Berger SL. The complex language of chromatin regulation during transcription. Nature. 2007;447(7143):407–12.
Article
CAS
PubMed
Google Scholar
Pfluger J, Wagner D. Histone modifications and dynamic regulation of genome accessibility in plants. Curr Opin Plant Biol. 2007;10(6):645–52.
Article
PubMed Central
CAS
PubMed
Google Scholar
Margueron R, Trojer P, Reinberg D. The key to development: interpreting the histone code? Curr Opin Genet Dev. 2005;15(2):163–76.
Article
CAS
PubMed
Google Scholar
Martin C, Zhang Y. The diverse functions of histone lysine methylation. Nat Rev Mol Cell Biol. 2005;6(11):838–49.
Article
CAS
PubMed
Google Scholar
Liu C, Lu F, Cui X, Cao X. Histone methylation in higher plants. Annu Rev Plant Biol. 2010;61:395–420.
Article
CAS
PubMed
Google Scholar
Lan F, Nottke AC, Shi Y. Mechanisms involved in the regulation of histone lysine demethylases. Curr Opin Cell Biol. 2008;20(3):316–25.
Article
PubMed Central
CAS
PubMed
Google Scholar
Shi Y, Lan F, Matson C, Mulligan P, Whetstine JR, Cole PA, et al. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell. 2004;119(7):941–53.
Article
CAS
PubMed
Google Scholar
Tsukada Y, Fang J, Erdjument-Bromage H, Warren ME, Borchers CH, Tempst P, et al. Histone demethylation by a family of JmjC domain-containing proteins. Nature. 2006;439(7078):811–6.
Article
CAS
PubMed
Google Scholar
Klose RJ, Kallin EM, Zhang Y. JmjC-domain-containing proteins and histone demethylation. Nat Rev Genet. 2006;7(9):715–27.
Article
CAS
PubMed
Google Scholar
Jiang D, Yang W, He Y, Amasino RM. Arabidopsis relatives of the human lysine-specific Demethylase1 repress the expression of FWA and FLOWERING LOCUS C and thus promote the floral transition. Plant Cell. 2007;19(10):2975–87.
Article
PubMed Central
CAS
PubMed
Google Scholar
Singh V, Roy S, Giri MK, Chaturvedi R, Chowdhury Z, Shah J, et al. Arabidopsis thaliana FLOWERING LOCUS D is required for systemic acquired resistance. Mol Plant Microbe Interact. 2013;26(9):1079–88.
Article
CAS
PubMed
Google Scholar
Singh V, Roy S, Singh D, Nandi AK. Arabidopsis flowering locus D influences systemic-acquired-resistance- induced expression and histone modifications of WRKY genes. J Biosci. 2014;39(1):119–26.
Article
CAS
PubMed
Google Scholar
Luo M, Hung F-Y, Yang S, Liu X, Wu K. Histone lysine demethylases and their functions in plants. Plant Mol Biol Rep. 2013;32(2):558–65.
Article
Google Scholar
Lu F, Cui X, Zhang S, Liu C, Cao X. JMJ14 is an H3K4 demethylase regulating flowering time in Arabidopsis. Cell Res. 2010;20(3):387–90.
Article
PubMed
Google Scholar
Yang H, Han Z, Cao Y, Fan D, Li H, Mo H, et al. A companion cell-dominant and developmentally regulated H3K4 demethylase controls flowering time in Arabidopsis via the repression of FLC expression. PLoS Genet. 2012;8(4):e1002664.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yang H, Mo H, Fan D, Cao Y, Cui S, Ma L. Overexpression of a histone H3K4 demethylase, JMJ15, accelerates flowering time in Arabidopsis. Plant Cell Rep. 2012;31(7):1297–308.
Article
CAS
PubMed
Google Scholar
Lu F, Li G, Cui X, Liu C, Wang XJ, Cao X. Comparative analysis of JmjC domain-containing proteins reveals the potential histone demethylases in Arabidopsis and rice. J Integr Plant Biol. 2008;50(7):886–96.
Article
CAS
PubMed
Google Scholar
Sun Q, Zhou DX. Rice jmjC domain-containing gene JMJ706 encodes H3K9 demethylase required for floral organ development. Proc Natl Acad Sci U S A. 2008;105(36):13679–84.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zhou D, Hu Y. Regulatory function of histone modifications in controlling rice gene expression and plant growth. Rice. 2010;3:103–11.
Article
Google Scholar
Chen X, Hu Y, Zhou DX. Epigenetic gene regulation by plant Jumonji group of histone demethylase. Biochim Biophys Acta. 2011;1809(8):421–6.
Article
CAS
PubMed
Google Scholar
Cui X, Jin P, Gu L, Lu Z, Xue Y, Wei L, et al. Control of transposon activity by a histone H3K4 demethylase in rice. Proc Natl Acad Sci U S A. 2013;110(5):1953–8.
Article
PubMed Central
CAS
PubMed
Google Scholar
Chen Q, Chen X, Wang Q, Zhang F, Lou Z, Zhang Q, et al. Structural basis of a histone H3 lysine 4 demethylase required for stem elongation in rice. PLoS Genet. 2013;9(1):e1003239.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li T, Chen X, Zhong X, Zhao Y, Liu X, Zhou S, et al. Jumonji C domain protein JMJ705-mediated removal of histone H3 lysine 27 trimethylation is involved in defense-related gene activation in rice. Plant Cell. 2013;25(11):4725–36.
Article
PubMed Central
CAS
PubMed
Google Scholar
Berr A, McCallum EJ, Alioua A, Heintz D, Heitz T, Shen WH. Arabidopsis histone methyltransferase SET DOMAIN GROUP8 mediates induction of the jasmonate/ethylene pathway genes in plant defense response to necrotrophic fungi. Plant Physiol. 2010;154(3):1403–14.
Article
PubMed Central
CAS
PubMed
Google Scholar
Berr A, Menard R, Heitz T, Shen WH. Chromatin modification and remodelling: a regulatory landscape for the control of Arabidopsis defence responses upon pathogen attack. Cell Microbiol. 2012;14(6):829–39.
Article
CAS
PubMed
Google Scholar
Palma K, Thorgrimsen S, Malinovsky FG, Fiil BK, Nielsen HB, Brodersen P, et al. Autoimmunity in Arabidopsis acd11 is mediated by epigenetic regulation of an immune receptor. PLoS Pathog. 2010;6(10):e1001137.
Article
PubMed Central
PubMed
Google Scholar
Alvarez-Venegas R, Sadder M, Hlavacka A, Baluska F, Xia Y, Lu G, et al. The Arabidopsis homolog of trithorax, ATX1, binds phosphatidylinositol 5-phosphate, and the two regulate a common set of target genes. Proc Natl Acad Sci U S A. 2006;103(15):6049–54.
Article
PubMed Central
CAS
PubMed
Google Scholar
Alvarez-Venegas R, Abdallat AA, Guo M, Alfano JR, Avramova Z. Epigenetic control of a transcription factor at the cross section of two antagonistic pathways. Epigenetics. 2007;2(2):106–13.
Article
PubMed
Google Scholar
Verdier V, Vera Cruz C, Leach JE. Controlling rice bacterial blight in Africa: needs and prospects. J Biotechnol. 2012;159(4):320–8.
Article
CAS
PubMed
Google Scholar
Sundaram R, Chatterjee S, Oliva R, Laha G, Cruz C, Leach J, et al. Update on bacterial blight of rice: Fourth international conference on bacterial blight. Rice. 2014;7:12.
Article
PubMed
Google Scholar
Zhang J, Li C, Wu C, Xiong L, Chen G, Zhang Q, et al. RMD: a rice mutant database for functional analysis of the rice genome. Nucleic Acids Res. 2006;34(Database issue):D745–748.
Article
PubMed Central
CAS
PubMed
Google Scholar
Jeon JS, Lee S, Jung KH, Jun SH, Jeong DH, Lee J, et al. T-DNA insertional mutagenesis for functional genomics in rice. Plant J. 2000;22(6):561–70.
Article
CAS
PubMed
Google Scholar
Chern M, Canlas PE, Fitzgerald HA, Ronald PC. Rice NRR, a negative regulator of disease resistance, interacts with Arabidopsis NPR1 and rice NH1. Plant J. 2005;43(5):623–35.
Article
CAS
PubMed
Google Scholar
Peng Y, Bartley LE, Chen X, Dardick C, Chern M, Ruan R, et al. OsWRKY62 is a negative regulator of basal and Xa21-mediated defense against Xanthomonas oryzae pv. oryzae in rice. Mol Plant. 2008;1(3):446–58.
Article
CAS
PubMed
Google Scholar
Antony G, Zhou J, Huang S, Li T, Liu B, White F, et al. Rice xa13 recessive resistance to bacterial blight is defeated by induction of the disease susceptibility gene Os-11N3. Plant Cell. 2010;22(11):3864–76.
Article
PubMed Central
CAS
PubMed
Google Scholar
Fang H, Liu X, Thorn G, Duan J, Tian L. Expression analysis of histone acetyltransferases in rice under drought stress. Biochem Biophys Res Commun. 2014;443(2):400–5.
Article
CAS
PubMed
Google Scholar
Mosher RA, Durrant WE, Wang D, Song J, Dong X. A comprehensive structure-function analysis of Arabidopsis SNI1 defines essential regions and transcriptional repressor activity. Plant Cell. 2006;18(7):1750–65.
Article
PubMed Central
CAS
PubMed
Google Scholar
Jaskiewicz M, Conrath U, Peterhansel C. Chromatin modification acts as a memory for systemic acquired resistance in the plant stress response. EMBO Rep. 2011;12(1):50–5.
Article
PubMed Central
CAS
PubMed
Google Scholar
De-La-Pena C, Rangel-Cano A, Alvarez-Venegas R. Regulation of disease-responsive genes mediated by epigenetic factors: interaction of Arabidopsis-Pseudomonas. Mol Plant Pathol. 2012;13(4):388–98.
Article
CAS
PubMed
Google Scholar
Kim KC, Lai Z, Fan B, Chen Z. Arabidopsis WRKY38 and WRKY62 transcription factors interact with histone deacetylase 19 in basal defense. Plant Cell. 2008;20(9):2357–71.
Article
PubMed Central
CAS
PubMed
Google Scholar
Choi SM, Song HR, Han SK, Han M, Kim CY, Park J, et al. HDA19 is required for the repression of salicylic acid biosynthesis and salicylic acid-mediated defense responses in Arabidopsis. Plant J. 2012;71(1):135–46.
Article
CAS
PubMed
Google Scholar
Ding B, Bellizzi Mdel R, Ning Y, Meyers BC, Wang GL. HDT701, a histone H4 deacetylase, negatively regulates plant innate immunity by modulating histone H4 acetylation of defense-related genes in rice. Plant Cell. 2012;24(9):3783–94.
Article
PubMed Central
CAS
PubMed
Google Scholar
Park CJ, Ronald PC. Cleavage and nuclear localization of the rice XA21 immune receptor. Nat Commun. 2012;3:920.
Article
PubMed Central
PubMed
Google Scholar
Zhang J, Guo D, Chang Y, You C, Li X, Dai X, et al. Non-random distribution of T-DNA insertions at various levels of the genome hierarchy as revealed by analyzing 13 804 T-DNA flanking sequences from an enhancer-trap mutant library. Plant J. 2007;49(5):947–59.
Article
CAS
PubMed
Google Scholar
Chen H, Wang S, Zhang Q. New gene for bacterial blight resistance in rice located on chromosome 12 identified from minghui 63, an elite restorer line. Phytopathology. 2002;92(7):750–4.
Article
CAS
PubMed
Google Scholar
Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(−Delta Delta C(T)) Method. Methods. 2001;25(4):402–8.
Article
CAS
PubMed
Google Scholar
Jackson JP, Johnson L, Jasencakova Z, Zhang X, PerezBurgos L, Singh PB, et al. Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. Chromosoma. 2004;112(6):308–15.
Article
CAS
PubMed
Google Scholar
Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10(1):57–63.
Article
PubMed Central
CAS
PubMed
Google Scholar
Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, et al. GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics. 2004;20(18):3710–5.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zhang J, Nallamilli BR, Mujahid H, Peng Z. OsMADS6 plays an essential role in endosperm nutrient accumulation and is subject to epigenetic regulation in rice (Oryza sativa). Plant J. 2010;64(4):604–17.
Article
CAS
PubMed
Google Scholar