Genome-wide profiling of histone H3 lysine 9 acetylation and dimethylation in arabidopsis reveals correlation between multiple histone marks and gene expression

Plant Molecular Biology

Volumn 72, Issue 6, 2010, Pages 585-595

  Zhou, Junli ^a,b   Wang, Xiangfeng ^a,b   He, Kun ^b,c   Charron, Jean Benoit F ^b   Elling, Axel A ^b,c   Deng, Xing Wang ^a,b,c  

^a NATIONAL INSTITUTE OF BIOLOGICAL SCIENCES   (China)

^b YALE UNIVERSITY   (United States)

^c PEKING UNIVERSITY   (China)

Author keywords

Arabidopsis; Epigenetics; H3K9ac; H3K9me2; Histone modification

Indexed keywords

ARABIDOPSIS;

ARABIDOPSIS PROTEIN; HDA19 PROTEIN, ARABIDOPSIS; HISTONE; HISTONE DEACETYLASE;

ACETYLATION; ARABIDOPSIS; ARTICLE; GENE EXPRESSION REGULATION; GENETIC EPIGENESIS; GENETICS; METABOLISM; METHYLATION; MUTATION; PLANT GENE; PLANT GENOME; TRANSCRIPTION INITIATION; TRANSPOSON;

ACETYLATION; ARABIDOPSIS; ARABIDOPSIS PROTEINS; DNA TRANSPOSABLE ELEMENTS; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENOME, PLANT; HISTONE DEACETYLASES; HISTONES; METHYLATION; MUTATION; TRANSCRIPTIONAL ACTIVATION;

EID: 77954460369     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11103-009-9594-7     Document Type: Article

References (57)

1. Agalioti T, Chen G, Thanos D (2002) Deciphering the transcriptional histone acetylation code for a human gene. Cell 111:381-392
2. Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen H, Shinn P et al (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301:653-657
3. Ausín I, Alonso-Blanco C, Jarillo JA, Ruiz-García L, Martínez-Zapater JM (2004) Regulation of flowering time by FVE, a retinoblastoma-associated protein. Nat Genet 36:162-166
4. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z et al (2007) High-resolution profiling of histone methylations in the human genome. Cell 129:823-837
5. Benhamed M, Bertrand C, Servet C, Zhou DX (2006) Arabidopsis GCN5, HD1, and TAF1/HAF2 interact to regulate histone acetylation required for light-responsive gene expression. Plant Cell 18:2893-2903
6. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Statist Soc Ser B 57:289-300
7. Bernatavichute YV, Zhang X, Cokus S, Pellegrini M, Jacobsen SE (2008) Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana. PLoS ONE 3:e3156
8. Bernstein BE, Humphrey EL, Erlich RL, Schneider R, Bouman P, Liu JS et al (2002) Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci USA 99:8695-8700
9. Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, Huebert DJ et al (2005) Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120:169-181
10. Bowler C, Benvenuto G, Laflamme P, Molino D, Probst AV, Tariq M et al (2004) Chromatin techniques for plant cells. Plant J 39: 776-789
11. Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M et al (2006) DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 38:1378-1385
12. Feng S, Shen Y, Sullivan JA, Rubio V, Xiong Y, Sun TP et al (2004) Arabidopsis CAND1, an unmodified CUL1-interacting protein, is involved in multiple developmental pathways controlled by ubiquitin/proteasome-mediated protein degradation. Plant Cell 16:1870-1882
13. Frank SR, Schroeder M, Fernandez P, Taubert S, Amati B (2001) Binding of c-Myc to chromatin mediates mitogen-induced acetylation of histone H4 and gene activation. Genes Dev 15:2069-2082
14. Fuchs J, Demidov D, Houben A, Schubert I (2006) Chromosomal histone modification patterns-from conservation to diversity. Trends Plant Sci 11:199-208
15. Gartler SM, Varadarajan KR, Luo P, Canfield TK, Traynor J, Francke U et al (2004) Normal histone modifications on the inactive X chromosome in ICF and Rett syndrome cells: implications for methyl-CpG binding proteins. BMC Biol 2:21
16. Hollander M, Wolfe DA (1999) Nonparametric statistical methods. Wiley, New York, pp 228-235
17. Houben A, Demidov D, Gernand D, Meister A, Leach CR, Schubert I (2003) Methylation of histone H3 in euchromatin of plant chromosomes depends on basic nuclear DNA content. Plant J 33:967-973
18. Jenuwein T, Allis CD (2001) Translating the histone code. Science 293:1074-1080
19. Jiao Y, Ma L, Strickland E, Deng XW (2005) Conservation and divergence of ight-Regulated genome Expression Patterns during Seedling Development in Rice and Arabidopsis. Plant Cell 17:3239-3256
20. 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
21. Kondo Y, Shen L, Yan PS, Huang TH, Issa JP (2004) Chromatin immunoprecipitation microarrays for identification of genes silenced by histone H3 lysine 9 methylation. Proc Natl Acad Sci USA 101:7398-7403
22. Kouzarides T (2007) Chromatin modifications and their function. Cell 128:693-705
23. Kuo MH, Zhou J, Jambeck P, Churchill ME, Allis CD (1998) Histone acetyltransferase activity of yeast Gcn5p is required for the activation of target genes in vivo. Genes Dev 12:627-639
24. Kurdistani SK, Tavazoie S, Grunstein M (2004) Mapping global histone acetylation patterns to gene expression. Cell 117:721-733
25. Lee J, He K, Stolc V, Lee H, Figueroa P, Gao Y et al (2007) Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development. Plant Cell 19:731-749
26. Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR et al (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature 430:471-476
27. Liu CL, Kaplan T, Kim M, Buratowski S, Schreiber SL, Friedman N et al (2005) Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol 3:e328
28. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25:402-408
29. Millar CB, Grunstein M (2006) Genome-wide patterns of histone modifications in yeast. Nat Rev Mol Cell Biol 7:657-666
30. Ng DW, Chandrasekharan MB, Hall TC (2006) Ordered histone modifications are associated with transcriptional poising and activation of the phaseolin promoter. Plant Cell 18:119-132
31. Pfluger J, Wagner D (2007) Histone modifications and dynamic regulation of genome accessibility in plants. Curr Opin Plant Biol 10:645-652
32. Pokholok DK, Harbison CT, Levine S, Cole M, Hannett NM, Lee TI et al (2005) Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122:517-527
33. Rao B, Shibata Y, Strahl BD, Lieb JD (2005) Dimethylation of histone H3 at lysine 36 demarcates regulatory and nonregulatory chromatin genome-wide. Mol Cell Biol 25:9447-9459
34. Ren XY, Vorst O, Fiers MW, Stiekema WJ, Nap JP (2006) In plants, highly expressed genes are the least compact. Trends Genet 22:528-532
35. Roh TY, Ngau WC, Cui K, Landsman D, Zhao K (2004) Highresolution genome-wide mapping of histone modifications. Nat Biotechnol 22:1013-1016
36. Roh TY, Cuddapah S, Zhao K (2005) Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Genes Dev 19:542-552
37. Roh TY, Cuddapah S, Cui K, Zhao K (2006) The genomic landscape of histone modifications in human T cells. Proc Natl Acad Sci USA 103:15782-15787
38. Schübeler D, MacAlpine DM, Scalzo D, Wirbelauer C, Kooperberg C, van Leeuwen F et al (2004) The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev 18:1263-1271
39. Sims RJ III, Nishioka K, Reinberg D (2003) Histone lysine methylation: a signature for chromatin function. Trends Genet 19:629-639
40. Sinha I, Wirén M, Ekwall K (2006) Genome-wide patterns of histone modifications in fission yeast. Chromosome Res 14:95-105
41. Smyth GK, Michaud J, Scott HS (2005) Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 21:2067-2075
42. Stolc V, Samanta MP, Tongprasit W, Sethi H, Liang S, Nelson DC et al (2005) Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proc Natl Acad Sci USA 102:4453-4458
43. Tariq M, Saze H, Probst AV, Lichota J, Habu Y, Paszkowski J (2003) Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin. Proc Natl Acad Sci USA 100:8823-8827
44. Tian L, Chen ZJ (2001) Blocking histone deacetylation in Arabidopsis induces pleiotropic effects on plant gene regulation and development. Proc Natl Acad Sci USA 98:200-205
45. Tian L, Wang J, Fong MP, Chen M, Cao H, Gelvin SB et al (2003) Genetic control of developmental changes induced by disruption of Arabidopsis histone deacetylase 1 (HD1) expression. Genetics 165:399-409
46. Turck F, Roudier F, Farrona S, Martin-Magniette ML, Guillaume E, Buisine N et al (2007) Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27. PLoS Genet 3:e86
47. Umlauf D, Goto Y, Cao R, Cerqueira F, Wagschal A, Zhang Y et al (2004) Imprinting along the Kcnq1 domain on mouse chromosome 7 involves repressive histone methylation and recruitment of Polycomb group complexes. Nat Genet 36:1296-1300
48. Verbsky ML, Richards EJ (2001) Chromatin remodeling in plants. Curr Opin Plant Biol 4:494-500
49. Wirén M, Silverstein RA, Sinha I, Walfridsson J, Lee HM, Laurenson P et al (2005) Genomewide analysis of nucleosome density histone acetylation and HDAC function in fission yeast. EMBO J 24:2906-2918
50. Wu K, Malik K, Tian L, Brown D, Miki B (2000) Functional analysis of a RPD3 histone deacetylase homolog in Arabidopsis thaliana. Plant Mol Biol 44:167-176
51. Yan PS, Chen CM, Shi H, Rahmatpanah F, Wei SH, Caldwell CW et al (2001) Dissecting complex epigenetic alterations in breast cancer using CpG island microarrays. Cancer Res 61:8375-8380
52. Zhang Y, Fatima N, Dufau ML (2005) Coordinated changes in DNA methylation and histone modifications regulate silencing/derepression of luteinizing hormone receptor gene transcription. Mol Cell Biol 25:7929-7939
53. Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H et al (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126: 1189-1201
54. Zhang X, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, Goodrich J et al (2007) Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol 5:e129
55. Zhao W, Soejima H, Higashimoto K, Nakagawachi T, Urano T, Kudo S et al (2005) The essential role of histone H3 Lys9 di-methylation and MeCP2 binding in MGMT silencing with poor DNA methylation of the promoter CpG island. J Biochem 137:431-440
56. Zilberman D, Cao X, Jacobsen SE (2003) ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science 299:716-719
57. Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S (2007) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 39:61-69