水稻组蛋白甲基转移酶和去乙酰化酶基因的功能研究
|
摘要
组蛋白修饰是表观遗传调控的重要机制之一,包括组蛋白甲基化、乙酰化、磷酸化、泛素化等其它组蛋白修饰,在动植物生长发育和基因表达调控中发挥着重要的作用。水稻是世界上重要的粮食作物,也是单子叶植物中的模式生物,有关水稻表观遗传调控机制的研究还很少报道,因此研究水稻中组蛋白修饰基因的功能具有重要的意义。
本研究主要以水稻的组蛋白甲基转移酶基因(Histone methyltransferase, HMTs)和组蛋白去乙酰化酶基因(Histone deacetylase, HDACs)为研究对象,通过生物信息学、克隆和转化等方法研究了HMTs和HDACs基因的结构、表达和功能,阐述了其在水稻表观遗传调控机制中的作用,主要获得以下结果：
1.通过同源序列研究发现,水稻中存在12个组蛋白甲基转移酶SUVH(Suppressor of variegation 3-9 homologue)家族基因和18个HDACs基因；对水稻组蛋白甲基转移酶中SUVH家族和HDAC家族基因进行了系统进化分析,并确定拟研究基因；基因结构分析发现,SUVH家族基因都由YDG-SRA、Pre-SET、SET三个保守的结构域组成；对SUVH和HDAC家族基因进行了水稻全生育期芯片的表达模式分析和愈伤、根、小苗、茎、叶、旗叶和幼穗等特异组织的表达谱分析,发现不同的SUVH家族基因具有相似的表达模式,但表达水平不同。
2.对SUVH和HDAC家族中拟研究基因SDG703、SDG704、SDG709、SDG710、SDG713、SDG714、SDG715、SDG726、SDG727、SDG728、HDT701、HDA704、HDA706进行了RNAi干涉载体构建,对基因SDG703、SDG704、SDG709、SDG713、SDG714、SDG715、SDG726、SDG728、HDA706、HDT702、HDA711构建了超量表达载体,并获得独立的转基因植株。
3.RNA水平检测SUVH和HDAC结果显示,在超量表达和RNAi植株中,各基因的表达量都有不同程度的上升和下降。
4.转基因SUVH成员SDG713和SDG728的下调表达分别引起了植株矮小致死和种子粒厚减小的表型；HDAC成员中HDA704的下调表达引起植株矮化和旗叶基部卷曲,外施赤霉素GA3不能互补HDA704的表型。
5.亚细胞定位显示SUVH家族SDG713位于细胞核内,与启动子融合的GFP在根尖、幼茎、雌蕊等组织中特异表达。
6.SUVH成员SDG714下调表达引起柱头数目增多等花的变态发育,同时引起miRNA159的上升表达和miRNA164的下降表达。
7.SUVH成员转基因材料的Western杂交结果显示,与野生型相比,SDG728在超量表达和：RNAi植株中分别引起H3K9me3修饰的上升和下降；SDG704、SDG726、SDG727在RNAi植株中H3K9me3修饰呈下降变化。
8.原核表达GST-SDG728和GST-SDG714组蛋白甲基化酶并进行活性实验,结果显示GST-SDG714可以使小牛核心组蛋白和原核表达重组寡聚组蛋白单甲基化和二甲基化；而GST-SDG728仅能使小牛核心组蛋白甲基化,而不能使原核表达重组寡聚组蛋白甲基化,表明SDG728具有三甲基化活性。
9.McrBC-PCR方法检测DNA甲基化结果显示,SDG728调控Tos17和一个Tyl-copia类反转座子Os08g03880的DNA甲基化。另外,SDG703、SDG713、SDG715等也影响上述两个反转座子的甲基化水平。
10.染色质免疫沉淀结果显示,SDG728调控Tos17和Os08g03880基因区域的H3K9me3水平,在SDG728超量表达植株中,H3K9me3明显增加；在RNAi植株中,H3K9me3则呈显著下降。
上述一系列的结果表明,水稻SUVH成员SDG728是一个组蛋白三甲基化酶,通过调控反转座子基因区域的组蛋白三甲基化水平来影响DNA甲基化水平,进而调控反转座子的表达,维持水稻的基因组稳定,揭示了表观遗传调控在调节转座元件基因表达过程中的分子机制。其它SUVH成员和HDAC成员的研究结果表明其在水稻组蛋白修饰和生长发育中起着重要的作用。
Histone modifications, including histone methylation, acetylation, phosphorylation, ubiqutination and others, play pivotal roles in plant development and gene regulation. There are few reports on the molecular mechanism of epigenetic regulation in monocots, especially in rice. Therefore it is of great significance to study the function of histone modification gene from rice.
This study mainly focused on the histone methyltransferase (HMTs) and histone deacetylase (HDACs). The function and the roles of these genes in epigenetic regulation were investigated by bioinformatics, cloning, transformation and other methods. Main results are shown as following:
1.12 SUVHs (Suppressor of variegation 3-9 homologue) histone methyltransferases and 18 HDACs (Histone deacetylase) were identified from rice. Sequence alignment and phylogenetic analysis of SUVHs and HDACs were performed to elucidate the evolution relationship of members within these two families. Gene structure analysis revealed that SUVH proteins contained three conserved domain including YDG (named after 3 conserved amino acids)-SRA (SET-and Ring finger-associated) and pre-SET, SET (named after 3 genes from Drosophila). To study the expression profiles of the rice SUVHs and HDAC genes, a serial Affimetrix microarray analysis of transcripts from various organs at different developmental stages were performed (http://crep.ncpgr.cn). The results revealed that most of the rice SVUH genes showed a similar expression pattern, whereas their expression levels in same tissues or organs were different.
2. Over-expression and RNAi vectors of SUVHs and HDACs genes were constructed and transformed into rice to get transgenic plants.
3. RNA level analysis indicated that there were the increased expression of each target genes in over-expression and decreased expression in RNAi transgenic plants.
4. Down-regulation of SDG713 and SDG728 (SUVHs) led to the lethal dwarf plant and reduced seed thickness, respectively. The dwarf phenotype and twist flag leaf was caused by reduced expression level of HDA704, which were not complemented by treating with gibberellin (GA3).
5. The expression pattern of the SDG713-GFP fusion protein showed that SDG713 was a widely expressed nuclear protein with high expressions in root tip, young stem, pistil and others tissues.
6. SDG714 RNA interference induced abnormal stigma development and led to the increased miR159 RNA level and decreased miR164 RNA level in rice (indica).
7. Western Blot results revealed that SDG728 was required to regulate H3K9me3 and SDG704, SDG726 and SDG727 participated in the regulation of H3K9me3.
8. The proteins of GST-SDG728 and GST-SDG714 which were expressed and purified from E.coli were used to study the methyltransferase activity in vitro. Results showed that SDG728 could methylate calf core histones, but not the synthesized non-methylated histones, whereas SDG714 showed a methyltransferase activity on both types of sbustrates. This observation indicated that SDG728 has a trimethyltransferase activity.
9. The results of McrBC-PCR denmostrated that DNA methylations of Tos17 and a Ty1-copia like retrotransposon (Os08g03880) were affected by SDG728 and other members such as SDG703, SDG713 and SDG715.
10. ChIP (Chromatin immunoprecipitation) data indicated that SDG728 was required for histone H3K9me3 on the Tosl 7 and Os08g03880 loci.
All those data demonstrated that SDG728 was a histone trimethyltransferase in rice, which regulated the DNA methylation on the gene region of transposable elements by the changes of histone H3K9me3. The fact that SDG728 could repress the retrotransposons and maintain the genome stability indirectly, suggested its role in regulating the retrotransposon expression of SDG728. Other members of SUVHs and HDACs played important roles in histone modification and rice development.
本研究主要以水稻的组蛋白甲基转移酶基因(Histone methyltransferase, HMTs)和组蛋白去乙酰化酶基因(Histone deacetylase, HDACs)为研究对象,通过生物信息学、克隆和转化等方法研究了HMTs和HDACs基因的结构、表达和功能,阐述了其在水稻表观遗传调控机制中的作用,主要获得以下结果：
1.通过同源序列研究发现,水稻中存在12个组蛋白甲基转移酶SUVH(Suppressor of variegation 3-9 homologue)家族基因和18个HDACs基因；对水稻组蛋白甲基转移酶中SUVH家族和HDAC家族基因进行了系统进化分析,并确定拟研究基因；基因结构分析发现,SUVH家族基因都由YDG-SRA、Pre-SET、SET三个保守的结构域组成；对SUVH和HDAC家族基因进行了水稻全生育期芯片的表达模式分析和愈伤、根、小苗、茎、叶、旗叶和幼穗等特异组织的表达谱分析,发现不同的SUVH家族基因具有相似的表达模式,但表达水平不同。
2.对SUVH和HDAC家族中拟研究基因SDG703、SDG704、SDG709、SDG710、SDG713、SDG714、SDG715、SDG726、SDG727、SDG728、HDT701、HDA704、HDA706进行了RNAi干涉载体构建,对基因SDG703、SDG704、SDG709、SDG713、SDG714、SDG715、SDG726、SDG728、HDA706、HDT702、HDA711构建了超量表达载体,并获得独立的转基因植株。
3.RNA水平检测SUVH和HDAC结果显示,在超量表达和RNAi植株中,各基因的表达量都有不同程度的上升和下降。
4.转基因SUVH成员SDG713和SDG728的下调表达分别引起了植株矮小致死和种子粒厚减小的表型；HDAC成员中HDA704的下调表达引起植株矮化和旗叶基部卷曲,外施赤霉素GA3不能互补HDA704的表型。
5.亚细胞定位显示SUVH家族SDG713位于细胞核内,与启动子融合的GFP在根尖、幼茎、雌蕊等组织中特异表达。
6.SUVH成员SDG714下调表达引起柱头数目增多等花的变态发育,同时引起miRNA159的上升表达和miRNA164的下降表达。
7.SUVH成员转基因材料的Western杂交结果显示,与野生型相比,SDG728在超量表达和：RNAi植株中分别引起H3K9me3修饰的上升和下降；SDG704、SDG726、SDG727在RNAi植株中H3K9me3修饰呈下降变化。
8.原核表达GST-SDG728和GST-SDG714组蛋白甲基化酶并进行活性实验,结果显示GST-SDG714可以使小牛核心组蛋白和原核表达重组寡聚组蛋白单甲基化和二甲基化；而GST-SDG728仅能使小牛核心组蛋白甲基化,而不能使原核表达重组寡聚组蛋白甲基化,表明SDG728具有三甲基化活性。
9.McrBC-PCR方法检测DNA甲基化结果显示,SDG728调控Tos17和一个Tyl-copia类反转座子Os08g03880的DNA甲基化。另外,SDG703、SDG713、SDG715等也影响上述两个反转座子的甲基化水平。
10.染色质免疫沉淀结果显示,SDG728调控Tos17和Os08g03880基因区域的H3K9me3水平,在SDG728超量表达植株中,H3K9me3明显增加；在RNAi植株中,H3K9me3则呈显著下降。
上述一系列的结果表明,水稻SUVH成员SDG728是一个组蛋白三甲基化酶,通过调控反转座子基因区域的组蛋白三甲基化水平来影响DNA甲基化水平,进而调控反转座子的表达,维持水稻的基因组稳定,揭示了表观遗传调控在调节转座元件基因表达过程中的分子机制。其它SUVH成员和HDAC成员的研究结果表明其在水稻组蛋白修饰和生长发育中起着重要的作用。
Histone modifications, including histone methylation, acetylation, phosphorylation, ubiqutination and others, play pivotal roles in plant development and gene regulation. There are few reports on the molecular mechanism of epigenetic regulation in monocots, especially in rice. Therefore it is of great significance to study the function of histone modification gene from rice.
This study mainly focused on the histone methyltransferase (HMTs) and histone deacetylase (HDACs). The function and the roles of these genes in epigenetic regulation were investigated by bioinformatics, cloning, transformation and other methods. Main results are shown as following:
1.12 SUVHs (Suppressor of variegation 3-9 homologue) histone methyltransferases and 18 HDACs (Histone deacetylase) were identified from rice. Sequence alignment and phylogenetic analysis of SUVHs and HDACs were performed to elucidate the evolution relationship of members within these two families. Gene structure analysis revealed that SUVH proteins contained three conserved domain including YDG (named after 3 conserved amino acids)-SRA (SET-and Ring finger-associated) and pre-SET, SET (named after 3 genes from Drosophila). To study the expression profiles of the rice SUVHs and HDAC genes, a serial Affimetrix microarray analysis of transcripts from various organs at different developmental stages were performed (http://crep.ncpgr.cn). The results revealed that most of the rice SVUH genes showed a similar expression pattern, whereas their expression levels in same tissues or organs were different.
2. Over-expression and RNAi vectors of SUVHs and HDACs genes were constructed and transformed into rice to get transgenic plants.
3. RNA level analysis indicated that there were the increased expression of each target genes in over-expression and decreased expression in RNAi transgenic plants.
4. Down-regulation of SDG713 and SDG728 (SUVHs) led to the lethal dwarf plant and reduced seed thickness, respectively. The dwarf phenotype and twist flag leaf was caused by reduced expression level of HDA704, which were not complemented by treating with gibberellin (GA3).
5. The expression pattern of the SDG713-GFP fusion protein showed that SDG713 was a widely expressed nuclear protein with high expressions in root tip, young stem, pistil and others tissues.
6. SDG714 RNA interference induced abnormal stigma development and led to the increased miR159 RNA level and decreased miR164 RNA level in rice (indica).
7. Western Blot results revealed that SDG728 was required to regulate H3K9me3 and SDG704, SDG726 and SDG727 participated in the regulation of H3K9me3.
8. The proteins of GST-SDG728 and GST-SDG714 which were expressed and purified from E.coli were used to study the methyltransferase activity in vitro. Results showed that SDG728 could methylate calf core histones, but not the synthesized non-methylated histones, whereas SDG714 showed a methyltransferase activity on both types of sbustrates. This observation indicated that SDG728 has a trimethyltransferase activity.
9. The results of McrBC-PCR denmostrated that DNA methylations of Tos17 and a Ty1-copia like retrotransposon (Os08g03880) were affected by SDG728 and other members such as SDG703, SDG713 and SDG715.
10. ChIP (Chromatin immunoprecipitation) data indicated that SDG728 was required for histone H3K9me3 on the Tosl 7 and Os08g03880 loci.
All those data demonstrated that SDG728 was a histone trimethyltransferase in rice, which regulated the DNA methylation on the gene region of transposable elements by the changes of histone H3K9me3. The fact that SDG728 could repress the retrotransposons and maintain the genome stability indirectly, suggested its role in regulating the retrotransposon expression of SDG728. Other members of SUVHs and HDACs played important roles in histone modification and rice development.
引文
1. Holliday R. Epigenetics:a historical overview. Epigenetics,2006,1:76-80
2. Nanney DL. Epigenetic Control Systems. Proc Natl Acad Sci U S A,1958,44: 712-717
3. Haig D. The (dual) origin of epigenetics. Cold Spring Harb Symp Quant Biol, 2004,69:67-70
4. Holliday R. The inheritance of epigenetic defects. Science,1987,238:163-170
5. Holliday R. Epigenetics:an overview. Dev Genet,1994,15:453-457
6. Riggs ADandPorter TN. Overview of epigenetic mechanisms. In Epigenetic mechanisms of gene regulation,1996,29-45
7. Allis CD, Jenuwein TandReinberg D. Epigenetics. Gottschling DE, editor. New York:Cold Spring Harbor Laboratory Press; 2006.2 p.
8. Wolffe APandMatzke MA. Epigenetics:regulation through repression. Science, 1999,286:481-486
9. Roloff TCandNuber UA. Chromatin, epigenetics and stem cells. Eur J Cell Biol, 2005,84:123-135
10. Avery OT, Macleod CMandMcCarty M. Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types:Induction of Transformation by a Desoxyribonucleic Acid Fraction Isolated from Pneumococcus Type Iii. J Exp Med,1944,79:137-158
11. Kornberg RD. Chromatin structure:a repeating unit of histones and DNA. Science, 1974,184:868-871
12. Luger K, Mader AW, Richmond RK, Sargent DFandRichmond TJ. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature,1997,389: 251-260
13. Luger K, Rechsteiner TJ, Flaus AJ, Waye MMandRichmond TJ. Characterization of nucleosome core particles containing histone proteins made in bacteria. J Mol Biol,1997,272:301-311
14. Arents GandMoudrianakis EN. Topography of the histone octamer surface: repeating structural motifs utilized in the docking of nucleosomal DNA. Proc Natl Acad Sci U S A,1993,90:10489-10493
15. Karpen GHandAllshire RC. The case for epigenetic effects on centromere identity and function. Trends Genet,1997,13:489-496
16. Holliday RandPugh JE. DNA modification mechanisms and gene activity during development. Science,1975,187:226-232
17. Riggs AD. X inactivation, differentiation, and DNA methylation; 1975.9-25 p.
18. Bird AP. The occurrence and transmission of a pattern of DNA methylation in Xenopus laevis ribosomal DNA. Philos Trans R Soc Lond B Biol Sci,1978,283: 325-327
19. Ehrlich M, Gama-Sosa MA, Huang LH, Midgett RM, Kuo KC, McCune RAandGehrke C. Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells. Nucleic Acids Res,1982,10:2709-2721
20. Posfai J, Bhagwat AS, Posfai GandRoberts RJ. Predictive motifs derived from cytosine methyltransferases. Nucleic Acids Res,1989,17:2421-2435
21. Bestor T. Structure of mammalian DNA methyltransferase as deduced from the inferred amino acid sequence and direct studies of the protein. Biochem Soc Trans, 1988,16:944-947
22. Finnegan EJ, Peacock WJandDennis ES. Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proc Natl Acad Sci U SA,1996,93:8449-8454
23. Chan SW, Henderson IRandJacobsen SE. Gardening the genome:DNA methylation in Arabidopsis thaliana. Nat Rev Genet,2005,6:351-360
24. Finnegan EJandDennis ES. Isolation and identification by sequence homology of a putative cytosine methyltransferase from Arabidopsis thaliana. Nucleic Acids Res,1993,21:2383-2388
25. Kishimoto N, Sakai H, Jackson J, Jacobsen SE, Meyerowitz EM, Dennis ESandFinnegan EJ. Site specificity of the Arabidopsis METI DNA methyltransferase demonstrated through hypermethylation of the superman locus. Plant Mol Biol,2001,46:171-183
26. Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff SandJacobsen SE. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science,2001,292:2077-2080
27. Ronemus MJ, Galbiati M, Ticknor C, Chen JandDellaporta SL. Demethylation-induced developmental pleiotropy in Arabidopsis. Science,1996, 273:654-657
28. Vongs A, Kakutani T, Martienssen RAandRichards EJ. Arabidopsis thaliana DNA methylation mutants. Science,1993,260:1926-1928
29. Henikoff SandComai L. A DNA methyltransferase homolog with a chromodomain exists in multiple polymorphic forms in Arabidopsis. Genetics,1998,149: 307-318
30. Bartee L, Malagnac FandBender J. Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Genes Dev,2001, 15:1753-1758
31. McCallum CM, Comai L, Greene EAandHenikoff S. Targeted screening for induced mutations. Nat Biotechnol,2000,18:455-457
32. Jackson JP, Lindroth AM, Cao XandJacobsen SE. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature,2002, 416:556-560
33. Cao X, Springer NM, Muszynski MG, Phillips RL, Kaeppler SandJacobsen SE. Conserved plant genes with similarity to mammalian de novo DNA methyltransferases. Proc Natl Acad Sci USA,2000,97:4979-4984
34. Okano M, Bell DW, Haber DAandLi E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell, 1999,99:247-257
35. Lyko F, Ramsahoye BH, Kashevsky H, Tudor M, Mastrangelo MA, Orr-Weaver TLandJaenisch R. Mammalian (cytosine-5) methyltransferases cause genomic DNA methylation and lethality in Drosophila. Nat Genet,1999,23:363-366
36. Hsieh CL. In vivo activity of murine de novo methyltransferases, Dnmt3a and Dnmt3b. Mol Cell Biol,1999,19:8211-8218
37. Okano M, Xie SandLi E. Dnmt2 is not required for de novo and maintenance methylation of viral DNA in embryonic stem cells. Nucleic Acids Res,1998,26: 2536-2540
38. Cao XandJacobsen SE. Role of the arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol,2002,12:1138-1144
39. Loidl P. A plant dialect of the histone language. Trends Plant Sci,2004,9:84-90
40. Fischle W, Wang YandAllis CD. Histone and chromatin cross-talk. Curr Opin Cell Biol,2003,15:172-183
41. Turner BM. Cellular memory and the histone code. Cell,2002,111:285-291
42. Jenuwein TandAllis CD. Translating the histone code. Science,2001,293: 1074-1080
43. Jaskelioff MandPeterson CL. Chromatin and transcription:histones continue to make their marks. Nat Cell Biol,2003,5:395-399
44. Fischle W, Wang Y, Jacobs SA, Kim Y, Allis CDandKhorasanizadeh S. Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. Genes Dev,2003,17:1870-1881
45. Zhang YandReinberg D. Transcription regulation by histone methylation:interplay between different covalent modifications of the core histone tails. Genes Dev, 2001,15:2343-2360
46. Lee JH, Cook JR, Yang ZH, Mirochnitchenko O, Gunderson SI, Felix AM, Herth N, Hoffmann RandPestka S. PRMT7, a new protein arginine methyltransferase that synthesizes symmetric dimethylarginine. JBiol Chem,2005,280:3656-3664
47. Lachner M, O'Sullivan RJandJenuwein T. An epigenetic road map for histone lysine methylation. J Cell Sci,2003,116:2117-2124
48. Bannister AJandKouzarides T. Reversing histone methylation. Nature,2005,436: 1103-1106
49. Lachner M, Sengupta R, Schotta GandJenuwein T. Trilogies of histone lysine methylation as epigenetic landmarks of the eukaryotic genome. Cold Spring Harb Symp Quant Biol,2004,69:209-218
50. Zhang X, Zhou LandCheng X. Crystal structure of the conserved core of protein arginine methyltransferase PRMT3. Embo J,2000,19:3509-3519
51. Weiss VH, McBride AE, Soriano MA, Filman DJ, Silver PAandHogle JM. The structure and oligomerization of the yeast arginine methyltransferase, Hmtl. Nat Struct Biol,2000,7:1165-1171
52. Ebbs MLandBender J. Locus-specific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase. Plant Cell,2006,18:1166-1176
53. Zhao W, Soejima H, Higashimoto K, Nakagawachi T, Urano T, Kudo S, Matsukura S, Matsuo S, Joh KandMukai T. 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,2005,137:431-440
54. Naumann K, Fischer A, Hofmann I, Krauss V, Phalke S, Irmler K, Hause G, Aurich AC, Dorn R, Jenuwein TandReuter G. Pivotal role of AtSUVH2 in heterochromatic histone methylation and gene silencing in Arabidopsis. Embo J, 2005,24:1418-1429
55. Kim SY, He Y, Jacob Y, Noh YS, Michaels SandAmasino R. Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyl transferase. Plant Cell,2005,17:3301-3310
56. Fang J, Wang HandZhang Y. Purification of histone methyltransferases from HeLa cells. Methods Enzymol,2004,377:213-226
57. Rea S, Eisenhaber F, O'Carroll D, Strahl BD, Sun ZW, Schmid M, Opravil S, Mechtler K, Ponting CP, Allis CDandJenuwein T. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature,2000,406: 593-599
58. Bedford MTandRichard S. Arginine methylation an emerging regulator of protein function. Mol Cell,2005,18:263-272
59. Boisvert FM, Cote J, Boulanger MCandRichard S. A proteomic analysis of arginine-methylated protein complexes. Mol Cell Proteomics,2003,2:1319-1330
60. Lin WJ, Gary JD, Yang MC, Clarke SandHerschman HR. The mammalian immediate-early TIS21 protein and the leukemia-associated BTG1 protein interact with a protein-arginine N-methyltransferase.J Biol Chem,1996,271: 15034-15044
61. Wang H, Huang ZQ, Xia L, Feng Q, Erdjument-Bromage H, Strahl BD, Briggs SD, Allis CD, Wong J, Tempst PandZhang Y. Methylation of histone H4 at arginine 3 facilitating transcriptional activation by nuclear hormone receptor. Science,2001,293:853-857
62. Frankel AandClarke S. PRMT3 is a distinct member of the protein arginine N-methyltransferase family. Conferral of substrate specificity by a zinc-finger domain. J Biol Chem,2000,275:32974-32982
63. Cook JR, Lee JH, Yang ZH, Krause CD, Herth N, Hoffmann RandPestka S. FBXO11/PRMT9, a new protein arginine methyltransferase, symmetrically dimethylates arginine residues. Biochem Biophys Res Commun,2006,342: 472-481
64. Schmitz RJ, Sung SandAmasino RM. Histone arginine methylation is required for vernalization-induced epigenetic silencing of FLC in winter-annual Arabidopsis thaliana. Proc Natl Acad Sci USA,2008,105:411-416
65. Pei Y, Niu L, Lu F, Liu C, Zhai J, Kong XandCao X. Mutations in the Type II protein arginine methyltransferase AtPRMT5 result in pleiotropic developmental defects in Arabidopsis. Plant Physiol,2007,144:1913-1923
66. Wang X, Zhang Y, Ma Q, Zhang Z, Xue Y, Bao SandChong K. SKB1-mediated symmetric dimethylation of histone H4R3 controls flowering time in Arabidopsis. Embo J,2007,26:1934-1941
67. Niu L, Lu F, Pei Y, Liu CandCao X. Regulation of flowering time by the protein arginine methyltransferase AtPRMT10. EMBO Rep,2007,8:1190-1195
68. Berger SL. Histone modifications in transcriptional regulation. Curr Opin Genet Dev,2002,12:142-148
69. Strahl BDandAllis CD. The language of covalent histone modifications. Nature, 2000,403:41-45
70. Zhang X, Tamaru H, Khan SI, Horton JR, Keefe LJ, Selker EUandCheng X. Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferase. Cell,2002,111:117-127
71. Zhang X, Yang Z, Khan SI, Horton JR, Tamaru H, Selker EUandCheng X. Structural basis for the product specificity of histone lysine methyltransferases. Mol Cell,2003,12:177-185
72. Jenuwein T. The epigenetic magic of histone lysine methylation. Febs J,2006, 273:3121-3135
73. Fuchs J, Demidov D, Houben AandSchubert I. Chromosomal histone modification patterns--from conservation to diversity. Trends Plant Sci,2006,11:199-208
74. Alvarez-Venegas R, Pien S, Sadder M, Witmer X, Grossniklaus UandAvramova Z. ATX-1, an Arabidopsis homolog of trithorax, activates flower homeotic genes. Curr Biol,2003,13:627-637
75. Boa S, Coert CandPatterton HG. Saccharomyces cerevisiae Set1p is a methyltransferase specific for lysine 4 of histone H3 and is required for efficient gene expression. Yeast,2003,20:827-835
76. Bernstein BE, Humphrey EL, Erlich RL, Schneider R, Bouman P, Liu JS, Kouzarides TandSchreiber SL. Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci U S A,2002,99:8695-8700
77. Santos-Rosa H, Schneider R, Bannister AJ, Sherriff J, Bernstein BE, Emre NC, Schreiber SL, Mellor JandKouzarides T. Active genes are tri-methylated at K4 of histone H3. Nature,2002,419:407-411
78. Strahl BD, Grant PA, Briggs SD, Sun ZW, Bone JR, Caldwell JA, Mollah S, Cook RG, Shabanowitz J, Hunt DFandAllis CD. Set2 is a nucleosomal histone H3-selective methyltransferase that mediates transcriptional repression. Mol Cell Biol,2002,22:1298-1306
79. Xiao T, Hall H, Kizer KO, Shibata Y, Hall MC, Borchers CHandStrahl BD. Phosphorylation of RNA polymerase Ⅱ CTD regulates H3 methylation in yeast. Genes Dev,2003,17:654-663
80. Krogan NJ, Kim M, Tong A, Golshani A, Cagney G, Canadien V, Richards DP, Beattie BK, Emili A, Boone C, Shilatifard A, Buratowski SandGreenblatt J. Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase Ⅱ. Mol Cell Biol,2003,23: 4207-4218
81. Li B, Howe L, Anderson S, Yates JR,3rdandWorkman JL. The Set2 histone methyltransferase functions through the phosphorylated carboxyl-terminal domain of RNA polymerase II. JBiol Chem,2003,278:8897-8903
82. Li J, Moazed DandGygi SP. Association of the histone methyltransferase Set2 with RNA polymerase II plays a role in transcription elongation. J Biol Chem, 2002,277:49383-49388
83. Schaft D, Roguev A, Kotovic KM, Shevchenko A, Sarov M, Shevchenko A, Neugebauer KMandStewart AF. The histone 3 lysine 36 methyltransferase, SET2, is involved in transcriptional elongation. Nucleic Acids Res,2003,31:2475-2482
84. Zhao Z, Yu Y, Meyer D, Wu CandShen WH. Prevention of early flowering by expression of FLOWERING LOCUS C requires methylation of histone H3 K36. Nat Cell Biol,2005,7:1256-1260
85. Berr A, Xu L, Gao J, Cognat V, Steinmetz A, Dong AandShen WH. 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
86. Cartagena JA, Matsunaga S, Seki M, Kurihara D, Yokoyama M, Shinozaki K, Fujimoto S, Azumi Y, Uchiyama SandFukui 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
87. Richards EJandElgin SC. Epigenetic codes for heterochromatin formation and silencing:rounding up the usual suspects. Cell,2002,108:489-500
88. Weiler KSandWakimoto BT. Heterochromatin and gene expression in Drosophila. Annu Rev Genet,1995,29:577-605
89. Eissenberg JC, James TC, Foster-Hartnett DM, Hartnett T, Ngan VandElgin SC. Mutation in a heterochromatin-specific chromosomal protein is associated with suppression of position-effect variegation in Drosophila melanogaster. Proc Natl Acad Sci USA,1990,87:9923-9927
90. Goll MGandBestor TH. Histone modification and replacement in chromatin activation. Genes Dev,2002,16:1739-1742
91. Peters AH, O'Carroll D, Scherthan H, Mechtler K, Sauer S, Schofer C, Weipoltshammer K, Pagani M, Lachner M, Kohlmaier A, Opravil S, Doyle M, Sibilia MandJenuwein T. Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability. Cell,2001,107:323-337
92. Noma K, Allis CDandGrewal SI. Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science,2001,293:1150-1155
93. Peters AH, Kubicek S, Mechtler K, O'Sullivan RJ, Derijck AA, Perez-Burgos L, Kohlmaier A, Opravil S, Tachibana M, Shinkai Y, Martens JHandJenuwein T. Partitioning and plasticity of repressive histone methylation states in mammalian chromatin. Mol Cell,2003,12:1577-1589
94. Rice JC, Briggs SD, Ueberheide B, Barber CM, Shabanowitz J, Hunt DF, Shinkai YandAllis CD. Histone methyltransferases direct different degrees of methylation to define distinct chromatin domains. Mol Cell,2003,12:1591-1598
95. Saccani SandNatoli G. Dynamic changes in histone H3 Lys 9 methylation occurring at tightly regulated inducible inflammatory genes. Genes Dev,2002,16: 2219-2224
96. Tachibana M, Ueda J, Fukuda M, Takeda N, Ohta T, Iwanari H, Sakihama T, Kodama T, Hamakubo TandShinkai Y. Histone methyltransferases G9a and GLP form heteromeric complexes and are both crucial for methylation of euchromatin at H3-K9. Genes Dev,2005,19:815-826
97. Nielsen SJ, Schneider R, Bauer UM, Bannister AJ, Morrison A, O'Carroll D, Firestein R, Cleary M, Jenuwein T, Herrera REandKouzarides T. Rb targets histone H3 methylation and HP1 to promoters. Nature,2001,412:561-565
98. Schultz DC, Ayyanathan K, Negorev D, Maul GGandRauscher FJ,3rd. SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP 1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins. Genes Dev,2002,16:919-932
99. Malagnac F, Bartee LandBender J. An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation. Embo J,2002,21: 6842-6852
100. Ding Y, Wang X, Su L, Zhai J, Cao S, Zhang D, Liu C, Bi Y, Qian Q, Cheng Z, Chu CandCao X. SDG714, a histone H3K9 methyltransferase, is involved in Tosl7 DNA methylation and transposition in rice. Plant Cell,2007,19:9-22
101. Hirochika H, Okamoto HandKakutani T. Silencing of retrotransposons in arabidopsis and reactivation by the ddml mutation. Plant Cell,2000,12:357-369
102. Kakutani T, Jeddeloh JA, Flowers SK, Munakata KandRichards EJ. Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proc Natl Acad Sci U S A,1996,93:12406-12411
103. Gendrel AV, Lippman Z, Yordan C, Colot VandMartienssen RA. Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science,2002,297:1871-1873
104. Kondo Y, Shen LandIssa JP. Critical role of histone methylation in tumor suppressor gene silencing in colorectal cancer. Mol Cell Biol,2003,23:206-215
105. Plath K, Fang J, Mlynarczyk-Evans SK, Cao R, Worringer KA, Wang H, de la Cruz CC, Otte AP, Panning BandZhang Y. Role of histone H3 lysine 27 methylation in X inactivation. Science,2003,300:131-135
106. Silva J, Mak W, Zvetkova I, Appanah R, Nesterova TB, Webster Z, Peters AH, Jenuwein T, Otte APandBrockdorff N. Establishment of histone h3 methylation on the inactive X chromosome requires transient recruitment of Eed-Enxl polycomb group complexes. Dev Cell,2003,4:481-495
107. Boggs BA, Cheung P, Heard E, Spector DL, Chinault ACandAllis CD. Differentially methylated forms of histone H3 show unique association patterns with inactive human X chromosomes. Nat Genet,2002,30:73-76
108. Heard E, Rougeulle C, Arnaud D, Avner P, Allis CDandSpector DL. Methylation of histone H3 at Lys-9 is an early mark on the X chromosome during X inactivation. Cell,2001,107:727-738
109. Peters AH, Mermoud JE, O'Carroll D, Pagani M, Schweizer D, Brockdorff NandJenuwein T. Histone H3 lysine 9 methylation is an epigenetic imprint of facultative heterochromatin. Nat Genet,2002,30:77-80
110. Min J, Zhang YandXu RM. Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. Genes Dev,2003,17: 1823-1828
111. Brown JL, Mucci D, Whiteley M, Dirksen MLandKassis JA. The Drosophila Polycomb group gene pleiohomeotic encodes a DNA binding protein with homology to the transcription factor YY1. Mol Cell,1998,1:1057-1064
112. Czermin B, Melfi R, McCabe D, Seitz V, Imhof AandPirrotta V. Drosophila enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites. Cell,2002,111:185-196
113. Horard B, Tatout C, Poux SandPirrotta V. Structure of a polycomb response element and in vitro binding of polycomb group complexes containing GAGA factor. Mol Cell Biol,2000,20:3187-3197
114. Mulholland NM, King IFandKingston RE. Regulation of Polycomb group complexes by the sequence-specific DNA binding proteins Zeste and GAGA. Genes Dev,2003,17:2741-2746
115. Simon JAandTamkun JW. Programming off and on states in chromatin: mechanisms of Polycomb and trithorax group complexes. Curr Opin Genet Dev, 2002,12:210-218
116. Cao R, Wang L, Wang H, Xia L, Erdjument-Bromage H, Tempst P, Jones RSandZhang Y. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science,2002,298:1039-1043
117. Muller J, Hart CM, Francis NJ, Vargas ML, Sengupta A, Wild B, Miller EL, O'Connor MB, Kingston REandSimon JA. Histone methyltransferase activity of a Drosophila Polycomb group repressor complex. Cell,2002,111:197-208
118. Feng Q, Wang H, Ng HH, Erdjument-Bromage H, Tempst P, Struhl KandZhang Y. Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain. Curr Biol,2002,12:1052-1058
119. Lacoste N, Utley RT, Hunter JM, Poirier GGandCote J. Disruptor of telomeric silencing-1 is a chromatin-specific histone H3 methyltransferase. J Biol Chem, 2002,277:30421-30424
120. Ng HH, Feng Q, Wang H, Erdjument-Bromage H, Tempst P, Zhang YandStruhl K. Lysine methylation within the globular domain of histone H3 by Dotl is important for telomeric silencing and Sir protein association. Genes Dev,2002,16: 1518-1527
121. van Leeuwen F, Gafken PRandGottschling DE. Dotlp modulates silencing in yeast by methylation of the nucleosome core. Cell,2002,109:745-756
122. Fang J, Feng Q, Ketel CS, Wang H, Cao R, Xia L, Erdjument-Bromage H, Tempst P, Simon JAandZhang Y. Purification and functional characterization of SET8, a nucleosomal histone H4-lysine 20-specific methyltransferase. Curr Biol,2002,12: 1086-1099
123. Nishioka K, Rice JC, Sarma K, Erdjument-Bromage H, Werner J, Wang Y, Chuikov S, Valenzuela P, Tempst P, Steward R, Lis JT, Allis CDandReinberg D. PR-Set7 is a nucleosome-specific methyltransferase that modifies lysine 20 of histone H4 and is associated with silent chromatin. Mol Cell,2002,9:1201-1213
124. Turner BM. Histone acetylation and an epigenetic code. Bioessays,2000,22: 836-845
125. Allfrey VGandMirsky AE. Structural Modifications of Histones and their Possible Role in the Regulation of RNA Synthesis. Science,1964,144:559
126. Brownell JE, Zhou J, Ranalli T, Kobayashi R, Edmondson DG, Roth SYandAllis CD. Tetrahymena histone acetyltransferase A:a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell,1996,84:843-851
127. Candau RandBerger SL. Structural and functional analysis of yeast putative adaptors. Evidence for an adaptor complex in vivo. J Biol Chem,1996,271: 5237-5245
128. Neuwald AFandLandsman D. GCN5-related histone N-acetyltransferases belong to a diverse superfamily that includes the yeast SPT10 protein. Trends Biochem Sci,1997,22:154-155
129. Bannister AJandKouzarides T. The CBP co-activator is a histone acetyltransferase. Nature,1996,384:641-643
130. Giles RH. Update CBP/p300 transgenic mice. Trends Genet,1998,14:214
131. Pandey R, Muller A, Napoli CA, Selinger DA, Pikaard CS, Richards EJ, Bender J, Mount DWandJorgensen RA. 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
132. Sterner DEandBerger SL. Acetylation of histones and transcription-related factors. Microbiol Mol Biol Rev,2000,64:435-459
133. Leo CandChen JD. The SRC family of nuclear receptor coactivators. Gene,2000, 245:1-11
134. Rundlett SE, Carmen AA, Suka N, Turner BMandGrunstein M. Transcriptional repression by UME6 involves deacetylation of lysine 5 of histone H4 by RPD3. Nature,1998,392:831-835
135. Rundlett SE, Carmen AA, Kobayashi R, Bavykin S, Turner BMandGrunstein M. HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription. Proc Natl Acad Sci U S A,1996,93: 14503-14508
136. De Rubertis F, Kadosh D, Henchoz S, Pauli D, Reuter G, Struhl KandSpierer P. The histone deacetylase RPD3 counteracts genomic silencing in Drosophila and yeast. Nature,1996,384:589-591
137. Vidal MandGaber RF. RPD3 encodes a second factor required to achieve maximum positive and negative transcriptional states in Saccharomyces cerevisiae. Mol Cell Biol,1991,11:6317-6327
138. Landry J, Sutton A, Tafrov ST, Heller RC, Stebbins J, Pillus LandSternglanz R. The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases. Proc Natl Acad Sci U S A,2000,97:5807-5811
139. Landry J, Slama JTandSternglanz R. Role of NAD(+) in the deacetylase activity of the SIR2-like proteins. Biochem Biophys Res Commun,2000,278:685-690
140. Imai S, Johnson FB, Marciniak RA, McVey M, Park PUandGuarente L. Sir2:an NAD-dependent histone deacetylase that connects chromatin silencing, metabolism, and aging. Cold Spring Harb Symp Quant Biol,2000,65:297-302
141. Imai S, Armstrong CM, Kaeberlein MandGuarente L. Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature, 2000,403:795-800
142. Lusser A, Kolle DandLoidl P. Histone acetylation:lessons from the plant kingdom. Trends Plant Sci,2001,6:59-65
143. Graessle S, Loidl PandBrosch G. Histone acetylation:plants and fungi as model systems for the investigation of histone deacetylases. Cell Mol Life Sci,2001,58: 704-720
144. Frye RA. Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins. Biochem Biophys Res Commun,2000,273:793-798
145. Lusser A, Brosch G, Loidl A, Haas HandLoidl P. Identification of maize histone deacetylase HD2 as an acidic nucleolar phosphoprotein. Science,1997,277:88-91
146. Waterborg JH. Sequence analysis of acetylation and methylation in two histone H3 variants of alfalfa. JBiol Chem,1990,265:17157-17161
147. Waterborg JH. Identification of five sites of acetylation in alfalfa histone H4. Biochemistry,1992,31:6211-6219
148. Kuo MHandAllis CD. Roles of histone acetyltransferases and deacetylases in gene regulation. Bioessays,1998,20:615-626
149. Pazin MJandKadonaga JT. What's up and down with histone deacetylation and transcription? Cell,1997,89:325-328
150. Tse C, Sera T, Wolffe APandHansen JC. Disruption of higher-order folding by core histone acetylation dramatically enhances transcription of nucleosomal arrays by RNA polymerase III. Mol Cell Biol,1998,18:4629-4638
151. Horn PJandPeterson CL. Molecular biology. Chromatin higher order folding--wrapping up transcription. Science,2002,297:1824-1827
152. Zamore PD, Tuschl T, Sharp PAandBartel DP. RNAi:double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell,2000,101:25-33
153. Elbashir SM, Martinez J, Patkaniowska A, Lendeckel WandTuschl T. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. Embo J,2001,20:6877-6888
154. Lee RC, Feinbaum RLandAmbros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell,1993,75: 843-854
155. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HRandRuvkun G. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature,2000,403:901-906
156. Moss EG. Heterochronic genes and the nature of developmental time. Curr Biol, 2007,17:R425-434
157. Pasquinelli AEandRuvkun G. Control of developmental timing by micrornas and their targets. Annu Rev Cell Dev Biol,2002,18:495-513
158. Rougvie AE. Intrinsic and extrinsic regulators of developmental timing:from miRNAs to nutritional cues. Development,2005,132:3787-3798
159. Wu G, Park MY, Conway SR, Wang JW, Weigel DandPoethig RS. The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell,2009,138:750-759
160. Wang JW, Czech BandWeigel D. miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana. Cell,2009,138: 738-749
161. Chandler VLandStam M. Chromatin conversations:mechanisms and implications of paramutation. Nat Rev Genet,2004,5:532-544
162. Chandler VL, Eggleston WBandDorweiler JE. Paramutation in maize. Plant Mol Biol,2000,43:121-145
163. Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, Lavine K, Mittal V, May B, Kasschau KD, Carrington JC, Doerge RW, Colot VandMartienssen R. Role of transposable elements in heterochromatin and epigenetic control. Nature,2004,430:471-476
164. Shen WH. NtSET1, a member of a newly identified subgroup of plant SET-domain-containing proteins, is chromatin-associated and its ectopic overexpression inhibits tobacco plant growth. Plant J,2001,28:371-383
165. Yu Y, Dong AandShen WH. Molecular characterization of the tobacco SET domain protein NtSET1 unravels its role in histone methylation, chromatin binding, and segregation. Plant J,2004,40:699-711
166. Baumbusch LO, Thorstensen T, Krauss V, Fischer A, Naumann K, Assalkhou R, Schulz I, Reuter GandAalen RB. The Arabidopsis thaliana genome contains at least 29 active genes encoding SET domain proteins that can be assigned to four evolutionarily conserved classes. Nucleic Acids Res,2001,29:4319-4333
167. Ebbs ML, Bartee LandBender J. H3 lysine 9 methylation is maintained on a transcribed inverted repeat by combined action of SUVH6 and SUVH4 methyltransferases. Mol Cell Biol,2005,25:10507-10515
168. Bertrand C, Bergounioux C, Domenichini S, Delarue MandZhou DX. Arabidopsis histone acetyltransferase AtGCN5 regulates the floral meristem activity through the WUSCHEL/AGAMOUS pathway. JBiol Chem,2003,278:28246-28251
169. Taunton J, Hassig CAandSchreiber SL. A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p. Science,1996,272:408-411
170. Grozinger CMandSchreiber SL. Deacetylase enzymes:biological functions and the use of small-molecule inhibitors. Chem Biol,2002,9:3-16
171. Moazed D. Enzymatic activities of Sir2 and chromatin silencing. Curr Opin Cell Biol,2001,13:232-238
172. Tian LandChen ZJ. Blocking histone deacetylation in Arabidopsis induces pleiotropic effects on plant gene regulation and development. Proc Natl Acad Sci USA,2001,98:200-205
173. Wu K, Malik K, Tian L, Brown DandMiki B. Functional analysis of a RPD3 histone deacetylase homologue in Arabidopsis thaliana. Plant Mol Biol,2000,44: 167-176
174. Zhou C, Zhang L, Duan J, Miki BandWu K. HISTONE DEACETYLASE19 is involved in jasmonic acid and ethylene signaling of pathogen response in Arabidopsis. Plant Cell,2005,17:1196-1204
175. Gonzalez D, Bowen AJ, Carroll TSandConlan RS. The transcription corepressor LEUNIG interacts with the histone deacetylase HDA19 and mediator components MED14 (SWP) and CDK8 (HEN3) to repress transcription. Mol Cell Biol,2007, 27:5306-5315
176. Kim KC, Lai Z, Fan BandChen Z. Arabidopsis WRKY38 and WRKY62 transcription factors interact with histone deacetylase 19 in basal defense. Plant Cell,2008,20:2357-2371
177. Aufsatz W, Mette MF, van der Winden J, Matzke MandMatzke AJ. HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double-stranded RNA. Embo J,2002,21:6832-6841
178. Murfett J, Wang XJ, Hagen GandGuilfoyle TJ. Identification of Arabidopsis histone deacetylase HDA6 mutants that affect transgene expression. Plant Cell, 2001,13:1047-1061
179. Jang IC, Pahk YM, Song SI, Kwon HJ, Nahm BHandKim JK. Structure and expression of the rice class-Ⅰ type histone deacetylase genes OsHDAC1-3: OsHDAC1 overexpression in transgenic plants leads to increased growth rate and altered architecture. Plant J,2003,33:531-541
180. Finnegan EJ. Is plant gene expression regulated globally? Trends Genet,2001,17: 361-365
181. Grozinger CM, Chao ED, Blackwell HE, Moazed DandSchreiber SL. Identification of a class of small molecule inhibitors of the sirtuin family of NAD-dependent deacetylases by phenotypic screening. J Biol Chem,2001,276: 38837-38843
182. Huang L, Sun Q, Qin F, Li C, Zhao YandZhou DX. Down-Regulation of a SILENT INFORMATION REGULATOR2-Related Histone Deacetylase Gene, OsSRT1, Induces DNA Fragmentation and Cell Death in Rice. Plant Physiol, 2007,144:1508-1519
183. Chung PJ, Kim YS, Jeong JS, Park SH, Nahm BHandKim JK. The histone deacetylase OsHDAC1 epigenetically regulates the OsNAC6 gene that controls seedling root growth in rice. Plant J,2009,59:764-776
184. Hecht AandGrunstein M. Mapping DNA interaction sites of chromosomal proteins using immunoprecipitation and polymerase chain reaction. Methods Enzymol, 1999,304:399-414
185. Orlando V, Strutt HandParo R. Analysis of chromatin structure by in vivo formaldehyde cross-linking. Methods,1997,11:205-214
186. Zilberman D, Gehring M, Tran RK, Ballinger TandHenikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet,2007,39:61-69
187. Church GMandGilbert W. Genomic sequencing. Proc Natl Acad Sci U S A,1984, 81:1991-1995
188. Hiei Y, Ohta S, Komari TandKumashiro T. Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. Plant J,1994,6:271-282
189. Tariq M, Saze H, Probst AV, Lichota J, Habu YandPaszkowski J. Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin. Proc Natl Acad Sci USA,2003,100:8823-8827
190. Marmorstein R. Structure of SET domain proteins:a new twist on histone methylation. Trends Biochem Sci,2003,28:59-62
191. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin FandHiggins DG. The CLUSTAL_X windows interface:flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res,1997,25:4876-4882
192. Kumar S, Tamura KandNei M. MEGA3:Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform,2004,5: 150-163
193. Letunic I, Copley RR, Pils B, Pinkert S, Schultz JandBork P. SMART 5:domains in the context of genomes and networks. Nucleic Acids Res,2006,34:D257-260
194. Collins RE, Tachibana M, Tamaru H, Smith KM, Jia D, Zhang X, Selker EU, Shinkai YandCheng X. In vitro and in vivo analyses of a Phe/Tyr switch controlling product specificity of histone lysine methyltransferases. J Biol Chem, 2005,280:5563-5570
195. Baulcombe D. RNA silencing in plants. Nature,2004,431:356-363
196. Montgomery MK. RNA interference:historical overview and significance. Methods Mol Biol,2004,265:3-21
197. Zhou HJ, Tsai SYandTsai MJ. RNAi technology and its use in studying the function of nuclear receptors and coregulators. Nucl Recept Signal,2003,1:e008
198. Eisen MB, Spellman PT, Brown POandBotstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A,1998,95: 14863-14868
199. Dai M, Zhao Y, Ma Q, Hu Y, Hedden P, Zhang QandZhou DX. The rice YABBY1 gene is involved in the feedback regulation of gibberellin metabolism. Plant Physiol,2007,144:121-133
200. Dai M, Hu Y, Zhao Y, Liu HandZhou DX. A WUSCHEL-LIKE HOMEOBOX gene represses a YABBY gene expression required for rice leaf development. Plant Physiol,2007,144:380-390
201. Dong A, Liu Z, Zhu Y, Yu F, Li Z, Cao KandShen WH. Interacting proteins and differences in nuclear transport reveal specific functions for the NAP1 family proteins in plants. Plant Physiol,2005,138:1446-1456
202. Hirochika H, Sugimoto K, Otsuki Y, Tsugawa HandKanda M. Retrotransposons of rice involved in mutations induced by tissue culture. Proc Natl Acad Sci U S A, 1996,93:7783-7788
203. Cheng C, Daigen MandHirochika H. Epigenetic regulation of the rice retrotransposon Tos17. Mol Genet Genomics,2006,276:378-390
204. Eriksson S, Bohlenius H, Moritz TandNilsson O. GA4 is the active gibberellin in the regulation of LEAFY transcription and Arabidopsis floral initiation. Plant Cell, 2006,18:2172-2181
205. Huang S, Cerny RE, Qi Y, Bhat D, Aydt CM, Hanson DD, Malloy KPandNess LA. Transgenic studies on the involvement of cytokinin and gibberellin in male development. Plant Physiol,2003,131:1270-1282
206. Ishii TandNishijima T. Inhibition of gibberellin-induced elongation growth of rice by feruloyl oligosaccharides. Plant Cell Physiol,1995,36:1447-1451
207. King KE, Moritz TandHarberd NP. Gibberellins are not required for normal stem growth in Arabidopsis thaliana in the absence of GAI and RGA. Genetics,2001, 159:767-776
208. Oh E, Yamaguchi S, Kamiya Y, Bae G, Chung WIandChoi G. Light activates the degradation of PIL5 protein to promote seed germination through gibberellin in Arabidopsis. Plant J,2006,47:124-139
209. Stavang JA, Lindgard B, Erntsen A, Lid SE, Moe RandOlsen JE. Thermoperiodic stem elongation involves transcriptional regulation of gibberellin deactivation in pea. Plant Physiol,2005,138:2344-2353
210. Cannon SB, Mitra A, Baumgarten A, Young NDandMay G. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol,2004,4:10
211. Kong H, Landherr LL, Frohlich MW, Leebens-Mack J, Ma HanddePamphilis CW. Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth. Plant J,2007,50:873-885
212. Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C, Zhang J, Zhang Y, Li R, Xu Z, Li S, Li X, Zheng H, Cong L, Lin L, Yin J, et al.,. The Genomes of Oryza sativa:a history of duplications. PLoS Biol,2005,3:e38
213. Ray S, Agarwal P, Arora R, Kapoor SandTyagi AK. Expression analysis of calcium-dependent protein kinase gene family during reproductive development and abiotic stress conditions in rice (Oryza sativa L. ssp. indica). Mol Genet Genomics,2007,278:493-505
214. Goodrich J, Puangsomlee P, Martin M, Long D, Meyerowitz EMandCoupland G. A Polycomb-group gene regulates homeotic gene expression in Arabidopsis. Nature,1997,386:44-51
215. Grossniklaus U, Vielle-Calzada JP, Hoeppner MAandGagliano WB. Maternal control of embryogenesis by MEDEA, a polycomb group gene in Arabidopsis. Science,1998,280:446-450
216. Kiyosue T, Ohad N, Yadegari R, Hannon M, Dinneny J, Wells D, Katz A, Margossian L, Harada JJ, Goldberg RBandFischer RL. Control of fertilization-independent endosperm development by the MEDEA polycomb gene in Arabidopsis. Proc Natl Acad Sci U S A,1999,96:4186-4191
217. Luo M, Bilodeau P, Dennis ES, Peacock WJandChaudhury A. Expression and parent-of-origin effects for FIS2, MEA, and FIE in the endosperm and embryo of developing Arabidopsis seeds. Proc Natl Acad Sci USA,2000,97:10637-10642
218. Vielle-Calzada JP, Thomas J, Spillane C, Coluccio A, Hoeppner MAandGrossniklaus U. Maintenance of genomic imprinting at the Arabidopsis medea locus requires zygotic DDM1 activity. Genes Dev,1999,13:2971-2982
219. Sun QandZhou DX. Rice jmjC domain-containing gene JMJ706 encodes H3K9 demethylase required for floral organ development. Proc Natl Acad Sci U S A, 2008,105:13679-13684
220. Turck F, Roudier F, Farrona S, Martin-Magniette ML, Guillaume E, Buisine N, Gagnot S, Martienssen RA, Coupland GandColot V. Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 21.PLoS Genet,2001,3:e86
221. Dillon SC, Zhang X, Trievel RCandCheng X. The SET-domain protein superfamily:protein lysine methyltransferases. Genome Biol,2005,6:227
222. Dong G, Ma DPandLi J. The histone methyltransferase SDG8 regulates shoot branching in Arabidopsis. Biochem Biophys Res Commun,2008,373:659-664
223. Lippman Z, May B, Yordan C, Singer TandMartienssen R. Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS Biol,2003,1:E67
224. Mathieu O, Probst AVandPaszkowski J. Distinct regulation of histone H3 methylation at lysines 27 and 9 by CpG methylation in Arabidopsis. Embo J,2005, 24:2783-2791
225. Tran RK, Zilberman D, de Bustos C, Ditt RF, Henikoff JQ Lindroth AM, Delrow J, Boyle T, Kwong S, Bryson TD, Jacobsen SEandHenikoff S. Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biol,2005,6:R90
226. Jain M, Nijhawan A, Arora R, Agarwal P, Ray S, Sharma P, Kapoor S, Tyagi AKandKhurana JP. F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol,2007,143:1467-1483
2. Nanney DL. Epigenetic Control Systems. Proc Natl Acad Sci U S A,1958,44: 712-717
3. Haig D. The (dual) origin of epigenetics. Cold Spring Harb Symp Quant Biol, 2004,69:67-70
4. Holliday R. The inheritance of epigenetic defects. Science,1987,238:163-170
5. Holliday R. Epigenetics:an overview. Dev Genet,1994,15:453-457
6. Riggs ADandPorter TN. Overview of epigenetic mechanisms. In Epigenetic mechanisms of gene regulation,1996,29-45
7. Allis CD, Jenuwein TandReinberg D. Epigenetics. Gottschling DE, editor. New York:Cold Spring Harbor Laboratory Press; 2006.2 p.
8. Wolffe APandMatzke MA. Epigenetics:regulation through repression. Science, 1999,286:481-486
9. Roloff TCandNuber UA. Chromatin, epigenetics and stem cells. Eur J Cell Biol, 2005,84:123-135
10. Avery OT, Macleod CMandMcCarty M. Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types:Induction of Transformation by a Desoxyribonucleic Acid Fraction Isolated from Pneumococcus Type Iii. J Exp Med,1944,79:137-158
11. Kornberg RD. Chromatin structure:a repeating unit of histones and DNA. Science, 1974,184:868-871
12. Luger K, Mader AW, Richmond RK, Sargent DFandRichmond TJ. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature,1997,389: 251-260
13. Luger K, Rechsteiner TJ, Flaus AJ, Waye MMandRichmond TJ. Characterization of nucleosome core particles containing histone proteins made in bacteria. J Mol Biol,1997,272:301-311
14. Arents GandMoudrianakis EN. Topography of the histone octamer surface: repeating structural motifs utilized in the docking of nucleosomal DNA. Proc Natl Acad Sci U S A,1993,90:10489-10493
15. Karpen GHandAllshire RC. The case for epigenetic effects on centromere identity and function. Trends Genet,1997,13:489-496
16. Holliday RandPugh JE. DNA modification mechanisms and gene activity during development. Science,1975,187:226-232
17. Riggs AD. X inactivation, differentiation, and DNA methylation; 1975.9-25 p.
18. Bird AP. The occurrence and transmission of a pattern of DNA methylation in Xenopus laevis ribosomal DNA. Philos Trans R Soc Lond B Biol Sci,1978,283: 325-327
19. Ehrlich M, Gama-Sosa MA, Huang LH, Midgett RM, Kuo KC, McCune RAandGehrke C. Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells. Nucleic Acids Res,1982,10:2709-2721
20. Posfai J, Bhagwat AS, Posfai GandRoberts RJ. Predictive motifs derived from cytosine methyltransferases. Nucleic Acids Res,1989,17:2421-2435
21. Bestor T. Structure of mammalian DNA methyltransferase as deduced from the inferred amino acid sequence and direct studies of the protein. Biochem Soc Trans, 1988,16:944-947
22. Finnegan EJ, Peacock WJandDennis ES. Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proc Natl Acad Sci U SA,1996,93:8449-8454
23. Chan SW, Henderson IRandJacobsen SE. Gardening the genome:DNA methylation in Arabidopsis thaliana. Nat Rev Genet,2005,6:351-360
24. Finnegan EJandDennis ES. Isolation and identification by sequence homology of a putative cytosine methyltransferase from Arabidopsis thaliana. Nucleic Acids Res,1993,21:2383-2388
25. Kishimoto N, Sakai H, Jackson J, Jacobsen SE, Meyerowitz EM, Dennis ESandFinnegan EJ. Site specificity of the Arabidopsis METI DNA methyltransferase demonstrated through hypermethylation of the superman locus. Plant Mol Biol,2001,46:171-183
26. Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff SandJacobsen SE. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science,2001,292:2077-2080
27. Ronemus MJ, Galbiati M, Ticknor C, Chen JandDellaporta SL. Demethylation-induced developmental pleiotropy in Arabidopsis. Science,1996, 273:654-657
28. Vongs A, Kakutani T, Martienssen RAandRichards EJ. Arabidopsis thaliana DNA methylation mutants. Science,1993,260:1926-1928
29. Henikoff SandComai L. A DNA methyltransferase homolog with a chromodomain exists in multiple polymorphic forms in Arabidopsis. Genetics,1998,149: 307-318
30. Bartee L, Malagnac FandBender J. Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Genes Dev,2001, 15:1753-1758
31. McCallum CM, Comai L, Greene EAandHenikoff S. Targeted screening for induced mutations. Nat Biotechnol,2000,18:455-457
32. Jackson JP, Lindroth AM, Cao XandJacobsen SE. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature,2002, 416:556-560
33. Cao X, Springer NM, Muszynski MG, Phillips RL, Kaeppler SandJacobsen SE. Conserved plant genes with similarity to mammalian de novo DNA methyltransferases. Proc Natl Acad Sci USA,2000,97:4979-4984
34. Okano M, Bell DW, Haber DAandLi E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell, 1999,99:247-257
35. Lyko F, Ramsahoye BH, Kashevsky H, Tudor M, Mastrangelo MA, Orr-Weaver TLandJaenisch R. Mammalian (cytosine-5) methyltransferases cause genomic DNA methylation and lethality in Drosophila. Nat Genet,1999,23:363-366
36. Hsieh CL. In vivo activity of murine de novo methyltransferases, Dnmt3a and Dnmt3b. Mol Cell Biol,1999,19:8211-8218
37. Okano M, Xie SandLi E. Dnmt2 is not required for de novo and maintenance methylation of viral DNA in embryonic stem cells. Nucleic Acids Res,1998,26: 2536-2540
38. Cao XandJacobsen SE. Role of the arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol,2002,12:1138-1144
39. Loidl P. A plant dialect of the histone language. Trends Plant Sci,2004,9:84-90
40. Fischle W, Wang YandAllis CD. Histone and chromatin cross-talk. Curr Opin Cell Biol,2003,15:172-183
41. Turner BM. Cellular memory and the histone code. Cell,2002,111:285-291
42. Jenuwein TandAllis CD. Translating the histone code. Science,2001,293: 1074-1080
43. Jaskelioff MandPeterson CL. Chromatin and transcription:histones continue to make their marks. Nat Cell Biol,2003,5:395-399
44. Fischle W, Wang Y, Jacobs SA, Kim Y, Allis CDandKhorasanizadeh S. Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. Genes Dev,2003,17:1870-1881
45. Zhang YandReinberg D. Transcription regulation by histone methylation:interplay between different covalent modifications of the core histone tails. Genes Dev, 2001,15:2343-2360
46. Lee JH, Cook JR, Yang ZH, Mirochnitchenko O, Gunderson SI, Felix AM, Herth N, Hoffmann RandPestka S. PRMT7, a new protein arginine methyltransferase that synthesizes symmetric dimethylarginine. JBiol Chem,2005,280:3656-3664
47. Lachner M, O'Sullivan RJandJenuwein T. An epigenetic road map for histone lysine methylation. J Cell Sci,2003,116:2117-2124
48. Bannister AJandKouzarides T. Reversing histone methylation. Nature,2005,436: 1103-1106
49. Lachner M, Sengupta R, Schotta GandJenuwein T. Trilogies of histone lysine methylation as epigenetic landmarks of the eukaryotic genome. Cold Spring Harb Symp Quant Biol,2004,69:209-218
50. Zhang X, Zhou LandCheng X. Crystal structure of the conserved core of protein arginine methyltransferase PRMT3. Embo J,2000,19:3509-3519
51. Weiss VH, McBride AE, Soriano MA, Filman DJ, Silver PAandHogle JM. The structure and oligomerization of the yeast arginine methyltransferase, Hmtl. Nat Struct Biol,2000,7:1165-1171
52. Ebbs MLandBender J. Locus-specific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase. Plant Cell,2006,18:1166-1176
53. Zhao W, Soejima H, Higashimoto K, Nakagawachi T, Urano T, Kudo S, Matsukura S, Matsuo S, Joh KandMukai T. 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,2005,137:431-440
54. Naumann K, Fischer A, Hofmann I, Krauss V, Phalke S, Irmler K, Hause G, Aurich AC, Dorn R, Jenuwein TandReuter G. Pivotal role of AtSUVH2 in heterochromatic histone methylation and gene silencing in Arabidopsis. Embo J, 2005,24:1418-1429
55. Kim SY, He Y, Jacob Y, Noh YS, Michaels SandAmasino R. Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyl transferase. Plant Cell,2005,17:3301-3310
56. Fang J, Wang HandZhang Y. Purification of histone methyltransferases from HeLa cells. Methods Enzymol,2004,377:213-226
57. Rea S, Eisenhaber F, O'Carroll D, Strahl BD, Sun ZW, Schmid M, Opravil S, Mechtler K, Ponting CP, Allis CDandJenuwein T. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature,2000,406: 593-599
58. Bedford MTandRichard S. Arginine methylation an emerging regulator of protein function. Mol Cell,2005,18:263-272
59. Boisvert FM, Cote J, Boulanger MCandRichard S. A proteomic analysis of arginine-methylated protein complexes. Mol Cell Proteomics,2003,2:1319-1330
60. Lin WJ, Gary JD, Yang MC, Clarke SandHerschman HR. The mammalian immediate-early TIS21 protein and the leukemia-associated BTG1 protein interact with a protein-arginine N-methyltransferase.J Biol Chem,1996,271: 15034-15044
61. Wang H, Huang ZQ, Xia L, Feng Q, Erdjument-Bromage H, Strahl BD, Briggs SD, Allis CD, Wong J, Tempst PandZhang Y. Methylation of histone H4 at arginine 3 facilitating transcriptional activation by nuclear hormone receptor. Science,2001,293:853-857
62. Frankel AandClarke S. PRMT3 is a distinct member of the protein arginine N-methyltransferase family. Conferral of substrate specificity by a zinc-finger domain. J Biol Chem,2000,275:32974-32982
63. Cook JR, Lee JH, Yang ZH, Krause CD, Herth N, Hoffmann RandPestka S. FBXO11/PRMT9, a new protein arginine methyltransferase, symmetrically dimethylates arginine residues. Biochem Biophys Res Commun,2006,342: 472-481
64. Schmitz RJ, Sung SandAmasino RM. Histone arginine methylation is required for vernalization-induced epigenetic silencing of FLC in winter-annual Arabidopsis thaliana. Proc Natl Acad Sci USA,2008,105:411-416
65. Pei Y, Niu L, Lu F, Liu C, Zhai J, Kong XandCao X. Mutations in the Type II protein arginine methyltransferase AtPRMT5 result in pleiotropic developmental defects in Arabidopsis. Plant Physiol,2007,144:1913-1923
66. Wang X, Zhang Y, Ma Q, Zhang Z, Xue Y, Bao SandChong K. SKB1-mediated symmetric dimethylation of histone H4R3 controls flowering time in Arabidopsis. Embo J,2007,26:1934-1941
67. Niu L, Lu F, Pei Y, Liu CandCao X. Regulation of flowering time by the protein arginine methyltransferase AtPRMT10. EMBO Rep,2007,8:1190-1195
68. Berger SL. Histone modifications in transcriptional regulation. Curr Opin Genet Dev,2002,12:142-148
69. Strahl BDandAllis CD. The language of covalent histone modifications. Nature, 2000,403:41-45
70. Zhang X, Tamaru H, Khan SI, Horton JR, Keefe LJ, Selker EUandCheng X. Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferase. Cell,2002,111:117-127
71. Zhang X, Yang Z, Khan SI, Horton JR, Tamaru H, Selker EUandCheng X. Structural basis for the product specificity of histone lysine methyltransferases. Mol Cell,2003,12:177-185
72. Jenuwein T. The epigenetic magic of histone lysine methylation. Febs J,2006, 273:3121-3135
73. Fuchs J, Demidov D, Houben AandSchubert I. Chromosomal histone modification patterns--from conservation to diversity. Trends Plant Sci,2006,11:199-208
74. Alvarez-Venegas R, Pien S, Sadder M, Witmer X, Grossniklaus UandAvramova Z. ATX-1, an Arabidopsis homolog of trithorax, activates flower homeotic genes. Curr Biol,2003,13:627-637
75. Boa S, Coert CandPatterton HG. Saccharomyces cerevisiae Set1p is a methyltransferase specific for lysine 4 of histone H3 and is required for efficient gene expression. Yeast,2003,20:827-835
76. Bernstein BE, Humphrey EL, Erlich RL, Schneider R, Bouman P, Liu JS, Kouzarides TandSchreiber SL. Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci U S A,2002,99:8695-8700
77. Santos-Rosa H, Schneider R, Bannister AJ, Sherriff J, Bernstein BE, Emre NC, Schreiber SL, Mellor JandKouzarides T. Active genes are tri-methylated at K4 of histone H3. Nature,2002,419:407-411
78. Strahl BD, Grant PA, Briggs SD, Sun ZW, Bone JR, Caldwell JA, Mollah S, Cook RG, Shabanowitz J, Hunt DFandAllis CD. Set2 is a nucleosomal histone H3-selective methyltransferase that mediates transcriptional repression. Mol Cell Biol,2002,22:1298-1306
79. Xiao T, Hall H, Kizer KO, Shibata Y, Hall MC, Borchers CHandStrahl BD. Phosphorylation of RNA polymerase Ⅱ CTD regulates H3 methylation in yeast. Genes Dev,2003,17:654-663
80. Krogan NJ, Kim M, Tong A, Golshani A, Cagney G, Canadien V, Richards DP, Beattie BK, Emili A, Boone C, Shilatifard A, Buratowski SandGreenblatt J. Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase Ⅱ. Mol Cell Biol,2003,23: 4207-4218
81. Li B, Howe L, Anderson S, Yates JR,3rdandWorkman JL. The Set2 histone methyltransferase functions through the phosphorylated carboxyl-terminal domain of RNA polymerase II. JBiol Chem,2003,278:8897-8903
82. Li J, Moazed DandGygi SP. Association of the histone methyltransferase Set2 with RNA polymerase II plays a role in transcription elongation. J Biol Chem, 2002,277:49383-49388
83. Schaft D, Roguev A, Kotovic KM, Shevchenko A, Sarov M, Shevchenko A, Neugebauer KMandStewart AF. The histone 3 lysine 36 methyltransferase, SET2, is involved in transcriptional elongation. Nucleic Acids Res,2003,31:2475-2482
84. Zhao Z, Yu Y, Meyer D, Wu CandShen WH. Prevention of early flowering by expression of FLOWERING LOCUS C requires methylation of histone H3 K36. Nat Cell Biol,2005,7:1256-1260
85. Berr A, Xu L, Gao J, Cognat V, Steinmetz A, Dong AandShen WH. 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
86. Cartagena JA, Matsunaga S, Seki M, Kurihara D, Yokoyama M, Shinozaki K, Fujimoto S, Azumi Y, Uchiyama SandFukui 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
87. Richards EJandElgin SC. Epigenetic codes for heterochromatin formation and silencing:rounding up the usual suspects. Cell,2002,108:489-500
88. Weiler KSandWakimoto BT. Heterochromatin and gene expression in Drosophila. Annu Rev Genet,1995,29:577-605
89. Eissenberg JC, James TC, Foster-Hartnett DM, Hartnett T, Ngan VandElgin SC. Mutation in a heterochromatin-specific chromosomal protein is associated with suppression of position-effect variegation in Drosophila melanogaster. Proc Natl Acad Sci USA,1990,87:9923-9927
90. Goll MGandBestor TH. Histone modification and replacement in chromatin activation. Genes Dev,2002,16:1739-1742
91. Peters AH, O'Carroll D, Scherthan H, Mechtler K, Sauer S, Schofer C, Weipoltshammer K, Pagani M, Lachner M, Kohlmaier A, Opravil S, Doyle M, Sibilia MandJenuwein T. Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability. Cell,2001,107:323-337
92. Noma K, Allis CDandGrewal SI. Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science,2001,293:1150-1155
93. Peters AH, Kubicek S, Mechtler K, O'Sullivan RJ, Derijck AA, Perez-Burgos L, Kohlmaier A, Opravil S, Tachibana M, Shinkai Y, Martens JHandJenuwein T. Partitioning and plasticity of repressive histone methylation states in mammalian chromatin. Mol Cell,2003,12:1577-1589
94. Rice JC, Briggs SD, Ueberheide B, Barber CM, Shabanowitz J, Hunt DF, Shinkai YandAllis CD. Histone methyltransferases direct different degrees of methylation to define distinct chromatin domains. Mol Cell,2003,12:1591-1598
95. Saccani SandNatoli G. Dynamic changes in histone H3 Lys 9 methylation occurring at tightly regulated inducible inflammatory genes. Genes Dev,2002,16: 2219-2224
96. Tachibana M, Ueda J, Fukuda M, Takeda N, Ohta T, Iwanari H, Sakihama T, Kodama T, Hamakubo TandShinkai Y. Histone methyltransferases G9a and GLP form heteromeric complexes and are both crucial for methylation of euchromatin at H3-K9. Genes Dev,2005,19:815-826
97. Nielsen SJ, Schneider R, Bauer UM, Bannister AJ, Morrison A, O'Carroll D, Firestein R, Cleary M, Jenuwein T, Herrera REandKouzarides T. Rb targets histone H3 methylation and HP1 to promoters. Nature,2001,412:561-565
98. Schultz DC, Ayyanathan K, Negorev D, Maul GGandRauscher FJ,3rd. SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP 1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins. Genes Dev,2002,16:919-932
99. Malagnac F, Bartee LandBender J. An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation. Embo J,2002,21: 6842-6852
100. Ding Y, Wang X, Su L, Zhai J, Cao S, Zhang D, Liu C, Bi Y, Qian Q, Cheng Z, Chu CandCao X. SDG714, a histone H3K9 methyltransferase, is involved in Tosl7 DNA methylation and transposition in rice. Plant Cell,2007,19:9-22
101. Hirochika H, Okamoto HandKakutani T. Silencing of retrotransposons in arabidopsis and reactivation by the ddml mutation. Plant Cell,2000,12:357-369
102. Kakutani T, Jeddeloh JA, Flowers SK, Munakata KandRichards EJ. Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proc Natl Acad Sci U S A,1996,93:12406-12411
103. Gendrel AV, Lippman Z, Yordan C, Colot VandMartienssen RA. Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science,2002,297:1871-1873
104. Kondo Y, Shen LandIssa JP. Critical role of histone methylation in tumor suppressor gene silencing in colorectal cancer. Mol Cell Biol,2003,23:206-215
105. Plath K, Fang J, Mlynarczyk-Evans SK, Cao R, Worringer KA, Wang H, de la Cruz CC, Otte AP, Panning BandZhang Y. Role of histone H3 lysine 27 methylation in X inactivation. Science,2003,300:131-135
106. Silva J, Mak W, Zvetkova I, Appanah R, Nesterova TB, Webster Z, Peters AH, Jenuwein T, Otte APandBrockdorff N. Establishment of histone h3 methylation on the inactive X chromosome requires transient recruitment of Eed-Enxl polycomb group complexes. Dev Cell,2003,4:481-495
107. Boggs BA, Cheung P, Heard E, Spector DL, Chinault ACandAllis CD. Differentially methylated forms of histone H3 show unique association patterns with inactive human X chromosomes. Nat Genet,2002,30:73-76
108. Heard E, Rougeulle C, Arnaud D, Avner P, Allis CDandSpector DL. Methylation of histone H3 at Lys-9 is an early mark on the X chromosome during X inactivation. Cell,2001,107:727-738
109. Peters AH, Mermoud JE, O'Carroll D, Pagani M, Schweizer D, Brockdorff NandJenuwein T. Histone H3 lysine 9 methylation is an epigenetic imprint of facultative heterochromatin. Nat Genet,2002,30:77-80
110. Min J, Zhang YandXu RM. Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. Genes Dev,2003,17: 1823-1828
111. Brown JL, Mucci D, Whiteley M, Dirksen MLandKassis JA. The Drosophila Polycomb group gene pleiohomeotic encodes a DNA binding protein with homology to the transcription factor YY1. Mol Cell,1998,1:1057-1064
112. Czermin B, Melfi R, McCabe D, Seitz V, Imhof AandPirrotta V. Drosophila enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites. Cell,2002,111:185-196
113. Horard B, Tatout C, Poux SandPirrotta V. Structure of a polycomb response element and in vitro binding of polycomb group complexes containing GAGA factor. Mol Cell Biol,2000,20:3187-3197
114. Mulholland NM, King IFandKingston RE. Regulation of Polycomb group complexes by the sequence-specific DNA binding proteins Zeste and GAGA. Genes Dev,2003,17:2741-2746
115. Simon JAandTamkun JW. Programming off and on states in chromatin: mechanisms of Polycomb and trithorax group complexes. Curr Opin Genet Dev, 2002,12:210-218
116. Cao R, Wang L, Wang H, Xia L, Erdjument-Bromage H, Tempst P, Jones RSandZhang Y. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science,2002,298:1039-1043
117. Muller J, Hart CM, Francis NJ, Vargas ML, Sengupta A, Wild B, Miller EL, O'Connor MB, Kingston REandSimon JA. Histone methyltransferase activity of a Drosophila Polycomb group repressor complex. Cell,2002,111:197-208
118. Feng Q, Wang H, Ng HH, Erdjument-Bromage H, Tempst P, Struhl KandZhang Y. Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain. Curr Biol,2002,12:1052-1058
119. Lacoste N, Utley RT, Hunter JM, Poirier GGandCote J. Disruptor of telomeric silencing-1 is a chromatin-specific histone H3 methyltransferase. J Biol Chem, 2002,277:30421-30424
120. Ng HH, Feng Q, Wang H, Erdjument-Bromage H, Tempst P, Zhang YandStruhl K. Lysine methylation within the globular domain of histone H3 by Dotl is important for telomeric silencing and Sir protein association. Genes Dev,2002,16: 1518-1527
121. van Leeuwen F, Gafken PRandGottschling DE. Dotlp modulates silencing in yeast by methylation of the nucleosome core. Cell,2002,109:745-756
122. Fang J, Feng Q, Ketel CS, Wang H, Cao R, Xia L, Erdjument-Bromage H, Tempst P, Simon JAandZhang Y. Purification and functional characterization of SET8, a nucleosomal histone H4-lysine 20-specific methyltransferase. Curr Biol,2002,12: 1086-1099
123. Nishioka K, Rice JC, Sarma K, Erdjument-Bromage H, Werner J, Wang Y, Chuikov S, Valenzuela P, Tempst P, Steward R, Lis JT, Allis CDandReinberg D. PR-Set7 is a nucleosome-specific methyltransferase that modifies lysine 20 of histone H4 and is associated with silent chromatin. Mol Cell,2002,9:1201-1213
124. Turner BM. Histone acetylation and an epigenetic code. Bioessays,2000,22: 836-845
125. Allfrey VGandMirsky AE. Structural Modifications of Histones and their Possible Role in the Regulation of RNA Synthesis. Science,1964,144:559
126. Brownell JE, Zhou J, Ranalli T, Kobayashi R, Edmondson DG, Roth SYandAllis CD. Tetrahymena histone acetyltransferase A:a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell,1996,84:843-851
127. Candau RandBerger SL. Structural and functional analysis of yeast putative adaptors. Evidence for an adaptor complex in vivo. J Biol Chem,1996,271: 5237-5245
128. Neuwald AFandLandsman D. GCN5-related histone N-acetyltransferases belong to a diverse superfamily that includes the yeast SPT10 protein. Trends Biochem Sci,1997,22:154-155
129. Bannister AJandKouzarides T. The CBP co-activator is a histone acetyltransferase. Nature,1996,384:641-643
130. Giles RH. Update CBP/p300 transgenic mice. Trends Genet,1998,14:214
131. Pandey R, Muller A, Napoli CA, Selinger DA, Pikaard CS, Richards EJ, Bender J, Mount DWandJorgensen RA. 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
132. Sterner DEandBerger SL. Acetylation of histones and transcription-related factors. Microbiol Mol Biol Rev,2000,64:435-459
133. Leo CandChen JD. The SRC family of nuclear receptor coactivators. Gene,2000, 245:1-11
134. Rundlett SE, Carmen AA, Suka N, Turner BMandGrunstein M. Transcriptional repression by UME6 involves deacetylation of lysine 5 of histone H4 by RPD3. Nature,1998,392:831-835
135. Rundlett SE, Carmen AA, Kobayashi R, Bavykin S, Turner BMandGrunstein M. HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription. Proc Natl Acad Sci U S A,1996,93: 14503-14508
136. De Rubertis F, Kadosh D, Henchoz S, Pauli D, Reuter G, Struhl KandSpierer P. The histone deacetylase RPD3 counteracts genomic silencing in Drosophila and yeast. Nature,1996,384:589-591
137. Vidal MandGaber RF. RPD3 encodes a second factor required to achieve maximum positive and negative transcriptional states in Saccharomyces cerevisiae. Mol Cell Biol,1991,11:6317-6327
138. Landry J, Sutton A, Tafrov ST, Heller RC, Stebbins J, Pillus LandSternglanz R. The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases. Proc Natl Acad Sci U S A,2000,97:5807-5811
139. Landry J, Slama JTandSternglanz R. Role of NAD(+) in the deacetylase activity of the SIR2-like proteins. Biochem Biophys Res Commun,2000,278:685-690
140. Imai S, Johnson FB, Marciniak RA, McVey M, Park PUandGuarente L. Sir2:an NAD-dependent histone deacetylase that connects chromatin silencing, metabolism, and aging. Cold Spring Harb Symp Quant Biol,2000,65:297-302
141. Imai S, Armstrong CM, Kaeberlein MandGuarente L. Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature, 2000,403:795-800
142. Lusser A, Kolle DandLoidl P. Histone acetylation:lessons from the plant kingdom. Trends Plant Sci,2001,6:59-65
143. Graessle S, Loidl PandBrosch G. Histone acetylation:plants and fungi as model systems for the investigation of histone deacetylases. Cell Mol Life Sci,2001,58: 704-720
144. Frye RA. Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins. Biochem Biophys Res Commun,2000,273:793-798
145. Lusser A, Brosch G, Loidl A, Haas HandLoidl P. Identification of maize histone deacetylase HD2 as an acidic nucleolar phosphoprotein. Science,1997,277:88-91
146. Waterborg JH. Sequence analysis of acetylation and methylation in two histone H3 variants of alfalfa. JBiol Chem,1990,265:17157-17161
147. Waterborg JH. Identification of five sites of acetylation in alfalfa histone H4. Biochemistry,1992,31:6211-6219
148. Kuo MHandAllis CD. Roles of histone acetyltransferases and deacetylases in gene regulation. Bioessays,1998,20:615-626
149. Pazin MJandKadonaga JT. What's up and down with histone deacetylation and transcription? Cell,1997,89:325-328
150. Tse C, Sera T, Wolffe APandHansen JC. Disruption of higher-order folding by core histone acetylation dramatically enhances transcription of nucleosomal arrays by RNA polymerase III. Mol Cell Biol,1998,18:4629-4638
151. Horn PJandPeterson CL. Molecular biology. Chromatin higher order folding--wrapping up transcription. Science,2002,297:1824-1827
152. Zamore PD, Tuschl T, Sharp PAandBartel DP. RNAi:double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell,2000,101:25-33
153. Elbashir SM, Martinez J, Patkaniowska A, Lendeckel WandTuschl T. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. Embo J,2001,20:6877-6888
154. Lee RC, Feinbaum RLandAmbros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell,1993,75: 843-854
155. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HRandRuvkun G. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature,2000,403:901-906
156. Moss EG. Heterochronic genes and the nature of developmental time. Curr Biol, 2007,17:R425-434
157. Pasquinelli AEandRuvkun G. Control of developmental timing by micrornas and their targets. Annu Rev Cell Dev Biol,2002,18:495-513
158. Rougvie AE. Intrinsic and extrinsic regulators of developmental timing:from miRNAs to nutritional cues. Development,2005,132:3787-3798
159. Wu G, Park MY, Conway SR, Wang JW, Weigel DandPoethig RS. The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell,2009,138:750-759
160. Wang JW, Czech BandWeigel D. miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana. Cell,2009,138: 738-749
161. Chandler VLandStam M. Chromatin conversations:mechanisms and implications of paramutation. Nat Rev Genet,2004,5:532-544
162. Chandler VL, Eggleston WBandDorweiler JE. Paramutation in maize. Plant Mol Biol,2000,43:121-145
163. Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, Lavine K, Mittal V, May B, Kasschau KD, Carrington JC, Doerge RW, Colot VandMartienssen R. Role of transposable elements in heterochromatin and epigenetic control. Nature,2004,430:471-476
164. Shen WH. NtSET1, a member of a newly identified subgroup of plant SET-domain-containing proteins, is chromatin-associated and its ectopic overexpression inhibits tobacco plant growth. Plant J,2001,28:371-383
165. Yu Y, Dong AandShen WH. Molecular characterization of the tobacco SET domain protein NtSET1 unravels its role in histone methylation, chromatin binding, and segregation. Plant J,2004,40:699-711
166. Baumbusch LO, Thorstensen T, Krauss V, Fischer A, Naumann K, Assalkhou R, Schulz I, Reuter GandAalen RB. The Arabidopsis thaliana genome contains at least 29 active genes encoding SET domain proteins that can be assigned to four evolutionarily conserved classes. Nucleic Acids Res,2001,29:4319-4333
167. Ebbs ML, Bartee LandBender J. H3 lysine 9 methylation is maintained on a transcribed inverted repeat by combined action of SUVH6 and SUVH4 methyltransferases. Mol Cell Biol,2005,25:10507-10515
168. Bertrand C, Bergounioux C, Domenichini S, Delarue MandZhou DX. Arabidopsis histone acetyltransferase AtGCN5 regulates the floral meristem activity through the WUSCHEL/AGAMOUS pathway. JBiol Chem,2003,278:28246-28251
169. Taunton J, Hassig CAandSchreiber SL. A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p. Science,1996,272:408-411
170. Grozinger CMandSchreiber SL. Deacetylase enzymes:biological functions and the use of small-molecule inhibitors. Chem Biol,2002,9:3-16
171. Moazed D. Enzymatic activities of Sir2 and chromatin silencing. Curr Opin Cell Biol,2001,13:232-238
172. Tian LandChen ZJ. Blocking histone deacetylation in Arabidopsis induces pleiotropic effects on plant gene regulation and development. Proc Natl Acad Sci USA,2001,98:200-205
173. Wu K, Malik K, Tian L, Brown DandMiki B. Functional analysis of a RPD3 histone deacetylase homologue in Arabidopsis thaliana. Plant Mol Biol,2000,44: 167-176
174. Zhou C, Zhang L, Duan J, Miki BandWu K. HISTONE DEACETYLASE19 is involved in jasmonic acid and ethylene signaling of pathogen response in Arabidopsis. Plant Cell,2005,17:1196-1204
175. Gonzalez D, Bowen AJ, Carroll TSandConlan RS. The transcription corepressor LEUNIG interacts with the histone deacetylase HDA19 and mediator components MED14 (SWP) and CDK8 (HEN3) to repress transcription. Mol Cell Biol,2007, 27:5306-5315
176. Kim KC, Lai Z, Fan BandChen Z. Arabidopsis WRKY38 and WRKY62 transcription factors interact with histone deacetylase 19 in basal defense. Plant Cell,2008,20:2357-2371
177. Aufsatz W, Mette MF, van der Winden J, Matzke MandMatzke AJ. HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double-stranded RNA. Embo J,2002,21:6832-6841
178. Murfett J, Wang XJ, Hagen GandGuilfoyle TJ. Identification of Arabidopsis histone deacetylase HDA6 mutants that affect transgene expression. Plant Cell, 2001,13:1047-1061
179. Jang IC, Pahk YM, Song SI, Kwon HJ, Nahm BHandKim JK. Structure and expression of the rice class-Ⅰ type histone deacetylase genes OsHDAC1-3: OsHDAC1 overexpression in transgenic plants leads to increased growth rate and altered architecture. Plant J,2003,33:531-541
180. Finnegan EJ. Is plant gene expression regulated globally? Trends Genet,2001,17: 361-365
181. Grozinger CM, Chao ED, Blackwell HE, Moazed DandSchreiber SL. Identification of a class of small molecule inhibitors of the sirtuin family of NAD-dependent deacetylases by phenotypic screening. J Biol Chem,2001,276: 38837-38843
182. Huang L, Sun Q, Qin F, Li C, Zhao YandZhou DX. Down-Regulation of a SILENT INFORMATION REGULATOR2-Related Histone Deacetylase Gene, OsSRT1, Induces DNA Fragmentation and Cell Death in Rice. Plant Physiol, 2007,144:1508-1519
183. Chung PJ, Kim YS, Jeong JS, Park SH, Nahm BHandKim JK. The histone deacetylase OsHDAC1 epigenetically regulates the OsNAC6 gene that controls seedling root growth in rice. Plant J,2009,59:764-776
184. Hecht AandGrunstein M. Mapping DNA interaction sites of chromosomal proteins using immunoprecipitation and polymerase chain reaction. Methods Enzymol, 1999,304:399-414
185. Orlando V, Strutt HandParo R. Analysis of chromatin structure by in vivo formaldehyde cross-linking. Methods,1997,11:205-214
186. Zilberman D, Gehring M, Tran RK, Ballinger TandHenikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet,2007,39:61-69
187. Church GMandGilbert W. Genomic sequencing. Proc Natl Acad Sci U S A,1984, 81:1991-1995
188. Hiei Y, Ohta S, Komari TandKumashiro T. Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. Plant J,1994,6:271-282
189. Tariq M, Saze H, Probst AV, Lichota J, Habu YandPaszkowski J. Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin. Proc Natl Acad Sci USA,2003,100:8823-8827
190. Marmorstein R. Structure of SET domain proteins:a new twist on histone methylation. Trends Biochem Sci,2003,28:59-62
191. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin FandHiggins DG. The CLUSTAL_X windows interface:flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res,1997,25:4876-4882
192. Kumar S, Tamura KandNei M. MEGA3:Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform,2004,5: 150-163
193. Letunic I, Copley RR, Pils B, Pinkert S, Schultz JandBork P. SMART 5:domains in the context of genomes and networks. Nucleic Acids Res,2006,34:D257-260
194. Collins RE, Tachibana M, Tamaru H, Smith KM, Jia D, Zhang X, Selker EU, Shinkai YandCheng X. In vitro and in vivo analyses of a Phe/Tyr switch controlling product specificity of histone lysine methyltransferases. J Biol Chem, 2005,280:5563-5570
195. Baulcombe D. RNA silencing in plants. Nature,2004,431:356-363
196. Montgomery MK. RNA interference:historical overview and significance. Methods Mol Biol,2004,265:3-21
197. Zhou HJ, Tsai SYandTsai MJ. RNAi technology and its use in studying the function of nuclear receptors and coregulators. Nucl Recept Signal,2003,1:e008
198. Eisen MB, Spellman PT, Brown POandBotstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A,1998,95: 14863-14868
199. Dai M, Zhao Y, Ma Q, Hu Y, Hedden P, Zhang QandZhou DX. The rice YABBY1 gene is involved in the feedback regulation of gibberellin metabolism. Plant Physiol,2007,144:121-133
200. Dai M, Hu Y, Zhao Y, Liu HandZhou DX. A WUSCHEL-LIKE HOMEOBOX gene represses a YABBY gene expression required for rice leaf development. Plant Physiol,2007,144:380-390
201. Dong A, Liu Z, Zhu Y, Yu F, Li Z, Cao KandShen WH. Interacting proteins and differences in nuclear transport reveal specific functions for the NAP1 family proteins in plants. Plant Physiol,2005,138:1446-1456
202. Hirochika H, Sugimoto K, Otsuki Y, Tsugawa HandKanda M. Retrotransposons of rice involved in mutations induced by tissue culture. Proc Natl Acad Sci U S A, 1996,93:7783-7788
203. Cheng C, Daigen MandHirochika H. Epigenetic regulation of the rice retrotransposon Tos17. Mol Genet Genomics,2006,276:378-390
204. Eriksson S, Bohlenius H, Moritz TandNilsson O. GA4 is the active gibberellin in the regulation of LEAFY transcription and Arabidopsis floral initiation. Plant Cell, 2006,18:2172-2181
205. Huang S, Cerny RE, Qi Y, Bhat D, Aydt CM, Hanson DD, Malloy KPandNess LA. Transgenic studies on the involvement of cytokinin and gibberellin in male development. Plant Physiol,2003,131:1270-1282
206. Ishii TandNishijima T. Inhibition of gibberellin-induced elongation growth of rice by feruloyl oligosaccharides. Plant Cell Physiol,1995,36:1447-1451
207. King KE, Moritz TandHarberd NP. Gibberellins are not required for normal stem growth in Arabidopsis thaliana in the absence of GAI and RGA. Genetics,2001, 159:767-776
208. Oh E, Yamaguchi S, Kamiya Y, Bae G, Chung WIandChoi G. Light activates the degradation of PIL5 protein to promote seed germination through gibberellin in Arabidopsis. Plant J,2006,47:124-139
209. Stavang JA, Lindgard B, Erntsen A, Lid SE, Moe RandOlsen JE. Thermoperiodic stem elongation involves transcriptional regulation of gibberellin deactivation in pea. Plant Physiol,2005,138:2344-2353
210. Cannon SB, Mitra A, Baumgarten A, Young NDandMay G. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol,2004,4:10
211. Kong H, Landherr LL, Frohlich MW, Leebens-Mack J, Ma HanddePamphilis CW. Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth. Plant J,2007,50:873-885
212. Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C, Zhang J, Zhang Y, Li R, Xu Z, Li S, Li X, Zheng H, Cong L, Lin L, Yin J, et al.,. The Genomes of Oryza sativa:a history of duplications. PLoS Biol,2005,3:e38
213. Ray S, Agarwal P, Arora R, Kapoor SandTyagi AK. Expression analysis of calcium-dependent protein kinase gene family during reproductive development and abiotic stress conditions in rice (Oryza sativa L. ssp. indica). Mol Genet Genomics,2007,278:493-505
214. Goodrich J, Puangsomlee P, Martin M, Long D, Meyerowitz EMandCoupland G. A Polycomb-group gene regulates homeotic gene expression in Arabidopsis. Nature,1997,386:44-51
215. Grossniklaus U, Vielle-Calzada JP, Hoeppner MAandGagliano WB. Maternal control of embryogenesis by MEDEA, a polycomb group gene in Arabidopsis. Science,1998,280:446-450
216. Kiyosue T, Ohad N, Yadegari R, Hannon M, Dinneny J, Wells D, Katz A, Margossian L, Harada JJ, Goldberg RBandFischer RL. Control of fertilization-independent endosperm development by the MEDEA polycomb gene in Arabidopsis. Proc Natl Acad Sci U S A,1999,96:4186-4191
217. Luo M, Bilodeau P, Dennis ES, Peacock WJandChaudhury A. Expression and parent-of-origin effects for FIS2, MEA, and FIE in the endosperm and embryo of developing Arabidopsis seeds. Proc Natl Acad Sci USA,2000,97:10637-10642
218. Vielle-Calzada JP, Thomas J, Spillane C, Coluccio A, Hoeppner MAandGrossniklaus U. Maintenance of genomic imprinting at the Arabidopsis medea locus requires zygotic DDM1 activity. Genes Dev,1999,13:2971-2982
219. Sun QandZhou DX. Rice jmjC domain-containing gene JMJ706 encodes H3K9 demethylase required for floral organ development. Proc Natl Acad Sci U S A, 2008,105:13679-13684
220. Turck F, Roudier F, Farrona S, Martin-Magniette ML, Guillaume E, Buisine N, Gagnot S, Martienssen RA, Coupland GandColot V. Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 21.PLoS Genet,2001,3:e86
221. Dillon SC, Zhang X, Trievel RCandCheng X. The SET-domain protein superfamily:protein lysine methyltransferases. Genome Biol,2005,6:227
222. Dong G, Ma DPandLi J. The histone methyltransferase SDG8 regulates shoot branching in Arabidopsis. Biochem Biophys Res Commun,2008,373:659-664
223. Lippman Z, May B, Yordan C, Singer TandMartienssen R. Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS Biol,2003,1:E67
224. Mathieu O, Probst AVandPaszkowski J. Distinct regulation of histone H3 methylation at lysines 27 and 9 by CpG methylation in Arabidopsis. Embo J,2005, 24:2783-2791
225. Tran RK, Zilberman D, de Bustos C, Ditt RF, Henikoff JQ Lindroth AM, Delrow J, Boyle T, Kwong S, Bryson TD, Jacobsen SEandHenikoff S. Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biol,2005,6:R90
226. Jain M, Nijhawan A, Arora R, Agarwal P, Ray S, Sharma P, Kapoor S, Tyagi AKandKhurana JP. F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol,2007,143:1467-1483
© 2004-2018 中国地质图书馆版权所有 京ICP备05064691号 京公网安备11010802017129号 地址：北京市海淀区学院路29号 邮编：100083 电话：办公室：(+86 10)66554848；文献借阅、咨询服务、科技查新：66554700 |