1 Hemberger M, Dean W, Reik W. Epigenetic dynamics of stem cells and cell lineage commitment: Digging Waddington’s canal. Nat Rev Mol Cell Biol, 2009, 10: 526-537??
[2]
3 The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature, 2012, 489: 57-74??
[3]
4 Deng D J, Liu Z J, Du Y T. Epigenetic alterations as cancer diagnostic, prognostic, and predictive biomarkers. Adv Genet, 2010, 71: 125-176??
[4]
5 Sun Y, Deng D, You W C, et al. Methylation of p16 CpG islands associated with malignant transformation of gastric dysplasia in a population-based study. Clin Cancer Res, 2004, 10: 5087-5093??
[5]
14 Barski A, Cuddapah S, Cui K, et al. High-resolution profiling of histone methylations in the human genome. Cell, 2007, 129: 823-837??
[6]
17 Bhutani N, Burns D M, Blau H M. DNA demethylation dynamics. Cell, 2011, 146: 866-872??
[7]
18 Xu Y, Wu F, Tan L, et al. Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells. Mol Cell, 2011, 42: 451-464
[8]
19 Ficz G, Branco M R, Seisenberger S, et al. Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature, 2011, 473: 398-402??
[9]
25 Bai H, Zhou J, Deng D J. Nucleosome positions and differential methylation status of various regions within MLH1 CpG island. Chin J Cancer Res, 2008, 20: 237-242??
[10]
26 Egger G, Aparicio A M, Escobar S G, et al. Inhibition of histone deacetylation does not block resilencing of p16 after 5-aza-2′-deox- ycytidine treatment. Cancer Res, 2007, 67: 346-353??
[11]
30 Yu L, Liu C, Vandeusen J, et al. Global assessment of promoter methylation in a mouse model of cancer identifies ID4 as a putativetumor-suppressor gene in human leukemia. Nat Genet, 2005, 37: 265-274??
[12]
33 Deng D J, Deng G R, Smith M F, et al. Simultaneous detection of CpG methylation and single nucleotide polymorphism by denaturing high performance liquid chromatography. Nucleic Acids Res, 2002, 30: 13E ??
[13]
34 Luo D, Zhang B, Lü L, et al. Methylation of CpG islands of p16 associated with progression of primary gastric carcinomas. Lab Invest, 2006, 86: 591-598
[14]
35 Deng D, Liu Z. Methods and nucleotide fragments of predicting the ability of tumor invasion and metastasis in vitro (in Chinese). PCT patent, WO2011095067, 2011-03-30
[15]
36 Deng D, Gao Y, Zhang B, et al. Methods and nucleotides for assessing tumor metastasis or prognosis in vitro (in Chinese). PCT patent, WO2012097477, 2011-01-21
[16]
37 Deng D, Zhang J, Liu Z, et al. Predicting ability of tumor development, metastasis, and patient’s survival, by extracting DNA from biological samples, detecting demethylation degree of cytosine in CpG island of DNA sequence of GFRA1 and determining tested samples (in Chinese). PCT patent, PCT/CN2012/000169, 2011-03-08
[17]
38 Du Y, Liu Z, Gu L, et al. Characterization of human gastric carcinoma-related methylation of 9 miR CpG islands and repression of their expressions in vitro and in vivo. BMC Cancer, 2012, 12: 249??
[18]
39 Dong C X, Deng D J, Pan K F, et al. Promoter methylation of p16 associated with Helicobacter pylori infection in precancerous gastric lesions: A population-based study. Int J Cancer, 2009, 124: 434-439??
[19]
41 Song M-Y, Pan K-F, Su H-J, et al. Identification of serum microRNAs as novel non-invasive biomarkers for early detection of gastric cancer. PLoS One, 2012, 7: e33608??
[20]
2 FaulK C, Dolinoy D C. Timing is everything: The when and how of environmentally induced changes in the epigenome of animals. Epigenetics, 2011, 6: 791-797??
[21]
6 Cao J, Zhou J, Gao Y, et al. Methylation of p16 CpG island associated with malignant progression of oral epithelial dysplasia: A prospective cohort study. Clin Cancer Res, 2009, 15: 5178-5183??
[22]
7 Hall G L, Shaw R J, Field E A, et al. p16 Promoter methylation is a potential predictor of malignant transformation in oral epithelial dysplasia. Cancer Epidemiol Biomarkers Prev, 2008, 17: 2174-2179??
[23]
8 Belinsky S A, Liechty K C, Gentry F D, et al. Promoter hypermethylation of multiple genes in sputum precedes lung cancer incidence in a high-risk cohort. Cancer Res, 2006, 66: 3338-3344??
[24]
9 Jin Z, Cheng Y, Gu W, et al. A multicenter, double-blinded validation study of methylation biomarkers for progression prediction in Barrett’s esophagus. Cancer Res, 2009, 69: 4112-4115
[25]
10 Zhou J, Cao J, Lu Z M, et al. A 115-bp MethyLight assay for detection of p16 (CDKN2A) methylation as a diagnostic biomarker in human tissues. BMC Med Genet, 2011, 12: 67
[26]
11 Lister R, Pelizzola M, Dowen R H, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature, 2009, 462: 315-322??
[27]
12 Laurent L, Wong E, Li G, et al. Dynamic changes in the human methylome during differentiation. Genome Res, 2010, 20: 320-331??
[28]
13 Chodavarapu R K, Feng S, Bernatavichute Y V, et al. Relationship between nucleosome positioning and DNA methylation. Nature, 2010, 466: 388-392??
[29]
15 Statham A L, Robinson M D, Song J Z, et al. Bisulphite-sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA. Genome Res, 2012, 22: 1120-1127??
[30]
16 Brinkman A B, Gu H, Bartels S J J, et al. Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res, 2012, 22: 1128-1138??
[31]
20 Irizarry R A, Ladd-Acosta C, Wen B, et al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet, 2009, 41: 178-186??
[32]
21 Doi A, Park I H, Wen B, et al. Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat Genet, 2009, 41: 1350-1353??
[33]
22 Yang P, Ma J, Zhang B, et al. CpG Site-specific hypermethylation of p16INK4α in peripheral blood lymphocytes of PAH-exposed workers. Cancer Epidemiol Biomarkers Prev, 2012, 21: 182-190??
[34]
23 Yan P S, Shi H, Rahmatpanah F, et al. Differential distribution of DNA methylation within the RASSF1A CpG island in breast cancer. Cancer Res, 2003, 63: 6178-6186
[35]
24 Lu Z M, Zhou J, Wang X, et al. Nucleosomes correlate with in vivo progression pattern of de novo methylation of p16 CpG islands in human gastric carcinogenesis. PLoS One, 2012, 7: e35928??
[36]
27 De Carvalho D D, Sharma S, You J S, et al. DNA methylation screening identifies driver epigenetic events of cancer cell survival. Cancer Cell, 2012, 21: 655-667??
[37]
28 Costello J F, Frühwald M C, Smiraglia D J, et al. Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nat Genet, 2000, 24: 132-138??
[38]
29 Gitan R S, Shi H, Chen C M, et al. Methylation-specific oligonucleotide microarray: A new potential for high-throughput methylation analysis. Genome Res, 2002, 12: 158-164??
[39]
31 Shen L, Kondo Y, Guo Y, et al. Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters. PLoS Genet, 2007, 3: 2023-2036
[40]
32 Liu Z J, Gao Y H, Zhang J, et al. DNA methylation markers as predictors of initiation and progression of gastric carcinomas. In: Noh H S, Mok Y J, Yang H K, eds. 9th International Gastric Cancer Congress. Pianoro, Bologna, Italy: MEDIMOND s.r.l., 2011. 13-17
[41]
40 Niwa T, Tsukamoto T, Toyoda T, et al. Inflammatory processes triggered by Helicobacter pylori infection cause aberrant DNA methylation in gastric epithelial cells. Cancer Res, 2010, 70: 1430-1440??