Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana

PLoS ONE

Volumn 3, Issue 9, 2008, Pages

  Bernatavichute, Yana V ^a   Zhang, Xiaoyu ^b   Cokus, Shawn ^a   Pellegrini, Matteo ^a   Jacobsen, Steven E ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS PROTEIN; HISTONE H3 LYSINE 9; UNCLASSIFIED DRUG; HISTONE; LYSINE; SMALL INTERFERING RNA;

ARABIDOPSIS; ARTICLE; CHROMATIN IMMUNOPRECIPITATION; CHROMOSOME ARM; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; DNA MICROARRAY; GENE EXPRESSION; GENE MAPPING; GENE SILENCING; GENETIC ASSOCIATION; GENOME ANALYSIS; NONHUMAN; PROMOTER REGION; REGULATORY MECHANISM; TRANSPOSON; CHEMISTRY; CHROMATIN; GENETIC EPIGENESIS; GENETIC TRANSCRIPTION; HETEROCHROMATIN; METABOLISM; METHYLATION; PLANT GENE; PLANT GENOME;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; DNA METHYLATION; DNA TRANSPOSABLE ELEMENTS; EPIGENESIS, GENETIC; GENES, PLANT; GENOME, PLANT; HETEROCHROMATIN; HISTONES; LYSINE; METHYLATION; RNA, SMALL INTERFERING; TRANSCRIPTION, GENETIC;

EID: 52349089796     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0003156     Document Type: Article

References (51)

1. Kouzarides T (2007) Chromatin modifications and their function. Cell 128: 693-705.
2. Martens JH, O'Sullivan RJ, Braunschweig U, Opravil S, Radolf M, et al. (2005) The profile of repeat-associated histone lysine methylation states in the mouse epigenome. Embo J 24: 800-812.
3. 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.
4. Lehnertz B, Ueda Y, Derijck AA, Braunschweig U, Perez-Burgos L, et al. (2003) Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr Biol 13: 1192-1200.
5. Tachibana M, Sugimoto K, Fukushima T, Shinkai Y (2001) Set domain-containing protein, G9a, is a novel lysine-preferring mammalian histone methyltransferase with hyperactivity and specific selectivity to lysines 9 and 27 of histone H3. J Biol Chem 276: 25309-25317.
6. Fuchs J, Demidov D, Houben A, Schubert I (2006) Chromosomal histone modification patterns-from conservation to diversity. Trends Plant Sci 11: 199-208.
7. Jackson JP, Lindroth AM, Cao X, Jacobsen SE (2002) Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416: 556-560.
8. Ebbs ML, Bartee L, Bender J (2005) H3 lysine 9 methylation is maintained on a transcribed inverted repeat by combined action of SUVH6 and SUVH4 methyltransferases. Molecular and Cellular Biology 25: 10507-10515.
9. Ebbs ML, Bender J (2006) Locus-specific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase. Plant Cell 18: 1166-1176.
10. Jasencakova Z, Soppe WJJ, 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 Journal 33: 471-480.
11. Cao X, Jacobsen SE (2002) Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc Natl Acad Sci U S A 99 Suppl 4: 16491-16498.
12. Onodera Y, Haag JR, Ream T, Nunes PC, Pontes O, et al. (2005) Plant nuclear RNA olymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 120: 613-622.
13. Herr AJ, Jensen MB, Dalmay T, Baulcombe DC (2005) RNA polymerase IV directs silencing of endogenous DNA. Science 308: 118-120.
14. Chan SW, Zilberman D, Xie Z, Johansen LK, Carrington JC, et al. (2004) RNA silencing genes control de novo DNA methylation. Science 303: 1336.
15. Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, et al. (2004) Genetic and functional diversification of small RNA pathways in plants. PLoS Biol 2: E104.
16. Zilberman D, Cao X, Jacobsen SE (2003) ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science 299: 716-719.
17. Li CF, Pontes O, El-Shami M, Henderson IR, Bernatavichute YV, et al. (2006) An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana. Cell 126: 93-106.
18. 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: 791-797.
19. Kanno T, Mette MF, Kreil DP, Aufsatz W, Matzke M, et al. (2004) Involvement of putative SNF2 chromatin remodeling protein DRD1 in RNA-directed DNA methylation. Curr Biol 14: 801-805.
20. Chan SW, Henderson R, Jacobsen SE (2005) Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet 6: 351-360.
21. Henderson IR, Jacobsen SE (2007) Epigenetic Inheritance in Plants. Nature 447: 418-424.
22. Bestor TH (2000) The DNA methyltransferases of mammals. Hum Mol Genet 9: 2395-2402.
23. Finnegan EJ, Kovac KA (2000) Plant DNA methyltransferases. Plant Mol Biol 43: 189-201.
24. Goll MG, Bestor TH (2005) Eukaryotic cytosine methyltransferases. Annu Rev Biochem 74: 481-514.
25. Vongs A, Kakutani T, Martienssen RA, Richards EJ (1993) Arabidopsis thaliana DNA methylation mutants. Science 260: 1926-1928.
26. Kankel MW, Ramsey DE, Stokes TL, Flowers SK, Haag JR, et al. (2003) Arabidopsis MET1 Cytosine Methyltransferase Mutants. Genetics 163: 1109-1122.
27. 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.
28. Woo H, Pontes O, Pickart CM, Richards EJ (2007) VIM1, a methylcytosine-binding protein required for centromeric heterchromatinization. Genes & Dev 21: 267-277.
29. Bostick M, Kim JK, Esteve PO, Clark A, Pradhan S, et al. (2007) UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science 317: 1760-1764.
30. Johnson LM, Bostick M, Zhang X, Kraft E, Henderson IR, et al. (2007) The SRA Methyl-Cytosine-Binding Domain Links DNA and Histone Methylation. Current Biology 17: 379.
31. Sharif J, Muto M, Takebayashi S, Suetake I, Iwamatsu A, et al. (2007) The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. Nature 450: 908-912.
32. Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, et al. (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452: 215-219.
33. Malagnac F, Bartee L, Bender J (2002) An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation. Embo J 21: 6842-6852.
34. Jackson JP, Johnson L, Jasencakova Z, Zhang X, PerezBurgos L, et al. (2004) Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. Chromosoma 112: 308-315.
35. Lindroth AM, Shultis 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.
36. Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, et al. (2005) DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Curr Biol 15: 154-159.
37. 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.
38. Tran RK, Zilberman D, de Bustos C, Ditt RF, Henikoff JG, et al. (2005) Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biol 6: R90.
39. 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.
40. Zilberman D, Henikoff S (2007) Genome-wide analysis of DNA methylation patterns. Development 134: 3959-3965.
41. Turck F, Roudier F, Farrona S, Martin-Magniette M, Guillaume E, et al. (2007) Arabidopsis TFL2/LHP1 Specifically Associates with Genes Marked by Trimethylation of Histone H3 Lysine 27. PLoS Genetics doi:10.1371/ journal.pgen.0030086.eor.
42. Gendrel AV, Lippman Z, Yordan C, Colot V, Martienssen RA (2002) Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science 297: 1871-1873.
43. Johnson L, Cao X, Jacobsen S (2002) Interplay between two epigenetic marks. DNA methylation and histone H3 lysine 9 methylation. Curr Biol 12: 1360-1367.
44. 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.
45. Tariq M, Saze H, Probst AV, Lichota J, Habu Y, et al. (2003) Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin. Proc Natl Acad Sci U S A 100: 8823-8827.
46. 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 Biology 5(5): e129.
47. Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, et al. (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature 430: 471-476.
48. Kent WJ (2002) BLAT-the BLAST-like alignment tool. Genome Res 12: 656-664.
49. Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, et al. (2005) A gene expression map of Arabidopsis thaliana development. Nat Genet 37: 501-506.
50. Matzke MA, Birchler JA (2005) RNAi-mediated pathways in the nucleus. Nat Rev Genet 6: 24-35.
51. Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, et al. (2005) Elucidation of the small RNA component of the transcriptome. Science 309: 1567-1569.