Epigenetic mechanisms of plant stress responses and adaptation

Agius F, Kapoor A, Zhu JK (2006) Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation. Proc Natl Acad Sci USA 103:11796–11801 Akimoto K, Katakami H, Kim HJ, Ogawa E, Sano CM, Wada Y, Sano H (2007) Epigenetic inheritance in rice plants. Ann Bot 100:205–217 Angaji SA, Hedayati SS, Hoseinpoor R, Poor SS, Shiravi S, Madani SD (2010) Application of RNA interference in plants. Plant Omics J 3:77–84 Angers B, Castonguay E, Massicotte R (2010) Environmentally induced phenotypes and DNA methylation: how to deal with unpredictable conditions until the next generation and after. Mol Ecol 19:1283–1295 Baek D, Jiang J, Chung JS, Wang B, Chen J, Xin Z, Shi H (2011) Regulated AtHKT1 gene expression by a distal enhancer element and DNA methylation in the promoter plays an important role in salt tolerance. Plant Cell Physiol 52:149–161 Bian XY, Rasheed MS, Seemanpillai MJ, Ali Rezaian M (2006) Analysis of silencing escape of tomato leaf curl virus: an evaluation of the role of DNA methylation. Mol Plant Microbe Interact 19:614–624 Boyko A, Blevins T, Yao Y, Golubov A, Bilichak A, Ilnytskyy Y, Hollunder J, Meins F Jr, Kovalchuk I (2010) Transgenerational adaptation of Arabidopsis to stress requires DNA methylation and the function of Dicer-like proteins. PLoS ONE 5(3):e9514 Cao X, Jacobsen SE (2002) Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol 12:1138–1144 Cao X, Aufsatz W, Zilberman D, Mette MF, Huang MS, Matzke M, Jacobsen SE (2003) Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Curr Biol 13:2212–2217 Chan SWL, Henderson IR, Jacobsen SE (2005) Gardening the genome: DNA methylation in Arabidopsis thaliana. Genetics 6:351–360 Chinnusamy V, Zhu JK (2009) Epigenetic regulation of stress responses in plants. Curr Opin Plant Biol 12:133–139 Chinnusamy V, Gong Z, Zhu JK (2008) Abscisic acid-mediated epigenetic processes in plant development and stress responses. J Integr Plant Biol 50:1187–1195 Choi CS, Sano H (2007) Abiotic-stress induces demethylation and transcriptional activation of a gene encoding a glycerophosphodiesterase-like protein in tobacco plants. Mol Genet Genomics 277:589–600 Correia B, Valledor L, Meijon M, Rodriguez JL, Dias MC, Santos C, Canal MJ, Rodriguez R, Pinto G (2013) Is the interplay between epigenetic markers related to the acclimation of cork oak plants to high temperatures? PLoS ONE 8(1):e53543 Dowen RH, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, Nery JR, Dixon JE, Ecker JR (2012) Widespread dynamic DNA methylation in response to biotic stress. Proc Natl Acad Sci USA 109(32):E2183–E2191 Dyachenko OV, Zakharchenko NS, Shevchuk TV, Bohnert HJ, Cushman JC, Buryanov YI (2006) Effect of hypermethylation of CCWGG sequences in DNA of Mesembryanthemum crystallinum plants on their adaptation to salt stress. Biochem 71:461–465 El-Shami M, Pontier D, Lahmy S, Braun L, Picart C, Vega D, Hakimi MA, Jacobsen SE, Cooke R, Lagrange T (2007) Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE binding platforms in RNAi-related components. Genes Dev 21:2539–2544 Emran AM, Tabei Y, Kobayashi K, Yamaoka N, Nishiguchi M (2012) Molecular analysis of transgenic melon plants showing virus resistance conferred by direct repeat of movement gene of Cucumber green mottle mosaic virus. Plant Cell Rep 31:1371–1377 Feng Q, Yang C, Lin X, Wang J, Ou X, Zhang C, Chenand Y, Liu B (2012) Salt and alkaline stress induced transgenerational alteration in DNA methylation of rice (Oryza sativa). Aus J Crop Sci 6:877–883 Finnegan EJ, Genger RK, Kovac K, Peacock WJ, Dennis ES (1998) DNA methylation and the promotion of flowering by vernalization. Proc Natl Acad Sci USA 95:5824–5829 Gohlke J, Scholz CJ, Kneitz S, Weber D, Fuchs J, Hedrich R, Deeken R (2013) DNA methylation mediated control of gene expression is critical for development of crown gall tumors. PLoS Genet 9(2):e1003267 Golldack D, Lüking I, Yang O (2011) Plant tolerance to drought and salinity: stress regulating transcription factors and their functional significance in the cellular transcriptional network. Plant Cell Rep 30:1383–1391 González RM, Ricardi MM, Iusem ND (2011) Atypical epigenetic mark in an atypical location: cytosine methylation at asymmetric (CNN) sites within the body of a non-repetitive tomato gene. BMC Plant Biol 11:94 Gowher H, Jeltsch A (2002) Molecular enzymology of the catalytic domains of the Dnmt3a and Dnmt3b DNA methyltransferases. J Biol Chem 277:20409–20414 Grativol C, Hemerly AS, Ferreira PC (2012) Genetic and epigenetic regulation of stress responses in natural plant populations. Biochim Biophys Acta 1819:176–185 Hashida SN, Uchiyama T, Martin C, Kishima Y, Sano Y, Mikami T (2006) The temperature-dependent change in methylation of the Antirrhinum transposon Tam3 is controlled by the activity of its transposase. Plant Cell 18:104–118 Hauser MT, Aufsatz W, Jonak C, Luschnig C (2011) Transgenerational epigenetic inheritance in plants. Biochim Biophys Acta 1809:459–468 Jackson JP, Lindroth AM, Cao X, Jacobsen SE (2002) Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416:556–560 Jasencakova Z, Soppe WJ, Meister A, Gernand D, Turner BM, Schubert I (2003) Histone modifications in Arabidopsis-high methylation of H3 lysine 9 are dispensable for constitutive heterochromatin. Plant J 33:471–480 Kanazawa A, Inaba J, Shimura H, Otagaki S, Tsukahara S, Matsuzawa A, Kim BM, Goto K, Masuta C (2011) Virus-mediated efficient induction of epigenetic modifications of 5 endogenous genes with phenotypic changes in plants. Plant J 65:156–168 Kankel MW, Ramsey DE, Stokes TL, Flowers SK, Haag JR, Jeddeloh JA, Riddle NC, Verbsky ML, Richards EJ (2003) Arabidopsis MET1 cytosine methyltransferase mutants. Genetics 163:1109–1122 Karan R, DeLeon T, Biradar H, Subudhi PK (2012) Salt stress induced variation in DNA methylation pattern and its influence on gene expression in contrasting rice genotypes. PLoS ONE 7(6):e40203 Karlsson M, Weber W, Fussenegger M (2011) De novo design and construction of an inducible gene expression system in mammalian cells. Methods Enzymol 497:239–253 Kato M, Miura A, Bender J, Jacobsen SE, Kakutani T (2003) Role of CG, non-CG methylation in immobilization of transposons in Arabidopsis. Curr Biol 13:421–426 Khraiwesh B, Arif MA, Seumel GI, Ossowski S, Weigel D, Reski R, Frank W (2010) Transcriptional control of gene expression by MicroRNAs. Cell 140:111–122 Kou HP, Li Y, Song XX, Ou XF, Xing SC, Ma J, Von Wettstein D, Liu B (2011) Salt stress induced variation in DNA methylation pattern and its influence on gene expression in contrasting rice genotypes. J Plant Physiol 168:1685–1693 Kovarik A, Koukalova B, Bezdek M, Opatrny Z (1997) Hypermethylation of tobacco heterochromatic loci in response to osmotic stress. Theor Appl Genet 95:301–306 Labra M, Ghiani A, Citterio S, Sgorbati S, Sala F, Vannini C, Ruffini-Castiglione M, Bracale M (2002) Analysis of cytosine methylation pattern in response to water deficit in pea root tips. Plant Biol 4:694–699 Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE (2001) Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292:2077–2080 Lira-Medeiros CF, Parisod C, Fernandes RA, Mata CS, Cardoso MA, Ferreira PCG (2010) Epigenetic variation in mangrove plants occurring in contrasting natural environment. PLoS ONE 5(4):e10326 Luna E, Ton J (2012) The epigenetic machinery controlling transgenerational systemic acquired resistance. Plant Signal Behav 7:615–618 Madlung A, Comai L (2004) The effect of stress on genome regulation and structure. Ann Bot 94:481–495 Mirouze M, Paszkowski J (2011) Epigenetic contribution to stress adaptation in plants. Curr Opin Plant Biol 14:267–274 Morales-Ruiz T, Ortega-Galisteo AP, Ponferrada-Marin MI, Martinez-Macias MI, Ariza RR, Roldan-Arjona T (2006) DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases. Proc Natl Acad Sci USA 103:6853–6858 Muthamilarasan M, Prasad M (2013) Plant innate immunity: an updated insight in defense mechanism. J Biosci. doi:10.1007/s12038-013-9302-2 Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL (2007) DNA demethylation in the Arabidopsis genome. Proc Natl Acad Sci USA 104:6752–6757 Qian Y, Cheng X, Liu Y, Jiang H, Zhu S, Cheng B (2010) An epigenetic change in rice cultivars under water stress conditions. Plant Cell Rep 29:1365–1376 Ramsahoye BH, Biniszkiewicz D, Lyko F, Clrk V, Bird AP, Jaenisch R (2000) Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc Natl Acad Sci USA 97:5237–5242 Rodríguez-Negrete EA, Carrillo-Tripp J, Rivera-Bustamante RF (2009) RNA silencing against geminivirus: complementary action of posttranscriptional gene silencing and transcriptional gene silencing in host recovery. J Virol 83:1332–1340 Sabbah M, Raise M, Tal M (1995) Methylation of DNA in NaCl-adapted cells of potato. Plant Cell Rep 14:467–470 Sahu PP, Rai NK, Chakraborty S, Singh M, Chandrappa PH, Ramesh B, Chattopadhyay D, Prasad M (2010) Tomato cultivar tolerant to Tomato leaf curl New Delhi virus infection induces virus-specific short interfering RNA accumulation and defence-associated host gene expression. Mol Plant Pathol 11:531–544 Sahu PP, Rai NK, Puranik S, Roy A, Khan M, Prasad M (2012) Dynamics of defense-related components in two contrasting genotypes of tomato upon infection with Tomato Leaf Curl New Delhi Virus. Mol Biotechnol 52:140–150 Santos AP, Serra T, Figueiredo DD, Barros P, Lourenço T, Chander S, Oliveira MM, Saibo NJ (2011) Transcription regulation of abiotic stress responses in rice: a combined action of transcription factors and epigenetic mechanisms. OMICS 15:839–857 Shaik R, Ramakrishna W (2012) Bioinformatic analysis of epigenetic and micro-RNA mediated regulation of drought responsive genes in rice. PLoS ONE 7(11):e49331 Sharma N, Sahu PP, Puranik S, Prasad M (2012) Recent advances in plant-virus interaction with emphasis on small interfering RNAs (siRNAs). Mol Biotechnol. doi: 10.1007/s12033-012-9615-7 Song Y, Ji D, Li S, Wang P, Li Q, Xiang F (2012) The dynamic changes of DNA methylation and histone modifications of salt responsive transcription factor genes in soybean. PLoS ONE 7(7):e41274 Soppe WJ, Jasencakova Z, Houben A, Kakutani T, Meister A, Huang MS, Jacobsen SE, Schubert I, Fransz PF (2002) DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J 21:6549–6559 Steward N, Kusano T, Sano H (2000) Expression of ZmMET1, a gene encoding a DNA methyltransferase from maize, is associated not only with DNA replication in actively proliferating cells, but also with altered DNA methylation status in cold-stressed quiescent cells. Nuc Acids Res 28:3250–3259 Suji KK, John A (2010) An epigenetic change in rice cultivars under water stress conditions. Elect J Plant Breed 1:1142–1143 Tariq M, Saze H, Probst AV, Lichota J, Habu Y, Paszkowski J (2003) Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin. Proc Natl Acad Sci USA 100:8823–8827 Tompa R, McCallum CM, Delrow J, Henikoff JG, van Steensel B, Henikoff S (2002) Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3. Curr Biol 12:65–68 Tougou M, Yamagishi N, Furutani N, Shizukawa Y, Takahata Y, Hidaka S (2007) Soybean dwarf virus-resistant transgenic soybeans with the sense coat protein gene. Plant Cell Rep 26:1967–1975 Uthup TK, Ravindran M, Bini K, Thakurdas S (2011) Divergent DNA methylation patterns associated with abiotic stress in Hevea brasiliensis. Mol Plant 4:996–1013 Vanyushin BF, Ashapkin VV (2011) DNA methylation in higher plants: past, present and future. Biochim Biophys Acta 1809:360–368 Verhoeven KJF, Jansen JJ, Dijk PJV, Biere A (2010) Stress-induced DNA methylation changes and their heritability in asexual dandelions. New Phytol 185:1108–1118 Wada Y, Miyamoto K, Kusano T, Sano H (2004) Association between up-regulation of stress-responsive genes and hypomethylation of genomic DNA in tobacco plants. Mol Genet Genomics 271:658–666 Wang WS, Pan YJ, Zhao XQ, Dwivedi D, Zhu LH, Ali J, Fu BY, Li ZK (2011) Drought-induced site-specific DNA methylation and its association with drought tolerance in rice (Oryza sativa L.). J Exp Bot 62:1951–1960 Wang Y, An C, Zhang X, Yao J, Zhang Y, Sun Y, Yu F, Amador DM, Mou Z (2013) The Arabidopsis elongator complex subunit2 epigenetically regulates plant immune responses. Plant Cell 25:762–776 Yadav RK, Chattopadhyay D (2011) Enhanced viral intergenic region-specific short interfering RNA accumulation and DNA methylation correlates with resistance against a geminivirus. Mol Plant Microbe Interact 24:1189–1197 Yaish MW, Colasanti J, Rothstein SJ (2011) The role of epigenetic processes in controlling flowering time in plants exposed to stress. J Exp Bot 62:3727–3735 Yao Y, Bilichak A, Golubov A, Kovalchuk I (2012) ddm1 plants are sensitive to methyl methane sulfonate and NaCl stresses and are deficient in DNA repair. Plant Cell Rep 31:1549–1561 Yu Y, Yang X, Wang H, Shi F, Liu Y, Liu J, Li L, Wang D, Liu B (2013a) Cytosine methylation alteration in natural populations of Leymus chinensis induced by multiple abiotic stresses. PLoS ONE 8(2):e55772 Yu A, Lepère G, Jay F, Wang J, Bapaume L, Wang Y, Abraham AL, Penterman J, Fischer RL, Voinnet O, Navarro L (2013b) Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense. Proc Natl Acad Sci USA. doi: 10.1073/pnas.1211757110 Zhang L, Wang Y, Zhang X, Zhang M, Han D, Qiu C, Han Z (2012) Dynamics of phytohormone and DNA methylation patterns changes during dormancy induction in strawberry (Fragaria × ananassa Duch.). Plant Cell Rep 31:155–165 Zheng Q, Rowley MJ, Böhmdorfer G, Sandhu D, Gregory BD, Wierzbicki AT (2013) RNA polymerase V targets transcriptional silencing components to promoters of protein-coding genes. Plant J 73:179–189 Zhu B, Zheng Y, Angliker H, Schwarz S, Thiry S, Siegmann M, Jost JP (2000) 5-Methylcytosine DNA glycosylase activity is also present in the human MBD4 (G/T mismatch glycosylase) and in a related avian sequence. Proc Natl Acad Sci USA 28:4157–4165 Zhu J, Kapoor A, Sridhar VV, Agius F, Zhu JK (2007) The DNA glycosylase/lyase ROS1 functions in pruning DNA methylation patterns in Arabidopsis. Curr Biol 17:54–59