Epigenetics, a mode for plants to respond to abiotic stresses

Ascenzi R, Gantt J S (1997). A drought-stress-inducible histone gene in Arabidopsis thaliana is a member of a distinct class of plant linker histone variants. Plant Mol Biol, 34(4): 629–641 Aufsatz W, Mette MF, van der Winden J, Matzke M, Matzke A J (2002). HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double-stranded RNA. EMBO J, 21(24): 6832–6841 Bartee L, Malagnac F, Bender J (2001). Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Genes Dev, 15(14): 1753–1758 Borsani O, Zhu J, Verslues P E, Sunkar R, Zhu J K (2005). Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell, 123(7): 1279–1291 Camporeale G, Oommen A M, Griffin J B, Sarath G, Zempleni J (2007). K12-biotinylated histone H4 marks heterochromatin in human lymphoblastoma cells. J Nutr Biochem, 18(11): 760–768 Chen L T, Luo M, Wang Y Y, Wu K (2010). Involvement of Arabidopsis histone deacetylase HDA6 in ABA and salt stress response. J Exp Bot, 61(12): 3345–3353 Chinnusamy E, Zhu J K (2009). Epigenetic regulation of stress responses in plants. Curr Opin Plant Biol, 12(2): 1–7 Choi C S, 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(5): 589–600 Dalmay T, Hamilton A, Rudd S, Angell S, Baulcombe D C (2000). An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell, 101(5): 543–553 Dyachenko O V, Zakharchenko N S, Shevchuk T V, Bohnert H J, Cushman J C, Buryanov Y I (2006). Effect of hypermethylation of CCWGG sequences in DNA of Mesembryanthemum crystallinum plants on their adaptation to salt stress. Biochemistry (Mosc), 71(4): 461–465 Finnegan E J, Kovac K A (2000). Plant DNA methyltransferases. Plant Mol Biol, 43(2–3): 189–201 Fu W Q, Wu K Q, Duan J (2007). Sequence and expression analysis of histone deacetylases in rice. Biochem Biophys Res Commun, 356(4): 843–850 Hashida S N, 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(1): 104–118 Henderson I R, Jacobsen S E (2007). Epigenetic inheritance in plants. Nature, 447(7143): 418–424 Johnson L, Cao X, Jacobsen S (2002). Interplay between two epigenetic marks. DNA methylation and histone H3 lysine 9 methylation. Curr Biol, 12(16): 1360–1367 Kim J M, To T K, Ishida J, Morosawa T, Kawashima M, Matsui A, Toyoda T, Kimura H, Shinozaki K, Seki M (2008). Alterations of lysine modifications on the histone H3 N-tail under drought stress conditions in Arabidopsis thaliana. Plant Cell Physiol, 49(10): 1580–1588 Kovarik A, Koukalova B, Bezdek M, Opatrn Z (1997). Hypermethylation of tobacco heterochromatic loci in response to osmotic stress. Theor Appl Genet, 95(1-2): 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 (Stuttgart), 4(6): 694–699 Lister R, O’Malley R C, Tonti-Filippini J, Gregory B D, Berry C C, Millar A H, Ecker J R (2008). Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell, 133(3): 523–536 Martienssen R (1998). Transposons, DNA methylation and gene control. Trends Genet, 14(7): 263–264 Mourrain P, Béclin C, Elmayan T, Feuerbach F, Godon C, Morel J B, Jouette D, Lacombe A M, Nikic S, Picault N, Rémoué K, Sanial M, Vo T A, Vaucheret H (2000). Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell, 101(5): 533–542 Nathan D, Ingvarsdottir K, Sterner D E, Bylebyl G R, Dokmanovic M, Dorsey J A, Whelan K A, Krsmanovic M, Lane W S, Meluh P B, Johnson E S, Berger S L (2006). Histone sumoylation is a negative regulator in Saccharomyces cerevisiae and shows dynamic interplay with positive-acting histone modifications. Genes Dev, 20(8): 966–976 Navarro L, Dunoyer P, Jay F, Arnold B, Dharmasiri N, Estelle M, Voinnet O, Jones J D G (2006). A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science, 312(5772): 436–439 Papa C M, Springer N M, Muszynski M G, Meeley R, Kaeppler S M (2001). Maize chromomethylase Zea methyltransferase2 is required for CpNpG methylation. Plant Cell, 13(8): 1919–1928 Phillips J R, Dalmay T, Bartels D (2007). The role of small RNAs in abiotic stress. FEBS Lett, 581(19): 3592–3597 Probst A V, Fagard M, Proux F, Mourrain P, Boutet S, Earley K, Lawrence R J, Pikaard C S, Murfett J, Furner I, Vaucheret H, Mittelsten Scheid O (2004). Arabidopsis histone deacetylase HDA6 is required for maintenance of transcriptional gene silencing and determines nuclear organization of rDNA repeats. Plant Cell, 16(4): 1021–1034 Qiu S P, Huang J, Pan L J, Wang M M, Zhang H S (2006). Salt induces expression of RH3.2A, encoding an H3.2-type histone H3 protein in rice (Oryza sativa L.). Yi Chuan Xue Bao, 33(9): 833–840 Schauer S E, Jacobsen S E, Meinke DW, Ray A (2002). DICER-LIKE1: blind men and elephants in Arabidopsis development. Trends Plant Sci, 7(11): 487–491 Scippa G S, Griffiths A, Chiatante D, Bray E A (2000). The H1 histone variant of tomato, H1-S, is targeted to the nucleus and accumulates in chromatin in response to water-deficit stress. Planta, 211(2): 173–181 Shen W H (2001). NtSET1, a member of a newly identified subgroup of plant SET-domain-containing proteins, is chromatin-associated and its ectopic overexpression inhibits tobacco plant growth. Plant J, 28(4): 371–383 Sokol A, Kwiatkowska A, Jerzmanowski A, Prymakowska-Bosak M (2007). Up-regulation of stress-inducible genes in tobacco and Arabidopsis cells in response to abiotic stresses and ABA treatment correlates with dynamic changes in histone H3 and H4 modifications. Planta, 227(1): 245–254 Sridha S, Wu K (2006). Identification of AtHD2C as a novel regulator of abscisic acid responses in Arabidopsis. Plant J, 46(1): 124–133 Sridhar V V, Kapoor A, Zhang K, Zhu J, Zhou T, Hasegawa P M, Bressan R A, Zhu J K (2007). Control of DNA methylation and heterochromatic silencing by histone H2B deubiquitination. Nature, 447(7145): 735–738 Steward N, Ito M, Yamaguchi Y, Koizumi N, Sano H (2002). Periodic DNA methylation in maize nucleosomes and demethylation by environmental stress. J Biol Chem, 277(40): 37741–37746 Stockinger E J, Mao Y, Regier M K, Triezenberg S J, Thomashow M F (2001). Transcriptional adaptor and histone acetyltransferase proteins in Arabidopsis and their interactions with CBF1, a transcriptional activator involved in cold-regulated gene expression. Nucleic Acids Res, 29(7): 1524–1533 Sunkar R, Chinnusamy V, Zhu J, Zhu J K (2007). Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends Plant Sci, 12(7): 310–309 Sunkar R, Kapoor A, Zhu J K (2006). Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance. Plant Cell, 18(8): 2051–2065 Sunkar R, Zhu J K (2004). Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell, 16(8): 2001–2019 Tsuji H, Saika H, Tsutsumi N, Hirai A, Nakazono M (2006). Dynamic and reversible changes in histone H3-Lys4 methylation and H3 acetylation occurring at submergence-inducible genes in rice. Plant Cell Physiol, 47(7): 995–1003 Vaistij F E, Jones L, Baulcombe D C (2002). Spreading of RNA targeting and DNA methylation in RNA silencing requires transcription of the target gene and a putative RNA-dependent RNA polymerase. Plant Cell, 14(4): 857–867 Wada Y (2005). Physiological functions of plant DNA methyltransferases. Plant Biotechnol, 22: 71–80 Wada Y, Ohya H, Yamaguchi Y, Koizumi N, Sano H (2003). Preferential de novo methylation of cytosine residues in non-CpG sequences by a domains rearranged DNA methyltransferase from tobacco plants. J Biol Chem, 278(43): 42386–42393 Yoder J A, Walsh C P, Bestor T H (1997). Cytosine methylation and the ecology of intragenomic parasites. Trends Genet, 13(8): 335–340 Zemach A, Grafi G (2003). Characterization of Arabidopsis thaliana methyl-CpG-binding domain (MBD) proteins. Plant J, 34(5): 565–572 Zhang K, Sridhar V V, Zhu J, Kapoor A, Zhu J K (2007). Distinctive core histone post-translational modification patterns in Arabidopsis thaliana. PLoS ONE, 2(11): e1210 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(4): 1196–1204 Zhu J K (2008). Epigenome sequencing comes of age. Cell, 133(3): 395–397