Histone modifications and expression of light-regulated genes in arabidopsis are cooperatively influenced by changing light conditions

Plant Physiology

Volumn 147, Issue 4, 2008, Pages 2070-2083

  Guo, Lan ^a,b   Zhou, Junli ^b   Elling, Axel A ^c   Charron, Jean Benoit F ^c   Xing, Wang Deng ^a,b,c  

^a PEKING UNIVERSITY   (China)

^b NATIONAL INSTITUTE OF BIOLOGICAL SCIENCES   (China)

^c YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA;

ARABIDOPSIS PROTEIN; HD1 PROTEIN, ARABIDOPSIS; HISTONE; HISTONE DEACETYLASE; MESSENGER RNA;

ACETYLATION; ARABIDOPSIS; ARTICLE; DARKNESS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; LIGHT; METABOLISM; PHOTOSYNTHESIS; PHYSIOLOGY; RADIATION EXPOSURE; SEEDLING;

ACETYLATION; ARABIDOPSIS; ARABIDOPSIS PROTEINS; DARKNESS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; HISTONE DEACETYLASES; HISTONES; LIGHT; PHOTOSYNTHETIC REACTION CENTER COMPLEX PROTEINS; RNA, MESSENGER; SEEDLING;

EID: 53749104815     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.108.122929     Document Type: Article

References (68)

1. Agalioti T, Lomvardas S, Parekh B, Yie J, Maniatis T, Thanos D (2000) Ordered recruitment of chromatin modifying and general transcription factors to the IFN-beta promoter. Cell 103: 667-678
2. Ahmad K, Henikoff S (2002) The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol Cell 9: 1191-1200
3. Ang LH, Chattopadhyay S, Wei N, Oyama T, Okada K, Batschauer A, Deng XW (1998) Molecular interaction between COP1 and HY5 defines a regulatory switch for light control of Arabidopsis development. Mol Cell 1: 213-222
4. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K (2007) High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837
5. Bastow R, Mylne JS, Lister C, Lippman Z, Martienssen RA, Dean C (2004) Vernalization requires epigenetic silencing of FLC by histone methylation. Nature 427: 164-167
6. 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
7. Benvenuto G, Formiggini F, Laflamme P, Malakhov M, Bowler C (2002) The photomorphogenesis regulator DET1 binds the amino-terminal tail of histone H2B in a nucleosome context. Curr Biol 12: 1529-1534
8. Bernstein BE, Tong JK, Schreiber SL (2000) Genomewide studies of histone deacetylase function in yeast. Proc Natl Acad Sci USA 97: 13708-13713
9. Bertrand C, Benhamed M, Li YF, Ayadi M, Lemonnier G, Renou JP, Delarue M, Zhou DX (2005) Arabidopsis HAF2 gene encoding TATA-binding protein (TBP)-associated factor TAF1, is required to integrate light signals to regulate gene expression and growth. J Biol Chem 280: 1465-1473
10. Chattopadhyay S, Ang LH, Puente P, Deng XW, Wei N (1998) Arabidopsis bZIP protein HY5 directly interacts with light-responsive promoters in mediating light control of gene expression. Plant Cell 10: 673-683
11. Chen ZJ, Tian L (2007) Roles of dynamic and reversible histone acetylation in plant development and polyploidy. Biochim Biophys Acta 1769: 295-307
12. Chory J, Peto CA (1990) Mutations in the DET1 gene affect cell-type-specific expression of light-regulated genes and chloroplast development in Arabidopsis. Proc Natl Acad Sci USA 87: 8776-8780
13. Chua YL, Brown AP, Gray JC (2001) Targeted histone acetylation and altered nuclease accessibility over short regions of the pea plastocyanin gene. Plant Cell 13: 599-612
14. Chua YL, Mott E, Brown AP, MacLean D, Gray JC (2004) Microarray analysis of chromatin-immunoprecipitated DNA identifies specific regions of tobacco genes associated with acetylated histones. Plant J 37: 789-800
15. Chua YL, Watson LA, Gray JC (2003) The transcriptional enhancer of the pea plastocyanin gene associates with the nuclear matrix and regulates gene expression through histone acetylation. Plant Cell 15: 1468-1479
16. Deng XW, Caspar T, Quail PH (1991) cop1: a regulatory locus involved in light-controlled development and gene expression in Arabidopsis. Genes Dev 5: 1172-1182
17. Devlin PF, Patel SR, Whitelam GC (1998) Phytochrome E influences internode elongation and flowering time in Arabidopsis. Plant Cell 10: 1479-1487
18. Devlin PF, Robson PR, Patel SR, Goosey L, Sharrock RA, Whitelam GC (1999) Phytochrome D acts in the shade-avoidance syndrome in Arabidopsis by controlling elongation growth and flowering time. Plant Physiol 119: 909-915
19. Dion MF, Altschuler SJ, Wu LF, Rando OJ (2005) Genomic characterization reveals a simple histone H4 acetylation code. Proc Natl Acad Sci USA 102: 5501-5506
20. Fankhauser C, Chory J (1997) Light control of plant development. Annu Rev Cell Dev Biol 13: 203-229
21. Folta KM, Kaufman LS (2006) Isolation of Arabidopsis nuclei and measurement of gene transcription rates using nuclear run-on assays. Nat Protocols 1: 3094-3100
22. 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
23. Garcia-Bassets I, Kwon YS, Telese F, Prefontaine GG, Hutt KR, Cheng CS, Ju BG, Ohgi KA, Wang J, Escoubet-Lozach L, et al (2007) Histone methylation-dependent mechanisms impose ligand dependency for gene activation by nuclear receptors. Cell 128: 505-518
24. Gendrel AV, Lippman Z, Martienssen R, Colot V (2005) Profiling histone modification patterns in plants using genomic tiling microarrays. Nat Methods 2: 213-218
25. He Y, Michaels SD, Amasino RM (2003) Regulation of flowering time by histone acetylation in Arabidopsis. Science 302: 1751-1754
26. Holm M, Deng XW (1999) Structural organization and interactions of COP1, a light-regulated developmental switch. Plant Mol Biol 41: 151-158
27. Holm M, Ma LG, Qu LJ, Deng XW (2002) Two interacting bZIP proteins are direct targets of COP1-mediated control of light-dependent gene expression in Arabidopsis. Genes Dev 16: 1247-1259
28. Jenuwein T, Allis CD (2001) Translating the histone code. Science 293: 1074-1080
29. Jiao Y, Lau OS, Deng XW (2007) Light-regulated transcriptional networks in higher plants. Nat Rev Genet 8: 217-230
30. Jiao Y, Ma L, Strickland E, Deng XW (2005) Conservation and divergence of light-regulated genome expression patterns during seedling development in rice and Arabidopsis. Plant Cell 17: 3239-3256
31. Kouzarides T (2007) Chromatin modifications and their function. Cell 128: 693-705
32. Kurdistani SK, Robyr D, Tavazoie S, Grunstein M (2002) Genome-wide binding map of the histone deacetylase Rpd3 in yeast. Nat Genet 31: 248-254
33. Kurdistani SK, Tavazoie S, Grunstein M (2004) Mapping global histone acetylation patterns to gene expression. Cell 117: 721-733
34. Lee DY, Hayes JJ, Pruss D, Wolffe AP (1993) A positive role for histone acetylation in transcription factor access to nucleosomal DNA. Cell 72: 73-84
35. Lee J, He K, Stolc V, Lee H, Figueroa P, Gao Y, Tongprasit W, Zhao H, Lee I, Deng XW (2007) Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development. Plant Cell 19: 731-749
36. Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouzé P, Rombauts S (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res 30: 325-327
37. Li B, Carey M, Workman JL (2007) The role of chromatin during transcription. Cell 128: 707-719
38. Loidl P (2004) A plant dialect of the histone language. Trends Plant Sci 9: 84-90
39. Ma L, Li J, Qu L, Hager J, Chen Z, Zhao H, Deng XW (2001) Light control of Arabidopsis development entails coordinated regulation of genome expression and cellular pathways. Plant Cell 13: 2589-2607
40. Ma L, Zhao H, Deng XW (2003) Analysis of the mutational effects of the COP/DET/FUS loci on genome expression profiles reveals their overlapping yet not identical roles in regulating Arabidopsis seedling development. Development 130: 969-981
41. McNellis TW, von Arnim AG, Araki T, Komeda Y, Misera S, Deng XW (1994) Genetic and molecular analysis of an allelic series of cop1 mutants suggests functional roles for the multiple protein domains. Plant Cell 6: 487-500
42. Millar CB, Grunstein M (2006) Genome-wide patterns of histone modifications in yeast. Nat Rev Mol Cell Biol 7: 657-666
43. Mockler TC, Guo H, Yang H, Duong H, Lin C (1999) Antagonistic actions of Arabidopsis cryptochromes and phytochrome B in the regulation of floral induction. Development 126: 2073-2082
44. Ni M, Tepperman JM, Quail PH (1998) PIF3, a phytochrome- interacting factor necessary for normal photoinduced signal transduction, is a novel basic helix-loop-helix protein. Cell 95: 657-667
45. Osterlund MT, Hardtke CS, Wei N, Deng XW (2000) Targeted destabilization of HY5 during light-regulated development of Arabidopsis. Nature 405: 462-466
46. Oyama T, Shimura Y, Okada K (1997) The Arabidopsis HY5 gene encodes a bZIP protein that regulates stimulus-induced development of root and hypocotyl. Genes Dev 11: 2983-2995
47. Pandey R, Muller A, Napoli CA, Selinger DA, Pikaard CS, Richards EJ, Bender J, Mount DW, Jorgensen RA (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
48. Pavri R, Zhu B, Li G, Trojer P, Mandal S, Shilatifard A, Reinberg D (2006) Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II. Cell 125: 703-717
49. Pepper A, Delaney T, Washburn T, Poole D, Chory J (1994) DET1, a negative regulator of light-mediated development and gene expression in Arabidopsis, encodes a novel nuclear-localized protein. Cell 78: 109-116
50. Rockwell NC, Su YS, Lagarias JC (2006) Phytochrome structure and signaling mechanisms. Annu Rev Plant Biol 57: 837-858
51. Saijo Y, Sullivan JA, Wang H, Yang J, Shen Y, Rubio V, Ma L, Hoecker U, Deng XW (2003) The COP1-SPA1 interaction defines a critical step in phytochrome A-mediated regulation of HY5 activity. Genes Dev 17: 2642-2647
52. Schroeder DF, Gahrtz M, Maxwell BB, Cook RK, Kan JM, Alonso JM, Ecker JR, Chory J (2002) De-etiolated 1 and damaged DNA binding protein 1 interact to regulate Arabidopsis photomorphogenesis. Curr Biol 12: 1462-1472
53. Somers DE, Sharrock RA, Tepperman JM, Quail PH (1991) The hy3 long hypocotyl mutant of Arabidopsis is deficient in phytochrome B. Plant Cell 3: 1263-1274
54. Sung S, Amasino RM (2004) Vernalization and epigenetics: how plants remember winter. Curr Opin Plant Biol 7: 4-10
55. Tessadori F, Kees Schulkes R, van Dreil R, Fransz P (2007) Light-regulated large-scale reorganization of chromatin during the floral transition in Arabidopsis. Plant J 50: 848-857
56. Thomas B (2006) Light signals and flowering. J Exp Bot 57: 3387-3393
57. 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
58. Tian L, Fong MP, Wang JJ, Wei NE, Jiang H, Doerge RW, Chen ZJ (2005) Reversible histone acetylation and deacetylation mediate genome-wide, promoter-dependent and locus-specific changes in gene expression during plant development. Genetics 169: 337-345
59. Tian L, Wang J, Fong MP, Chen M, Cao H, Gelvin SB, Chen ZJ (2003) Genetic control of developmental changes induced by disruption of Arabidopsis histone deacetylase 1 (AtHD1) expression. Genetics 165: 399-409
60. Wagner D (2003) Chromatin regulation of plant development. Curr Opin Plant Biol 6: 20-28
61. Wang H, Ma L, Habashi J, Li J, Zhao H, Deng XW (2002) Analysis of farred light-regulated genome expression profiles of phytochrome A pathway mutants in Arabidopsis. Plant J 32: 723-733
62. Wei N, Kwok SF, von Arnim AG, Lee A, McNellis TW, Piekos B, Deng XW (1994) Arabidopsis COP8, COP10, and COP11 genes are involved in repression of photomorphogenic development in darkness. Plant Cell 6: 629-643
63. Whitelam GC, Patel S, Devlin PF (1998) Phytochromes and photomorphogenesis in Arabidopsis. Philos Trans R Soc Lond B Biol Sci 353: 1445-1453
64. Wolffe AP, Hayes JJ (1999) Chromatin disruption and modification. Nucleic Acids Res 27: 711-720
65. 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
66. Yanagawa Y, Sullivan JA, Komatsu S, Gusmaroli G, Suzuki G, Yin J, Ishibashi T, Saijo Y, Rubio V, Kimura S, et al (2004) Arabidopsis COP10 forms a complexwith DDB1 and DET1 in vivo and enhances the activity of ubiquitin conjugating enzymes. Genes Dev 18: 2172-2181
67. Zhang K, Sridhar VV, Zhu J, Kapoor A, Zhu JK (2007a) Distinctive core histone post-translational modification patterns in Arabidopsis thaliana. PLoS One 11: e1210
68. Zhang X, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, Goodrich J, Jacobsen SE (2007b) Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol 5: e129