Histone modifications in transcriptional activation during plant development

Biochimica et Biophysica Acta - Gene Regulatory Mechanisms

Volumn 1809, Issue 10, 2011, Pages 567-576

  Berr, Alexandre ^a   Shafiq, Sarfraz ^a   Shen, Wen Hui ^a  

^a UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

Arabidopsis thaliana; Epigenetic regulation; FLC transcription; Histone acetylation; Histone methylation; Histone monoubiquitination

Indexed keywords

LYSINE; RNA POLYMERASE II;

ARABIDOPSIS; CELL DIFFERENTIATION; DEMETHYLATION; ENVIRONMENTAL STRESS; EVOLUTIONARY ADAPTATION; GAMETOGENESIS; GENE EXPRESSION; GENE FUNCTION; HISTONE ACETYLATION; HISTONE METHYLATION; HISTONE MODIFICATION; HISTONE UBIQUITINATION; NONHUMAN; PLANT DEVELOPMENT; PLANT RESPONSE; PRIORITY JOURNAL; REPRESSOR GENE; REVIEW; TRANSCRIPTION INITIATION;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CHROMATIN; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION, PLANT; HISTONES; METHYLATION; PLANTS; RNA POLYMERASE II; TRANSCRIPTIONAL ACTIVATION; UBIQUITIN;

ARABIDOPSIS; ARABIDOPSIS THALIANA; EUKARYOTA;

EID: 80053435772     PISSN: 18749399     EISSN: 18764320     Source Type: Journal    
DOI: 10.1016/j.bbagrm.2011.07.001     Document Type: Review

References (138)

1. Andrews A.J., Luger K. Nucleosome structure(s) and stability: variations on a theme. Annu. Rev. Biophys. 2011, 40:99-117.
2. Nelissen H., Boccardi T.M., Himanen K., Van Lijsebettens M. Impact of core histone modifications on transcriptional regulation and plant growth. Crit. Rev. Plant Sci. 2007, 26:243-263.
3. Shen W.-H., Xu L. Chromatin remodeling in stem cell maintenance in Arabidopsis thaliana. Mol. Plant 2009, 2:600-609.
4. Alvarez M.E., Nota F., Cambiagno D.A. Epigenetic control of plant immunity. Mol. Plant Pathol. 2010, 11:563-576.
5. Berr A., Shen W.H. Molecular mechanisms in epigenetic regulation of plant growth and development. Plant Developmental Biology-Biotechnological Perspectives 2010, Vol. 2:325-344.
6. Strahl B.D., Allis C.D. The language of covalent histone modifications. Nature 2000, 403:41-45.
7. Roudier F., Teixeira F.K., Colot V. Chromatin indexing in Arabidopsis: an epigenomic tale of tails and more. Trends Genet. 2009, 25:511-517.
8. Lee K.K., Workman J.L. Histone acetyltransferase complexes: one size doesn't fit all. Nat. Rev. Mol. Cell Biol. 2007, 8:284-295.
9. Earley K.W., Shook M.S., Brower-Toland B., Hicks L., Pikaard C.S. In vitro specificities of Arabidopsis co-activator histone acetyltransferases: implications for histone hyperacetylation in gene activation. Plant J. 2007, 52:615-626.
10. Zhang K., Sridhar V.V., Zhu J., Kapoor A., Zhu J.-K. Distinctive core histone post-translational modification patterns in Arabidopsis thaliana. PLoS ONE 2007, 2:e1210.
11. Bertrand C., Bergounioux C., Domenichini S., Delarue M., Zhou D.-X. Arabidopsis histone acetyltransferase AtGCN5 regulates the floral meristem activity through the WUSCHEL/AGAMOUS pathway. J. Biol. Chem. 2003, 278:28246-28251.
12. Benhamed M., Bertrand C., Servet C., Zhou D.-X. Arabidopsis GCN5, HD1, and TAF1/HAF2 interact to regulate histone acetylation required for light-responsive gene expression. Plant Cell 2006, 18:2893-2903.
13. Mao Y., Pavangadkar K.A., Thomashow M.F., Triezenberg S.J. Physical and functional interactions of Arabidopsis ADA2 transcriptional coactivator proteins with the acetyltransferase GCN5 and with the cold-induced transcription factor CBF1. Biochim. Biophys. Acta (BBA) Gene Struct. Expr. 2006, 1759:69-79.
14. Stockinger E.J., Mao Y., Regier M.K., Triezenberg S.J., Thomashow M.F. Transcriptional adaptor and histone acetyltransferase proteins in Arabidopsis and their interactions with CBF1, a transcriptional activator involved in cold-regulated gene expression. Nucleic Acids Res. 2001, 29:1524-1533.
15. Benhamed M., Martin-Magniette M.-L., Taconnat L., Bitton F., Servet C., De Clercq R., De Meyer B., Buysschaert C., Rombauts S., Villarroel R., Aubourg S., Beynon J., Bhalerao R.P., Coupland G., Gruissem W., Menke F.L.H., Weisshaar B., Renou J.-P., Zhou D.-X., Hilson P. Genome-scale Arabidopsis promoter array identifies targets of the histone acetyltransferase GCN5. Plant J. 2008, 56:493-504.
16. Nelissen H., De Groeve S., Fleury D., Neyt P., Bruno L., Bitonti M.B., Vandenbussche F., Van der Straeten D., Yamaguchi T., Tsukaya H., Witters E., De Jaeger G., Houben A., Van Lijsebettens M. Plant Elongator regulates auxin-related genes during RNA polymerase II transcription elongation. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:1678-1683.
17. Sanmartin M., Sauer M., Munoz A., Zouhar J., Ordonez A., van de Ven W.T., Caro E., de la Paz Sanchez M., Raikhel N.V., Gutierrez C., Sanchez-Serrano J.J., Rojo E. A molecular switch for initiating cell differentiation in Arabidopsis. Curr. Biol. 2011, 21:999-1008.
18. Bordoli L., Netsch M., Lüthi U., Lutz W., Eckner R. Plant orthologs of p300/CBP: conservation of a core domain in metazoan p300/CBP acetyltransferase-related proteins. Nucleic Acids Res. 2001, 29:589-597.
19. Bertrand C., Benhamed M., Li Y.-F., Ayadi M., Lemonnier G., Renou J.-P., Delarue M., Zhou D.-X. 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. 2005, 280:1465-1473.
20. Pandey R., Müller A., Napoli C.A., Selinger D.A., Pikaard C.S., Richards E.J., Bender J., Mount D.W., Jorgensen R.A. Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Res. 2002, 30:5036-5055.
21. Fong P.M., Tian L., Chen Z.J. Arabidopsis thaliana histone deacetylase 1 (AtHD1) is localized in euchromatic regions and demonstrates histone deacetylase activity in vitro. Cell Res. 2006, 16:479-488.
22. Tian L., Chen Z.J. Blocking histone deacetylation in Arabidopsis induces pleiotropic effects on plant gene regulation and development. Proc. Natl. Acad. Sci. U. S. A. 2001, 98:200-205.
23. Tian L., Wang J., Fong M.P., Chen M., Cao H., Gelvin S.B., Chen Z.J. Genetic control of developmental changes induced by disruption of Arabidopsis Histone Deacetylase 1 (AtHD1) expression. Genetics 2003, 165:399-409.
24. Tian L., Fong M.P., Wang J.J., Wei N.E., Jiang H., Doerge R.W., Chen Z.J. Reversible histone acetylation and deacetylation mediate genome-wide, promoter-dependent and locus-specific changes in gene expression during plant development. Genetics 2005, 169:337-345.
25. 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, 17:1196-1204.
26. Earley K., Lawrence R.J., Pontes O., Reuther R., Enciso A.J., Silva M., Neves N., Gross M., Viegas W., Pikaard C.S. Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale gene silencing in nucleolar dominance. Genes Dev. 2006, 20:1283-1293.
27. Probst A.V., Fagard M., Proux F., Mourrain P., Boutet S., Earley K., Lawrence R.J., Pikaard C.S., Murfett J., Furner I., Vaucheret H., Scheid O.M. Arabidopsis histone deacetylase HDA6 is required for maintenance of transcriptional gene silencing and determines nuclear organization of rDNA repeats. Plant Cell 2004, 16:1021-1034.
28. Aufsatz W., Mette M.F., van der Winden J., Matzke M., Matzke A.J.M. HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double-stranded RNA. EMBO J. 2002, 21:6832-6841.
29. Lippman Z., May B., Yordan C., Singer T., Martienssen R. Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS Biol. 2003, 1:e67.
30. May B.P., Lippman Z.B., Fang Y., Spector D.L., Martienssen R.A. Differential regulation of strand-specific transcripts from Arabidopsis centromeric satellite repeats. PLoS Genet. 2005, 1:e79.
31. Murfett J., Wang X.-J., Hagen G., Guilfoyle T.J. Identification of Arabidopsis histone deacetylase HDA6 mutants that affect transgene expression. Plant Cell 2001, 13:1047-1061.
32. Xu C.-R., Liu C., Wang Y.-L., Li L.-C., Chen W.-Q., Xu Z.-H., Bai S.-N. Histone acetylation affects expression of cellular patterning genes in the Arabidopsis root epidermis. Proc. Natl. Acad. Sci. U. S. A. 2005, 102:14469-14474.
33. Dangl M., Brosch G., Haas H., Loidl P., Lusser A. Comparative analysis of HD2 type histone deacetylases in higher plants. Planta 2001, 213:280-285.
34. Lusser A., Brosch G., Loidl A., Haas H., Loidl P. Identification of maize histone deacetylase HD2 as an acidic nucleolar phosphoprotein. Science 1997, 277:88-91.
35. Wu K., Tian L., Malik K., Brown D., Miki B. Functional analysis of HD2 histone deacetylase homologues in Arabidopsis thaliana. Plant J. 2000, 22:19-27.
36. Wu K., Tian L., Zhou C., Brown D., Miki B. Repression of gene expression by Arabidopsis HD2 histone deacetylases. Plant J. 2003, 34:241-247.
37. Zhou C., Labbe H., Sridha S., Wang L., Tian L., Latoszek-Green M., Yang Z., Brown D., Miki B., Wu K. Expression and function of HD2-type histone deacetylases in Arabidopsis development. Plant J. 2004, 38:715-724.
38. Lawrence R.J., Earley K., Pontes O., Silva M., Chen Z.J., Neves N., Viegas W., Pikaard C.S. A concerted DNA methylation/histone methylation switch regulates rRNA gene dosage control and nucleolar dominance. Mol. Cell 2004, 13:599-609.
39. Wang C., Gao F., Wu J., Dai J., Wei C., Li Y. Arabidopsis putative deacetylase AtSRT2 regulates basal defense by suppressing PAD4, EDS5 and SID2 expression. Plant Cell Physiol. 2010, 51:1291-1299.
40. Pickart C.M. Mechanisms underlying ubiquitination. Annu. Rev. Biochem. 2001, 70:503-533.
41. Smalle J., Vierstra R.D. The ubiquitin 26s proteasome proteolytic pathway. Annu. Rev. Plant Biol. 2004, 55:555-590.
42. Xu P., Duong D.M., Seyfried N.T., Cheng D., Xie Y., Robert J., Rush J., Hochstrasser M., Finley D., Peng J. Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation. Cell 2009, 137:133-145.
43. Hicke L. Protein regulation by monoubiquitin. Nat. Rev. Mol. Cell Biol. 2001, 2:195-201.
44. Zhang Y. Transcriptional regulation by histone ubiquitination and deubiquitination. Genes Dev. 2003, 17:2733-2740.
45. Weake V.M., Workman J.L. Histone ubiquitination: triggering gene activity. Mol. Cell 2008, 29:653-663.
46. Bratzel F., López-Torrejón G., Koch M., Del Pozo J.C., Calonje M. Keeping cell identity in Arabidopsis requires PRC1 RING-finger homologs that catalyze H2A monoubiquitination. Curr. Biol. 2010, 20:1853-1859.
47. Chen D., Molitor A., Liu C., Shen W.-H. The Arabidopsis PRC1-like ring-finger proteins are necessary for repression of embryonic traits during vegetative growth. Cell Res. 2010, 20:1332-1344.
48. Xu L., Shen W.-H. Polycomb silencing of KNOX genes confines shoot stem cell niches in Arabidopsis. Curr. Biol. 2008, 18:1966-1971.
49. Fleury D., Himanen K., Cnops G., Nelissen H., Boccardi T.M., Maere S., Beemster G.T.S., Neyt P., Anami S., Robles P., Micol J.L., Inzé D., Van Lijsebettens M. The Arabidopsis thaliana homolog of yeast BRE1 has a function in cell cycle regulation during early leaf and root growth. Plant Cell 2007, 19:417-432.
50. Liu Y., Koornneef M., Soppe W.J.J. The absence of histone H2B monoubiquitination in the Arabidopsis hub1 (rdo4) mutant reveals a role for chromatin remodeling in seed dormancy. Plant Cell 2007, 19:433-444.
51. Xu L., Ménard R., Berr A., Fuchs J., Cognat V., Meyer D., Shen W.-H. The E2 ubiquitin-conjugating enzymes, AtUBC1 and AtUBC2, play redundant roles and are involved in activation of FLC expression and repression of flowering in Arabidopsis thaliana. Plant J. 2009, 57:279-288.
52. Cao Y., Dai Y., Cui S., Ma L. Histone H2B monoubiquitination in the chromatin of FLOWERING LOCUS C regulates flowering time in Arabidopsis. Plant Cell 2008, 20:2586-2602.
53. Gu X., Jiang D., Wang Y., Bachmair A., He Y. Repression of the floral transition via histone H2B monoubiquitination. Plant J. 2009, 57:522-533.
54. Liu Y., Wang F., Zhang H., He H., Ma L., Deng X.W. Functional characterization of the Arabidopsis ubiquitin-specific protease gene family reveals specific role and redundancy of individual members in development. Plant J. 2008, 55:844-856.
55. Yan N., Doelling J.H., Falbel T.G., Durski A.M., Vierstra R.D. The ubiquitin-specific protease family from Arabidopsis. AtUBP1 and 2 are required for the resistance to the amino acid analog canavanine. Plant Physiol. 2000, 124:1828-1843.
56. Sridhar V.V., Kapoor A., Zhang K., Zhu J., Zhou T., Hasegawa P.M., Bressan R.A., Zhu J.-K. Control of DNA methylation and heterochromatic silencing by histone H2B deubiquitination. Nature 2007, 447:735-738.
57. Luo M., Luo M.-Z., Buzas D., Finnegan J., Helliwell C., Dennis E.S., Peacock W.J., Chaudhury A. UBIQUITIN-SPECIFIC PROTEASE 26 is required for seed development and the repression of PHERES1 in Arabidopsis. Genetics 2008, 180:229-236.
58. Schmitz R.J., Tamada Y., Doyle M.R., Zhang X., Amasino R.M. Histone H2B deubiquitination is required for transcriptional activation of FLOWERING LOCUS C and for proper control of flowering in Arabidopsis. Plant Physiol. 2009, 149:1196-1204.
59. Ng D.W., Wang T., Chandrasekharan M.B., Aramayo R., Kertbundit S., Hall T.C. Plant SET domain-containing proteins: structure, function and regulation. Biochim. Biophys. Acta 2007, 1769:316-329.
60. Liu C., Lu F., Cui X., Cao X. Histone methylation in higher plants. Annu. Rev. Plant Biol. 2010, 61:395-420.
61. Demidov D., Hesse S., Tewes A., Rutten T., Fuchs J., Ashtiyani R.K., Lein S., Fischer A., Reuter G., Houben A. Aurora1 phosphorylation activity on histone H3 and its cross-talk with other post-translational histone modifications in Arabidopsis. Plant J. 2009, 59:221-230.
62. Berr A., McCallum E.J., Ménard R., Meyer D., Fuchs J., Dong A., Shen W.-H. Arabidopsis SET DOMAIN GROUP2 is required for H3K4 trimethylation and is crucial for both sporophyte and gametophyte development. Plant Cell 2010, 22:3232-3248.
63. Guo L., Yu Y., Law J.A., Zhang X. SET DOMAIN GROUP2 is the major histone H3 lysine 4 trimethyltransferase in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:18557-18562.
64. Alvarez-Venegas R., Pien S., Sadder M., Witmer X., Grossniklaus U., Avramova Z. ATX-1, an Arabidopsis homolog of trithorax, activates flower homeotic genes. Curr. Biol. 2003, 13:627-637.
65. Alvarez-Venegas R., Avramova Z. Methylation patterns of histone H3 Lys 4, Lys 9 and Lys 27 in transcriptionally active and inactive Arabidopsis genes and in atx1 mutants. Nucleic Acids Res. 2005, 33:5199-5207.
66. Alvarez-Venegas R., Abdallat A.A., Guo M., Alfano J.R., Avramova Z. Epigenetic control of a transcription factor at the cross section of two antagonistic pathways. Epigenetics 2007, 2:106-113.
67. Ding Y., Avramova Z., Fromm M. The Arabidopsis trithorax-like factor ATX1 functions in dehydration stress responses via ABA-dependent and ABA-independent pathways. Plant J. 2011, 66:735-744.
68. Saleh A., Alvarez-Venegas R., Yilmaz M., Le O., Hou G., Sadder M., Al-Abdallat A., Xia Y., Lu G., Ladunga I., Avramova Z. The highly similar Arabidopsis homologs of trithorax ATX1 and ATX2 encode proteins with divergent biochemical functions. Plant Cell 2008, 20:568-579.
69. Pien S., Fleury D., Mylne J.S., Crevillen P., Inzé D., Avramova Z., Dean C., Grossniklaus U. ARABIDOPSIS TRITHORAX1 dynamically regulates FLOWERING LOCUS C activation via histone 3 lysine 4 trimethylation. Plant Cell 2008, 20:580-588.
70. Berr A., Xu L., Gao J., Cognat V., Steinmetz A., Dong A., Shen W.-H. SET DOMAIN GROUP25 encodes a histone methyltransferase and is involved in FLOWERING LOCUS C activation and repression of flowering. Plant Physiol. 2009, 151:1476-1485.
71. Tamada Y., Yun J.-Y., Woo S.c., Amasino R.M. ARABIDOPSIS TRITHORAX-RELATED7 is required for methylation of lysine 4 of histone H3 and for transcriptional activation of FLOWERING LOCUS C. Plant Cell 2009, 21:3257-3269.
72. Cartagena J.A., Matsunaga S., Seki M., Kurihara D., Yokoyama M., Shinozaki K., Fujimoto S., Azumi Y., Uchiyama S., Fukui K. The Arabidopsis SDG4 contributes to the regulation of pollen tube growth by methylation of histone H3 lysines 4 and 36 in mature pollen. Dev. Biol. 2008, 315:355-368.
73. Thorstensen T., Grini P., Mercy I., Alm V., Erdal S., Aasland R., Aalen R. The Arabidopsis SET-domain protein ASHR3 is involved in stamen development and interacts with the bHLH transcription factor ABORTED MICROSPORES (AMS). Plant Mol. Biol. 2008, 66:47-59.
74. Berr A., McCallum E.J., Alioua A., Heintz D., Heitz T., Shen W.-H. Arabidopsis histone methyltransferase SET DOMAIN GROUP8 mediates induction of the jasmonate/ethylene pathway genes in plant defense response to necrotrophic fungi. Plant Physiol. 2010, 154:1403-1414.
75. Cazzonelli C.I., Cuttriss A.J., Cossetto S.B., Pye W., Crisp P., Whelan J., Finnegan E.J., Turnbull C., Pogson B.J. Regulation of carotenoid composition and shoot branching in Arabidopsis by a chromatin modifying histone methyltransferase, SDG8. Plant Cell 2009, 21:39-53.
76. Grini P.E., Thorstensen T., Alm V., Vizcay-Barrena G., Windju S.S., Jfcyrillicrstad T.S., Wilson Z.A., Aalen R.B. The ASH1 HOMOLOG 2 (ASHH2) histone H3 methyltransferase is required for ovule and anther development in Arabidopsis. PLoS ONE 2009, 4:e7817.
77. Kim S.Y., He Y., Jacob Y., Noh Y.-S., Michaels S., Amasino R. Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyltransferase. Plant Cell 2005, 17:3301-3310.
78. Palma K., Thorgrimsen S., Malinovsky F.G., Fiil B.K., Nielsen H.B., Brodersen P., Hofius D., Petersen M., Mundy J. Autoimmunity in Arabidopsis acd11 is mediated by epigenetic regulation of an immune receptor. PLoS Pathog. 2010, 6:e1001137.
79. Xu L., Zhao Z., Dong A., Soubigou-Taconnat L., Renou J.-P., Steinmetz A., Shen W.-H. Di- and tri- but not monomethylation on histone H3 lysine 36 marks active transcription of genes involved in flowering time regulation and other processes in Arabidopsis thaliana. Mol. Cell. Biol. 2008, 28:1348-1360.
80. Zhao Z., Yu Y., Meyer D., Wu C., Shen W.-H. Prevention of early flowering by expression of FLOWERING LOCUS C requires methylation of histone H3 K36. Nat. Cell Biol. 2005, 7:1256-1260.
81. He Y., Michaels S.D., Amasino R.M. Regulation of flowering time by histone acetylation in Arabidopsis. Science 2003, 302:1751-1754.
82. Jiang D., Yang W., He Y., Amasino R.M. 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, 19:2975-2987.
83. Yu C.-W., Liu X., Luo M., Chen C., Lin X., Tian G., Lu Q., Cui Y., Wu K. HISTONE DEACETYLASE6 interacts with FLOWERING LOCUS D and regulates flowering in Arabidopsis. Plant Physiol. 2011, 156:173-184.
84. Tsukada Y., Fang J., Erdjument-Bromage H., Warren M.E., Borchers C.H., Tempst P., Zhang Y. Histone demethylation by a family of JmjC domain-containing proteins. Nature 2006, 439:811-816.
85. Lu F., Cui X., Zhang S., Liu C., Cao X. JMJ14 is an H3K4 demethylase regulating flowering time in Arabidopsis. Cell Res. 2010, 20:387-390.
86. Deleris A., Greenberg M.V.C., Ausin I., Law R.W.Y., Moissiard G., Schubert D., Jacobsen S.E. Involvement of a Jumonji-C domain-containing histone demethylase in DRM2-mediated maintenance of DNA methylation. EMBO Rep. 2010, 11:950-955.
87. Searle I.R., Pontes O., Melnyk C.W., Smith L.M., Baulcombe D.C. JMJ14, a JmjC domain protein, is required for RNA silencing and cell-to-cell movement of an RNA silencing signal in Arabidopsis. Genes Dev. 2010, 24:986-991.
88. Noh B., Lee S.-H., Kim H.-J., Yi G., Shin E.-A., Lee M., Jung K.-J., Doyle M.R., Amasino R.M., Noh Y.-S. Divergent roles of a pair of homologous jumonji/zinc-finger-class transcription factor proteins in the regulation of Arabidopsis flowering time. Plant Cell 2004, 16:2601-2613.
89. Yu X., Li L., Li L., Guo M., Chory J., Yin Y. Modulation of brassinosteroid-regulated gene expression by jumonji domain-containing proteins ELF6 and REF6 in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:7618-7623.
90. Lu F., Cui X., Zhang S., Jenuwein T., Cao X. Arabidopsis REF6 is a histone H3 lysine 27 demethylase. Nat. Genet. 2011, 43:715-719.
91. Inagaki S., Miura-Kamio A., Nakamura Y., Lu F., Cui X., Cao X., Kimura H., Saze H., Kakutani T. Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome. EMBO J. 2010, 29:3496-3506.
92. Miura A., Nakamura M., Inagaki S., Kobayashi A., Saze H., Kakutani T. An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites. EMBO J. 2009, 28:1078-1086.
93. Saze H., Shiraishi A., Miura A., Kakutani T. Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana. Science 2008, 319:462-465.
94. Yun M., Wu J., Workman J.L., Li B. Readers of histone modifications. Cell Res. 2011, 21:564-578.
95. Zeng L., Zhou M.-M. Bromodomain: an acetyl-lysine binding domain. FEBS Lett. 2002, 513:124-128.
96. Chua Y.L., Channelière S., Mott E., Gray J.C. The bromodomain protein GTE6 controls leaf development in Arabidopsis by histone acetylation at ASYMMETRIC LEAVES1. Genes Dev. 2005, 19:2245-2254.
97. Duque P., Chua N.-H. IMB1, a bromodomain protein induced during seed imbibition, regulates ABA- and phyA-mediated responses of germination in Arabidopsis. Plant J. 2003, 35:787-799.
98. Gaudin V., Libault M., Pouteau S., Juul T., Zhao G., Lefebvre D., Grandjean O. Mutations in LIKE HETEROCHROMATIN PROTEIN 1 affect flowering time and plant architecture in Arabidopsis. Development 2001, 128:4847-4858.
99. Exner V., Aichinger E., Shu H., Wildhaber T., Alfarano P., Caflisch A., Gruissem W., Köhler C., Hennig L. The chromodomain of LIKE HETEROCHROMATIN PROTEIN 1 is essential for H3K27me3 binding and function during Arabidopsis development. PLoS ONE 2009, 4:e5335.
100. Mylne J.S., Barrett L., Tessadori F., Mesnage S., Johnson L., Bernatavichute Y.V., Jacobsen S.E., Fransz P., Dean C. LHP1, the Arabidopsis homologue of HETEROCHROMATIN PROTEIN1, is required for epigenetic silencing of FLC. Proc. Natl. Acad. Sci. U. S. A. 2006, 103:5012-5017.
101. Vezzoli A., Bonadies N., Allen M.D., Freund S.M.V., Santiveri C.M., Kvinlaug B.T., Huntly B.J.P., Gottgens B., Bycroft M. Molecular basis of histone H3K36me3 recognition by the PWWP domain of Brpf1. Nat. Struct. Mol. Biol. 2010, 17:617-619.
102. Hoppmann V., Thorstensen T., Kristiansen P.E., Veiseth S.V., Rahman M.A., Finne K., Aalen R.B., Aasland R. The CW domain, a new histone recognition module in chromatin proteins. EMBO J. 2011, 18:1939-1952.
103. Oh S., Park S., van Nocker S. Genic and global functions for Paf1C in chromatin modification and gene expression in Arabidopsis. PLoS Genet. 2008, 4:e1000077.
104. Roudier F., Ahmed I., Berard C., Sarazin A., Mary-Huard T., Cortijo S., Bouyer D., Caillieux E., Duvernois-Berthet E., Al-Shikhley L., Giraut L., Despres B., Drevensek S., Barneche F., Derozier S., Brunaud V., Aubourg S., Schnittger A., Bowler C., Martin-Magniette M.-L., Robin S., Caboche M., Colot V. Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J. 2011, 18:1928-1938.
105. Zhang X., Bernatavichute Y., Cokus S., Pellegrini M., Jacobsen S. Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol. 2009, 10:R62.
106. de la Paz Sanchez M., Gutierrez C. Arabidopsis ORC1 is a PHD-containing H3K4me3 effector that regulates transcription. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:2065-2070.
107. Saitoh Y., Miyagi S., Ariga H., Tsutsumi K. Functional domains involved in the interaction between Orc1 and transcriptional repressor AlF-C that bind to an origin/promoter of the rat aldolase B gene. Nucleic Acids Res. 2002, 30:5205-5212.
108. Lee W.Y., Lee D., Chung W.-I., Kwon C.S. Arabidopsis ING and Alfin1-like protein families localize to the nucleus and bind to H3K4me3/2 via plant homeodomain fingers. Plant J. 2009, 58:511-524.
109. Greb T., Mylne J.S., Crevillen P., Geraldo N., An H., Gendall A.R., Dean C. The PHD finger protein VRN5 functions in the epigenetic silencing of Arabidopsis FLC. Curr. Biol. 2007, 17:73-78.
110. Sung S., Schmitz R.J., Amasino R.M. A PHD finger protein involved in both the vernalization and photoperiod pathways in Arabidopsis. Genes Dev. 2006, 20:3244-3248.
111. Sung S., Amasino R.M. Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nature 2004, 427:159-164.
112. Jiang D., Gu X., He Y. Establishment of the winter-annual growth habit via FRIGIDA-mediated histone methylation at FLOWERING LOCUS C in Arabidopsis. Plant Cell 2009, 21:1733-1746.
113. Fuchs J., Demidov D., Houben A., Schubert I. Chromosomal histone modification patterns - from conservation to diversity. Trends Plant Sci. 2006, 11:199-208.
114. Caro E., Castellano M.M., Gutierrez C. A chromatin link that couples cell division to root epidermis patterning in Arabidopsis. Nature 2007, 447:213-217.
115. Charron J.-B.F., He H., Elling A.A., Deng X.W. Dynamic landscapes of four histone modifications during deetiolation in Arabidopsis. Plant Cell 2009, 21:3732-3748.
116. Turck F., Roudier F., Farrona S., Martin-Magniette M.-L., Guillaume E., Buisine N., Gagnot S., Martienssen R.A., Coupland G., Colot V. Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27. PLoS Genet. 2007, 3:e86.
117. Bernstein B.E., Kamal M., Lindblad-Toh K., Bekiranov S., Bailey D.K., Huebert D.J., McMahon S., Karlsson E.K., Kulbokas Iii E.J., Gingeras T.R., Schreiber S.L., Lander E.S. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 2005, 120:169-181.
118. Schübeler D., MacAlpine D.M., Scalzo D., Wirbelauer C., Kooperberg C., van Leeuwen F., Gottschling D.E., O'Neill L.P., Turner B.M., Delrow J., Bell S.P., Groudine M. The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev. 2004, 18:1263-1271.
119. Santos-Rosa H., Schneider R., Bannister A.J., Sherriff J., Bernstein B.E., Emre N.C.T., Schreiber S.L., Mellor J., Kouzarides T. Active genes are tri-methylated at K4 of histone H3. Nature 2002, 419:407-411.
120. Zhang X., Bernatavichute Y., Cokus S., Pellegrini M., Jacobsen S. Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol. 2009, 10:R62.
121. Filion G.J., van Bemmel J.G., Braunschweig U., Talhout W., Kind J., Ward L.D., Brugman W., de Castro I.J., Kerkhoven R.M., Bussemaker H.J., van Steensel B. Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell 2010, 143:212-224.
122. Selth L.A., Sigurdsson S., Svejstrup J.Q. Transcript elongation by RNA polymerase II. Annu. Rev. Biochem. 2010, 79:271-293.
123. Venters B.J., Pugh B.F. How eukaryotic genes are transcribed. Critical Rev. Biochem. Mol. Biol. 2009, 44:117-141.
124. Choi K., Kim J., Hwang H.-J., Kim S., Park C., Kim S.Y., Lee I. The FRIGIDA complex activates transcription of FLC, a strong flowering repressor in Arabidopsis, by recruiting chromatin modification factors. Plant Cell 2011, 23:289-303.
125. March-Díaz R., Reyes J.C. The beauty of being a variant: H2A.Z and the SWR1 complex in plants. Mol. Plant 2009, 2:565-577.
126. Choi K., Park C., Lee J., Oh M., Noh B., Lee I. Arabidopsis homologs of components of the SWR1 complex regulate flowering and plant development. Development 2007, 134:1931-1941.
127. Deal R.B., Topp C.N., McKinney E.C., Meagher R.B. Repression of flowering in Arabidopsis requires activation of FLOWERING LOCUS C expression by the histone variant H2A.Z. Plant Cell 2007, 19:74-83.
128. Noh Y.-S., Amasino R.M. PIE1, an ISWI family gene, is required for FLC activation and floral repression in Arabidopsis. Plant Cell 2003, 15:1671-1682.
129. Lu P.Y., Lévesque N., Kobor M.S. NuA4 and SWR1-C: two chromatin-modifying complexes with overlapping functions and components. Biochem. Cell Biol. 2009, 87:799-815.
130. He Y., Doyle M.R., Amasino R.M. PAF1-complex-mediated histone methylation of FLOWERING LOCUS C chromatin is required for the vernalization-responsive, winter-annual habit in Arabidopsis. Genes Dev. 2004, 18:2774-2784.
131. Oh S., Zhang H., Ludwig P., van Nocker S. A mechanism related to the yeast transcriptional regulator Paf1c is required for expression of the Arabidopsis FLC/MAF MADS box gene family. Plant Cell 2004, 16:2940-2953.
132. Zhang H., Ransom C., Ludwig P., van Nocker S. Genetic analysis of early flowering mutants in Arabidopsis defines a class of pleiotropic developmental regulator required for expression of the flowering-time switch Flowering Locus C. Genetics 2003, 164:347-358.
133. Zhang H., Van Nocker S. The VERNALIZATION INDEPENDENCE 4 gene encodes a novel regulator of FLOWERING LOCUS C. Plant J. 2002, 31:663-673.
134. Park S., Oh S., Ek-Ramos J., van Nocker S. PLANT HOMOLOGOUS TO PARAFIBROMIN is a component of the PAF1 complex and assists in regulating expression of genes within H3K27me3-enriched chromatin. Plant Physiol. 2010, 153:821-831.
135. Yu X., Michaels S.D. The Arabidopsis Paf1c complex component CDC73 participates in the modification of FLOWERING LOCUS C chromatin. Plant Physiol. 2010, 153:1074-1084.
136. Ding Y., Avramova Z., Fromm M. Two distinct roles of ARABIDOPSIS HOMOLOG OF TRITHORAX1 (ATX1) at promoters and within transcribed regions of ATX1-regulated genes. Plant Cell 2011, 23:350-363.
137. Jiang D., Kong N.C., Gu X., Li Z., He Y. Arabidopsis COMPASS-Like complexes mediate histone H3 lysine-4 trimethylation to control floral transition and plant development. PLoS Genet. 2011, 7:e1001330.
138. Tenney K., Gerber M., Ilvarsonn A., Schneider J., Gause M., Dorsett D., Eissenberg J.C., Shilatifard A. Drosophila Rtf1 functions in histone methylation, gene expression, and Notch signaling. Proc. Natl. Acad. Sci. U. S. A. 2006, 103:11970-11974.