Cokus SJ, Feng S, Zhang X, et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning[J]. Nature, 2008, 452(7184):215-219.
[2]
Lister R, O''Malley RC, Tonti-Filippini J, et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis[J]. Cell, 2008, 133(3):523-536.
[3]
Zilberman D, Gehring M, Tran RK, et al. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription[J]. Nature Genetics, 2006, 39(1):61-69.
[4]
Zemach A, McDaniel IE, Silva P, et al. Genome-wide evolutionary analysis of eukaryotic DNA methylation[J]. Science, 2010, 328(5980):916-919.
[5]
Sheldon CC, Finnegan EJ, Rouse DT, et al. The control of flowering by vernalization[J]. Curr Opin Plant Biol, 2000, 3(5):418-422.
[6]
Fraga MF, Ca?al M, Rodríguez R. Phase-change related epigenetic and physiological changes in Pinus radiata D. Don[J]. Planta, 2002, 215(4):672-678.
[7]
Peerbolte R, Leenhouts K, Hooykaas-van Slogteren GM, et al. Clones from a shooty tobacco crown gall tumor II:irregular T-DNA structures and organization, T-DNA methylation and conditional expression of opine genes[J]. Plant Mol Biol, 1986, 7:285-299.
[8]
Bernstein BE, Meissner A, Lander ES. The mammalian epigenome[J]. Cell, 2007, 128(4):669-681.
[9]
Chan SW, Zilberman D, Xie Z, et al. RNA silencing genes control de novo DNA methylation[J]. Science, 2004, 303(5662):1336-1336.
[10]
Cao X, Aufsatz W, Zilberman D, et al. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation[J]. Current Biology, 2003, 13(24):2212-2217.
[11]
Lindroth AM, Cao X, Jackson JP, et al. Requirement of CHROMO-METHYLASE3 for maintenance of CpXpG methylation[J]. Science, 2001, 292(5524):2077-2080.
[12]
Goodrich J, Tweedie S. Remembrance of things past:chromatin remodeling in plant development[J]. Annual Review of Cell and Developmental Biology, 2002, 18(1):707-746.
[13]
Toyota M, Ho C, Ahuja N, et al. Identification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification[J]. Cancer Res, 1999, 59:2307-2312.
[14]
Hatada I, Hayashizaki Y, Hirotsune S, et al. A genomic scanning method for higher organisms using restriction sites as landmarks[J]. Proc Natl Acad Sci USA, 1991, 88(21):9523-9527.
[15]
Frommer M, McDonald LE, Millar DS, et al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands[J]. Proc Natl Acad Sci USA, 1992, 89:1827-1831.
[16]
Beck S, Rakyan VK. The methylome:approaches for global DNA methylation profiling[J]. Trends Genet, 2008, 24(5):231-237.
[17]
Weber M, Davies JJ, Wittig D, et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells[J]. Nature Genetics, 2005, 37(8):853-862.
[18]
http://www. plob. org/2012/01/09/1614. html.
[19]
Mensaert K, Denil S, Trooskens G, et al. Next-generation technolo-gies and data analytical approaches for epigenomics[J]. Enviro-nmental and Molecular Mutagenesis, 2014, 55(3):155-170.
[20]
Rohde C, Zhang Y, Jurkowski TP, et al. Bisulfite sequencing data presentation and compilation(BDPC)web server—a useful tool for DNA methylation analysis[J]. Nucleic Acids Research, 2008, 36(5):e34.
[21]
Down TA, Rakyan VK, Turner DJ, et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis[J]. Nature Biotechnology, 2008, 26(7):779-785.
[22]
Takai D, Jones PA. The CpG island searcher:a new WWW resource[J]. In Silico Biology, 2003, 3(3):235-240.
[23]
Grunau C, Renault E, Rosenthal A, et al. MethDB-a public database for DNA methylation data[J]. Nucleic Acids Research, 2001, 29(1):270-274.
[24]
Amoreira C, Hindermann W, Grunau C. An improved version of the DNA Methylation database(MethDB)[J]. Nucleic Acids Research, 2003, 31(1):75-77.
[25]
Kumaki Y, Oda M, Okano M. QUMA:quantification tool for methylation analysis[J]. Nucleic Acids Research, 2008, 36(suppl 2):W170-W175.
[26]
Li LC, Dahiya R. MethPrimer:designing primers for methylation PCRs[J]. Bioinformatics, 2002, 18(11):1427-1431.
[27]
Bird AP. CpG-rich islands and the function of DNA methylation[J]. Nature, 1985, 321(6067):209-213.
[28]
Zhang X, Yazaki J, Sundaresan A, et al. Genome-wide high-resolution mapping and functional analysis of dna methylation in Arabidopsis[J]. Cell, 2006, 126(6):1189-1201.
[29]
Tran RK, Henikoff JG, Zilberman D, et al. DNA Methylation profiling identifies CG methylation clusters in Arabidopsis genes[J]. Current Biology, 2005, 15(2):154-159.
[30]
Hsieh TF, Ibarra CA, Silva P, et al. Genome-wide demethylation of Arabidopsis endosperm[J]. Science, 2009, 324:1451-1454.
[31]
Aina R, Sgorbati S, Santagostino A, et al. Specific hypomethylation of DNA is induced by heavy metals in white clover and industrial hemp[J]. Physiologia Plantarum, 2004, 121(3):472-480.
Papa CM, Springer NM, Muszynski MG, et al. Maize chromomethy-lase Zea methyltransferase2 is required for CpNpG methylation[J]. The Plant Cell Online, 2001, 13(8):1919-1928.
[35]
Bartee L, Malagnac F, Bender J. Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene[J]. Genes & Development, 2001, 15(14):1753-1758.
[36]
Huang THM, Laux DE, Hamlin BC, et al. Identification of DNA methylation markers for human breast carcinomas using the methylation-sensitive restriction fingerprinting technique[J]. Cancer Research, 1997, 57(6):1030-1034.
[37]
Reyna-Lopez GE, Simpson J, Ruiz-Herrera J. Differences in DNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphisms[J]. Molecular and General Genetics MGG, 1997, 253(6):703-710.
[38]
朱燕. DNA 甲基化的分析与状态检测[J]. 现代预防医学, 2006, 32(9):1070-1073.
[39]
Yegnasubramanian S, Lin X, Haffner MC, et al. Combination of methylated-DNA precipitation and methylation-sensitive restriction enzymes(COMPARE-MS)for the rapid, sensitive and quantitative detection of DNA methylation[J]. Nucleic Acids Research, 2006, 34(3):e19.
[40]
Thu KL, Vucic EA, Kennett JY, et al. Methylated DNA immunoprecipitation[J]. J Vis Exp:JoVE, 2009(23):935.
[41]
Serre D, Lee BH, Ting AH. MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome[J]. Nucleic Acids Research, 2010, 38(2):391-399.
Krueger F, Kreck B, Franke A, et al. DNA methylome analysis using short bisulfite sequencing data[J]. Nature Methods, 2012, 9(2):145-151.
[44]
Wang LS, Burke C, Hasson H, et al. A phase 1b study of the effects of black raspberries on rectal polyps in patients with familial adeno-matous polyposis[J]. Cancer Prev Res, 2014, 7:666-674.
[45]
Li N, Ye M, Li Y, et al. Whole genome DNA methylation analysis based on high throughput sequencing technology[J]. Methods, 2010, 52(3):203-212.
[46]
Xi Y, Li W. BSMAP:whole genome bisulfite sequence MAPping program[J]. BMC Bioinformatics, 2009, 10(1):232.
[47]
Wang Y, Leung FC. An evaluation of new criteria for CpG islands in the human genome as gene markers[J]. Bioinformatics, 2004, 20(7):1170-1177.
[48]
Ioshikhes IP, Zhang MQ. Large-scale human promoter mapping using CpG islands[J]. Nature Genetics, 2000, 26(1):61-63.
[49]
Grunau C, Renault E, Roizes G. DNA methylation database “MethDB”:a user guide[J]. J Nutr, 2002, 132:2435S-2439S.
[50]
Negre V, Grunau C. The MethDB DAS server:adding an epigenetic information layer to the human genome[J]. Epigenetics, 2006, 1(2):101-105.
[51]
Pattyn F, Hoebeeck J, Robbrecht P, et al. methBLAST and meth-PrimerDB:web-tools for PCR based methylation analysis[J]. BMC Bioinformatics, 2006, 7(1):496.
[52]
Laird PW. Principles and challenges of genome-wide DNA methylation analysis[J]. Nature Reviews Genetics, 2010, 11(3):191-203.