Techniques used in studies of epigenome dysregulation due to aberrant DNA methylation: An emphasis on fetal-based adult diseases

Reproductive Toxicology

Volumn 23, Issue 3, 2007, Pages 267-282

  Ho, Shuk mei ^a   Tang, Wan yee ^a  

^a UNIVERSITY OF CINCINNATI COLLEGE OF MEDICINE   (United States)

Author keywords

Chromatin remodeling; Cytosine methylation; Epigenetics; Fetal based adult disease; Genome wide methylation profiling; Methylation sensitive restriction fingerprinting; Restriction landmark genomic scanning (RLGS)

Indexed keywords

BISULFITE;

ADULT DISEASE; CHROMATIN IMMUNOPRECIPITATION; COMPUTER MODEL; DATA BASE; DIFFERENTIAL METHYLATION HYBRIDIZATION; DNA METHYLATION; DNA MICROARRAY; EPIGENETICS; GENE CONTROL; GENE EXPRESSION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; METHODOLOGY; METHYLATION CPG ISLAND AMPLIFICATION REPRESENTATIONAL DIFFERENCE ANALYSIS; METHYLATION SENSITIVE RESTRICTION FINGERPRINTING; RESTRICTION LANDMARK GENOMIC SCANNING; REVIEW;

DNA METHYLATION; EPIGENESIS, GENETIC; FEMALE; GENE EXPRESSION PROFILING; GENETIC PREDISPOSITION TO DISEASE; HUMANS; MODELS, GENETIC; MOLECULAR BIOLOGY; PREGNANCY; PRENATAL EXPOSURE DELAYED EFFECTS;

EID: 34247136384     PISSN: 08906238     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.reprotox.2007.01.004     Document Type: Review

References (145)

1. Liu Y., and Freedman B.I. Genetics of progressive renal failure in diabetic kidney disease. Kidney Int Suppl (2005) S94-S97
2. Kroll T.G. Molecular events in follicular thyroid tumors. Cancer Treat Res 122 (2004) 85-105
3. Moore M.A. Converging pathways in leukemogenesis and stem cell self-renewal. Exp Hematol 33 (2005) 719-737
4. Scher H.I., and Sawyers C.L. Biology of progressive, castration-resistant prostate cancer: directed therapies targeting the androgen-receptor signaling axis. J Clin Oncol 23 (2005) 8253-8261
5. Tusie Luna M.T. Genes and type 2 diabetes mellitus. Arch Med Res 36 (2005) 210-222
6. Soussi T., Ishioka C., Claustres M., and Beroud C. Locus-specific mutation databases: pitfalls and good practice based on the p53 experience. Nat Rev Cancer 6 (2006) 83-90
7. Garg V. Insights into the genetic basis of congenital heart disease. Cell Mol Life Sci 63 (2006) 1141-1148
8. Verschure P.J., Visser A.E., and Rots M.G. Step out of the groove: epigenetic gene control systems and engineered transcription factors. Adv Genet 56 (2006) 163-204
9. Jiang Y.H., Bressler J., and Beaudet A.L. Epigenetics and human disease. Annu Rev Genomics Hum Genet 5 (2004) 479-510
10. Rodenhiser D., and Mann M. Epigenetics and human disease: translating basic biology into clinical applications. CMAJ 174 (2006) 341-348
11. Jaenisch R., and Bird A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 33 Suppl (2003) 245-254
12. Morris K.V. siRNA-mediated transcriptional gene silencing: the potential mechanism and a possible role in the histone code. Cell Mol Life Sci 62 (2005) 3057-3066
13. Cheung P., and Lau P. Epigenetic regulation by histone methylation and histone variants. Mol Endocrinol 19 (2005) 563-573
14. Esteller M. Aberrant DNA methylation as a cancer-inducing mechanism. Annu Rev Pharmacol Toxicol 45 (2005) 629-656
15. Gluckman P.D., and Hanson M.A. The developmental origins of the metabolic syndrome. Trends Endocrinol Metab 15 (2004) 183-187
16. Dolinoy D.C., Weidman J.R., and Jirtle R.L. Epigenetic gene regulation: linking early developmental environment to adult disease. Reprod Toxicol 23 (2007) 297-307
17. Santos F., and Dean W. Epigenetic reprogramming during early development in mammals. Reproduction 127 (2004) 643-651
18. Weidman J.R., Maloney K.A., and Jirtle R.L. Comparative phylogenetic analysis reveals multiple non-imprinted isoforms of opossum Dlk1. Mamm Genome 17 (2006) 157-167
19. Anway M.D., Cupp A.S., Uzumcu M., and Skinner M.K. Epigenetic transgenerational actions of endocrine disruptors and male fertility. Science 308 (2005) 1466-1469
20. Ho S.M., Tang W.Y., Belmonte dF, and Prins G.S. Developmental exposure to estradiol and bisphenol A increases susceptibility to prostate carcinogenesis and epigenetically regulates phosphodiesterase type 4 variant 4. Cancer Res 66 (2006) 5624-5632
21. Dolinoy D.C., Weidman J.R., Waterland R.A., and Jirtle R.L. Maternal genistein alters coat color and protects Avy mouse offspring from obesity by modifying the fetal epigenome. Environ Health Perspect 114 (2006) 567-572
22. Fernandez-Twinn D.S., and Ozanne S.E. Mechanisms by which poor early growth programs type-2 diabetes, obesity and the metabolic syndrome. Physiol Behav 88 (2006) 234-243
23. Barker D.J., Osmond C., Simmonds S.J., and Wield G.A. The relation of small head circumference and thinness at birth to death from cardiovascular disease in adult life. BMJ 306 (1993) 422-426
24. Ravelli A.C., van der Meulen J.H., Michels R.P., et al. Glucose tolerance in adults after prenatal exposure to famine. Lancet 351 (1998) 173-177
25. Dennison E.M., Arden N.K., Keen R.W., et al. Birthweight, vitamin D receptor genotype and the programming of osteoporosis. Paediatr Perinat Epidemiol 15 (2001) 211-219
26. Thompson C., Syddall H., Rodin I., et al. Birth weight and the risk of depressive disorder in late life. Br J Psychiatry 179 (2001) 450-455
27. Veurink M., Koster M., and Berg L.T. The history of DES, lessons to be learned. Pharm World Sci 27 (2005) 139-143
28. Demerath E.W., Cameron N., Gillman M.W., et al. Telomeres and telomerase in the fetal origins of cardiovascular disease: a review. Hum Biol 76 (2004) 127-146
29. Lee H.K., Park K.S., Cho Y.M., et al. Mitochondria-based model for fetal origin of adult disease and insulin resistance. Ann N Y Acad Sci 1042 (2005) 1-18
30. Rakyan V.K., Blewitt M.E., Druker R., et al. Metastable epialleles in mammals. Trends Genet 18 (2002) 348-351
31. Tollefsbol T.O. Methods of epigenetic analysis. Methods Mol Biol 287 (2004) 1-8
32. Chiang P.K., Gordon R.K., Tal J., et al. S-Adenosylmethionine and methylation. FASEB J 10 (1996) 471-480
33. Singal R., and Ginder G.D. DNA methylation. Blood 93 (1999) 4059-4070
34. Murphy S.K., and Jirtle R.L. Imprinted genes as potential genetic and epigenetic toxicologic targets. Environ Health Perspect 108 Suppl 1 (2000) 5-11
35. Costello J.F., and Plass C. Methylation matters. J Med Genet 38 (2001) 285-303
36. Antequera F., and Bird A. Number of CpG islands and genes in human and mouse. Proc Natl Acad Sci USA 90 (1993) 11995-11999
37. Lyko F., and Brown R. DNA methyltransferase inhibitors and the development of epigenetic cancer therapies. J Natl Cancer Inst 97 (2005) 1498-1506
38. Bird A., Tate P., Nan X., et al. Studies of DNA methylation in animals. J Cell Sci Suppl 19 (1995) 37-39
39. Monk M., Boubelik M., and Lehnert S. Temporal and regional changes in DNA methylation in the embryonic, extraembryonic and germ cell lineages during mouse embryo development. Development 99 (1987) 371-382
40. Kafri T., Ariel M., Brandeis M., et al. Developmental pattern of gene-specific DNA methylation in the mouse embryo and germ line. Genes Dev 6 (1992) 705-714
41. Issa J.P. CpG-island methylation in aging and cancer. Curr Top Microbiol Immunol 249 (2000) 101-118
42. Waterland R.A., and Jirtle R.L. Transposable elements: targets for early nutritional effects on epigenetic gene regulation. Mol Cell Biol 23 (2003) 5293-5300
43. Niculescu M.D., Craciunescu C.N., and Zeisel S.H. Gene expression profiling of choline-deprived neural precursor cells isolated from mouse brain. Brain Res Mol Brain Res 134 (2005) 309-322
44. Li S., Washburn K.A., Moore R., et al. Developmental exposure to diethylstilbestrol elicits demethylation of estrogen-responsive lactoferrin gene in mouse uterus. Cancer Res 57 (1997) 4356-4359
45. Newbold R.R., Padilla-Banks E., and Jefferson W.N. Adverse effects of the model environmental estrogen diethylstilbestrol are transmitted to subsequent generations. Endocrinology 147 (2006) S11-S17
46. Li S., Hansman R., Newbold R., et al. Neonatal diethylstilbestrol exposure induces persistent elevation of c-fos expression and hypomethylation in its exon-4 in mouse uterus. Mol Carcinog 38 (2003) 78-84
47. Anway M.D., Leathers C., and Skinner MK. Endocrine disruptor vinclozolin induced epigenetic transgenerational adult onset disease. Endocrinology 147 (2006) 5515-5523
48. Huang T.H., Laux D.E., Hamlin B.C., et al. Identification of DNA methylation markers for human breast carcinomas using the methylation-sensitive restriction fingerprinting technique. Cancer Res 57 (1997) 1030-1034
49. Wu M., and Ho S.M. PMP24, a gene identified by MSRF, undergoes DNA hypermethylation-associated gene silencing during cancer progression in an LNCaP model. Oncogene 23 (2004) 250-259
50. Lo K.W., Tsang Y.S., Kwong J., et al. Promoter hypermethylation of the EDNRB gene in nasopharyngeal carcinoma. Int J Cancer 98 (2002) 651-655
51. Lv Z., Zhang M., Bi J., et al. Promoter hypermethylation of a novel gene, ZHX2, in hepatocellular carcinoma. Am J Clin Pathol 125 (2006) 740-746
52. Rodic N., Oka M., Hamazaki T., et al. DNA methylation is required for silencing of ant4, an adenine nucleotide translocase selectively expressed in mouse embryonic stem cells and germ cells. Stem Cells 23 (2005) 1314-1323
53. Hatada I., Hayashizaki Y., Hirotsune S., et al. A genomic scanning method for higher organisms using restriction sites as landmarks. Proc Natl Acad Sci USA 88 (1991) 9523-9527
54. Akama T.O., Okazaki Y., Ito M., et al. Restriction landmark genomic scanning (RLGS-M)-based genome-wide scanning of mouse liver tumors for alterations in DNA methylation status. Cancer Res 57 (1997) 3294-3299
55. Yoshikawa H., de la M.S., Nagai H., et al. Chromosomal assignment of human genomic NotI restriction fragments in a two-dimensional electrophoresis profile. Genomics 31 (1996) 28-35
56. Costello J.F., Plass C., and Cavenee W.K. Aberrant methylation of genes in low-grade astrocytomas. Brain Tumor Pathol 17 (2000) 49-56
57. Matsuyama T., Kimura M.T., Koike K., et al. Global methylation screening in the Arabidopsis thaliana and Mus musculus genome: applications of virtual image restriction landmark genomic scanning (Vi-RLGS). Nucleic Acids Res 31 (2003) 4490-4496
58. Rouillard J.M., Erson A.E., Kuick R., et al. Virtual genome scan: a tool for restriction landmark-based scanning of the human genome. Genome Res 11 (2001) 1453-1459
59. Asaga S., Ueda M., Jinno H., et al. Identification of a new breast cancer-related gene by restriction landmark genomic scanning. Anticancer Res 26 (2006) 35-42
60. Wu R., Lin L., Beer D.G., et al. Amplification and overexpression of the L-MYC proto-oncogene in ovarian carcinomas. Am J Pathol 162 (2003) 1603-1610
61. Motiwala T., Ghoshal K., Das A., et al. Suppression of the protein tyrosine phosphatase receptor type O gene (PTPRO) by methylation in hepatocellular carcinomas. Oncogene 22 (2003) 6319-6331
62. Sato K., Fukata H., Kogo Y., et al. Neonatal exposure to diethylstilbestrol alters the expression of DNA methyltransferases and methylation of genomic DNA in the epididymis of mice. Endocr J 53 (2006) 331-337
63. Lisitsyn N., Lisitsyn N., and Wigler M. Cloning the differences between two complex genomes. Science 259 (1993) 946-951
64. Schutte M., da Costa L.T., Moskaluk C.A., et al. Isolation of YAC insert sequences by representational difference analysis. Nucleic Acids Res 23 (1995) 4127-4133
65. Toyota M., Ho C., Ahuja N., et al. Identification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification. Cancer Res 59 (1999) 2307-2312
66. Koinuma K., Kaneda R., Toyota M., et al. Screening for genomic fragments that are methylated specifically in colorectal carcinoma with a methylated MLH1 promoter. Carcinogenesis 26 (2005) 2078-2085
67. Yamada Y., Toyota M., Hirokawa Y., et al. Identification of differentially methylated CpG islands in prostate cancer. Int J Cancer 112 (2004) 840-845
68. Ueki T., Toyota M., Skinner H., et al. Identification and characterization of differentially methylated CpG islands in pancreatic carcinoma. Cancer Res 61 (2001) 8540-8546
69. Asada K., Asada R., Yoshiji H., et al. DNA cytosine methylation profile in various cancer-related genes is altered in cultured rat hepatocyte cell lines as compared with primary hepatocytes. Oncol Rep 15 (2006) 1241-1248
70. Cross S.H., Charlton J.A., Nan X., and Bird A.P. Purification of CpG islands using a methylated DNA binding column. Nat Genet 6 (1994) 236-244
71. Huang T.H., Perry M.R., and Laux D.E. Methylation profiling of CpG islands in human breast cancer cells. Hum Mol Genet 8 (1999) 459-470
72. Yan P.S., Perry M.R., Laux D.E., et al. CpG island arrays: an application toward deciphering epigenetic signatures of breast cancer. Clin Cancer Res 6 (2000) 1432-1438
73. Ahluwalia A., Yan P., Hurteau J.A., et al. DNA methylation and ovarian cancer. I. Analysis of CpG island hypermethylation in human ovarian cancer using differential methylation hybridization. Gynecol Oncol 82 (2001) 261-268
74. Yan P.S., Shi H., Rahmatpanah F., et al. Differential distribution of DNA methylation within the RASSF1A CpG island in breast cancer. Cancer Res 63 (2003) 6178-6186
75. van Doorn R., Zoutman W.H., Dijkman R., et al. Epigenetic profiling of cutaneous T-cell lymphoma: promoter hypermethylation of multiple tumor suppressor genes including BCL7a, PTPRG, and p73. J Clin Oncol 23 (2005) 3886-3896
76. Day J.K., Bauer A.M., DesBordes C., et al. Genistein alters methylation patterns in mice. J Nutr 132 (2002) 2419S-2423S
77. Yan P.S., Wei S.H., and Huang T.H. Differential methylation hybridization using CpG island arrays. Methods Mol Biol 200 (2002) 87-100
78. Craig J.M., Kraus J., and Cremer T. Removal of repetitive sequences from FISH probes using PCR-assisted affinity chromatography. Hum Genet 100 (1997) 472-476
79. Heisler L.E., Torti D., Boutros P.C., et al. CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome. Nucleic Acids Res 33 (2005) 2952-2961
80. Frommer M., McDonald L.E., Millar D.S., et al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci USA 89 (1992) 1827-1831
81. Gitan R.S., Shi H., Chen C.M., et al. Methylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis. Genome Res 12 (2002) 158-164
82. Shi H., Wei S.H., Leu Y.W., et al. Triple analysis of the cancer epigenome: an integrated microarray system for assessing gene expression, DNA methylation, and histone acetylation. Cancer Res 63 (2003) 2164-2171
83. Yang H., Chen C.M., Yan P., et al. The androgen receptor gene is preferentially hypermethylated in follicular non-Hodgkin's lymphomas. Clin Cancer Res 9 (2003) 4034-4042
84. Hou P., Shen J.Y., Ji M.J., et al. Microarray-based method for detecting methylation changes of p16(Ink4a) gene 5′-CpG islands in gastric carcinomas. World J Gastroenterol 10 (2004) 3553-3558
85. Yu Y.P., Paranjpe S., Nelson J., et al. High throughput screening of methylation status of genes in prostate cancer using an oligonucleotide methylation array. Carcinogenesis 26 (2005) 471-479
86. Guo J., Burger M., Nimmrich I., et al. Differential DNA methylation of gene promoters in small B-cell lymphomas. Am J Clin Pathol 124 (2005) 430-439
87. Zhou D., Qiao W., Yang L., and Lu Z. Bisulfite-modified target DNA array for aberrant methylation analysis. Anal Biochem 351 (2006) 26-35
88. Kramer J.A., Pettit S.D., Amin R.P., et al. Overview on the application of transcription profiling using selected nephrotoxicants for toxicology assessment. Environ Health Perspect 112 (2004) 460-464
89. Suzuki H., Gabrielson E., Chen W., et al. A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer. Nat Genet 31 (2002) 141-149
90. Chiba T., Yokosuka O., Arai M., et al. Identification of genes up-regulated by histone deacetylase inhibition with cDNA microarray and exploration of epigenetic alterations on hepatoma cells. J Hepatol 41 (2004) 436-445
91. Dannenberg L.O., and Edenberg H.J. Epigenetics of gene expression in human hepatoma cells: expression profiling the response to inhibition of DNA methylation and histone deacetylation. BMC Genomics 7 (2006) 181
92. Li L., Shi H., Yiannoutsos C., et al. Epigenetic hypothesis tests for methylation and acetylation in a triple microarray system. J Comput Biol 12 (2005) 370-390
93. Holliday R., and Ho T. DNA methylation and epigenetic inheritance. Methods 27 (2002) 179-183
94. Boyle G.M., Martyn A.C., and Parsons P.G. Histone deacetylase inhibitors and malignant melanoma. Pigment Cell Res 18 (2005) 160-166
95. Glaser K.B., Staver M.J., Waring J.F., et al. Gene expression profiling of multiple histone deacetylase (HDAC) inhibitors: defining a common gene set produced by HDAC inhibition in T24 and MDA carcinoma cell lines. Mol Cancer Ther 2 (2003) 151-163
96. Weber M., Davies J.J., Wittig D., et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37 (2005) 853-862
97. Gebhard C., Schwarzfischer L., Pham T.H., et al. Genome-wide profiling of CpG methylation identifies novel targets of aberrant hypermethylation in myeloid leukemia. Cancer Res 66 (2006) 6118-6128
98. Shi H., Guo J., Duff D.J., et al. Discovery of novel epigenetic markers in non-Hodgkin's lymphoma. Carcinogenesis 28 (2007) 60-70
99. Wojdacz T.K., and Hansen L.L. Techniques used in studies of age-related DNA methylation changes. Ann N Y Acad Sci 1067 (2006) 479-487
100. Kuras L. Characterization of protein-DNA association in vivo by chromatin immunoprecipitation. Methods Mol Biol 284 (2004) 147-162
101. Davuluri R.V., Grosse I., and Zhang M.Q. Computational identification of promoters and first exons in the human genome. Nat Genet 29 (2001) 412-417
102. Weinmann A.S., Yan P.S., Oberley M.J., et al. Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev 16 (2002) 235-244
103. Ren B., Robert F., Wyrick J.J., et al. Genome-wide location and function of DNA binding proteins. Science 290 (2000) 2306-2309
104. Ren B., Cam H., Takahashi Y., et al. E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. Genes Dev 16 (2002) 245-256
105. Mao D.Y., Watson J.D., Yan P.S., et al. Analysis of Myc bound loci identified by CpG island arrays shows that Max is essential for Myc-dependent repression. Curr Biol 13 (2003) 882-886
106. Oberley M.J., Tsao J., Yau P., and Farnham P.J. High-throughput screening of chromatin immunoprecipitates using CpG-island microarrays. Methods Enzymol 376 (2004) 315-323
107. Wilson I.M., Davies J.J., Weber M., et al. Epigenomics: mapping the methylome. Cell Cycle 5 (2006) 155-158
108. Karimi M., Johansson S., Stach D., et al. LUMA (LUminometric Methylation Assay)-a high throughput method to the analysis of genomic DNA methylation. Exp Cell Res 312 (2006) 1989-1995
109. Cedar H., Solage A., Glaser G., and Razin A. Direct detection of methylated cytosine in DNA by use of the restriction enzyme MspI. Nucleic Acids Res 6 (1979) 2125-2132
110. Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res 11 (2001) 3-11
111. Tost J., El Abdalaoui H., and Gut I.G. Serial pyrosequencing for quantitative DNA methylation analysis. Biotechniques 40 (2006) 721-2, 724, 726
112. Shiao Y.H., Crawford E.B., Anderson L.M., et al. Allele-specific germ cell epimutation in the spacer promoter of the 45S ribosomal RNA gene after Cr(III) exposure. Toxicol Appl Pharmacol 205 (2005) 290-296
113. Mill J., Dempster E., Caspi A., et al. Evidence for monozygotic twin (MZ) discordance in methylation level at two CpG sites in the promoter region of the catechol-O-methyltransferase (COMT) gene. Am J Med Genet B Neuropsychiatr Genet 141 (2006) 421-425
114. White H.E., Durston V.J., Harvey J.F., and Cross N.C. Quantitative analysis of SNRPN (correction of SRNPN) gene methylation by pyrosequencing as a diagnostic test for Prader-Willi syndrome and Angelman syndrome. Clin Chem 52 (2006) 1005-1013
115. Shaw R.J., Liloglou T., Rogers S.N., et al. Promoter methylation of P16, RARbeta, E-cadherin, cyclin A1 and cytoglobin in oral cancer: quantitative evaluation using pyrosequencing. Br J Cancer 94 (2006) 561-568
116. Xinarianos G., McRonald F.E., Risk J.M., et al. Frequent genetic and epigenetic abnormalities contribute to the deregulation of cytoglobin in non-small cell lung cancer. Hum Mol Genet 15 (2006) 2038-2044
117. Kang S., Kim J., Kim H.B., et al. Methylation of p16INK4a is a non-rare event in cervical intraepithelial neoplasia. Diagn Mol Pathol 15 (2006) 74-82
118. Mirmohammadsadegh A., Marini A., Nambiar S., et al. Epigenetic silencing of the PTEN gene in melanoma. Cancer Res 66 (2006) 6546-6552
119. Smith L.M. The future of DNA sequencing. Science 262 (1993) 530-532
120. Hillenkamp F., Karas M., Beavis R.C., and Chait B.T. Matrix-assisted laser desorption/ionization mass spectrometry of biopolymers. Anal Chem 63 (1991) 1193A-1203A
121. Puapaiboon U., Jai-Nhuknan J., and Cowan J.A. Characterization of a multi-functional metal-mediated nuclease by MALDI-TOF mass spectrometry. Nucleic Acids Res 29 (2001) 3652-3656
122. Fu D.J., Tang K., Braun A., et al. Sequencing exons 5 to 8 of the p53 gene by MALDI-TOF mass spectrometry. Nat Biotechnol 16 (1998) 381-384
123. Schatz P., Dietrich D., and Schuster M. Rapid analysis of CpG methylation patterns using RNase T1 cleavage and MALDI-TOF. Nucleic Acids Res 32 (2004) e167
124. Tost J., Schatz P., Schuster M., et al. Analysis and accurate quantification of CpG methylation by MALDI mass spectrometry. Nucleic Acids Res 31 (2003) e50
125. Sauer S., Lechner D., Berlin K., et al. A novel procedure for efficient genotyping of single nucleotide polymorphisms. Nucleic Acids Res 28 (2000) E13
126. Ehrich M., Nelson M.R., Stanssens P., et al. Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc Natl Acad Sci USA 102 (2005) 15785-15790
127. Fraga M.F., and Esteller M. DNA methylation: a profile of methods and applications. Biotechniques 33 (2002) 632 634, 636-42, 649
128. Ramsahoye B.H. Measurement of genome wide DNA methylation by reversed-phase high-performance liquid chromatography. Methods 27 (2002) 156-161
129. Chakrabarty D., Yu K.W., and Paek K.Y. Detection of DNA methylation changes during somatic embryogenesis of Siberian ginseng (Eleuterococcus senticosus). Plant Sci 165 (2003) 61-68
130. 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 10 (2004) 5087-5093
131. Luo D., Zhang B., Lv L., et al. Methylation of CpG islands of p16 associated with progression of primary gastric carcinomas. Lab Invest 86 (2006) 591-598
132. Tryndyak V.P., Muskhelishvili L., Kovalchuk O., et al. Effect of long-term tamoxifen exposure on genotoxic and epigenetic changes in rat liver: implications for tamoxifen-induced hepatocarcinogenesis. Carcinogenesis 27 (2006) 1713-1720
133. Song L., James S.R., Kazim L., and Karpf A.R. Specific method for the determination of genomic DNA methylation by liquid chromatography-electrospray ionization tandem mass spectrometry. Anal Chem 77 (2005) 504-510
134. Gama-Sosa M.A., Midgett R.M., Slagel V.A., et al. Tissue-specific differences in DNA methylation in various mammals. Biochim Biophys Acta 740 (1983) 212-219
135. Fisher D.H., and Giese R.W. Determination of 5-methylcytosine in DNA by gas chromatography-electron-capture detection. J Chromatogr 452 (1988) 51-60
136. Leonard S.A., Wong S.C., and Nyce J.W. Quantitation of 5-methylcytosine by one-dimensional high-performance thin-layer chromatography. J Chromatogr 645 (1993) 189-192
137. Cortacero-Ramirez S., Segura-Carretero A., Cruces-Blanco C., et al. Simultaneous determination of multiple constituents in real beer samples of different origins by capillary zone electrophoresis. Anal Bioanal Chem 380 (2004) 831-837
138. Zhu X., Leav I., Leung Y.K., et al. Dynamic regulation of estrogen receptor-beta expression by DNA methylation during prostate cancer development and metastasis. Am J Pathol 164 (2004) 2003-2012
139. Herman J.G., Graff J.R., Myohanen S., et al. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci USA 93 (1996) 9821-9826
140. Derks S., Lentjes M.H., Hellebrekers D.M., et al. Methylation-specific PCR unraveled. Cell Oncol 26 (2004) 291-299
141. Xiong Z., and Laird P.W. COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res 25 (1997) 2532-2534
142. Bian Y.S., Yan P., Osterheld M.C., et al. Promoter methylation analysis on microdissected paraffin-embedded tissues using bisulfite treatment and PCR-SSCP. Biotechniques 30 (2001) 66-72
143. Clement G., Bosman F.T., Fontolliet C., and Benhattar J. Monoallelic methylation of the APC promoter is altered in normal gastric mucosa associated with neoplastic lesions. Cancer Res 64 (2004) 6867-6873
144. Eads C.A., Danenberg K.D., Kawakami K., et al. MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res 28 (2000) E32
145. Ogino S., Kawasaki T., Brahmandam M., et al. Precision and performance characteristics of bisulfite conversion and real-time PCR (MethyLight) for quantitative DNA methylation analysis. J Mol Diagn 8 (2006) 209-217