染色质修饰基因HUB1和CHR5及转录因子MYB44在拟南芥防卫反应中的功能研究
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摘要
植物在整个生长过程中都会受到各种病菌的侵染,为了生存及保护自己植物进化出了自己独特的免疫系统。是否能够迅速准确地启动免疫反应从而成功抵抗病菌侵染,主要依赖于植物能否适时而准确地调控自身防卫相关基因的转录表达。植物察觉病菌侵染后,会将胁迫信号传递到细胞核内,激活转录因子并将防卫信号放大并且传递,进而诱发下游一系列防卫相关基因的表达。在众多的植物基因的转录调控机制中转录因子和染色质修饰介导的基因转录调控是植物基因转录调控最重要的两大调控机制。染色质修饰主要包括围绕核小体的组蛋白修饰和依赖ATP提供能量的染色质重塑复合体蛋白介导的染色质构型调控。本研究证明转录因子和染色质修饰相关基因介导的基因转录调控参与拟南芥抗病防卫反应。
1.组蛋白H2B单泛素化调控拟南芥中抗病基因的表达
抗病基因调控是植物免疫反应的最重要调控环节。本章研究发现拟南芥E3连接酶基因HUB1(HISTONE MONOUBIQUITINATION1)和HUB2参与自体免疫突变体bon1中R(Resistance)基因SNC1(SUPPRESSOR OF nprl-1, CONSTITUTIVE1)的表达调控。SNC1在bon1中组成性上调表达,同时NC1基因位点H2B单泛素化(H2Bub)的水平比野生型显著地增加。突变HUB1或者其同源基因HUB2都可以显著地抑制bon1的自体免疫反应。SNC1在bon1中的上调表达与其基因位点H2Bub修饰相关。同时我们发现在野生型拟南芥中病菌侵染后SNC1和HUB1的表达及SNC1基因位点的H2Bubi的水平都会增加。以上结果证明H2Bub在自体免疫突变体bon1的R基因调控中起着关键的作用,并且H2Bub很有可能参与了病菌侵染后R基因的表达调控。
2.拟南芥CHD亚类染色质重塑基因CHR5在拟南芥免疫反应中的功能研究
依赖ATP提供能量的染色质重塑蛋白复合体可以通过水解ATP获得能量改变染色质的构型,染色质构型改变是真核生物调控基因转录表达的重要机制之一。本研究通过对一个拟南芥CHD类染色质重塑基因CHR(Chromatin Remodeling5)的鉴定和功能分析,证明其与植物免疫反应相关。通过对自体免疫突变体bon1潜在的抑制突变体的遗传筛选发现CHR5功能缺失突变体可以显著地抑制bon1的免疫反应。bon1中组成性激活表达的NB-LRR类的R基因SNC1及PR基因及植物防卫激素水杨酸(SA)的累积,都显著地被CHR5基因突变抑制。bon1突变体对丁香假单胞菌番茄致病变种Pst DC3000(Pseudomonas syringae pv. tomato DC3000)的组成性抗性也被CHR5基因突变明显的抑制。同时揭示了CHR5与HUB1和DDM1在bon1相关的免疫反应调控中的相互关系。通过对chr5突变体的对病菌Psm E4326(Pseudomonas. syringae pv. maculicola ES4326)的抗病实验证明CHR5正调控拟南芥对病菌的基本防卫反应。最后通过RNAseq对CHR5基因突变体进行了全基因组转录表达分析发现CHR5主要与一些植物防卫反应相关的基因的转录表达相关,并证明CHR5可能主要参与植物的胁迫应答反应。
3. AtMYB44通过水杨酸信号通路正调控拟南芥对丁香假单胞菌的抗性
AtMYB44属于植物R2R3型第22亚类的MYB转录因子。研究证明AtMYB44是一个重要的胁迫响应基因。本研究发现AtMYB44基因的表达能够被植物激素水杨酸(salicylic acid,SA)处理和半活体营养型病菌丁香假单胞菌番茄致病变种(Pseudomonas syringae pv. tomato DC3000, Pst DC3000)侵染显著地诱导表达,且AtMYB44的诱导表达需要SA的积累及NPR1蛋白的参与。AtMYB44过表达的转基因拟南芥比野生型显著地更抗pst DC3000的侵染,且病菌侵染后过表达植物会有更强PR1激活表达并产生更多的活性氧。相反AtMYB44基因功能缺失突变体atmyb44’比野生型更感病,同时病菌侵染后atmyb44突变体中PR1的激活表达也会减弱。进一步的遗传杂交实验证明,AtMYB44过表达植物的所有抗病表型都需要SA积累和NPR1蛋白的参与。上述结果证明AtMYB44通过依赖于NPR1的SA防卫信号通路正调控拟南芥对Pst DC3000的抗病性。
Due to their sessile lifestyle, plants are in constant conflict with pathogens throughout their life cycles. In order to fend off a wide range of microbial pathogen attacks, plants have developed sophisticated immunity system to defend themselves. Plant immunity responses against pathogen infection largely depend on the plant's capacity to reprogram rapidly and specifically the transcription of a large number of the host genes. In a pathogen stress type-dependent manner, external signals are trans-located into the nucleus to activate transcription factors, resulting in the increased expression of particular sets of defense-related genes. Among mechanisms of transcriptional regulation, transcription factors and chromatin modification accomplished through the activity of histone-modifying enzymes and ATP dependent chromatin-remodeling complexes are emerging as two key processes in the orchestration of plant immunity responses.
1. Regulation of disease resistance gene expression by H2B monoubiquitination in Arabidopsis
Regulation of disease resistance (R) genes is one key event in plant immunity response. Here we show that two Arabidopsis E3ubiquitin ligase genes HUB1(HISTONE MONOUBIQUITINATION1) and HUB2are involved in the regulation of the R gene SNC1(SUPPRESSOR OFnpr1-1, CONSTITUTIVE1) in the autoimmune mutant bon1. The SNC1gene is up-regulated in bon1and the SNC1locus has a higher monoubiquitination of H2B. The loss of HUB1or HUB2function largely suppresses the autoimmune phenotypes in bon1. Thus the up-expression of SNC1in bon1is dependent on H2B modification at the SNC1locus. Furthermore, the expression of SNC1and HUB1are moderately up-regulated by pathogen infection and H2B monoubiquitination at SNC1is enhanced by pathogen infection. Together, this study indicates that H2B monoubiquitination is critical for R gene up-regulation in autoimmune mutants and it might also contribute to R gene regulation during immune responses.
2. Characterize and function studies of one plant helicase-like domain (CHD) chromatin remodeling factor chromatin remodeling5(CHR5) in Arabidopsis innate immunity
ATP-dependent chromatin remodeling complexes use the energy of ATP hydrolysis to alter the structure of chromatin, which is an important mechanism in the regulation of eukaryotic gene expression. In this study, we characterized the function of chromatin remodeling5(CHR5), a member of plant helicase-like domain(CHD) chromatin remodeling factor, in Arabidopsis innate immunity. We found that knock out CHR5gene can largely suppress the autoimmunity in bon1-1by a genetic screen of the potential suppressor of the autoimmunity mutant bon1-1.The constitutively expression of the SNC1and PR1gene and the accumulation of SA in bon1-1were all largely suppressed by CHR5mutation. And the constitutively pathogen resistance in bon1-1was also disappeared in the chr5bon1-1double mutants.While chr5single mutants exhibit defects in basal resistance against the bacterial pathogen P. syringae pv.maculicola ES4326(Psm E4326). Furthermore, we approved that CHR5may regulate the expression of SNC1in a locus specific manner. After RNAseq data analysis, we found that the expression many important defense response genes were significantly changed in chr5mutants. Our study indicates that CHR5is a negative regulator of plant immunity and may regulate gene expression at chromatin level.
3. AtMYB44positively modulates disease resistance to Pseudomonas syringae through the salicylic acid signalling pathway in Arabidopsis
AtMYB44which belongs to sub-group22of the R2R3MYB transcription factor family is one well known stress response related gene. Here, we found that the expression of AtMYB44is sensitive to the phytophormone salicylic acid (SA) treatment and the hemibiotrophic pathogen Pseudomonas syringae pv. tomato DC3000(Pst DC3000) infection. And the induction expression of AtMYB44by Pst DC3000requires both the SA accumulation and the NPR1gene. AtMYB44over-expression up-regulated PR genes induction expression and ROS accumulation by Pst DC3000, leading to enhanced resistance to the Pst DC3000. While the knockout mutant atmyb44shows opposite effects. Induction of PR1by Pst DC3000is reduced in atmyb44mutants. AtMYB44over-expression phenotypes, such as retarded growth, up-regelated PR1and resistance to Pst DC3000are reversed by SA depletion and NPR1mutation. Thus, AtMYB44positive regulates Arabidopsis defense response against Pst DC3000through SA signaling pathway.
1.组蛋白H2B单泛素化调控拟南芥中抗病基因的表达
抗病基因调控是植物免疫反应的最重要调控环节。本章研究发现拟南芥E3连接酶基因HUB1(HISTONE MONOUBIQUITINATION1)和HUB2参与自体免疫突变体bon1中R(Resistance)基因SNC1(SUPPRESSOR OF nprl-1, CONSTITUTIVE1)的表达调控。SNC1在bon1中组成性上调表达,同时NC1基因位点H2B单泛素化(H2Bub)的水平比野生型显著地增加。突变HUB1或者其同源基因HUB2都可以显著地抑制bon1的自体免疫反应。SNC1在bon1中的上调表达与其基因位点H2Bub修饰相关。同时我们发现在野生型拟南芥中病菌侵染后SNC1和HUB1的表达及SNC1基因位点的H2Bubi的水平都会增加。以上结果证明H2Bub在自体免疫突变体bon1的R基因调控中起着关键的作用,并且H2Bub很有可能参与了病菌侵染后R基因的表达调控。
2.拟南芥CHD亚类染色质重塑基因CHR5在拟南芥免疫反应中的功能研究
依赖ATP提供能量的染色质重塑蛋白复合体可以通过水解ATP获得能量改变染色质的构型,染色质构型改变是真核生物调控基因转录表达的重要机制之一。本研究通过对一个拟南芥CHD类染色质重塑基因CHR(Chromatin Remodeling5)的鉴定和功能分析,证明其与植物免疫反应相关。通过对自体免疫突变体bon1潜在的抑制突变体的遗传筛选发现CHR5功能缺失突变体可以显著地抑制bon1的免疫反应。bon1中组成性激活表达的NB-LRR类的R基因SNC1及PR基因及植物防卫激素水杨酸(SA)的累积,都显著地被CHR5基因突变抑制。bon1突变体对丁香假单胞菌番茄致病变种Pst DC3000(Pseudomonas syringae pv. tomato DC3000)的组成性抗性也被CHR5基因突变明显的抑制。同时揭示了CHR5与HUB1和DDM1在bon1相关的免疫反应调控中的相互关系。通过对chr5突变体的对病菌Psm E4326(Pseudomonas. syringae pv. maculicola ES4326)的抗病实验证明CHR5正调控拟南芥对病菌的基本防卫反应。最后通过RNAseq对CHR5基因突变体进行了全基因组转录表达分析发现CHR5主要与一些植物防卫反应相关的基因的转录表达相关,并证明CHR5可能主要参与植物的胁迫应答反应。
3. AtMYB44通过水杨酸信号通路正调控拟南芥对丁香假单胞菌的抗性
AtMYB44属于植物R2R3型第22亚类的MYB转录因子。研究证明AtMYB44是一个重要的胁迫响应基因。本研究发现AtMYB44基因的表达能够被植物激素水杨酸(salicylic acid,SA)处理和半活体营养型病菌丁香假单胞菌番茄致病变种(Pseudomonas syringae pv. tomato DC3000, Pst DC3000)侵染显著地诱导表达,且AtMYB44的诱导表达需要SA的积累及NPR1蛋白的参与。AtMYB44过表达的转基因拟南芥比野生型显著地更抗pst DC3000的侵染,且病菌侵染后过表达植物会有更强PR1激活表达并产生更多的活性氧。相反AtMYB44基因功能缺失突变体atmyb44’比野生型更感病,同时病菌侵染后atmyb44突变体中PR1的激活表达也会减弱。进一步的遗传杂交实验证明,AtMYB44过表达植物的所有抗病表型都需要SA积累和NPR1蛋白的参与。上述结果证明AtMYB44通过依赖于NPR1的SA防卫信号通路正调控拟南芥对Pst DC3000的抗病性。
Due to their sessile lifestyle, plants are in constant conflict with pathogens throughout their life cycles. In order to fend off a wide range of microbial pathogen attacks, plants have developed sophisticated immunity system to defend themselves. Plant immunity responses against pathogen infection largely depend on the plant's capacity to reprogram rapidly and specifically the transcription of a large number of the host genes. In a pathogen stress type-dependent manner, external signals are trans-located into the nucleus to activate transcription factors, resulting in the increased expression of particular sets of defense-related genes. Among mechanisms of transcriptional regulation, transcription factors and chromatin modification accomplished through the activity of histone-modifying enzymes and ATP dependent chromatin-remodeling complexes are emerging as two key processes in the orchestration of plant immunity responses.
1. Regulation of disease resistance gene expression by H2B monoubiquitination in Arabidopsis
Regulation of disease resistance (R) genes is one key event in plant immunity response. Here we show that two Arabidopsis E3ubiquitin ligase genes HUB1(HISTONE MONOUBIQUITINATION1) and HUB2are involved in the regulation of the R gene SNC1(SUPPRESSOR OFnpr1-1, CONSTITUTIVE1) in the autoimmune mutant bon1. The SNC1gene is up-regulated in bon1and the SNC1locus has a higher monoubiquitination of H2B. The loss of HUB1or HUB2function largely suppresses the autoimmune phenotypes in bon1. Thus the up-expression of SNC1in bon1is dependent on H2B modification at the SNC1locus. Furthermore, the expression of SNC1and HUB1are moderately up-regulated by pathogen infection and H2B monoubiquitination at SNC1is enhanced by pathogen infection. Together, this study indicates that H2B monoubiquitination is critical for R gene up-regulation in autoimmune mutants and it might also contribute to R gene regulation during immune responses.
2. Characterize and function studies of one plant helicase-like domain (CHD) chromatin remodeling factor chromatin remodeling5(CHR5) in Arabidopsis innate immunity
ATP-dependent chromatin remodeling complexes use the energy of ATP hydrolysis to alter the structure of chromatin, which is an important mechanism in the regulation of eukaryotic gene expression. In this study, we characterized the function of chromatin remodeling5(CHR5), a member of plant helicase-like domain(CHD) chromatin remodeling factor, in Arabidopsis innate immunity. We found that knock out CHR5gene can largely suppress the autoimmunity in bon1-1by a genetic screen of the potential suppressor of the autoimmunity mutant bon1-1.The constitutively expression of the SNC1and PR1gene and the accumulation of SA in bon1-1were all largely suppressed by CHR5mutation. And the constitutively pathogen resistance in bon1-1was also disappeared in the chr5bon1-1double mutants.While chr5single mutants exhibit defects in basal resistance against the bacterial pathogen P. syringae pv.maculicola ES4326(Psm E4326). Furthermore, we approved that CHR5may regulate the expression of SNC1in a locus specific manner. After RNAseq data analysis, we found that the expression many important defense response genes were significantly changed in chr5mutants. Our study indicates that CHR5is a negative regulator of plant immunity and may regulate gene expression at chromatin level.
3. AtMYB44positively modulates disease resistance to Pseudomonas syringae through the salicylic acid signalling pathway in Arabidopsis
AtMYB44which belongs to sub-group22of the R2R3MYB transcription factor family is one well known stress response related gene. Here, we found that the expression of AtMYB44is sensitive to the phytophormone salicylic acid (SA) treatment and the hemibiotrophic pathogen Pseudomonas syringae pv. tomato DC3000(Pst DC3000) infection. And the induction expression of AtMYB44by Pst DC3000requires both the SA accumulation and the NPR1gene. AtMYB44over-expression up-regulated PR genes induction expression and ROS accumulation by Pst DC3000, leading to enhanced resistance to the Pst DC3000. While the knockout mutant atmyb44shows opposite effects. Induction of PR1by Pst DC3000is reduced in atmyb44mutants. AtMYB44over-expression phenotypes, such as retarded growth, up-regelated PR1and resistance to Pst DC3000are reversed by SA depletion and NPR1mutation. Thus, AtMYB44positive regulates Arabidopsis defense response against Pst DC3000through SA signaling pathway.
引文
1. Abe H, Urao T, Ito T, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2003) Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signaling. Plant Cell 15:63-78
2. Abe H, Yamaguchi-Shinozaki K, Urao T, Iwasaki T, Hosokawa D, Shinozaki K (1997) Role of arabidopsis MYC and MYB homologs in drought-and abscisic acid-regulated gene expression. Plant Cell 9:1859-1868
3. Agarwal M, Hao Y, Kapoor A, Dong CH, Fujii H, Zheng X, Zhu JK (2006) A R2R3 type MYB transcription factor is involved in the cold regulation of CBF genes and in acquired freezing tolerance. J Biol Chem 281:37636-37645
4. Ali GS, Reddy A (2008) PAMP-triggered immunity:Early events in the activation of FLAGELLIN SENSITIVE2. Plant Signal Behav 3:423-426
5. Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen H, Shinn P, Stevenson DK, Zimmerman J, Barajas P, Ecker JR (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301:653-657
6. Alvarez-Venegas R, Abdallat AA, Guo M, Alfano JR, Avramova Z (2007) Epigenetic control of a transcription factor at the cross section of two antagonistic pathways. Epigenetics 2:106-113
7. Alvarez-Venegas R, Al Abdallat A, Guo M, Alfano JR, Avramova Z (2007) Epigenetic control of a transcription factor at the cross section of two antagonistic pathways. Epigenetics 2:106-113
8. Alvarez-Venegas R, Avramova Z (2005) Methylation patterns of histone H3 Lys 4, Lys 9 and Lys 8 27 in transcriptionally active and inactive Arabidopsis genes and in atxl mutants. Nucleic Acids Res 33:5199-5207
9. Axtell MJ, Staskawicz BJ (2003) Initiation of RPS2-specified disease resistance in Arabidopsis is coupled to the AvrRpt2-directed elimination of RIN4. Cell 112:369-377
10. Berke L, Sanchez-Perez GF, Snel B (2012) Contribution of the epigenetic mark H3K27me3 to functional divergence after whole genome duplication in Arabidopsis. Genome Biol 13:R94
11. Berr A, McCallum EJ, Alioua A, Heintz D, Heitz T, Shen WH (2010) Arabidopsis Histone Methyltransferase SET DOMAIN GROUP8 Mediates Induction of the Jasmonate/Ethylene Pathway Genes in Plant Defense Response to Necrotrophic Fungi. Plant Physiology 154: 1403-1414
12. Berr A, McCallum EJ, Alioua A, Heintz D, Heitz T, Shen WH (2010) Arabidopsis histone methyltransferase SET DOMAIN GROUP8 mediates induction of the jasmonate/ethylene pathway genes in plant defense response to necrotrophic fungi. Plant Physiol 154:1403-1414
13. Berr A, Menard R, Heitz T, Shen WH (2012) Chromatin modification and remodelling:a regulatory landscape for the control of Arabidopsis defence responses upon pathogen attack. Cellular Microbiology 14:829-839
14. Bowles D (1998) Signal transduction in the wound response of tomato plants. Philos Trans R Soc Lond B Biol Sci 353:1495-1510
15. Bowles DJ (1994) Signalling events in the wound response of tomato plants. Biochem Soc Symp 60: 155-164
16. Bray S, Musisi H, Bienz M (2005) Brel is required for Notch signaling and histone modification. Dev Cell 8:279-286
17. Broekaert WF, Delaure SL, De Bolle MF, Cammue BP (2006) The role of ethylene in host-pathogen interactions. Annu Rev Phytopathol 44:393-416
18. Brzeski J, Jerzmanowski A (2003) Deficient in DNA methylation 1 (DDM1) defines a novel family of chromatin-remodeling factors. J Biol Chem 278:823-828
19. Cao H, Bowling SA, Gordon AS, Dong X (1994) Characterization of an Arabidopsis Mutant That Is Nonresponsive to Inducers of Systemic Acquired Resistance. Plant Cell 6:1583-1592
20. Cao Y, Dai Y, Cui S, Ma L (2008) Histone H2B monoubiquitination in the chromatin of FLOWERING LOCUS C regulates flowering time in Arabidopsis. Plant Cell 20:2586-2602
21. Catanzariti AM, Dodds PN, Ve T, Kobe B, Ellis JG, Staskawicz BJ (2010) The AvrM effector from flax rust has a structured C-terminal domain and interacts directly with the M resistance protein. Mol Plant Microbe Interact 23:49-57
22. Chellappan P, Vanitharani R, Ogbe F, Fauquet CM (2005) Effect of temperature on geminivirus-induced RNA silencing in plants. Plant Physiology 138:1828-1841
23. Chen HM, Xue L, Chintamanani S, Germain H, Lin HQ, Cui HT, Cai R, Zuo JR, Tang XY, Li X, Guo HW, Zhou JM (2009) ETHYLENE INSENSITIVE3 and ETHYLENE INSENSITIVE3-LIKE1 Repress SALICYLIC ACID INDUCTION DEFICIENT2 Expression to Negatively Regulate Plant Innate Immunity in Arabidopsis. Plant Cell 21:2527-2540
24. Cheng H, Song SS, Xiao LT, Soo HM, Cheng ZW, Xie DX, Peng JR (2009) Gibberellin Acts through Jasmonate to Control the Expression of MYB21, MYB24, and MYB57 to Promote Stamen Filament Growth in Arabidopsis. Plos Genetics 5
25. Chinchilla D, Bauer Z, Regenass M, Boller T, Felix G (2006) The Arabidopsis receptor kinase FLS2 binds flg22 and determines the specificity of flagellin perception. Plant Cell 18:465-476
26. Chinchilla D, Zipfel C, Robatzek S, Kemmerling B, Nurnberger T, Jones JD, Felix G, Boller T (2007) A flagellin-induced complex of the receptor FLS2 and BAK1 initiates plant defence. Nature 448:497-500
27. Choi SM, Song HR, Han SK, Han M, Kim CY, Park J, Lee YH, Jeon JS, Noh YS, Noh B (2012) HDA19 is required for the repression of salicylic acid biosynthesis and salicylic acid-mediated defense responses in Arabidopsis. Plant J 71:135-146
28. Chung HS, Koo AJ, Gao X, Jayanty S, Thines B, Jones AD, Howe GA (2008) Regulation and function of Arabidopsis JASMONATE ZIM-domain genes in response to wounding and herbivory. Plant Physiol 146:952-964
29. Clapier CR, Cairns BR (2009) The biology of chromatin remodeling complexes. Annu Rev Biochem 78:273-304
30. Clapier CR, Cairns BR (2009) The Biology of Chromatin Remodeling Complexes. Annual Review of Biochemistry 78:273-304
31. Collier SM, Moffett P (2009) NB-LRRs work a "bait and switch" on pathogens. Trends Plant Sci 14: 521-529
32. Cominelli E, Galbiati M, Vavasseur A, Conti L, Sala T, Vuylsteke M, Leonhardt N, Dellaporta SL, Tonelli C (2005) A guard-cell-specific MYB transcription factor regulates stomatal movements and plant drought tolerance. Curr Biol 15:1196-1200
33. Dangl JL, Jones JD (2001) Plant pathogens and integrated defence responses to infection. Nature 411:826-833
34. Daniel X, Lacomme C, Morel JB, Roby D (1999) A novel myb oncogene homologue in Arabidopsis thaliana related to hypersensitive cell death. Plant J 20:57-66
35. Dasgupta P, Chellappan SP (2007) Chromatin immunoprecipitation assays:molecular analysis of chromatin modification and gene regulation. Methods Mol Biol 383:135-152
36. Day B, Dahlbeck D, Staskawicz BJ (2006) NDR1 interaction with RIN4 mediates the differential activation of multiple disease resistance pathways in Arabidopsis. Plant Cell 18:2782-2791
37. De-La-Pena C, Rangel-Cano A, Alvarez-Venegas R (2012) Regulation of disease-responsive genes mediated by epigenetic factors:interaction of Arabidopsis-Pseudomonas. Mol Plant Pathol 13: 388-398
38. De Jong CF, Takken FL, Cai X, de Wit PJ, Joosten MH (2002) Attenuation of Cf-mediated defense responses at elevated temperatures correlates with a decrease in elicitor-binding sites. Mol Plant Microbe Interact 15:1040-1049
39. De Torres M, Mansfield JW, Grabov N, Brown IR, Ammouneh H, Tsiamis G, Forsyth A, Robatzek S, Grant M, Boch J (2006) Pseudomonas syringae effector AvrPtoB suppresses basal defence in Arabidopsis. Plant J 47:368-382
40. De Torres Zabala M, Bennett MH, Truman WH, Grant MR (2009) Antagonism between salicylic and abscisic acid reflects early host-pathogen conflict and moulds plant defence responses. Plant J 59:375-386
41. De Vos M, Van Oosten VR, Van Poecke RM, Van Pelt JA, Pozo MJ, Mueller MJ, Buchala AJ, Metraux JP, Van Loon LC, Dicke M, Pieterse CM (2005) Signal signature and transcriptome changes of Arabidopsis during pathogen and insect attack. Mol Plant Microbe Interact 18:923-937
42. De Vos M, Van Zaanen W, Koornneef A, Korzelius JP, Dicke M, Van Loon LC, Pieterse CMJ (2006) Herbivore-induced resistance against microbial pathogens in Arabidopsis. Plant Physiology 142: 352-363
43. Delaney TP, Uknes S, Vernooij B, Friedrich L, Weymann K, Negrotto D, Gaffney T, Gut-Rella M, Kessmann H, Ward E, Ryals J (1994) A central role of salicylic Acid in plant disease resistance. Science 266:1247-1250
44. Dennis K, Fan T, Geiman T, Yan Q, Muegge K (2001) Lsh, a member of the SNF2 family, is required for genome-wide methylation. Genes Dev 15:2940-2944
45. Dhawan R, Luo H, Foerster AM, Abuqamar S, Du HN, Briggs SD, Mittelsten Scheid O, Mengiste T (2009) HISTONE MONOUBIQUITINATION1 interacts with a subunit of the mediator complex and regulates defense against necrotrophic fungal pathogens in Arabidopsis. Plant Cell 21: 1000-1019
46. Dias AP, Braun EL, McMullen MD, Grotewold E (2003) Recently duplicated maize R2R3 Myb genes provide evidence for distinct mechanisms of evolutionary divergence after duplication. Plant Physiol 131:610-620
47. Dong X (2004) NPR1, all things considered. Curr Opin Plant Biol 7:547-552
48. Dong X, Li X, Zhang Y, Fan W, Kinkema M, Clarke J (2001) Regulation of systemic acquired resistance by NPR1 and its partners. Novartis Found Symp 236:165-173; discussion 173-165
49. Dover J, Schneider J, Tawiah-Boateng MA, Wood A, Dean K, Johnston M, Shilatifard A (2002) Methylation of histone H3 by COMPASS requires ubiquitination of histone H2B by Rad6. J Biol Chem 277:28368-28371
50. Du H, Zhang L, Liu L, Tang XF, Yang WJ, Wu YM, Huang YB, Tang YX (2009) Biochemical and molecular characterization of plant MYB transcription factor family. Biochemistry (Mosc) 74:1-11
51.Dubos C, Stracke R, Grotewold E, Weisshaar B, Martin C, Lepiniec L (2010) MYB transcription factors in Arabidopsis. Trends Plant Sci 15:573-581
52. Durrant WE, Dong X (2004) Systemic acquired resistance. Annu Rev Phytopathol 42:185-209
53. Durrant WE, Wang S, Dong X (2007) Arabidopsis SNI1 and RAD51D regulate both gene transcription and DNA recombination during the defense response. Proc Natl Acad Sci U S A 104: 4223-4227
54. Eulgem T, Somssich IE (2007) Networks of WRKY transcription factors in defense signaling. Curr Opin Plant Biol 10:366-371
55. Farmer EE (2007) Plant biology:jasmonate perception machines. Nature 448:659-660
56. Felix G, Duran JD, Volko S, Boller T (1999) Plants have a sensitive perception system for the most conserved domain of bacterial flagellin. Plant J 18:265-276
57. Feys B, Benedetti CE, Penfold CN, Turner JG (1994) Arabidopsis Mutants Selected for Resistance to the Phytotoxin Coronatine Are Male Sterile, Insensitive to Methyl Jasmonate, and Resistant to a Bacterial Pathogen. Plant Cell 6:751-759
58. Feys BJ, Wiermer M, Bhat RA, Moisan LJ, Medina-Escobar N, Neu C, Cabral A, Parker JE (2005) Arabidopsis SENESCENCE-ASSOCIATED GENE101 stabilizes and signals within an ENHANCED DISEASE SUSCEPTIBILITY 1 complex in plant innate immunity.Plant Cell 17: 2601-2613
59. Fisher AJ, Franklin KA (2011) Chromatin remodelling in plant light signalling. Physiol Plant 142: 305-313
60. Flaus A, Martin DM, Barton GJ, Owen-Hughes T (2006) Identification of multiple distinct Snf2 subfamilies with conserved structural motifs. Nucleic Acids Res 34:2887-2905
61. Fleury D, Himanen K, Cnops G, Nelissen H, Boccardi TM, Maere S, Beemster GT, Neyt P, Anami S, Robles P, Micol JL, Inze D, Van Lijsebettens M (2007) The Arabidopsis thaliana homolog of yeast BRE1 has a function in cell cycle regulation during early leaf and root growth. Plant Cell 19: 417-432
62. Fleury D, Himanen K, Cnops G, Nelissen H, Boccardi TM, Maere S, Beemster GTS, Neyt P, Anami S, Robles P, Micol JL, Inze D, Van Lijsebettens M (2007) The Arabidopsis thaliana homolog of yeast BRE1 has a function in cell cycle regulation during early leaf and root growth. Plant Cell 19: 417-432
63. Fu DL, Uauy C, Distelfeld A, Blechl A, Epstein L, Chen XM, Sela HA, Fahima T, Dubcovsky J (2009) A Kinase-START Gene Confers Temperature-Dependent Resistance to Wheat Stripe Rust. Science 323:1357-1360
64. Fu ZQ, Dong X (2013) Systemic acquired resistance:turning local infection into global defense. Annu Rev Plant Biol 64:839-863
65. Gaffney T, Friedrich L, Vernooij B, Negrotto D, Nye G, Uknes S, Ward E, Kessmann H, Ryals J (1993) Requirement of salicylic Acid for the induction of systemic acquired resistance. Science 261: 754-756
66. Gao M, Wang X, Wang D, Xu F, Ding X, Zhang Z, Bi D, Cheng YT, Chen S, Li X, Zhang Y (2009) Regulation of cell death and innate immunity by two receptor-like kinases in Arabidopsis. Cell Host Microbe 6:34-44
67. Gendrel AV, Lippman Z, Martienssen R, Colot V (2005) Profiling histone modification patterns in plants using genomic tiling microarrays. Nat Methods 2:213-218
68. Geng F, Laurent BC (2004) Roles of SWI/SNF and HATs throughout the dynamic transcription of a yeast glucose-repressible gene. EMBO J 23:127-137
69. Gfeller A, Dubugnon L, Liechti R, Farmer EE (2010) Jasmonate biochemical pathway. Sci Signal 3: cm3
70. Glover BJ, Perez-Rodriguez M, Martin C (1998) Development of several epidermal cell types can be specified by the same MYB-related plant transcription factor. Development 125:3497-3508
71. Gomez-Gomez L, Boller T (2002) Flagellin perception:a paradigm for innate immunity. Trends Plant Sci 7:251-256
72. Gonzalez A, Mendenhall J, Huo Y, Lloyd A (2009) TTG1 complex MYBs, MYB5 and TT2, control outer seed coat differentiation. Dev Biol 325:412-421
73. Gonzalez A, Zhao M, Leavitt JM, Lloyd AM (2008) Regulation of the anthocyanin biosynthetic pathway by the TTGl/bHLH/Myb transcriptional complex in Arabidopsis seedlings. Plant J 53: 814-827
74. Gou M, Hua J (2012) Complex regulation of an R gene SNC1 revealed by auto-immune mutants. Plant Signal Behav 7:213-216
75. Grennan AK (2008) Ethylene response factors in jasmonate signaling and defense response. Plant Physiol 146:1457-1458
76. Guo M, Tian F, Wamboldt Y, Alfano JR (2009) The majority of the type Ⅲ effector inventory of Pseudomonas syringae pv. tomato DC3000 can suppress plant immunity. Mol Plant Microbe Interact 22:1069-1080
77. Han SK, Sang Y, Rodrigues A, Biol F, Wu MF, Rodriguez PL, Wagner D (2012) The SW12/SNF2 chromatin remodeling ATPase BRAHMA represses abscisic acid responses in the absence of the stress stimulus in Arabidopsis. Plant Cell 24:4892-4906
78. Hauck P, Thilmony R, He SY (2003) A Pseudomonas syringae type Ⅲ effector suppresses cell wall-based extracellular defense in susceptible Arabidopsis plants. Proc Natl Acad Sci U S A 100: 8577-8582
79. Heyse KS, Weber SE, Lipps HJ (2009) Histone modifications are specifically relocated during gene activation and nuclear differentiation. BMC Genomics 10:554
80. Hicke L (2001) Protein regulation by monoubiquitin. Nat Rev Mol Cell Biol 2:195-201
81. Higashi K, Ishiga Y, Inagaki Y, Toyoda K, Shiraishi T, Ichinose Y (2008) Modulation of defense signal transduction by flagellin-induced WRKY41 transcription factor in Arabidopsis thaliana. Mol Genet Genomics 279:303-312
82. Howe GA, Jander G (2008) Plant immunity to insect herbivores. Annu Rev Plant Biol 59:41-66
83. Hua J (2013) Modulation of plant immunity by light, circadian rhythm, and temperature. Curr Opin Plant Biol 16:406-413
84. Hua J, Grisafi P, Cheng SH, Fink GR (2001) Plant growth homeostasis is controlled by the Arabidopsis BON1 and BAP1 genes. Genes Dev 15:2263-2272
85. Hua, J., Chang, C., Sun, Q.,& Meyerowitz, E. M. (1995). Ethylene insensitivity conferred by Arabidopsis ERS gene. Science.269:1712-1714.
86. Jambunathan N, Siani JM, McNellis TW (2001) A humidity-sensitive Arabidopsis copine mutant exhibits precocious cell death and increased disease resistance. Plant Cell 13:2225-2240
87. Jaskiewicz M, Conrath U, Peterhansel C (2011) Chromatin modification acts as a memory for systemic acquired resistance in the plant stress response. EMBO Rep 12:50-55
88. Jeddeloh JA, Stokes TL, Richards EJ (1999) Maintenance of genomic methylation requires a SW12/SNF2-like protein. Nat Genet 22:94-97
89. Jia Y, McAdams SA, Bryan GT, Hershey HP, Valent B (2000) Direct interaction of resistance gene and avirulence gene products confers rice blast resistance. EMBO J 19:4004-4014
90. Jung C, Seo JS, Han SW, Koo YJ, Kim CH, Song SI, Nahm BH, Choi YD, Cheong JJ (2008) Overexpression of AtMYB44 enhances stomatal closure to confer abiotic stress tolerance in transgenic Arabidopsis. Plant Physiol 146:623-635
91. Jung C, Shim JS, Seo JS, Lee HY, Kim CH, Choi YD, Cheong JJ (2010) Non-specific phytohormonal induction of AtMYB44 and suppression of jasmonate-responsive gene activation in Arabidopsis thaliana. Mol Cells 29:71-76
92. Kakutani T, Jeddeloh JA, Richards EJ (1995) Characterization of an Arabidopsis thaliana DNA hypomethylation mutant. Nucleic Acids Res 23:130-137
93. Katagiri F, Tsuda K (2010) Understanding the plant immune system. Mol Plant Microbe Interact 23: 1531-1536
94. Kato M, Miura A, Bender J, Jacobsen SE, Kakutani T (2003) Role of CG and non-CG methylation in immobilization of transposons in arabidopsis. Current Biology 13:421-426
95. Kazan K, Manners JM (2008) Jasmonate signaling:toward an integrated view. Plant Physiol 146: 1459-1468
96. Kim J, Hake SB, Roeder RG (2005) The human homolog of yeast BRE1 functions as a transcriptional coactivator through direct activator interactions. Mol Cell 20:759-770
97. Kim KC, Lai Z, Fan B, Chen Z (2008) Arabidopsis WRKY38 and WRKY62 transcription factors interact with histone deacetylase 19 in basal defense. Plant Cell 20:2357-2371
98. Kim TH, Hauser F, Ha T, Xue SW, Bohmer M, Nishimura N, Munemasa S, Hubbard K, Peine N, Lee BH, Lee S, Robert N, Parker JE, Schroeder JI (2011) Chemical Genetics Reveals Negative Regulation of Abscisic Acid Signaling by a Plant Immune Response Pathway. Current Biology 21: 990-997
99. Kouzarides T (2007) Chromatin modifications and their function. Cell 128:693-705
100. Krebs JE, Fry CJ, Samuels ML, Peterson CL (2000) Global role for chromatin remodeling enzymes in mitotic gene expression. Cell 102:587-598
101. Kumar D, Park S, Forouhar F, Yang Y, Vlot A, Fridman E, Chiang Y, Acton T, Shulaev V, Montelione G, Pichersky E, Tong L, Klessig D (2005) Identification of SA-binding protein 2 (SABP2) as a critical component of plant innate immunity. Phytopathology 95:S55-S55
102. Lawton K, Weymann K, Friedrich L, Vernooij B, Uknes S, Ryals J (1995) Systemic acquired resistance in Arabidopsis requires salicylic acid but not ethylene. Mol Plant Microbe Interact 8: 863-870
103. Lee JS, Shukla A, Schneider J, Swanson SK, Washburn MP, Florens L, Bhaumik SR, Shilatifard A (2007) Histone crosstalk between H2B monoubiquitination and H3 methylation mediated by COMPASS. Cell 131:1084-1096
104. Lehti-Shiu MD, Zou C, Hanada K, Shiu SH (2009) Evolutionary history and stress regulation of plant receptor-like kinase/pelle genes. Plant Physiol 150:12-26
105. Lennartsson A, Ekwall K (2009) Histone modification patterns and epigenetic codes. Biochim Biophys Acta 1790:863-868
106. Leon-Reyes A, Du YJ, Koornneef A, Proietti S, Korbes AP, Memelink J, Pieterse CMJ, Ritsema T (2010) Ethylene Signaling Renders the Jasmonate Response of Arabidopsis Insensitive to Future Suppression by Salicylic Acid. Molecular Plant-Microbe Interactions 23:187-197
107. Li J, Brader Q Palva ET (2004) The WRKY70 transcription factor:a node of convergence for jasmonate-mediated and salicylate-mediated signals in plant defense. Plant Cell 16:319-331
108. Li L, Yu X, Thompson A, Guo M, Yoshida S, Asami T, Chory J, Yin Y (2009) Arabidopsis MYB30 is a direct target of BES1 and cooperates with BES1 to regulate brassinosteroid-induced gene expression. Plant J 58:275-286
109. Li Y, Gou M, Sun Q, Hua J (2010) Requirement of calcium binding, myristoylation, and protein-protein interaction for the Copine BON1 function in Arabidopsis. J Biol Chem 285: 29884-29891
110. Li Y, Tessaro MJ, Li X, Zhang Y (2010) Regulation of the expression of plant resistance gene SNC1 by a protein with a conserved BAT2 domain. Plant Physiol 153:1425-1434
111. Li Y, Yang S, Yang H, Hua J (2007) The TIR-NB-LRR gene SNC1 is regulated at the transcript level by multiple factors. Mol Plant Microbe Interact 20:1449-1456
112. Liu R, Chen L, Jia Z, Lu B, Shi H, Shao W, Dong H (2011) Transcription factor AtMYB44 regulates induced expression of the ETHYLENE INSENSITIVE2 gene in Arabidopsis responding to a harpin protein. Mol Plant Microbe Interact 24:377-389
113. Liu Y, Koornneef M, Soppe WJ (2007) The absence of histone H2B monoubiquitination in the Arabidopsis hubl (rdo4) mutant reveals a role for chromatin remodeling in seed dormancy. Plant Cell 19:433-444
114. Lorenzo O, Chico JM, Sanchez-Serrano JJ, Solano R (2004) JASMONATE-INSENSITIVEI encodes a MYC transcription factor essential to discriminate between different jasmonate-regulated defense responses in Arabidopsis. Plant Cell 16:1938-1950
115. Lorenzo O, Piqueras R, Sanchez-Serrano JJ, Solano R (2003) ETHYLENE RESPONSE FACTOR1 integrates signals from ethylene and jasmonate pathways in plant defense. Plant Cell 15:165-178
116. Lu B, Sun W, Zhang S, Zhang C, Qian J, Wang X, Gao R, Dong H (2011) HrpN Ea-induced deterrent effect on phloem feeding of the green peach aphid Myzus persicae requires AtGSL5 and AtMYB44 genes in Arabidopsis thaliana. J Biosci 36:123-137
117. Lu BB, Li XJ, Sun WW, Li L, Gao R, Zhu Q, Tian SM, Fu MQ, Yu HL, Tang XM, Zhang CL, Dong HS (2013) AtMYB44 regulates resistance to the green peach aphid and diamondback moth by activating EIN2-affected defences in Arabidopsis. Plant Biol (Stuttg) 15:841-850
118. Mackey D, Belkhadir Y, Alonso JM, Ecker JR, Dangl JL (2003) Arabidopsis RIN4 is a target of the type III virulence effector AvrRpt2 and modulates RPS2-mediated resistance. Cell 112:379-389
119. Mackey D, Holt BF,3rd, Wiig A, Dangl JL (2002) RIN4 interacts with Pseudomonas syringae type Ⅲ effector molecules and is required for RPM1-mediated resistance in Arabidopsis. Cell 108: 743-754
120. Mandaokar A, Browse J (2009) MYB108 Acts Together with MYB24 to Regulate Jasmonate-Mediated Stamen Maturation in Arabidopsis. Plant Physiology 149:851-862
121. Mang HG, Qian W, Zhu Y, Qian J, Kang HG, Klessig DF, Hua J (2012) Abscisic acid deficiency antagonizes high-temperature inhibition of disease resistance through enhancing nuclear accumulation of resistance proteins SNC1 and RPS4 in Arabidopsis. Plant Cell 24:1271-1284
122. March-Diaz R, Garcia-Dominguez M, Lozano-Juste J, Leon J, Florencio FJ, Reyes JC (2008) Histone H2A.Z and homologues of components of the SWR1 complex are required to control immunity in Arabidopsis. Plant J 53:475-487
123. Matus JT, Aquea F, Arce-Johnson P (2008) Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes. BMC Plant Biol 8:83
124. McGrath KC, Dombrecht B, Manners JM, Schenk PM, Edgar CI, Maclean DJ, Scheible WR, Udvardi MK, Kazan K (2005) Repressor- and activator-type ethylene response factors functioning in jasmonate signaling and disease resistance identified via a genome-wide screen of Arabidopsis transcription factor gene expression. Plant Physiol 139:949-959
125. Medzhitov R, Janeway CA, Jr. (1997) Innate immunity:the virtues of a nonclonal system of recognition. Cell 91:295-298
126. Millar AA, Gubler F (2005) The Arabidopsis GAMYB-like genes, MYB33 and MYB65, are MicroRNA-regulated genes that redundantly facilitate anther development. Plant Cell 17:705-721
127. Mohrmann L, Langenberg K, Krijgsveld J, Kal AJ, Heck AJ, Verrijzer CP (2004) Differential targeting of two distinct SWI/SNF-related Drosophila chromatin-remodeling complexes. Mol Cell Biol 24:3077-3088
128. Mohrmann L, Verrijzer CP (2005) Composition and functional specificity of SWI2/SNF2 class chromatin remodeling complexes. Biochim Biophys Acta 1681:59-73
129. Mou Z, Fan WH, Dong XN (2003) Inducers of plant systemic acquired resistance regulate NPR1 function through redox changes. Cell 113:935-944
130. Mu RL, Cao YR, Liu YF, Lei G, Zou HF, Liao Y, Wang HW, Zhang WK, Ma B, Du JZ, Yuan M, Zhang JS, Chen SY (2009) An R2R3-type transcription factor gene AtMYB59 regulates root growth and cell cycle progression in Arabidopsis. Cell Research 19:1291-1304
131. Muller D, Schmitz G, Theres K (2006) Blind homologous R2R3 Myb genes control the pattern of lateral meristem initiation in Arabidopsis. Plant Cell 18:586-597
132. Muller S, Feldman MF, Cornelis GR (2001) The Type Ⅲ secretion system of Gram-negative bacteria:a potential therapeutic target? Expert Opin Ther Targets 5:327-339
133. Mur LA, Kenton P, Atzorn R, Miersch O, Wasternack C (2006) The outcomes of concentration-specific interactions between salicylate and jasmonate signaling include synergy, antagonism, and oxidative stress leading to cell death. Plant Physiol 140:249-262
134. Noel L, Moores TL, van Der Biezen EA, Parniske M, Daniels MJ, Parker JE, Jones JD (1999) Pronounced intraspecific haplotype divergence at the RPP5 complex disease resistance locus of Arabidopsis. Plant Cell 11:2099-2112
135. Nurnberger T, Kemmerling B (2006) Receptor protein kinases-pattern recognition receptors in plant immunity. Trends Plant Sci 11:519-522
136. Oh JE, Kwon Y, Kim JH, Noh H, Hong SW, Lee H (2011) A dual role for MYB60 in stomatal regulation and root growth of Arabidopsis thaliana under drought stress. Plant Mol Biol 77:91-103
137. Palma K, Thorgrimsen S, Malinovsky FQ Fiil BK, Nielsen HB, Brodersen P, Hofius D, Petersen M, Mundy J (2010) Autoimmunity in Arabidopsis acd11 is mediated by epigenetic regulation of an immune receptor. PLoS Pathog 6:e1001137
138. Pan X, Welti R, Wang X (2008) Simultaneous quantification of major phytohormones and related compounds in crude plant extracts by liquid chromatography-electrospray tandem mass spectrometry. Phytochemistry 69:1773-1781
139. Pape S, Thurow C, Gatz C (2010) The Arabidopsis PR-1 promoter contains multiple integration sites for the coactivator NPR1 and the repressor SNI1. Plant Physiol 154:1805-1818
140. Paz-Ares J, Ghosal D, Wienand U, Peterson PA, Saedler H (1987) The regulatory c1 locus of Zea mays encodes a protein with homology to myb proto-oncogene products and with structural similarities to transcriptional activators. EMBO J 6:3553-3558
141. Penninckx IA, Thomma BP, Buchala A, Metraux JP, Broekaert WF (1998) Concomitant activation of jasmonate and ethylene response pathways is required for induction of a plant defensin gene in Arabidopsis. Plant Cell 10:2103-2113
142. Pickart CM (2004) Back to the future with ubiquitin. Cell 116:181-190
143. Pieterse CM, Leon-Reyes A, Van der Ent S, Van Wees SC (2009) Networking by small-molecule hormones in plant immunity. Nat Chem Biol 5:308-316
144. Pieterse CM, Van der Does D, Zamioudis C, Leon-Reyes A, Van Wees SC (2012) Hormonal modulation of plant immunity. Annu Rev Cell Dev Biol 28:489-521
145. Pointner J, Persson J, Prasad P, Norman-Axelsson U, Stralfors A, Khorosjutina O, Krietenstein N, Svensson JP, Ekwall K, Korber P (2012) CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S. pombe. EMBO J 31:4388-4403
146. Proft M, Struhl K (2002) Hogl kinase converts the Skol-Cyc8-Tupl repressor complex into an activator that recruits SAGA and SWI/SNF in response to osmotic stress. Mol Cell 9:1307-1317
147. Qu F, Ye XH, Hou GC, Sato S, Clemente TE, Morris TJ (2005) RDR6 has a broad-spectrum but temperature-dependent antiviral defense role in Nicotiana benthamiana. Journal of Virology 79: 15209-15217
148. Quan TK, Hartzog GA (2010) Histone H3K4 and K36 methylation, Chdl and Rpd3S oppose the functions of Saccharomyces cerevisiae Spt4-Spt5 in transcription. Genetics 184:321-334
149. Raffaele S, Vailleau F, Leger A, Joubes J, Miersch O, Huard C, Blee E, Mongrand S, Domergue F, Roby D (2008) A MYB transcription factor regulates very-long-chain fatty acid biosynthesis for activation of the hypersensitive cell death response in Arabidopsis. Plant Cell 20:752-767
150. Reyes JL, Chua NH (2007) ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination. Plant J 49:592-606
151. Robert JM (1971) [The modern concept of the gene]. Orthod Fr 42:43-53
152. 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 ML, Robin S, Caboche M, Colot V (2011) Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J 30:1928-1938
153. Sato M, Tsuda K, Wang L, Coller J, Watanabe Y, Glazebrook J, Katagiri F (2010) Network Modeling Reveals Prevalent Negative Regulatory Relationships between Signaling Sectors in Arabidopsis Immune Signaling. Plos Pathogens 6
154. Scheuermann JC, Gutierrez L, Muller J (2012) Histone H2A monoubiquitination and Polycomb repression:the missing pieces of the puzzle. Fly (Austin) 6:162-168
155. Schneider R, Grosschedl R (2007) Dynamics and interplay of nuclear architecture, genome organization, and gene expression. Genes Dev 21:3027-3043
156. Scott IM, Clarke SM, Wood JE, Mur LA (2004) Salicylate accumulation inhibits growth at chilling temperature in Arabidopsis. Plant Physiol 135:1040-1049
157. Sebald J, Morettini S, Podhraski V, Lass-Florl C, Lusser A (2012) CHD1 contributes to intestinal resistance against infection by P. aeruginosa in Drosophila melanogaster. PLoS One 7:e43144
158. Seo PJ, Lee SB, Suh MC, Park MJ, Go YS, Park CM (2011) The MYB96 transcription factor regulates cuticular wax biosynthesis under drought conditions in Arabidopsis. Plant Cell 23: 1138-1152
159. Seo PJ, Park CM (2010) MYB96-mediated abscisic acid signals induce pathogen resistance response by promoting salicylic acid biosynthesis in Arabidopsis. New Phytol 186:471-483
160. Seo PJ, Xiang F, Qiao M, Park JY, Lee YN, Kim SG, Lee YH, Park WJ, Park CM (2009) The MYB96 transcription factor mediates abscisic acid signaling during drought stress response in Arabidopsis. Plant Physiol 151:275-289
161. Sheard LB, Tan X, Mao H, Withers J, Ben-Nissan G, Hinds TR, Kobayashi Y, Hsu FF, Sharon M, Browse J, He SY, Rizo J, Howe GA, Zheng N (2010) Jasmonate perception by inositol-phosphate-potentiated COI1-JAZ co-receptor. Nature 468:400-405
162. Shim JS, Jung C, Lee S, Min K, Lee YW, Choi Y, Lee JS, Song JT, Kim JK, Choi YD (2013) AtMYB44 regulates WRKY70 expression and modulates antagonistic interaction between salicylic acid and jasmonic acid signaling. Plant J 73:483-495
163. Shin R, Burch AY, Huppert KA, Tiwari SB, Murphy AS, Guilfoyle TJ, Schachtman DP (2007) The Arabidopsis transcription factor MYB77 modulates auxin signal transduction. Plant Cell 19: 2440-2453
164. Singh Sandhu K, Li G, Sung WK, Ruan Y (2011) Chromatin interaction networks and higher order architectures of eukaryotic genomes. J Cell Biochem 112:2218-2221
165. Smalle J, Vierstra RD (2004) The ubiquitin 26S proteasome proteolytic pathway. Annual Review of Plant Biology 55:555-590
166. Spoel SH, Johnson JS, Dong X (2007) Regulation of tradeoffs between plant defenses against pathogens with different lifestyles. Proc Natl Acad Sci U S A 104:18842-18847
167. Spoel SH, Koornneef A, Claessens SM, Korzelius JP, Van Pelt JA, Mueller MJ, Buchala AJ, Metraux JP, Brown R, Kazan K, Van Loon LC, Dong X, Pieterse CM (2003) NPR1 modulates cross-talk between salicylate-and jasmonate-dependent defense pathways through a novel function in the cytosol. Plant Cell 15:760-770
168. Spoel SH, Koornneef A, Claessens SMC, Korzelius JP, Van Pelt JA, Mueller MJ, Buchala AJ, Metraux JP, Brown R, Kazan K, Van Loon LC, Dong XN, Pieterse CMJ (2003) NPR1 modulates cross-talk between salicylate- and jasmonate-dependent defense pathways through a novel function in the cytosol. Plant Cell 15:760-770
169. Sridhar VV, Kapoor A, Zhang K, Zhu J, Zhou T, Hasegawa PM, Bressan RA, Zhu JK (2007) Control of DNA methylation and heterochromatic silencing by histone H2B deubiquitination. Nature 447:735-738
170. Stokes TL, Kunkel BN, Richards EJ (2002) Epigenetic variation in Arabidopsis disease resistance. Genes Dev 16:171-182
171. Stracke R, Ishihara H, Huep G, Barsch A, Mehrtens F, Niehaus K, Weisshaar B (2007) Differential regulation of closely related R2R3-MYB transcription factors controls flavonol accumulation in different parts of the Arabidopsis thaliana seedling. Plant J 50:660-677
172. Stracke R, Werber M, Weisshaar B (2001) The R2R3-MYB gene family in Arabidopsis thaliana. Curr Opin Plant Biol 4:447-456
173. Szittya G, Silhavy D, Molnar A, Havelda Z, Lovas A, Lakatos L, Banfalvi Z, Burgyan J (2003) Low temperature inhibits RNA silencing-mediated defence by the control of siRNA generation. Embo Journal 22:633-640
174. Takeuchi K, Gyohda A, Tominaga M, Kawakatsu M, Hatakeyama A, Ishii N, Shimaya K, Nishimura T, Riemann M, Nick P, Hashimoto M, Komano T, Endo A, Okamoto T, Jikumaru Y, Kamiya Y, Terakawa T, Koshiba T (2011) RSOsPR10 expression in response to environmental stresses is regulated antagonistically by jasmonate/ethylene and salicylic acid signaling pathways in rice roots. Plant Cell Physiol 52:1686-1696
175. Terakura S, Ueno Y, Tagami H, Kitakura S, Machida C, Wabiko H, Aiba H, Otten L, Tsukagoshi H, Nakamura K, Machida Y (2007) An oncoprotein from the plant pathogen agrobacterium has histone chaperone-like activity. Plant Cell 19:2855-2865
176. Thorstensen T, Grini PE, Aalen RB (2011) SET domain proteins in plant development. Biochim Biophys Acta 1809:407-420
177. Tian L, Fong MP, Wang JJ, Wei NE, Jiang H, Doerge RW, Chen ZJ (2005) Reversible histone acetylation and deacetylation mediate genome-wide, promoter-dependent and locus-specific changes in gene expression during plant development. Genetics 169:337-345
178. Tominaga-Wada R, Nukumizu Y, Sato S, Wada T (2013) Control of plant trichome and root-hair development by a tomato (Solanum lycopersicum) R3 MYB transcription factor. PLoS One 8: e54019
179. Ton J, De Vos M, Robben C, Buchala A, Metraux JP, Van Loon LC, Pieterse CM (2002) Characterization of Arabidopsis enhanced disease susceptibility mutants that are affected in systemically induced resistance. Plant J 29:11-21
180. Ton J, Flors V, Mauch-Mani B (2009) The multifaceted role of ABA in disease resistance. Trends Plant Sci 14:310-317
181.Tsukiyama T, Palmer J, Landel CC, Shiloach J, Wu C (1999) Characterization of the imitation switch subfamily of ATP-dependent chromatin-remodeling factors in Saccharomyces cerevisiae. Genes Dev 13:686-697
182. Tuttle JR, Idris AM, Brown JK, Haigler CH, Robertson D (2008) Geminivirus-mediated gene silencing from Cotton leaf crumple virus is enhanced by low temperature in cotton. Plant Physiology 148:41-50
183. van Verk MC, Bol JF, Linthorst HJ (2011) Prospecting for genes involved in transcriptional regulation of plant defenses, a bioinformatics approach. BMC Plant Biol 11:88
184. Vanholme B, Grunewald W, Bateman A, Kohchi T, Gheysen G (2007) The tify family previously known as ZIM. Trends Plant Sci 12:239-244
185. Verhage A, van Wees SC, Pieterse CM (2010) Plant immunity:it's the hormones talking, but what do they say? Plant Physiol 154:536-540
186. Vernooij B, Friedrich L, Morse A, Reist R, Kolditz-Jawhar R, Ward E, Uknes S, Kessmann H, Ryals J (1994) Salicylic Acid Is Not the Translocated Signal Responsible for Inducing Systemic Acquired Resistance but Is Required in Signal Transduction. Plant Cell 6:959-965
187. Vlot AC, Dempsey DA, Klessig DF (2009) Salicylic Acid, a multifaceted hormone to combat disease. Annu Rev Phytopathol 47:177-206
188. Vlot AC, Klessig DF, Park SW (2008) Systemic acquired resistance:the elusive signal(s). Curr Opin Plant Biol 11:436-442
189. Vongs A, Kakutani T, Martienssen RA, Richards EJ (1993) Arabidopsis thaliana DNA methylation mutants. Science 260:1926-1928
190. Walley JW, Rowe HC, Xiao Y, Chehab EW, Kliebenstein DJ, Wagner D, Dehesh K (2008) The chromatin remodeler SPLAYED regulates specific stress signaling pathways. PLoS Pathog 4: e1000237
191. Wang C, Gao F, Wu J, Dai J, Wei C, Li Y (2010) Arabidopsis putative deacetylase AtSRT2 regulates basal defense by suppressing PAD4, EDS5 and SID2 expression. Plant Cell Physiol 51:1291-1299
192. Wang D, Amornsiripanitch N, Dong X (2006) A genomic approach to identify regulatory nodes in the transcriptional network of systemic acquired resistance in plants. PLoS Pathog 2:e123
193. Wang G, Ellendorff U, Kemp B, Mansfield JW, Forsyth A, Mitchell K, Bastas K, Liu CM, Woods-Tor A, Zipfel C, de Wit PJ, Jones JD, Tor M, Thomma BP (2008) A genome-wide functional investigation into the roles of receptor-like proteins in Arabidopsis. Plant Physiol 147:503-517
194. Wang XC, Niu QW, Teng C, Li C, Mu JY, Chua NH, Zuo JR (2009) Overexpression of PGA37/MYB118 and MYB115 promotes vegetative-to-embryonic transition in Arabidopsis. Cell Research 19:224-235
195. Wang Y, Bao Z, Zhu Y, Hua J (2009) Analysis of temperature modulation of plant defense against biotrophic microbes. Mol Plant Microbe Interact 22:498-506
196. Wang Z, Meng P, Zhang X, Ren D, Yang S (2011) BON1 interacts with the protein kinases BIR1 and BAK1 in modulation of temperature-dependent plant growth and cell death in Arabidopsis. Plant J 67:1081-1093
197. Wang ZX, Yamanouchi U, Katayose Y, Sasaki T, Yano M (2001) Expression of the Pib rice-blast-resistance gene family is up-regulated by environmental conditions favouring infection and by chemical signals that trigger secondary plant defences. Plant Molecular Biology 47:653-661
198. Wiermer M, Feys BJ, Parker JE (2005) Plant immunity:the EDS1 regulatory node. Curr Opin Plant Biol 8:383-389
199. Wildermuth MC, Dewdney J, Wu G, Ausubel FM (2001) Isochorismate synthase is required to synthesize salicylic acid for plant defence. Nature 414:562-565
200. Wilkins O, Nahal H, Foong J, Provart NJ, Campbell MM (2009) Expansion and diversification of the Populus R2R3-MYB family of transcription factors. Plant Physiol 149:981-993
201. Wu C (1997) Chromatin remodeling and the control of gene expression. J Biol Chem 272: 28171-28174
202. Wu K, Zhang L, Zhou C, Yu CW, Chaikam V (2008) HDA6 is required for jasmonate response, senescence and flowering in Arabidopsis. J Exp Bot 59:225-234
203. Xia S, Cheng YT, Huang S, Win J, Soards A, Jinn TL, Jones JD, Kamoun S, Chen S, Zhang Y, Li X (2013) Regulation of transcription of nucleotide-binding leucine-rich repeat-encoding genes SNC1 and RPP4 via H3K4 trimethylation. Plant Physiol 162:1694-1705
204. Xiao S, Brown S, Patrick E, Brearley C, Turner JG (2003) Enhanced transcription of the Arabidopsis disease resistance genes RPW8.1 and RPW8.2 via a salicylic acid-dependent amplification circuit is required for hypersensitive cell death. Plant Cell 15:33-45
205. Xu L, Menard R, Berr A, Fuchs J, Cognat V, Meyer D, Shen WH (2009) 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 57: 279-288
206. Yahr TL, Wolfgang MC (2006) Transcriptional regulation of the Pseudomonas aeruginosa type Ⅲ secretion system. Mol Microbiol 62:631-640
207. Yamaguchi K, Yamada K, Kawasaki T (2013) Receptor-like cytoplasmic kinases are pivotal components in pattern recognition receptor-mediated signaling in plant immunity. Plant Signal Behav 8
208. Yang H, Li Y, Hua J (2006) The C2 domain protein BAP1 negatively regulates defense responses in Arabidopsis. Plant J 48:238-248
209. Yang HJ, Yang SH, Li YQ, Hua J (2007) The Arabidopsis BAP1 and BAP2 genes are general inhibitors of programmed cell death. Plant Physiology 145:135-146
210. Yang J, Kloepper JW, Ryu CM (2009) Rhizosphere bacteria help plants tolerate abiotic stress. Trends Plant Sci 14:1-4
211. Yang S, Hua J (2004) A haplotype-specific Resistance gene regulated by BONZAI1 mediates temperature-dependent growth control in Arabidopsis. Plant Cell 16:1060-1071
212. Yang S, Yang H, Grisafi P, Sanchatjate S, Fink GR, Sun Q, Hua J (2006) The BON/CPN gene family represses cell death and promotes cell growth in Arabidopsis. Plant J 45:166-179
213. Yang SH, Hua J (2004) A haplotype-specific Resistance gene regulated by BONZAI1 mediates temperature-dependent growth control in Arabidopsis. Plant Cell 16:1060-1071
214. Yanhui C, Xiaoyuan Y, Kun H, Meihua L, Jigang L, Zhaofeng G, Zhiqiang L, Yunfei Z, Xiaoxiao W, Xiaoming Q, Yunping S, Li Z, Xiaohui D, Jingchu L, Xing-Wang D, Zhangliang C, Hongya G, Li-Jia Q (2006) The MYB transcription factor superfamily of Arabidopsis:expression analysis and phylogenetic comparison with the rice MYB family. Plant Mol Biol 60:107-124
215. Yasuda M, Ishikawa A, Jikumaru Y, Seki M, Umezawa T, Asami T, Maruyama-Nakashita A, Kudo T, Shinozaki K, Yoshida S, Nakashita H (2008) Antagonistic interaction between systemic acquired resistance and the abscisic acid-mediated abiotic stress response in Arabidopsis. Plant Cell 20: 1678-1692
216. Yi H, Richards EJ (2007) A cluster of disease resistance genes in Arabidopsis is coordinately regulated by transcriptional activation and RNA silencing. Plant Cell 19:2929-2939
217. Yoshioka K, Kachroo P, Tsui F, Sharma SB, Shah J, Klessig DF (2001) Environmentally sensitive, SA-dependent defense responses in the cpr22 mutant of Arabidopsis. Plant J 26:447-459
218. Yun MY, Wu J, Workman JL, Li B (2011)Readers of histone modifications. Cell Research 21: 564-578
219. Zander M, La Camera S, Lamotte O, Metraux JP, Gatz C (2010) Arabidopsis thaliana class-II TGA transcription factors are essential activators of jasmonic acid/ethylene-induced defense responses. Plant J 61:200-210
220. Zhang X, Germann S, Blus BJ, Khorasanizadeh S, Gaudin V, Jacobsen SE (2007) The Arabidopsis LHP1 protein colocalizes with histone H3 Lys27 trimethylation. Nat Struct Mol Biol 14:869-871
221. Zhang XC, Zhang XF, Singh J, Li DW, Qu F (2012) Temperature-Dependent Survival of Turnip Crinkle Virus-Infected Arabidopsis Plants Relies on an RNA Silencing-Based Defense That Requires DCL2, AG02, and HEN1. Journal of Virology 86:6847-6854
222. Zhang Y, Goritschnig S, Dong X, Li X (2003) A gain-of-function mutation in a plant disease resistance gene leads to constitutive activation of downstream signal transduction pathways in suppressor of nprl-1, constitutive 1. Plant Cell 15:2636-2646
223. Zhang ZB, Zhu J, Gao JF, Wang C, Li H, Li H, Zhang HQ, Zhang S, Wang DM, Wang QX, Huang H, Xia HJ, Yang ZN (2007) Transcription factor AtMYB103 is required for anther development by regulating tapetum development, callose dissolution and exine formation in Arabidopsis. Plant Journal 52:528-538
224. Zhong R, Lee C, Zhou J, McCarthy RL, Ye ZH (2008) A battery of transcription factors involved in the regulation of secondary cell wall biosynthesis in Arabidopsis. Plant Cell 20:2763-2782
225. Zhou C, Zhang L, Duan J, Miki B, Wu K (2005) HISTONE DEACETYLASE19 is involved in jasmonic acid and ethylene signaling of pathogen response in Arabidopsis. Plant Cell 17: 1196-1204
226. Zhou JM, Chai J (2008) Plant pathogenic bacterial type III effectors subdue host responses. Curr Opin Microbiol 11:179-185
227. Zhou W, Zhu P, Wang J, Pascual G, Ohgi KA, Lozach J, Glass CK, Rosenfeld MG (2008) Histone H2A monoubiquitination represses transcription by inhibiting RNA polymerase II transcriptional elongation. Mol Cell 29:69-80
228. Zhu Y, Mang HG, Sun Q, Qian J, Hipps A, Hua J (2012) Gene Discovery Using Mutagen-Induced Polymorphisms and Deep Sequencing:Application to Plant Disease Resistance. Genetics 192: 139-U171
229. Zhu Y, Qian W, Hua J (2010) Temperature modulates plant defense responses through NB-LRR proteins. PLoS Pathog 6:e1000844
230. Zhu Z, An F, Feng Y, Li P, Xue L, A M, Jiang Z, Kim JM, To TK, Li W, Zhang X, Yu Q, Dong Z, Chen WQ, Seki M, Zhou JM, Guo H (2011) Derepression of ethylene-stabilized transcription factors (EIN3/EIL1) mediates jasmonate and ethylene signaling synergy in Arabidopsis. Proc Natl Acad Sci U S A 108:12539-12544
231.Zipfel C (2008) Pattern-recognition receptors in plant innate immunity. Curr Opin Immunol 20: 10-16
232. Zipfel C (2009) Early molecular events in PAMP-triggered immunity. Curr Opin Plant Biol 12: 414-42
2. Abe H, Yamaguchi-Shinozaki K, Urao T, Iwasaki T, Hosokawa D, Shinozaki K (1997) Role of arabidopsis MYC and MYB homologs in drought-and abscisic acid-regulated gene expression. Plant Cell 9:1859-1868
3. Agarwal M, Hao Y, Kapoor A, Dong CH, Fujii H, Zheng X, Zhu JK (2006) A R2R3 type MYB transcription factor is involved in the cold regulation of CBF genes and in acquired freezing tolerance. J Biol Chem 281:37636-37645
4. Ali GS, Reddy A (2008) PAMP-triggered immunity:Early events in the activation of FLAGELLIN SENSITIVE2. Plant Signal Behav 3:423-426
5. Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen H, Shinn P, Stevenson DK, Zimmerman J, Barajas P, Ecker JR (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301:653-657
6. Alvarez-Venegas R, Abdallat AA, Guo M, Alfano JR, Avramova Z (2007) Epigenetic control of a transcription factor at the cross section of two antagonistic pathways. Epigenetics 2:106-113
7. Alvarez-Venegas R, Al Abdallat A, Guo M, Alfano JR, Avramova Z (2007) Epigenetic control of a transcription factor at the cross section of two antagonistic pathways. Epigenetics 2:106-113
8. Alvarez-Venegas R, Avramova Z (2005) Methylation patterns of histone H3 Lys 4, Lys 9 and Lys 8 27 in transcriptionally active and inactive Arabidopsis genes and in atxl mutants. Nucleic Acids Res 33:5199-5207
9. Axtell MJ, Staskawicz BJ (2003) Initiation of RPS2-specified disease resistance in Arabidopsis is coupled to the AvrRpt2-directed elimination of RIN4. Cell 112:369-377
10. Berke L, Sanchez-Perez GF, Snel B (2012) Contribution of the epigenetic mark H3K27me3 to functional divergence after whole genome duplication in Arabidopsis. Genome Biol 13:R94
11. Berr A, McCallum EJ, Alioua A, Heintz D, Heitz T, Shen WH (2010) Arabidopsis Histone Methyltransferase SET DOMAIN GROUP8 Mediates Induction of the Jasmonate/Ethylene Pathway Genes in Plant Defense Response to Necrotrophic Fungi. Plant Physiology 154: 1403-1414
12. Berr A, McCallum EJ, Alioua A, Heintz D, Heitz T, Shen WH (2010) Arabidopsis histone methyltransferase SET DOMAIN GROUP8 mediates induction of the jasmonate/ethylene pathway genes in plant defense response to necrotrophic fungi. Plant Physiol 154:1403-1414
13. Berr A, Menard R, Heitz T, Shen WH (2012) Chromatin modification and remodelling:a regulatory landscape for the control of Arabidopsis defence responses upon pathogen attack. Cellular Microbiology 14:829-839
14. Bowles D (1998) Signal transduction in the wound response of tomato plants. Philos Trans R Soc Lond B Biol Sci 353:1495-1510
15. Bowles DJ (1994) Signalling events in the wound response of tomato plants. Biochem Soc Symp 60: 155-164
16. Bray S, Musisi H, Bienz M (2005) Brel is required for Notch signaling and histone modification. Dev Cell 8:279-286
17. Broekaert WF, Delaure SL, De Bolle MF, Cammue BP (2006) The role of ethylene in host-pathogen interactions. Annu Rev Phytopathol 44:393-416
18. Brzeski J, Jerzmanowski A (2003) Deficient in DNA methylation 1 (DDM1) defines a novel family of chromatin-remodeling factors. J Biol Chem 278:823-828
19. Cao H, Bowling SA, Gordon AS, Dong X (1994) Characterization of an Arabidopsis Mutant That Is Nonresponsive to Inducers of Systemic Acquired Resistance. Plant Cell 6:1583-1592
20. Cao Y, Dai Y, Cui S, Ma L (2008) Histone H2B monoubiquitination in the chromatin of FLOWERING LOCUS C regulates flowering time in Arabidopsis. Plant Cell 20:2586-2602
21. Catanzariti AM, Dodds PN, Ve T, Kobe B, Ellis JG, Staskawicz BJ (2010) The AvrM effector from flax rust has a structured C-terminal domain and interacts directly with the M resistance protein. Mol Plant Microbe Interact 23:49-57
22. Chellappan P, Vanitharani R, Ogbe F, Fauquet CM (2005) Effect of temperature on geminivirus-induced RNA silencing in plants. Plant Physiology 138:1828-1841
23. Chen HM, Xue L, Chintamanani S, Germain H, Lin HQ, Cui HT, Cai R, Zuo JR, Tang XY, Li X, Guo HW, Zhou JM (2009) ETHYLENE INSENSITIVE3 and ETHYLENE INSENSITIVE3-LIKE1 Repress SALICYLIC ACID INDUCTION DEFICIENT2 Expression to Negatively Regulate Plant Innate Immunity in Arabidopsis. Plant Cell 21:2527-2540
24. Cheng H, Song SS, Xiao LT, Soo HM, Cheng ZW, Xie DX, Peng JR (2009) Gibberellin Acts through Jasmonate to Control the Expression of MYB21, MYB24, and MYB57 to Promote Stamen Filament Growth in Arabidopsis. Plos Genetics 5
25. Chinchilla D, Bauer Z, Regenass M, Boller T, Felix G (2006) The Arabidopsis receptor kinase FLS2 binds flg22 and determines the specificity of flagellin perception. Plant Cell 18:465-476
26. Chinchilla D, Zipfel C, Robatzek S, Kemmerling B, Nurnberger T, Jones JD, Felix G, Boller T (2007) A flagellin-induced complex of the receptor FLS2 and BAK1 initiates plant defence. Nature 448:497-500
27. Choi SM, Song HR, Han SK, Han M, Kim CY, Park J, Lee YH, Jeon JS, Noh YS, Noh B (2012) HDA19 is required for the repression of salicylic acid biosynthesis and salicylic acid-mediated defense responses in Arabidopsis. Plant J 71:135-146
28. Chung HS, Koo AJ, Gao X, Jayanty S, Thines B, Jones AD, Howe GA (2008) Regulation and function of Arabidopsis JASMONATE ZIM-domain genes in response to wounding and herbivory. Plant Physiol 146:952-964
29. Clapier CR, Cairns BR (2009) The biology of chromatin remodeling complexes. Annu Rev Biochem 78:273-304
30. Clapier CR, Cairns BR (2009) The Biology of Chromatin Remodeling Complexes. Annual Review of Biochemistry 78:273-304
31. Collier SM, Moffett P (2009) NB-LRRs work a "bait and switch" on pathogens. Trends Plant Sci 14: 521-529
32. Cominelli E, Galbiati M, Vavasseur A, Conti L, Sala T, Vuylsteke M, Leonhardt N, Dellaporta SL, Tonelli C (2005) A guard-cell-specific MYB transcription factor regulates stomatal movements and plant drought tolerance. Curr Biol 15:1196-1200
33. Dangl JL, Jones JD (2001) Plant pathogens and integrated defence responses to infection. Nature 411:826-833
34. Daniel X, Lacomme C, Morel JB, Roby D (1999) A novel myb oncogene homologue in Arabidopsis thaliana related to hypersensitive cell death. Plant J 20:57-66
35. Dasgupta P, Chellappan SP (2007) Chromatin immunoprecipitation assays:molecular analysis of chromatin modification and gene regulation. Methods Mol Biol 383:135-152
36. Day B, Dahlbeck D, Staskawicz BJ (2006) NDR1 interaction with RIN4 mediates the differential activation of multiple disease resistance pathways in Arabidopsis. Plant Cell 18:2782-2791
37. De-La-Pena C, Rangel-Cano A, Alvarez-Venegas R (2012) Regulation of disease-responsive genes mediated by epigenetic factors:interaction of Arabidopsis-Pseudomonas. Mol Plant Pathol 13: 388-398
38. De Jong CF, Takken FL, Cai X, de Wit PJ, Joosten MH (2002) Attenuation of Cf-mediated defense responses at elevated temperatures correlates with a decrease in elicitor-binding sites. Mol Plant Microbe Interact 15:1040-1049
39. De Torres M, Mansfield JW, Grabov N, Brown IR, Ammouneh H, Tsiamis G, Forsyth A, Robatzek S, Grant M, Boch J (2006) Pseudomonas syringae effector AvrPtoB suppresses basal defence in Arabidopsis. Plant J 47:368-382
40. De Torres Zabala M, Bennett MH, Truman WH, Grant MR (2009) Antagonism between salicylic and abscisic acid reflects early host-pathogen conflict and moulds plant defence responses. Plant J 59:375-386
41. De Vos M, Van Oosten VR, Van Poecke RM, Van Pelt JA, Pozo MJ, Mueller MJ, Buchala AJ, Metraux JP, Van Loon LC, Dicke M, Pieterse CM (2005) Signal signature and transcriptome changes of Arabidopsis during pathogen and insect attack. Mol Plant Microbe Interact 18:923-937
42. De Vos M, Van Zaanen W, Koornneef A, Korzelius JP, Dicke M, Van Loon LC, Pieterse CMJ (2006) Herbivore-induced resistance against microbial pathogens in Arabidopsis. Plant Physiology 142: 352-363
43. Delaney TP, Uknes S, Vernooij B, Friedrich L, Weymann K, Negrotto D, Gaffney T, Gut-Rella M, Kessmann H, Ward E, Ryals J (1994) A central role of salicylic Acid in plant disease resistance. Science 266:1247-1250
44. Dennis K, Fan T, Geiman T, Yan Q, Muegge K (2001) Lsh, a member of the SNF2 family, is required for genome-wide methylation. Genes Dev 15:2940-2944
45. Dhawan R, Luo H, Foerster AM, Abuqamar S, Du HN, Briggs SD, Mittelsten Scheid O, Mengiste T (2009) HISTONE MONOUBIQUITINATION1 interacts with a subunit of the mediator complex and regulates defense against necrotrophic fungal pathogens in Arabidopsis. Plant Cell 21: 1000-1019
46. Dias AP, Braun EL, McMullen MD, Grotewold E (2003) Recently duplicated maize R2R3 Myb genes provide evidence for distinct mechanisms of evolutionary divergence after duplication. Plant Physiol 131:610-620
47. Dong X (2004) NPR1, all things considered. Curr Opin Plant Biol 7:547-552
48. Dong X, Li X, Zhang Y, Fan W, Kinkema M, Clarke J (2001) Regulation of systemic acquired resistance by NPR1 and its partners. Novartis Found Symp 236:165-173; discussion 173-165
49. Dover J, Schneider J, Tawiah-Boateng MA, Wood A, Dean K, Johnston M, Shilatifard A (2002) Methylation of histone H3 by COMPASS requires ubiquitination of histone H2B by Rad6. J Biol Chem 277:28368-28371
50. Du H, Zhang L, Liu L, Tang XF, Yang WJ, Wu YM, Huang YB, Tang YX (2009) Biochemical and molecular characterization of plant MYB transcription factor family. Biochemistry (Mosc) 74:1-11
51.Dubos C, Stracke R, Grotewold E, Weisshaar B, Martin C, Lepiniec L (2010) MYB transcription factors in Arabidopsis. Trends Plant Sci 15:573-581
52. Durrant WE, Dong X (2004) Systemic acquired resistance. Annu Rev Phytopathol 42:185-209
53. Durrant WE, Wang S, Dong X (2007) Arabidopsis SNI1 and RAD51D regulate both gene transcription and DNA recombination during the defense response. Proc Natl Acad Sci U S A 104: 4223-4227
54. Eulgem T, Somssich IE (2007) Networks of WRKY transcription factors in defense signaling. Curr Opin Plant Biol 10:366-371
55. Farmer EE (2007) Plant biology:jasmonate perception machines. Nature 448:659-660
56. Felix G, Duran JD, Volko S, Boller T (1999) Plants have a sensitive perception system for the most conserved domain of bacterial flagellin. Plant J 18:265-276
57. Feys B, Benedetti CE, Penfold CN, Turner JG (1994) Arabidopsis Mutants Selected for Resistance to the Phytotoxin Coronatine Are Male Sterile, Insensitive to Methyl Jasmonate, and Resistant to a Bacterial Pathogen. Plant Cell 6:751-759
58. Feys BJ, Wiermer M, Bhat RA, Moisan LJ, Medina-Escobar N, Neu C, Cabral A, Parker JE (2005) Arabidopsis SENESCENCE-ASSOCIATED GENE101 stabilizes and signals within an ENHANCED DISEASE SUSCEPTIBILITY 1 complex in plant innate immunity.Plant Cell 17: 2601-2613
59. Fisher AJ, Franklin KA (2011) Chromatin remodelling in plant light signalling. Physiol Plant 142: 305-313
60. Flaus A, Martin DM, Barton GJ, Owen-Hughes T (2006) Identification of multiple distinct Snf2 subfamilies with conserved structural motifs. Nucleic Acids Res 34:2887-2905
61. Fleury D, Himanen K, Cnops G, Nelissen H, Boccardi TM, Maere S, Beemster GT, Neyt P, Anami S, Robles P, Micol JL, Inze D, Van Lijsebettens M (2007) The Arabidopsis thaliana homolog of yeast BRE1 has a function in cell cycle regulation during early leaf and root growth. Plant Cell 19: 417-432
62. Fleury D, Himanen K, Cnops G, Nelissen H, Boccardi TM, Maere S, Beemster GTS, Neyt P, Anami S, Robles P, Micol JL, Inze D, Van Lijsebettens M (2007) The Arabidopsis thaliana homolog of yeast BRE1 has a function in cell cycle regulation during early leaf and root growth. Plant Cell 19: 417-432
63. Fu DL, Uauy C, Distelfeld A, Blechl A, Epstein L, Chen XM, Sela HA, Fahima T, Dubcovsky J (2009) A Kinase-START Gene Confers Temperature-Dependent Resistance to Wheat Stripe Rust. Science 323:1357-1360
64. Fu ZQ, Dong X (2013) Systemic acquired resistance:turning local infection into global defense. Annu Rev Plant Biol 64:839-863
65. Gaffney T, Friedrich L, Vernooij B, Negrotto D, Nye G, Uknes S, Ward E, Kessmann H, Ryals J (1993) Requirement of salicylic Acid for the induction of systemic acquired resistance. Science 261: 754-756
66. Gao M, Wang X, Wang D, Xu F, Ding X, Zhang Z, Bi D, Cheng YT, Chen S, Li X, Zhang Y (2009) Regulation of cell death and innate immunity by two receptor-like kinases in Arabidopsis. Cell Host Microbe 6:34-44
67. Gendrel AV, Lippman Z, Martienssen R, Colot V (2005) Profiling histone modification patterns in plants using genomic tiling microarrays. Nat Methods 2:213-218
68. Geng F, Laurent BC (2004) Roles of SWI/SNF and HATs throughout the dynamic transcription of a yeast glucose-repressible gene. EMBO J 23:127-137
69. Gfeller A, Dubugnon L, Liechti R, Farmer EE (2010) Jasmonate biochemical pathway. Sci Signal 3: cm3
70. Glover BJ, Perez-Rodriguez M, Martin C (1998) Development of several epidermal cell types can be specified by the same MYB-related plant transcription factor. Development 125:3497-3508
71. Gomez-Gomez L, Boller T (2002) Flagellin perception:a paradigm for innate immunity. Trends Plant Sci 7:251-256
72. Gonzalez A, Mendenhall J, Huo Y, Lloyd A (2009) TTG1 complex MYBs, MYB5 and TT2, control outer seed coat differentiation. Dev Biol 325:412-421
73. Gonzalez A, Zhao M, Leavitt JM, Lloyd AM (2008) Regulation of the anthocyanin biosynthetic pathway by the TTGl/bHLH/Myb transcriptional complex in Arabidopsis seedlings. Plant J 53: 814-827
74. Gou M, Hua J (2012) Complex regulation of an R gene SNC1 revealed by auto-immune mutants. Plant Signal Behav 7:213-216
75. Grennan AK (2008) Ethylene response factors in jasmonate signaling and defense response. Plant Physiol 146:1457-1458
76. Guo M, Tian F, Wamboldt Y, Alfano JR (2009) The majority of the type Ⅲ effector inventory of Pseudomonas syringae pv. tomato DC3000 can suppress plant immunity. Mol Plant Microbe Interact 22:1069-1080
77. Han SK, Sang Y, Rodrigues A, Biol F, Wu MF, Rodriguez PL, Wagner D (2012) The SW12/SNF2 chromatin remodeling ATPase BRAHMA represses abscisic acid responses in the absence of the stress stimulus in Arabidopsis. Plant Cell 24:4892-4906
78. Hauck P, Thilmony R, He SY (2003) A Pseudomonas syringae type Ⅲ effector suppresses cell wall-based extracellular defense in susceptible Arabidopsis plants. Proc Natl Acad Sci U S A 100: 8577-8582
79. Heyse KS, Weber SE, Lipps HJ (2009) Histone modifications are specifically relocated during gene activation and nuclear differentiation. BMC Genomics 10:554
80. Hicke L (2001) Protein regulation by monoubiquitin. Nat Rev Mol Cell Biol 2:195-201
81. Higashi K, Ishiga Y, Inagaki Y, Toyoda K, Shiraishi T, Ichinose Y (2008) Modulation of defense signal transduction by flagellin-induced WRKY41 transcription factor in Arabidopsis thaliana. Mol Genet Genomics 279:303-312
82. Howe GA, Jander G (2008) Plant immunity to insect herbivores. Annu Rev Plant Biol 59:41-66
83. Hua J (2013) Modulation of plant immunity by light, circadian rhythm, and temperature. Curr Opin Plant Biol 16:406-413
84. Hua J, Grisafi P, Cheng SH, Fink GR (2001) Plant growth homeostasis is controlled by the Arabidopsis BON1 and BAP1 genes. Genes Dev 15:2263-2272
85. Hua, J., Chang, C., Sun, Q.,& Meyerowitz, E. M. (1995). Ethylene insensitivity conferred by Arabidopsis ERS gene. Science.269:1712-1714.
86. Jambunathan N, Siani JM, McNellis TW (2001) A humidity-sensitive Arabidopsis copine mutant exhibits precocious cell death and increased disease resistance. Plant Cell 13:2225-2240
87. Jaskiewicz M, Conrath U, Peterhansel C (2011) Chromatin modification acts as a memory for systemic acquired resistance in the plant stress response. EMBO Rep 12:50-55
88. Jeddeloh JA, Stokes TL, Richards EJ (1999) Maintenance of genomic methylation requires a SW12/SNF2-like protein. Nat Genet 22:94-97
89. Jia Y, McAdams SA, Bryan GT, Hershey HP, Valent B (2000) Direct interaction of resistance gene and avirulence gene products confers rice blast resistance. EMBO J 19:4004-4014
90. Jung C, Seo JS, Han SW, Koo YJ, Kim CH, Song SI, Nahm BH, Choi YD, Cheong JJ (2008) Overexpression of AtMYB44 enhances stomatal closure to confer abiotic stress tolerance in transgenic Arabidopsis. Plant Physiol 146:623-635
91. Jung C, Shim JS, Seo JS, Lee HY, Kim CH, Choi YD, Cheong JJ (2010) Non-specific phytohormonal induction of AtMYB44 and suppression of jasmonate-responsive gene activation in Arabidopsis thaliana. Mol Cells 29:71-76
92. Kakutani T, Jeddeloh JA, Richards EJ (1995) Characterization of an Arabidopsis thaliana DNA hypomethylation mutant. Nucleic Acids Res 23:130-137
93. Katagiri F, Tsuda K (2010) Understanding the plant immune system. Mol Plant Microbe Interact 23: 1531-1536
94. Kato M, Miura A, Bender J, Jacobsen SE, Kakutani T (2003) Role of CG and non-CG methylation in immobilization of transposons in arabidopsis. Current Biology 13:421-426
95. Kazan K, Manners JM (2008) Jasmonate signaling:toward an integrated view. Plant Physiol 146: 1459-1468
96. Kim J, Hake SB, Roeder RG (2005) The human homolog of yeast BRE1 functions as a transcriptional coactivator through direct activator interactions. Mol Cell 20:759-770
97. Kim KC, Lai Z, Fan B, Chen Z (2008) Arabidopsis WRKY38 and WRKY62 transcription factors interact with histone deacetylase 19 in basal defense. Plant Cell 20:2357-2371
98. Kim TH, Hauser F, Ha T, Xue SW, Bohmer M, Nishimura N, Munemasa S, Hubbard K, Peine N, Lee BH, Lee S, Robert N, Parker JE, Schroeder JI (2011) Chemical Genetics Reveals Negative Regulation of Abscisic Acid Signaling by a Plant Immune Response Pathway. Current Biology 21: 990-997
99. Kouzarides T (2007) Chromatin modifications and their function. Cell 128:693-705
100. Krebs JE, Fry CJ, Samuels ML, Peterson CL (2000) Global role for chromatin remodeling enzymes in mitotic gene expression. Cell 102:587-598
101. Kumar D, Park S, Forouhar F, Yang Y, Vlot A, Fridman E, Chiang Y, Acton T, Shulaev V, Montelione G, Pichersky E, Tong L, Klessig D (2005) Identification of SA-binding protein 2 (SABP2) as a critical component of plant innate immunity. Phytopathology 95:S55-S55
102. Lawton K, Weymann K, Friedrich L, Vernooij B, Uknes S, Ryals J (1995) Systemic acquired resistance in Arabidopsis requires salicylic acid but not ethylene. Mol Plant Microbe Interact 8: 863-870
103. Lee JS, Shukla A, Schneider J, Swanson SK, Washburn MP, Florens L, Bhaumik SR, Shilatifard A (2007) Histone crosstalk between H2B monoubiquitination and H3 methylation mediated by COMPASS. Cell 131:1084-1096
104. Lehti-Shiu MD, Zou C, Hanada K, Shiu SH (2009) Evolutionary history and stress regulation of plant receptor-like kinase/pelle genes. Plant Physiol 150:12-26
105. Lennartsson A, Ekwall K (2009) Histone modification patterns and epigenetic codes. Biochim Biophys Acta 1790:863-868
106. Leon-Reyes A, Du YJ, Koornneef A, Proietti S, Korbes AP, Memelink J, Pieterse CMJ, Ritsema T (2010) Ethylene Signaling Renders the Jasmonate Response of Arabidopsis Insensitive to Future Suppression by Salicylic Acid. Molecular Plant-Microbe Interactions 23:187-197
107. Li J, Brader Q Palva ET (2004) The WRKY70 transcription factor:a node of convergence for jasmonate-mediated and salicylate-mediated signals in plant defense. Plant Cell 16:319-331
108. Li L, Yu X, Thompson A, Guo M, Yoshida S, Asami T, Chory J, Yin Y (2009) Arabidopsis MYB30 is a direct target of BES1 and cooperates with BES1 to regulate brassinosteroid-induced gene expression. Plant J 58:275-286
109. Li Y, Gou M, Sun Q, Hua J (2010) Requirement of calcium binding, myristoylation, and protein-protein interaction for the Copine BON1 function in Arabidopsis. J Biol Chem 285: 29884-29891
110. Li Y, Tessaro MJ, Li X, Zhang Y (2010) Regulation of the expression of plant resistance gene SNC1 by a protein with a conserved BAT2 domain. Plant Physiol 153:1425-1434
111. Li Y, Yang S, Yang H, Hua J (2007) The TIR-NB-LRR gene SNC1 is regulated at the transcript level by multiple factors. Mol Plant Microbe Interact 20:1449-1456
112. Liu R, Chen L, Jia Z, Lu B, Shi H, Shao W, Dong H (2011) Transcription factor AtMYB44 regulates induced expression of the ETHYLENE INSENSITIVE2 gene in Arabidopsis responding to a harpin protein. Mol Plant Microbe Interact 24:377-389
113. Liu Y, Koornneef M, Soppe WJ (2007) The absence of histone H2B monoubiquitination in the Arabidopsis hubl (rdo4) mutant reveals a role for chromatin remodeling in seed dormancy. Plant Cell 19:433-444
114. Lorenzo O, Chico JM, Sanchez-Serrano JJ, Solano R (2004) JASMONATE-INSENSITIVEI encodes a MYC transcription factor essential to discriminate between different jasmonate-regulated defense responses in Arabidopsis. Plant Cell 16:1938-1950
115. Lorenzo O, Piqueras R, Sanchez-Serrano JJ, Solano R (2003) ETHYLENE RESPONSE FACTOR1 integrates signals from ethylene and jasmonate pathways in plant defense. Plant Cell 15:165-178
116. Lu B, Sun W, Zhang S, Zhang C, Qian J, Wang X, Gao R, Dong H (2011) HrpN Ea-induced deterrent effect on phloem feeding of the green peach aphid Myzus persicae requires AtGSL5 and AtMYB44 genes in Arabidopsis thaliana. J Biosci 36:123-137
117. Lu BB, Li XJ, Sun WW, Li L, Gao R, Zhu Q, Tian SM, Fu MQ, Yu HL, Tang XM, Zhang CL, Dong HS (2013) AtMYB44 regulates resistance to the green peach aphid and diamondback moth by activating EIN2-affected defences in Arabidopsis. Plant Biol (Stuttg) 15:841-850
118. Mackey D, Belkhadir Y, Alonso JM, Ecker JR, Dangl JL (2003) Arabidopsis RIN4 is a target of the type III virulence effector AvrRpt2 and modulates RPS2-mediated resistance. Cell 112:379-389
119. Mackey D, Holt BF,3rd, Wiig A, Dangl JL (2002) RIN4 interacts with Pseudomonas syringae type Ⅲ effector molecules and is required for RPM1-mediated resistance in Arabidopsis. Cell 108: 743-754
120. Mandaokar A, Browse J (2009) MYB108 Acts Together with MYB24 to Regulate Jasmonate-Mediated Stamen Maturation in Arabidopsis. Plant Physiology 149:851-862
121. Mang HG, Qian W, Zhu Y, Qian J, Kang HG, Klessig DF, Hua J (2012) Abscisic acid deficiency antagonizes high-temperature inhibition of disease resistance through enhancing nuclear accumulation of resistance proteins SNC1 and RPS4 in Arabidopsis. Plant Cell 24:1271-1284
122. March-Diaz R, Garcia-Dominguez M, Lozano-Juste J, Leon J, Florencio FJ, Reyes JC (2008) Histone H2A.Z and homologues of components of the SWR1 complex are required to control immunity in Arabidopsis. Plant J 53:475-487
123. Matus JT, Aquea F, Arce-Johnson P (2008) Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes. BMC Plant Biol 8:83
124. McGrath KC, Dombrecht B, Manners JM, Schenk PM, Edgar CI, Maclean DJ, Scheible WR, Udvardi MK, Kazan K (2005) Repressor- and activator-type ethylene response factors functioning in jasmonate signaling and disease resistance identified via a genome-wide screen of Arabidopsis transcription factor gene expression. Plant Physiol 139:949-959
125. Medzhitov R, Janeway CA, Jr. (1997) Innate immunity:the virtues of a nonclonal system of recognition. Cell 91:295-298
126. Millar AA, Gubler F (2005) The Arabidopsis GAMYB-like genes, MYB33 and MYB65, are MicroRNA-regulated genes that redundantly facilitate anther development. Plant Cell 17:705-721
127. Mohrmann L, Langenberg K, Krijgsveld J, Kal AJ, Heck AJ, Verrijzer CP (2004) Differential targeting of two distinct SWI/SNF-related Drosophila chromatin-remodeling complexes. Mol Cell Biol 24:3077-3088
128. Mohrmann L, Verrijzer CP (2005) Composition and functional specificity of SWI2/SNF2 class chromatin remodeling complexes. Biochim Biophys Acta 1681:59-73
129. Mou Z, Fan WH, Dong XN (2003) Inducers of plant systemic acquired resistance regulate NPR1 function through redox changes. Cell 113:935-944
130. Mu RL, Cao YR, Liu YF, Lei G, Zou HF, Liao Y, Wang HW, Zhang WK, Ma B, Du JZ, Yuan M, Zhang JS, Chen SY (2009) An R2R3-type transcription factor gene AtMYB59 regulates root growth and cell cycle progression in Arabidopsis. Cell Research 19:1291-1304
131. Muller D, Schmitz G, Theres K (2006) Blind homologous R2R3 Myb genes control the pattern of lateral meristem initiation in Arabidopsis. Plant Cell 18:586-597
132. Muller S, Feldman MF, Cornelis GR (2001) The Type Ⅲ secretion system of Gram-negative bacteria:a potential therapeutic target? Expert Opin Ther Targets 5:327-339
133. Mur LA, Kenton P, Atzorn R, Miersch O, Wasternack C (2006) The outcomes of concentration-specific interactions between salicylate and jasmonate signaling include synergy, antagonism, and oxidative stress leading to cell death. Plant Physiol 140:249-262
134. Noel L, Moores TL, van Der Biezen EA, Parniske M, Daniels MJ, Parker JE, Jones JD (1999) Pronounced intraspecific haplotype divergence at the RPP5 complex disease resistance locus of Arabidopsis. Plant Cell 11:2099-2112
135. Nurnberger T, Kemmerling B (2006) Receptor protein kinases-pattern recognition receptors in plant immunity. Trends Plant Sci 11:519-522
136. Oh JE, Kwon Y, Kim JH, Noh H, Hong SW, Lee H (2011) A dual role for MYB60 in stomatal regulation and root growth of Arabidopsis thaliana under drought stress. Plant Mol Biol 77:91-103
137. Palma K, Thorgrimsen S, Malinovsky FQ Fiil BK, Nielsen HB, Brodersen P, Hofius D, Petersen M, Mundy J (2010) Autoimmunity in Arabidopsis acd11 is mediated by epigenetic regulation of an immune receptor. PLoS Pathog 6:e1001137
138. Pan X, Welti R, Wang X (2008) Simultaneous quantification of major phytohormones and related compounds in crude plant extracts by liquid chromatography-electrospray tandem mass spectrometry. Phytochemistry 69:1773-1781
139. Pape S, Thurow C, Gatz C (2010) The Arabidopsis PR-1 promoter contains multiple integration sites for the coactivator NPR1 and the repressor SNI1. Plant Physiol 154:1805-1818
140. Paz-Ares J, Ghosal D, Wienand U, Peterson PA, Saedler H (1987) The regulatory c1 locus of Zea mays encodes a protein with homology to myb proto-oncogene products and with structural similarities to transcriptional activators. EMBO J 6:3553-3558
141. Penninckx IA, Thomma BP, Buchala A, Metraux JP, Broekaert WF (1998) Concomitant activation of jasmonate and ethylene response pathways is required for induction of a plant defensin gene in Arabidopsis. Plant Cell 10:2103-2113
142. Pickart CM (2004) Back to the future with ubiquitin. Cell 116:181-190
143. Pieterse CM, Leon-Reyes A, Van der Ent S, Van Wees SC (2009) Networking by small-molecule hormones in plant immunity. Nat Chem Biol 5:308-316
144. Pieterse CM, Van der Does D, Zamioudis C, Leon-Reyes A, Van Wees SC (2012) Hormonal modulation of plant immunity. Annu Rev Cell Dev Biol 28:489-521
145. Pointner J, Persson J, Prasad P, Norman-Axelsson U, Stralfors A, Khorosjutina O, Krietenstein N, Svensson JP, Ekwall K, Korber P (2012) CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S. pombe. EMBO J 31:4388-4403
146. Proft M, Struhl K (2002) Hogl kinase converts the Skol-Cyc8-Tupl repressor complex into an activator that recruits SAGA and SWI/SNF in response to osmotic stress. Mol Cell 9:1307-1317
147. Qu F, Ye XH, Hou GC, Sato S, Clemente TE, Morris TJ (2005) RDR6 has a broad-spectrum but temperature-dependent antiviral defense role in Nicotiana benthamiana. Journal of Virology 79: 15209-15217
148. Quan TK, Hartzog GA (2010) Histone H3K4 and K36 methylation, Chdl and Rpd3S oppose the functions of Saccharomyces cerevisiae Spt4-Spt5 in transcription. Genetics 184:321-334
149. Raffaele S, Vailleau F, Leger A, Joubes J, Miersch O, Huard C, Blee E, Mongrand S, Domergue F, Roby D (2008) A MYB transcription factor regulates very-long-chain fatty acid biosynthesis for activation of the hypersensitive cell death response in Arabidopsis. Plant Cell 20:752-767
150. Reyes JL, Chua NH (2007) ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination. Plant J 49:592-606
151. Robert JM (1971) [The modern concept of the gene]. Orthod Fr 42:43-53
152. 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 ML, Robin S, Caboche M, Colot V (2011) Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J 30:1928-1938
153. Sato M, Tsuda K, Wang L, Coller J, Watanabe Y, Glazebrook J, Katagiri F (2010) Network Modeling Reveals Prevalent Negative Regulatory Relationships between Signaling Sectors in Arabidopsis Immune Signaling. Plos Pathogens 6
154. Scheuermann JC, Gutierrez L, Muller J (2012) Histone H2A monoubiquitination and Polycomb repression:the missing pieces of the puzzle. Fly (Austin) 6:162-168
155. Schneider R, Grosschedl R (2007) Dynamics and interplay of nuclear architecture, genome organization, and gene expression. Genes Dev 21:3027-3043
156. Scott IM, Clarke SM, Wood JE, Mur LA (2004) Salicylate accumulation inhibits growth at chilling temperature in Arabidopsis. Plant Physiol 135:1040-1049
157. Sebald J, Morettini S, Podhraski V, Lass-Florl C, Lusser A (2012) CHD1 contributes to intestinal resistance against infection by P. aeruginosa in Drosophila melanogaster. PLoS One 7:e43144
158. Seo PJ, Lee SB, Suh MC, Park MJ, Go YS, Park CM (2011) The MYB96 transcription factor regulates cuticular wax biosynthesis under drought conditions in Arabidopsis. Plant Cell 23: 1138-1152
159. Seo PJ, Park CM (2010) MYB96-mediated abscisic acid signals induce pathogen resistance response by promoting salicylic acid biosynthesis in Arabidopsis. New Phytol 186:471-483
160. Seo PJ, Xiang F, Qiao M, Park JY, Lee YN, Kim SG, Lee YH, Park WJ, Park CM (2009) The MYB96 transcription factor mediates abscisic acid signaling during drought stress response in Arabidopsis. Plant Physiol 151:275-289
161. Sheard LB, Tan X, Mao H, Withers J, Ben-Nissan G, Hinds TR, Kobayashi Y, Hsu FF, Sharon M, Browse J, He SY, Rizo J, Howe GA, Zheng N (2010) Jasmonate perception by inositol-phosphate-potentiated COI1-JAZ co-receptor. Nature 468:400-405
162. Shim JS, Jung C, Lee S, Min K, Lee YW, Choi Y, Lee JS, Song JT, Kim JK, Choi YD (2013) AtMYB44 regulates WRKY70 expression and modulates antagonistic interaction between salicylic acid and jasmonic acid signaling. Plant J 73:483-495
163. Shin R, Burch AY, Huppert KA, Tiwari SB, Murphy AS, Guilfoyle TJ, Schachtman DP (2007) The Arabidopsis transcription factor MYB77 modulates auxin signal transduction. Plant Cell 19: 2440-2453
164. Singh Sandhu K, Li G, Sung WK, Ruan Y (2011) Chromatin interaction networks and higher order architectures of eukaryotic genomes. J Cell Biochem 112:2218-2221
165. Smalle J, Vierstra RD (2004) The ubiquitin 26S proteasome proteolytic pathway. Annual Review of Plant Biology 55:555-590
166. Spoel SH, Johnson JS, Dong X (2007) Regulation of tradeoffs between plant defenses against pathogens with different lifestyles. Proc Natl Acad Sci U S A 104:18842-18847
167. Spoel SH, Koornneef A, Claessens SM, Korzelius JP, Van Pelt JA, Mueller MJ, Buchala AJ, Metraux JP, Brown R, Kazan K, Van Loon LC, Dong X, Pieterse CM (2003) NPR1 modulates cross-talk between salicylate-and jasmonate-dependent defense pathways through a novel function in the cytosol. Plant Cell 15:760-770
168. Spoel SH, Koornneef A, Claessens SMC, Korzelius JP, Van Pelt JA, Mueller MJ, Buchala AJ, Metraux JP, Brown R, Kazan K, Van Loon LC, Dong XN, Pieterse CMJ (2003) NPR1 modulates cross-talk between salicylate- and jasmonate-dependent defense pathways through a novel function in the cytosol. Plant Cell 15:760-770
169. Sridhar VV, Kapoor A, Zhang K, Zhu J, Zhou T, Hasegawa PM, Bressan RA, Zhu JK (2007) Control of DNA methylation and heterochromatic silencing by histone H2B deubiquitination. Nature 447:735-738
170. Stokes TL, Kunkel BN, Richards EJ (2002) Epigenetic variation in Arabidopsis disease resistance. Genes Dev 16:171-182
171. Stracke R, Ishihara H, Huep G, Barsch A, Mehrtens F, Niehaus K, Weisshaar B (2007) Differential regulation of closely related R2R3-MYB transcription factors controls flavonol accumulation in different parts of the Arabidopsis thaliana seedling. Plant J 50:660-677
172. Stracke R, Werber M, Weisshaar B (2001) The R2R3-MYB gene family in Arabidopsis thaliana. Curr Opin Plant Biol 4:447-456
173. Szittya G, Silhavy D, Molnar A, Havelda Z, Lovas A, Lakatos L, Banfalvi Z, Burgyan J (2003) Low temperature inhibits RNA silencing-mediated defence by the control of siRNA generation. Embo Journal 22:633-640
174. Takeuchi K, Gyohda A, Tominaga M, Kawakatsu M, Hatakeyama A, Ishii N, Shimaya K, Nishimura T, Riemann M, Nick P, Hashimoto M, Komano T, Endo A, Okamoto T, Jikumaru Y, Kamiya Y, Terakawa T, Koshiba T (2011) RSOsPR10 expression in response to environmental stresses is regulated antagonistically by jasmonate/ethylene and salicylic acid signaling pathways in rice roots. Plant Cell Physiol 52:1686-1696
175. Terakura S, Ueno Y, Tagami H, Kitakura S, Machida C, Wabiko H, Aiba H, Otten L, Tsukagoshi H, Nakamura K, Machida Y (2007) An oncoprotein from the plant pathogen agrobacterium has histone chaperone-like activity. Plant Cell 19:2855-2865
176. Thorstensen T, Grini PE, Aalen RB (2011) SET domain proteins in plant development. Biochim Biophys Acta 1809:407-420
177. Tian L, Fong MP, Wang JJ, Wei NE, Jiang H, Doerge RW, Chen ZJ (2005) Reversible histone acetylation and deacetylation mediate genome-wide, promoter-dependent and locus-specific changes in gene expression during plant development. Genetics 169:337-345
178. Tominaga-Wada R, Nukumizu Y, Sato S, Wada T (2013) Control of plant trichome and root-hair development by a tomato (Solanum lycopersicum) R3 MYB transcription factor. PLoS One 8: e54019
179. Ton J, De Vos M, Robben C, Buchala A, Metraux JP, Van Loon LC, Pieterse CM (2002) Characterization of Arabidopsis enhanced disease susceptibility mutants that are affected in systemically induced resistance. Plant J 29:11-21
180. Ton J, Flors V, Mauch-Mani B (2009) The multifaceted role of ABA in disease resistance. Trends Plant Sci 14:310-317
181.Tsukiyama T, Palmer J, Landel CC, Shiloach J, Wu C (1999) Characterization of the imitation switch subfamily of ATP-dependent chromatin-remodeling factors in Saccharomyces cerevisiae. Genes Dev 13:686-697
182. Tuttle JR, Idris AM, Brown JK, Haigler CH, Robertson D (2008) Geminivirus-mediated gene silencing from Cotton leaf crumple virus is enhanced by low temperature in cotton. Plant Physiology 148:41-50
183. van Verk MC, Bol JF, Linthorst HJ (2011) Prospecting for genes involved in transcriptional regulation of plant defenses, a bioinformatics approach. BMC Plant Biol 11:88
184. Vanholme B, Grunewald W, Bateman A, Kohchi T, Gheysen G (2007) The tify family previously known as ZIM. Trends Plant Sci 12:239-244
185. Verhage A, van Wees SC, Pieterse CM (2010) Plant immunity:it's the hormones talking, but what do they say? Plant Physiol 154:536-540
186. Vernooij B, Friedrich L, Morse A, Reist R, Kolditz-Jawhar R, Ward E, Uknes S, Kessmann H, Ryals J (1994) Salicylic Acid Is Not the Translocated Signal Responsible for Inducing Systemic Acquired Resistance but Is Required in Signal Transduction. Plant Cell 6:959-965
187. Vlot AC, Dempsey DA, Klessig DF (2009) Salicylic Acid, a multifaceted hormone to combat disease. Annu Rev Phytopathol 47:177-206
188. Vlot AC, Klessig DF, Park SW (2008) Systemic acquired resistance:the elusive signal(s). Curr Opin Plant Biol 11:436-442
189. Vongs A, Kakutani T, Martienssen RA, Richards EJ (1993) Arabidopsis thaliana DNA methylation mutants. Science 260:1926-1928
190. Walley JW, Rowe HC, Xiao Y, Chehab EW, Kliebenstein DJ, Wagner D, Dehesh K (2008) The chromatin remodeler SPLAYED regulates specific stress signaling pathways. PLoS Pathog 4: e1000237
191. Wang C, Gao F, Wu J, Dai J, Wei C, Li Y (2010) Arabidopsis putative deacetylase AtSRT2 regulates basal defense by suppressing PAD4, EDS5 and SID2 expression. Plant Cell Physiol 51:1291-1299
192. Wang D, Amornsiripanitch N, Dong X (2006) A genomic approach to identify regulatory nodes in the transcriptional network of systemic acquired resistance in plants. PLoS Pathog 2:e123
193. Wang G, Ellendorff U, Kemp B, Mansfield JW, Forsyth A, Mitchell K, Bastas K, Liu CM, Woods-Tor A, Zipfel C, de Wit PJ, Jones JD, Tor M, Thomma BP (2008) A genome-wide functional investigation into the roles of receptor-like proteins in Arabidopsis. Plant Physiol 147:503-517
194. Wang XC, Niu QW, Teng C, Li C, Mu JY, Chua NH, Zuo JR (2009) Overexpression of PGA37/MYB118 and MYB115 promotes vegetative-to-embryonic transition in Arabidopsis. Cell Research 19:224-235
195. Wang Y, Bao Z, Zhu Y, Hua J (2009) Analysis of temperature modulation of plant defense against biotrophic microbes. Mol Plant Microbe Interact 22:498-506
196. Wang Z, Meng P, Zhang X, Ren D, Yang S (2011) BON1 interacts with the protein kinases BIR1 and BAK1 in modulation of temperature-dependent plant growth and cell death in Arabidopsis. Plant J 67:1081-1093
197. Wang ZX, Yamanouchi U, Katayose Y, Sasaki T, Yano M (2001) Expression of the Pib rice-blast-resistance gene family is up-regulated by environmental conditions favouring infection and by chemical signals that trigger secondary plant defences. Plant Molecular Biology 47:653-661
198. Wiermer M, Feys BJ, Parker JE (2005) Plant immunity:the EDS1 regulatory node. Curr Opin Plant Biol 8:383-389
199. Wildermuth MC, Dewdney J, Wu G, Ausubel FM (2001) Isochorismate synthase is required to synthesize salicylic acid for plant defence. Nature 414:562-565
200. Wilkins O, Nahal H, Foong J, Provart NJ, Campbell MM (2009) Expansion and diversification of the Populus R2R3-MYB family of transcription factors. Plant Physiol 149:981-993
201. Wu C (1997) Chromatin remodeling and the control of gene expression. J Biol Chem 272: 28171-28174
202. Wu K, Zhang L, Zhou C, Yu CW, Chaikam V (2008) HDA6 is required for jasmonate response, senescence and flowering in Arabidopsis. J Exp Bot 59:225-234
203. Xia S, Cheng YT, Huang S, Win J, Soards A, Jinn TL, Jones JD, Kamoun S, Chen S, Zhang Y, Li X (2013) Regulation of transcription of nucleotide-binding leucine-rich repeat-encoding genes SNC1 and RPP4 via H3K4 trimethylation. Plant Physiol 162:1694-1705
204. Xiao S, Brown S, Patrick E, Brearley C, Turner JG (2003) Enhanced transcription of the Arabidopsis disease resistance genes RPW8.1 and RPW8.2 via a salicylic acid-dependent amplification circuit is required for hypersensitive cell death. Plant Cell 15:33-45
205. Xu L, Menard R, Berr A, Fuchs J, Cognat V, Meyer D, Shen WH (2009) 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 57: 279-288
206. Yahr TL, Wolfgang MC (2006) Transcriptional regulation of the Pseudomonas aeruginosa type Ⅲ secretion system. Mol Microbiol 62:631-640
207. Yamaguchi K, Yamada K, Kawasaki T (2013) Receptor-like cytoplasmic kinases are pivotal components in pattern recognition receptor-mediated signaling in plant immunity. Plant Signal Behav 8
208. Yang H, Li Y, Hua J (2006) The C2 domain protein BAP1 negatively regulates defense responses in Arabidopsis. Plant J 48:238-248
209. Yang HJ, Yang SH, Li YQ, Hua J (2007) The Arabidopsis BAP1 and BAP2 genes are general inhibitors of programmed cell death. Plant Physiology 145:135-146
210. Yang J, Kloepper JW, Ryu CM (2009) Rhizosphere bacteria help plants tolerate abiotic stress. Trends Plant Sci 14:1-4
211. Yang S, Hua J (2004) A haplotype-specific Resistance gene regulated by BONZAI1 mediates temperature-dependent growth control in Arabidopsis. Plant Cell 16:1060-1071
212. Yang S, Yang H, Grisafi P, Sanchatjate S, Fink GR, Sun Q, Hua J (2006) The BON/CPN gene family represses cell death and promotes cell growth in Arabidopsis. Plant J 45:166-179
213. Yang SH, Hua J (2004) A haplotype-specific Resistance gene regulated by BONZAI1 mediates temperature-dependent growth control in Arabidopsis. Plant Cell 16:1060-1071
214. Yanhui C, Xiaoyuan Y, Kun H, Meihua L, Jigang L, Zhaofeng G, Zhiqiang L, Yunfei Z, Xiaoxiao W, Xiaoming Q, Yunping S, Li Z, Xiaohui D, Jingchu L, Xing-Wang D, Zhangliang C, Hongya G, Li-Jia Q (2006) The MYB transcription factor superfamily of Arabidopsis:expression analysis and phylogenetic comparison with the rice MYB family. Plant Mol Biol 60:107-124
215. Yasuda M, Ishikawa A, Jikumaru Y, Seki M, Umezawa T, Asami T, Maruyama-Nakashita A, Kudo T, Shinozaki K, Yoshida S, Nakashita H (2008) Antagonistic interaction between systemic acquired resistance and the abscisic acid-mediated abiotic stress response in Arabidopsis. Plant Cell 20: 1678-1692
216. Yi H, Richards EJ (2007) A cluster of disease resistance genes in Arabidopsis is coordinately regulated by transcriptional activation and RNA silencing. Plant Cell 19:2929-2939
217. Yoshioka K, Kachroo P, Tsui F, Sharma SB, Shah J, Klessig DF (2001) Environmentally sensitive, SA-dependent defense responses in the cpr22 mutant of Arabidopsis. Plant J 26:447-459
218. Yun MY, Wu J, Workman JL, Li B (2011)Readers of histone modifications. Cell Research 21: 564-578
219. Zander M, La Camera S, Lamotte O, Metraux JP, Gatz C (2010) Arabidopsis thaliana class-II TGA transcription factors are essential activators of jasmonic acid/ethylene-induced defense responses. Plant J 61:200-210
220. Zhang X, Germann S, Blus BJ, Khorasanizadeh S, Gaudin V, Jacobsen SE (2007) The Arabidopsis LHP1 protein colocalizes with histone H3 Lys27 trimethylation. Nat Struct Mol Biol 14:869-871
221. Zhang XC, Zhang XF, Singh J, Li DW, Qu F (2012) Temperature-Dependent Survival of Turnip Crinkle Virus-Infected Arabidopsis Plants Relies on an RNA Silencing-Based Defense That Requires DCL2, AG02, and HEN1. Journal of Virology 86:6847-6854
222. Zhang Y, Goritschnig S, Dong X, Li X (2003) A gain-of-function mutation in a plant disease resistance gene leads to constitutive activation of downstream signal transduction pathways in suppressor of nprl-1, constitutive 1. Plant Cell 15:2636-2646
223. Zhang ZB, Zhu J, Gao JF, Wang C, Li H, Li H, Zhang HQ, Zhang S, Wang DM, Wang QX, Huang H, Xia HJ, Yang ZN (2007) Transcription factor AtMYB103 is required for anther development by regulating tapetum development, callose dissolution and exine formation in Arabidopsis. Plant Journal 52:528-538
224. Zhong R, Lee C, Zhou J, McCarthy RL, Ye ZH (2008) A battery of transcription factors involved in the regulation of secondary cell wall biosynthesis in Arabidopsis. Plant Cell 20:2763-2782
225. Zhou C, Zhang L, Duan J, Miki B, Wu K (2005) HISTONE DEACETYLASE19 is involved in jasmonic acid and ethylene signaling of pathogen response in Arabidopsis. Plant Cell 17: 1196-1204
226. Zhou JM, Chai J (2008) Plant pathogenic bacterial type III effectors subdue host responses. Curr Opin Microbiol 11:179-185
227. Zhou W, Zhu P, Wang J, Pascual G, Ohgi KA, Lozach J, Glass CK, Rosenfeld MG (2008) Histone H2A monoubiquitination represses transcription by inhibiting RNA polymerase II transcriptional elongation. Mol Cell 29:69-80
228. Zhu Y, Mang HG, Sun Q, Qian J, Hipps A, Hua J (2012) Gene Discovery Using Mutagen-Induced Polymorphisms and Deep Sequencing:Application to Plant Disease Resistance. Genetics 192: 139-U171
229. Zhu Y, Qian W, Hua J (2010) Temperature modulates plant defense responses through NB-LRR proteins. PLoS Pathog 6:e1000844
230. Zhu Z, An F, Feng Y, Li P, Xue L, A M, Jiang Z, Kim JM, To TK, Li W, Zhang X, Yu Q, Dong Z, Chen WQ, Seki M, Zhou JM, Guo H (2011) Derepression of ethylene-stabilized transcription factors (EIN3/EIL1) mediates jasmonate and ethylene signaling synergy in Arabidopsis. Proc Natl Acad Sci U S A 108:12539-12544
231.Zipfel C (2008) Pattern-recognition receptors in plant innate immunity. Curr Opin Immunol 20: 10-16
232. Zipfel C (2009) Early molecular events in PAMP-triggered immunity. Curr Opin Plant Biol 12: 414-42