerve growth factor-induced differentiation of PC12 cells by recruiting histone deacetylase 2. Mol Cell Biol 25: 751-766.
55. Kato M, Miura A, Bender J, Jacobsen SE, Kakutani T, (2003) Role of CG and non-CG methylation in immobilization of transposons in Arabidopsis. Curr Biol 13: 421-426.
56. Chan SW, Henderson IR, Zhang X, Shah G, Chien JS, et al. (2006) RNAi, DRD1, and histone methylation actively target developmentally important non-CG DNA methylation in Arabidopsis. PLoS Genet 2: e83 doi:10.1371/journal.pgen.0020083.
57. Johnson LM, Bostick M, Zhang X, Kraft E, Henderson I, et al. (2007) The SRA methyl-cytosine-binding domain links DNA and histone methylation. Curr Biol 17: 379-384.
58. Mathieu O, Probst AV, Paszkowski J, (2005) Distinct regulation of histone H3 methylation at lysines 27 and 9 by CpG methylation in Arabidopsis. EMBO J 24: 2783-2791.
59. Onodera Y, Haag J, Ream T, Nunes PC, Pontes O, et al. (2005) Plant nuclear RNA polymerase IV mediates siRNA and DNA-methylation-dependent heterochromatin formation. Cell 120: 613-622.
60. Matsui A, Ishida J, Morosawa T, Mochizuki Y, Kaminuma E, et al. (2008) Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array. Plant Cell Physiol 49: 1135-1149.
61. Kim JM, To TK, Ishida J, Morosawa T, Kawashima M, et al. (2008) Alterations of lysine modifications on the histone H3 N-tail under drought stress conditions in Arabidopsis thaliana. Plant Cell Physiol 49: 1580-1588.
62. Kimura H, Hayashi-Takanaka Y, Goto Y, Takizawa N, Nozaki N, (2008) The organization of histone H3 modifications as revealed by a panel of specific monoclonal antibodies. Cell Struct Funct 33: 61-73.
63. Schmittgen TD, Livak KJ, (2008) Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc 3: 1101-1108.