Regulatory mechanism of histone epigenetic modifications in plants

Epigenetics

Volumn 4, Issue 1, 2009, Pages 15-18

  Zhou, Dao Xiu ^a  

^a INSTITUTE OF PLANT SCIENCES PARIS SACLAY IPS2   (France)

Author keywords

Chromatin; Demethylation; Histone acetylation; Methylation; Plant

Indexed keywords

HISTONE; HISTONE H3; LYSINE; SMALL INTERFERING RNA;

ARTICLE; CELL DIFFERENTIATION; CELL DIVISION; DNA METHYLATION; DNA MODIFICATION; DNA RNA HYBRIDIZATION; ENZYME MODIFICATION; EPIGENETICS; EUCHROMATIN; GENE EXPRESSION; GENE REPRESSION; HETEROCHROMATIN; INHERITANCE; NONHUMAN; PLANT CELL; PLANT DEVELOPMENT; PLANT GENETICS; PLANT GENOME; PROTEIN FUNCTION; PROTEIN METHYLATION; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING; REGULATORY MECHANISM; RNA INTERFERENCE; SEQUENCE HOMOLOGY; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION;

EID: 66349127923     PISSN: 15592294     EISSN: 15592308     Source Type: Journal    
DOI: 10.4161/epi.4.1.7371     Document Type: Article

References (44)

1. Kouzarides T. Chromatin modifications and their function. Cell 2007; 128:693-705.
2. Shahbazian MD, Grunstein M. Function of site-specific histone acetylation and deacetylation Ann Rev Biochem 2007; 76:75-100.
3. Cloos PA, Christensen J, Agger K, Helin K. Erasing the methyl mark: histone demethylases at the center of cellular differentiation and disease. Genes Dev 2008; 22:1115-40.
4. Shi Y, Lan F, Matson C, Mulligan P, Whetstine JR, Cole PA, et al. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 2004; 119:941-53.
5. Zhang K, Scidar VV, Zhu J, Kapoor A, Zhu JK. Distinctive core histone post-translational modification patterns in Arabidopsis thaliana. PlosONe 2007; 2:1210.
6. Earley KW, Shook MS, Brower-Toland B, Hicks L, Pikaard CS. In vitro specificities of Arabidopsis co-activator histone acetyltransferases: implications for histone hyperacetylation in gene activation. Plant J 2007; 52:615-26.
7. Benhamed M, Bertrand C, Servet C, Zhou DX. Arabidopsis GCN5, HD1 and TAF1/HAF2 interact to regulate histone acetylation required for light-responsive gene expression. Plant Cell 2006; 18:2893-903.
8. Ausín I, Alonso-Blanco C, Jarillo JA, Ruiz-García L, Martínez-Zapater JM. Regulation of flowering time by FVE, a retinoblastoma-associated protein. Nat Genet 2004; 36:162-6.
9. Ng DW, Chandrasekharan MB, Hall TC. Ordered histone modifications are associated withtranscriptional poising and activation of the phaseolin promoter. Plant Cell 2006; 18:119-32.
10. Servet C, Benhamed M, Latrasse D, Kim W, Delarue M, Zhou DX. Characterization of a phosphatase 2C protein as an interacting partner of the histone acetyltransferase GCN5 in Arabidopsis. Biochim Biophys Acta 2008; 1779:376-82.
11. Turck F, Roudier F, Farrona S, Martin-Magniette ML, Guillaume E, Buisine N, et al. Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27. PLoS Genet 2007; 3:86.
12. Zhang X, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, Goodrich J, et al. Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol 2007; 5:129.
13. Pandey R, Muller A, Napoli CA, Selinger DA, Pikaard CS, et al. Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Res 2002; 30:5036-55.
14. Vlachonasios KE, Thomashow MF, Triezenberg SJ. Disruption mutations of ADA2b and GCN5 transcriptional adaptor genes dramatically affect Arabidopsis growth, development and gene expression. Plant Cell 2003; 15:626-38.
15. Bertrand C, Bergounioux C, Domenichini S, Delarue M, Zhou DX. Arabidopsis histone acetyltransferase AtGCN5 regulates the floral meristem activity through the WUSCHEL/AGAMOUS Pathway. J Biol Chem 2003; 278:28246-51.
16. Benhamed M, Martin-Magniette ML, Taconnat L, Bitton F, Servet C, et al. Genome-scale Arabidopsis promoter array identifies targets of the histone acetyltransferase GCN5. Plant J 2008; 56:493-504. Epub 2008.
17. Lusser A, Brosch G, Loidl A, Haas H and Loidl P. Identification of maize histone deacetylase HD2 as an acidic nucleolar phosphoprotein. Science 1997; 277:88-91.
18. Tian L, Fong MP, Wang JJ, Wei NE, Jiang H, Doerge RW, et al. Reversible histone acetylation and deacetylation mediate genome-wide, promoter-dependent and locus-specific changes in gene expression during plant development. Genetics 2005; 169:337-45.
19. Tian L, Chen ZJ. Blocking histone deacetylation in Arabidopsis induces pleiotropic effects on plant gene regulation and development. Proc Natl Acad Sci USA 2001; 98:200-5.
20. Frye RA. Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins. Biochem Biophys Res Commun 2000; 273:793-8.
21. Huang L, Sun Q, Qin F, Li C, Zhao Y, Zhou DX. Downregulation of a Silent Information Regulator2-related gene induces DNA fragmentation and cell death in rice. Plant Physiol 2007; 144:1508-19.
22. Jackson JP, Lindroth AM, Cao X, Jacobsen SE. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 2002; 416:556-60.
23. Ebbs ML, Bartee L and Bender J. H3 lysine 9 methylation is maintained on a transcribed inverted repeat by combined action of SUVH6 and SUVH4 methyltransferases. Mol Cell Biol 2005; 25:10507-15.
24. Naumann K, Fischer A, Hofmann I, Krauss V, Phalke S, Irmler K, et al. Pivotal role of AtSUVH2 in heterochromatic histone methylation and gene silencing in Arabidopsis. EMBO J 2005; 24:1418-29.
25. Ebbs ML, Bender J. Locus-specific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase. Plant Cell 2006; 18:1166-76.
26. Ding Y, Wang X, Su L, Zhai J, et al. SDG714, a histone H3K9 methyltransferase, is involved in Tos17 DNA methylation and transposition in rice. Plant Cell 2007; 19:9-22.
27. Pien S, Grossniklaus U. Polycomb group and trithorax group proteins in Arabidopsis. Biochim Biophys Acta 2007; 1769:375-82.
28. Makarevich G, Leroy O, Akinci U, Schubert D, Clarenz O, Goodrich J, et al. Different polycomb group complexes regulate common target genes in Arabidopsis. EMBO Rep 2006; 7:947-52.
29. Köhler C, Hennig L, Spillane C, Pien S, Gruissem W, Grossniklaus U. The Polycomb-group protein MEDEA regulates seed development by controlling expression of the MADS-box gene PHERES1. Genes Dev 2003; 17:1540-53.
30. Zhang H, Rider SD, Henderson JT, et al. The CHD3 remodeler PICKLE promotes trimethylation of histone H3 lysine 27. J Biol Chem 2008; 283:22637-48.
31. Jiang D, Yang W, He Y, Amasino RM. Arabidopsis relatives of the human lysine-specific Demethylase1 repress the expression of FWA and FLOWERING LOCUS C and thus promote the floral transition. Plant Cell 2007; 19:2975-87.
32. Sun Q and Zhou DX. The rice jmjC domain-containing gene JMJ706 encodes a histone H3 lysine 9 (H3K9) demethylase required for floral organ development. Proc Natl Acad Sci USA 2008; 105:13679-84.
33. Soppe WJ, Jasencakova Z, Houben A, Kakutani T, Meister A, Huang MS, et al. DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J 2002; 21:6549-59.
34. Tariq M, Saze H, Probst AV, Lichota J, Habu Y, Paszkowski J. Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin. Proc Natl Acad Sci USA 2003; 100:8823-7.
35. Mathieu O, Probst AV, Paszkowski J. Distinct regulation of histone H3 methylation at lysines 27 and 9 by CpG methylation in Arabidopsis. EMBO J 2005; 24:2783-91.
36. Gendrel AV, Lippman Z, Yordan C, Colot V, Martienssen RA. Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science 2002; 297:1871-3.
37. Johnson LM, Bostick M, Zhang X, Kraft E, Henderson I, Callis J, Jacobsen SE. The SRA methyl-cytosine-binding domain links DNA and histone methylation. Curr Biol 2007; 17:379-84.
38. Lindroth AM, Shultis D, Jasencakova Z, Fuchs J, Johnson L, Schubert D, et al. Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J 2004; 23:4286-96.
39. Saze H, Shiraishi A, Miura A and Kakutani T. Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana. Science 2008; 319:462-5.
40. Matzke M, Kanno T, Huettel B, Daxinger L, Matzke AJ. Targets of RNA-directed DNA methylation. Curr Opin Plant Biol 2007; 10:512-9.
41. Aufsatz W, Mette MF, van der Winden J, Matzke M and Matzke AJ. HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double-stranded RNA. EMBO J 2002; 21:6832-41.
42. Eraley K, Lawrence RJ, Pontes O, Ruether R, Enciso AJ, Silva M, et al. Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale gene silencing in nucleolar dominance. Genes Dev 2006; 20:1283-93.
43. Grewal SI, Jia S. Heterochromatin revisited. Nat Rev Genet 2007; 8:35-46.
44. Zhou C, Zhang L, Duan J, Miki B, Wu K. HISTONE DEACETYLASE19 is involved in jasmonic acid and ethylene signaling of pathogen response in Arabidopsis. Plant Cell 2005; 17:1196-204.