Weber M, Hellmann I, Stadler M B, et al .Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome[J]. Nat Genet, 2007,39(4): 457.
Feng Q, Yang C, Lin X, et al. Salt and alkaline stress induced transgenerational alteration in DNA methylation of rice (Oryza sativa) [J]. Aus J Crop Sci,2012,6: 877.
[4]
Verhoeven K J F, Jansen J J, Dijk P J V,et al. Stress-induced DNA methylation changes and their heritability in asexual dandelions[J]. New Phytol, 2010,185: 1108.
[5]
Kovalchuk O, Burke P, Arkhipov A, et al. Genome hypermethylation in Pinus silvestris of chemobvl-a mechanism for radiation adaption[J]. Mutat Res, 2003,529: 13.
[6]
Rahavi M R, Migicovsky Z, Titov V, er al. Transgenerational adaption to heavy metal salts in Arabidopsis[J]. Front Plant Sci, 2011,2: 91.
[7]
Boyko A, Blevins T, Yao Y,et al. Transgenerational adaptation of Arabidopsis to stress requires DNA methylation and the function of Dicer-like proteins[J]. PLoS ONE, 2010,5: e9514.
[8]
Schwander T, Leimar O. Genes as leaders and followers in evolution[J]. Trends Ecol Evol, 2011, 26(3): 143.
[9]
Turner B M. Epigenetic responses to environmental change and their evolutionary implications[J]. Philos T R Soc B, 2009, 364(1534): 3403.
[10]
Zaratiegui M, Irvine D V, Martienssen R A. Noncoding RNAs and gene silencing[J]. Cell, 2007, 128(4): 763.
[11]
Rapp R A, Wendel J F. Epigenetics and plant evolution[J]. New Phytologist, 2005, 168(1): 81.
[12]
Jenuwein T, Allis C D. Translating the histone code[J]. Science, 2001, 293(5532): 1074.
[13]
Tian L, Fong M P, Wang J J, et al. Reversible histone acetylation and deacetylation mediate genome-wide, promoter-dependent and locus-specific changes in gene expression during plant development[J]. Genetics, 2005, 169(1): 337.
[14]
Halfmann R, Lindquist S. Epigenetics in the extreme: prions and the inheritance of environmentally acquired traits[J]. Science, 2010, 330(6004): 629.
[15]
Rollins R A, Haghighi F, Edwards J R,et al.Large-scale structure of genomic methylation patterns[J].Genome Res,2006,16(2): 157.
[16]
Cokus S J, Feng S, Zhang X, et al.Shotgun bisulphite sequencing of the Arabidopsisgenome reveals DNA methylation patterning[J].Nature,2008,452(7184): 215.
[17]
Nair S S, Coolen M W, Stirzaker C, et al.Comparison of methyl-DNA immunoprecipitation(MeDIP)and methyl-CpG binding domain(MBD)protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias[J]. Epigenetics,2011,6(1): 34.
[18]
Wojdacz T K, Dobrovic A.Methylation-sensitive high resolution melting (MS-HRM): a new approach for sensitive and high-throughput assessment of methylation[J].Nucleic Acids Res,2007,35(6): e41.
[19]
O\'Neill L P, Turner B M.Immunoprecipitation of chromatin[J].Method Enzymol,1995,274: 189.
[20]
Miura H, Tomaru Y.ChIP on chip for transcriptional regulatory network analysis[J].Tanpakushitsu Kakusan Koso,2004,49(17 Suppl): 2710.
[21]
Nix D A, Courdy S J, Boucher K M.Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks[J].BMC Bioinfor,2008,9(1): 523.
[22]
Hamilton A J, Baulcombe D C.A species of small antisense RNA in posttranscriptional gene silencing in plants[J].Science,1999,286(5441): 950.
[23]
Shi R, Chiang V L. Facile means for quantifying microRNA expression by real-time PCR[J].Biotechniques, 2005,39(4): 519.
[24]
Mestdagh P, Feys T, Bernard N, et al. High-throughput stem-loop RT-qPCR miRNA expression profiling using minute amounts of input RNA[J].Nucleic Acids Res,2008,36(21): 143.
[25]
Liu C G, Calin G A, Meloon B, et al. An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues[J].Proc Natil Acad Sci USA, 2004,101(26): 9740.
Flatscher R, Frajman B, Sch?nswetter P, et al. Environmental heterogeneity and phenotypic divergence: can heritable epigenetic variation aid speciation[J]. Genet Res Int, 2012, doi: 10.1155/2012/698421.
Bird A. Perceptions of epigenetics[J]. Nature, 2007, 447(7143): 396.
[34]
Jablonka E, Lamb M J. The changing concept of epigenetics[J]. Ann NY Acad Sci, 2002, 981(1): 82.
[35]
Oliver Galm, Stefan Wilop, Christian Lüders. Clinical implications of aberrant DNA methylation patterns in acute myelogenous leukemia[J]. Ann Hematol, 2005, 84: 39.
[36]
Bird A. DNA methylation patterns and epigenetic memory[J]. Genes Dev, 2002, 16(1): 6.
[37]
Goll M G, Bestor T H. Eukaryotic cytosine methylltransferases[J]. Annu Rev Biochem, 2005, 74: 481.
[38]
Goldberg A D, Allis C D, Bernstein E. Epigenetics: a landscape takes shape[J]. Cell, 2007, 128(4): 635.
[39]
Bernstein B E, Meissner A, Lander E S. The mammalian epigenome[J]. Cell, 2007, 128(4): 669.
[40]
Shelley L Berger. The complex language of chromatin regulation during transcription[J]. Nature, 2007,447(7143): 407.
[41]
E Jean Finnegan, W James Peacock, Elizabeth S Dennis. DNA methylation, a key regulator of plant development and other processes[J]. Curr Opin Genet Dev,2000,10(2): 217.
[42]
Chan S W, Henderson I R, Jacobsen S E. Gardening the genome: DNA methylation in Arabidopsis thaliana[J]. Nat Rev Genet, 2005,6: 351.
[43]
Paun O, Bateman R M, Fay M F, et al. Stable epigenetic effects impact adaptation in allopolyploid orchids (Dactylorhiza: Orchidaceae) [J]. Mol Biol Evol, 2010, 27(11): 2465.
[44]
Ha M, Pang M, Agarwal V, et al. Interspecies regulation of microRNAs and their targets[J]. Biochim Biophys Acta, 2008, 1779(11): 735.
[45]
Ha M, Ng D W K, Li W H, et al. Coordinated histone modifications are associated with gene expression variation within and between species[J]. Genome Res, 2011, 21(4): 590.
[46]
Hollister J D, Smith L M, Guo Y L, et al. Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata[J]. Proc Natl Acad Sci, 2011, 108(6): 2322.
Yuan Yuan, Wang Zhouyong, Jiang Chao, et al. Exploiting genes and functional diversity of chlorogenic acid and luteolin biosyntheses in Lonicera japonicaand their substitutes[J]. Gene, 2014, 534(2): 408.
Ashikawa I. Surveying CpG methylation at 5\'-CCGG in the genomes of rice cultivars[J]. Plant Mol Biol, 2001, 45(1): 31.
[53]
Knox M R, Ellis T H. Stability and inheritance of methylation states at Pstl sites in Pisum[J]. Mol Genet Genomics, 2001, 265(3): 497.
[54]
Cervera M T, Ruiz-Garcia L, Martinez-Zapater J. Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers[J]. Mol Genet Genomics, 2002, 268(4): 543.
[55]
Wang Y, Lin X, Dong B, et al. DNA methylation polymorphism in a set of elite rice cultivars and its possible contribution to inter-cultivar differential gene expression[J]. Cellular Mol Biol Lett, 2004, 9(3): 543.
[56]
Wang X, Zhang Y, Ma Q, et al. SKB1-mediated symmetric dimethylation of histone H4R3 controls flowering time in Arabidopsis[J]. EMBO J, 2007, 26(7): 1934.
[57]
Baek D, Jiang J, Chung J S, et al. Regulated AtHKT1 gene expression by a distal enhancer element and DNA methylation in the promoter plays an important role in salt tolerance[J]. Plant Cell Physiol, 2011, 52: 149.
[58]
Dyachenko O V, Zakharchenko N S, Shevchuk T V, et al. Effect of hypermethylation of CCWGG sequences in DNA of Mesembryanthemum crystallimom plants on their adaptation to salt stress[J]. Biochemistry, 2006, 71: 461.
[59]
Gonzalez R M, Ricardi M M, Iusem N D. Atypical epigenetic mark in an atypical location: cytosine methylation at asymmetric (CNN) sites within the body of a non-repetitive tomato gene[J]. BMC Plant Biol, 2011, 11: 94.
[60]
Hashida S N, Uchiyama T, Martin C, et al. The temperature-dependent change in methylation of the Antirrhinum transposon Tam3 is controlled by the activity of its transposase[J]. Plant Cell, 2006, 18: 104.
[61]
Song Y, Ji D, Li S, et al. The dynamic changes of DNA methylation and histone modifications of salt responsive transcription factor genes in soybean[J]. PLoS ONE, 2012,7: e41274.
[62]
Steward N, Kusano T, Sano H. 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[J]. Nuc Acids Res, 2000, 28: 3250.
[63]
Wada Y, Miyamoto K, Kusano T, et al. Association between up-regulation of stress-responsive genes and hypomethylation of genomic DNA in tobacco plants[J]. Mol Genet Genomics, 2004, 271: 658.
[64]
Chang-Sun Choi, Hiroshi Sano. Abiotic-stress induces demethylation and transcriptional activation of a gene encoding a glycerophosphodiesterase-like protein in tobacco plants[J]. Mol Genet Genomics,2007, 277: 589.
[65]
Mirouze M, Paszkowski J. Epigenetic contribution to stress adaptation in plants[J]. Curr Opin Plant Biol,2011,14: 267.
[66]
Hauser M T, Aufsatz W, Jonak C, et al. Transgenerational epigenetic inheritance in plants[J]. Biochim Biophys Acta,2011,1809: 459.