Methylation analysis by DNA immunoprecipitation

Journal of Cellular Physiology

Volumn 222, Issue 3, 2010, Pages 522-531

  Thu, Kelsie L ^a   Pikor, Larissa A ^a   Kennett, Jennifer Y ^a   Alvarez, Carlos E ^b   Lam, Wan L ^a  

^a BRITISH COLUMBIA CANCER RESEARCH CENTRE   (Canada)

^b THE OHIO STATE UNIVERSITY COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

BIOINFORMATICS; CPG ISLAND; DNA DETERMINATION; DNA METHYLATION; EPIGENETICS; GENOME; IMMUNOPRECIPITATION; INFORMATION; INFORMATION PROCESSING; METHODOLOGY; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SHORT SURVEY;

COMPUTATIONAL BIOLOGY; CPG ISLANDS; DNA; DNA METHYLATION; GENE EXPRESSION REGULATION; GENOMICS; HUMANS; IMMUNOPRECIPITATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; PROMOTER REGIONS, GENETIC; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA;

EID: 73649115248     PISSN: 00219541     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcp.22009     Document Type: Short Survey

References (106)

1. Adorjan P, Distler J, Lipscher E, Model F, Muller J, Pelet C, Braun A, Florl AR, Gutig D, Grabs G, Howe A, Kursar M, Lesche R, Leu E, Lewin A, Maier S, Muller V,Otto T, Scholz C, Schulz WA, Seifert HH, Schwope I, Ziebarth H, Berlin K, Piepenbrock C, Olek A. 2002. Tumour class prediction and discovery by microarray-based DNA methylation analysis. Nucleic Acids Res 30:e21.
2. Alkan C, Kidd JM,Marques-BonetT, Aksay G, Antonacci F, Hormozdiari F, Kitzman JO, Baker C, Malig M, Mutlu O, Sahinalp SC, Gibbs RA, Eichler EE. 2009. Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet 41:1061-1067.
3. Ansorge WJ. 2009. Next-generation DNA sequencing techniques. Nat Biotechnol 25:195-203.
4. Bailey VJ, Easwaran H, Zhang Y, Griffiths E, Belinsky SA, Herman JG, Baylin SB, Carraway HE, Wang TH. 2009. MS-qFRET: A quantum dot-based method for analysis of DNA methylation. Genome Res 19:1455-1461.
5. Ball MP, Li JB, Gao Y, Lee JH, LeProust EM, Park IH, Xie B, Daley GQ, Church GM. 2009. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol 27:361-368.
6. Beck S, Rakyan VK. 2008. The methylome: Approaches for globalDNAmethylation profiling. Trends Genet 24:231-237.
7. Belinsky SA, Liechty KC, Gentry FD, Wolf HJ, Rogers J, Vu K, Haney J, Kennedy TC, Hirsch FR, Miller Y, Franklin WA, Herman JG, Baylin SB, Bunn PA, Byers T. 2006. Promoter hypermethylation of multiple genes in sputum precedes lung cancer incidence in a high-risk cohort. Cancer Res 66:3338-3344.
8. Belinsky SA, Schiller JH, Stidley CA. 2008. DNA methylation biomarkers to assess therapy and chemoprevention for non-small cell lung cancer. Nutr Rev 66:S24-S26.
9. Bentley DR. 2006. Whole-genome re-sequencing. Curr Opin Genet Dev 16:545-552.
10. Berger SL, Kouzarides T, Shiekhattar R, Shilatifard A. 2009. An operational definition of epigenetics. Genes Dev 23:781-783.
11. Berman BP, Weisenberger DJ, Laird PW. 2009. Locking in on the human methylome. Nat Biotechnol 27:341-342.
12. Bernstein BE, Meissner A, Lander ES. 2007. The mammalian epigenome. Cell 128:669-681.
13. BibikovaM, Fan JB. 2009. GoldenGate assay forDNAmethylation profiling. Methods Mol Biol 507:149-163.
14. Bibikova M, Lin Z, Zhou L, Chudin E, Garcia EW, Wu B, Doucet D, Thomas NJ, Wang Y, Vollmer E, Goldmann T, Seifart C, Jiang W, Barker DL, Chee MS, Floros J, Fan JB. 2006. High-throughput DNA methylation profiling using universal bead arrays. Genome Res 16:383-393.
15. Bird AP, Southern EM. 1978. Use of restriction enzymes to study eukaryotic DNA methylation: I. The methylation pattern in ribosomal DNA from Xenopus laevis. J Mol Biol 118:27-47.
16. Bird A, Taggart M, Frommer M, MillerOJ, Macleod D. 1985. A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Cell 40:91-99.
17. Boks MP, Derks EM, Weisenberger DJ, Strengman E, Janson E, Sommer IE, Kahn RS, Ophoff RA. 2009. The relationship ofDNAmethylationwith age, gender and genotype in twins and healthy controls. PLoS ONE 4:e6767.
18. Brown CJ, Lafreniere RG, Powers VE, Sebastio G, Ballabio A, Pettigrew AL, Ledbetter DH, Levy E, Craig IW,Willard HF. 1991. Localization of the Xinactivation centre on the human X chromosome in Xq13. Nature 349:82-84.
19. Brunner AL, Johnson DS, Kim SW, Valouev A, Reddy TE, Neff NF, Anton E, Medina C, Nguyen L, Chiao E, Oyolu CB, Schroth GP, Absher DM, Baker JC, Myers RM. 2009. Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res 19:1044-1056.
20. Buller A, Pandya A, Jackson-Cook C, Bodurtha J, Tekin M, Wilkinson DS, Garrett CT, Ferreira-Gonzalez A. 2000. Validation of a multiplex methylation-sensitive PCR assay for the diagnosis of Prader-Willi and Angelman's syndromes. Mol Diagn 5:239-243.
21. Byun HM, Siegmund KD, Pan F, Weisenberger DJ, Kanel G, Laird PW, Yang AS. 2009. Epigenetic profiling of somatic tissues from human autopsy specimens identifies tissue- and individual-specific DNA methylation patterns. Hum Mol Genet 18:4808-4817.
22. Callinan PA, Feinberg AP. 2006. The emerging science of epigenomics. Hum Mol Genet 15:R95-R101.
23. Chang SC, Tucker T, Thorogood NP, Brown CJ. 2006. Mechanisms of X-chromosome inactivation. Front Biosci 11:852-866.
24. Chari R, Coe BP, Wedseltoft C, Benetti M, Wilson IM, Vucic EA, MacAulay C, Ng RT, Lam WL. 2008. SIGMA2: A system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes. BMC Bioinformatics 9:422.
25. Cheng AS, Culhane AC, Chan MW, Venkataramu CR, Ehrich M, Nasir A, Rodriguez BA, Liu J, Yan PS, Quackenbush J, Nephew KP, Yeatman TJ, Huang TH. 2008. Epithelial progeny of estrogen-exposed breast progenitor cells display a cancer-like methylome. Cancer Res 68:1786-1796.
26. Chi B, deLeeuw RJ, Coe BP, Ng RT, MacAulay C, LamWL. 2008. MD-SeeGH: A platform for integrative analysis of multi-dimensional genomic data. BMC Bioinformatics 9:243.
27. Coe BP, Ylstra B, Carvalho B, Meijer GA, Macaulay C, Lam WL. 2007. Resolving the resolution of array CGH. Genomics 89:647-653.
28. Coffee B, Keith K, Albizua I,Malone T, Mowrey J, Sherman SL, Warren ST. 2009. Incidence of fragile X syndrome by newborn screening for methylated FMR1 DNA. Am J Hum Genet 85:503-514.
29. Costello JF, Fruhwald MC, Smiraglia DJ, Rush LJ, Robertson GP, GaoX,Wright FA, Feramisco JD, Peltomaki P, Lang JC, Schuller DE, Yu L, Bloomfield CD, Caligiuri MA, Yates A, Nishikawa R, Su Huang H, Petrelli NJ, Zhang X, O'Dorisio MS, Held WA, Cavenee WK, Plass C. 2000. Aberrant CpG-island methylation has non-random and tumour-typespecific patterns. Nat Genet 24:132-138.
30. Deng J, Shoemaker R, Xie B, Gore A, LeProust EM, Antosiewicz-Bourget J, Egli D, Maherali N, Park IH, Yu J, Daley GQ, Eggan K, Hochedlinger K, Thomson J, Wang W, Gao Y, Zhang K. 2009. Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotechnol 27:353-360.
31. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Graf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Backdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavare S, Beck S. 2008. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol 26:779-785.
32. Eads CA, Danenberg KD, Kawakami K, Saltz LB, BlakeC, Shibata D, Danenberg PV, Laird PW. 2000. MethyLight: A high-throughput assay to measure DNA methylation. Nucleic Acids Res 28:E32.
33. Eckhardt F, Beck S, Gut IG, Berlin K. 2004. Future potential of the Human Epigenome Project. Expert Rev Mol Diagn 4:609-618.
34. Ellis L, Atadja PW, Johnstone RW. 2009. Epigenetics in cancer: Targeting chromatin modifications. Mol Cancer Ther 8:1409-1420.
35. Esteller M. 2005. Aberrant DNA methylation as a cancer-inducing mechanism. Annu Rev Pharmacol Toxicol 45:629-656.
36. Esteller M. 2007. Epigenetic gene silencing in cancer: The DNA hypermethylome. Hum Mol Genet 16:R50-R59.
37. Feinberg AP, Vogelstein B. 1983. Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301:89-92.
38. Fraga MF, Ballestar E, Paz MF, Ropero S, Setien F, Ballestar ML, Heine-Suner D, Cigudosa JC, Urioste M, Benitez J, Boix-Chornet M, Sanchez-Aguilera A, Ling C, Carlsson E, Poulsen P, Vaag A, Stephan Z, Spector TD, Wu YZ, Plass C, Esteller M. 2005. Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci USA 102:10604-10609.
39. Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, Paul CL. 1992. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci USA 89:1827-1831.
40. Gagneur J, Sinha H, Perocchi F, Bourgon R, Huber W, Steinmetz LM. 2009. Genome-wide allele- and strand-specific expression profiling. Mol Syst Biol 5:274.
41. Gebhard C, Schwarzfischer L, Pham TH, Schilling E, Klug M, Andreesen R, Rehli M. 2006. Genome-wide profiling of CpG methylation identifies novel targets of aberrant hypermethylation in myeloid leukemia. Cancer Res 66:6118-6128.
42. Gimelbrant A, Hutchinson JN, Thompson BR, Chess A. 2007. Widespread monoallelic expression on human autosomes. Science 318:1136-1140.
43. Gitan RS, Shi H, Chen CM, Yan PS, Huang TH. 2002. Methylation-specific oligonucleotide microarray: A new potential for high-throughput methylation analysis. Genome Res 12:158-164.
44. Graff JR, Herman JG, Myohanen S, Baylin SB, Vertino PM. 1997. Mapping patterns of CpG island methylation in normal and neoplastic cells implicates both upstream and downstream regions in de novo methylation. J Biol Chem 272:22322-22329.
45. Hatada I, Hayashizaki Y, Hirotsune S, Komatsubara H, Mukai T. 1991. A genomic scanning method for higher organisms using restriction sites as landmarks. Proc Natl Acad Sci USA 88:9523-9527.
46. Heisler LE, Torti D, Boutros PC, Watson J, Chan C, Winegarden N, Takahashi M, Yau P, Huang TH, Farnham PJ, Jurisica I, Woodgett JR, Bremner R, Penn LZ, Der SD. 2005. CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome. Nucleic Acids Res 33:2952-2961.
47. Hellman A, Chess A. 2007. Gene body-specific methylation on the active X chromosome. Science 315:1141-1143.
48. Herman JG, Graff JR, Myohanen S, Nelkin BD, Baylin SB. 1996. Methylation-specific PCR: A novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci USA 93:9821-9826.
49. Horard B, Eymery A, Fourel G, Vassetzky N, Puechberty J, Roizes G, Lebrigand K, Barbry P, LaugraudA,Gautier C, Simon EB, Devaux F,Magdinier F, Vourc'hC,Gilson E. 2009.Global analysis of DNA methylation and transcription of human repetitive sequences. Epigenetics 4:339-350.
50. Huang TH, Perry MR, Laux DE. 1999. Methylation profiling of CpG islands in human breast cancer cells. Hum Mol Genet 8:459-470.
51. Irizarry RA, Ladd-Acosta C, Carvalho B, Wu H, Brandenburg SA, Jeddeloh JA, Wen B, Feinberg AP. 2008. Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res 18:780-790.
52. Ishkanian AS,Malloff CA, Watson SK, DeLeeuw RJ, Chi B, Coe BP, Snijders A, Albertson DG, Pinkel D, Marra MA, Ling V, MacAulay C, Lam WL. 2004. A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet 36:299-303.
53. Jacinto FV, Ballestar E, Ropero S, Esteller M. 2007. Discovery of epigenetically silenced genes by methylated DNA immunoprecipitation in colon cancer cells. Cancer Res 67:11481-11486.
54. Jacinto FV, Ballestar E, Esteller M. 2008. Methyl-DNA immunoprecipitation (MeDIP): Hunting down the DNA methylome. Biotechniques 44:35 37, 39 passim.
55. Jaenisch R, Bird A. 2003. Epigenetic regulation of gene expression: How the genome integrates intrinsic and environmental signals. Nat Genet 33:245-254.
56. Jiang H, Wong WH. 2008. SeqMap: Mapping massive amount of oligonucleotides to the genome. Bioinformatics 24:2395-2396.
57. Jones PA. 2002. DNA methylation and cancer. Oncogene 21:5358-5360.
58. Jones PA, Baylin SB. 2002. The fundamental role of epigenetic events in cancer. Nat Rev Genet 3:415-428.
59. Kent WJ. 2002. BLAT-The BLAST-like alignment tool. Genome Res 12:656-664.
60. Keshet I, Schlesinger Y, Farkash S, Rand E, Hecht M, Segal E, Pikarski E, Young RA, NiveleauA, Cedar H, Simon I. 2006. Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat Genet 38:149-153.
61. Khojasteh M, Lam WL, Ward RK, MacAulay C. 2005. A stepwise framework for the normalization of array CGH data. BMC Bioinformatics 6:274.
62. Khulan B, Thompson RF, Ye K, Fazzari MJ, SuzukiM, Stasiek E, Figueroa ME,Glass JL, Chen Q, Montagna C, Hatchwell E, Selzer RR, Richmond TA, Green RD, Melnick A, Greally JM. 2006. Comparative isoschizomer profiling of cytosine methylation: The HELP assay. Genome Res 16:1046-1055.
63. Kim YJ, Teletia N, Ruotti V, Maher CA, Chinnaiyan AM, Stewart R, Thomson JA, Patel JM. 2009. ProbeMatch: Rapid alignment of oligonucleotides to genome allowing both gaps and mismatches. Bioinformatics 25:1424-1425.
64. Korshunova Y, Maloney RK, Lakey N, Citek RW, Bacher B, Budiman A, Ordway JM, McCombie WR, Leon J, Jeddeloh JA, McPherson JD. 2008. Massively parallel bisulphite pyrosequencing reveals the molecular complexity of breast cancer-associated cytosine-methylation patterns obtained from tissue and serum DNA. Genome Res 18:19-29.
65. Kosaki K, McGinniss MJ, Veraksa AN, McGinnis WJ, Jones KL. 1997. Prader-Willi and Angelman syndromes: Diagnosis with a bisulfite-treated methylation-specific PCRmethod. Am J Med Genet 73:308-313.
66. Kuo KC, McCune RA, Gehrke CW, Midgett R, EhrlichM. 1980. Quantitative reversed-phase high performance liquid chromatographic determination of major and modified deoxyribonucleosides in DNA. Nucleic Acids Res 8:4763-4776.
67. Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
68. Li H, Ruan J, Durbin R. 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18:1851-1858.
69. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR. 2009. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462:315-322.
70. Lockwood WW, Chari R, Chi B, Lam WL. 2006. Recent advances in array comparative genomic hybridization technologies and their applications in human genetics. Eur J Hum Genet 14:139-148.
71. Magdalena J, Goval JJ. 2009. Methyl DNA immunoprecipitation. Methods Mol Biol 567:237-247.
72. Mardis ER. 2008. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387-402.
73. Nosaka K, Maeda M, Tamiya S, Sakai T, Mitsuya H, Matsuoka M. 2000. Increasing methylation of the CDKN2A gene is associated with the progression of adult T-cell leukemia. Cancer Res 60:1043-1048.
74. Odom DT, Zizlsperger N, Gordon DB, Bell GW, Rinaldi NJ, Murray HL, Volkert TL, Schreiber J, Rolfe PA, Gifford DK, Fraenkel E, BellGI, Young RA. 2004. Control of pancreas and liver gene expression by HNF transcription factors. Science 303:1378-1381.
75. O'Riain C, O'Shea DM, Yang Y, Le Dieu R, Gribben JG, Summers K, Yeboah-Afari J, Bhaw-Rosun L , Fleischmann C, Mein CA, Crook T, Smith P, Kelly G, Rosenwald A, OttG,Campo E, Rimsza LM, Smeland EB, Chan WC, Johnson N, Gascoyne RD, Reimer S, Braziel RM, Wright GW, Staudt LM, Lister TA, Fitzgibbon J. 2009. Array-based DNA methylation profiling in follicular lymphoma. Leukemia 23:1858-1866.
76. Palmisano WA, Divine KK, Saccomanno G, Gilliland FD, Baylin SB, Herman JG, Belinsky SA. 2000. Predicting lung cancer by detecting aberrant promoter methylation in sputum. Cancer Res 60:5954-5958.
77. Park PJ. 2009. ChIP-seq: Advantages and challenges of a maturing technology. Nat Rev Genet 10:669-680.
78. Pelizzola M, Koga Y,Urban AE, Krauthammer M, Weissman S, Halaban R, Molinaro AM. 2008. MEDME: An experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment. Genome Res 18:1652-1659.
79. Pfeifer GP, Rauch TA. 2009. DNA methylation patterns in lung carcinomas. Semin Cancer Biol 19:181-187.
80. Quackenbush J. 2002. Microarray data normalization and transformation. Nat Genet 32:496-501.
81. Rakyan VK, Down TA, Thorne NP, Flicek P, Kulesha E, Graf S, Tomazou EM, Backdahl L, Johnson N, Herberth M, Howe KL, Jackson DK, Miretti MM, Fiegler H, Marioni JC, Birney E, Hubbard TJ,Carter NP, Tavare S, Beck S. 2008. An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res 18:1518-1529.
82. Rauch T, Pfeifer GP. 2005. Methylated-CpG island recovery assay: A new technique for the rapid detection of methylated-CpG islands in cancer. Lab Invest 85:1172-1180.
83. Rauch TA, Wu X, Zhong X, Riggs AD, Pfeifer GP. 2009. A human B cell methylome at 100-base pair resolution. Proc Natl Acad Sci USA 106:671-678.
84. Schilling E, Rehli M. 2007. Global, comparative analysis of tissue-specific promoter CpG methylation. Genomics 90:314-323.
85. Selker EU, Tountas NA, Cross SH, Margolin BS, Murphy JG, Bird AP, Freitag M. 2003. The methylated component of the Neurospora crassa genome. Nature 422:893-897.
86. Serre D, Gurd S, Ge B, Sladek R, Sinnett D, Harmsen E, Bibikova M, Chudin E, Barker DL, Dickinson T, Fan JB, Hudson TJ. 2008. Differential allelic expression in the human genome: Arobust approach to identify genetic and epigenetic cis-actingmechanisms regulating gene expression. PLoS Genet 4:e1000006.
87. Shames DS, Girard L, Gao B, Sato M, Lewis CM, Shivapurkar N, Jiang A, Perou CM, Kim YH, Pollack JR, Fong KM, Lam CL, Wong M, Shyr Y, Nanda R, Olopade OI, Gerald W, Euhus DM, Shay JW, Gazdar AF, Minna JD. 2006. A genome-wide screen for promoter methylation in lung cancer identifies novel methylation markers for multiple malignancies. PLoS Med 3:e486.
88. Shen Y, Fouse SD, Fan G. 2009. Genome-Wide DNA Methylation Profiling: The mDIP-Chip Technology. Methods Mol Biol 568:203-216.
89. Shivapurkar N, Sherman ME, Stastny V, Echebiri C, Rader JS, Nayar R, Bonfiglio TA, Gazdar AF, Wang SS. 2007. Evaluation of candidate methylation markers to detect cervical neoplasia. Gynecol Oncol 107:549-553.
90. Siegfried Z, Cedar H. 1997. DNA methylation: A molecular lock. Curr Biol 7:R305-R307.
91. Suzuki MM, Bird A. 2008. DNA methylation landscapes: Provocative insights from epigenomics. Nat Rev Genet 9:465-476.
92. Suzuki H, Gabrielson E, ChenW,Anbazhagan R, van EngelandM, Weijenberg MP, Herman JG, Baylin SB. 2002. A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer. Nat Genet 31:141-149.
93. Tan AC, Jimeno A, Lin SH, Wheelhouse J, Chan F, Solomon A, Rajeshkumar NV, Rubio-Viqueira B, Hidalgo M. 2009. Characterizing DNA methylation patterns in pancreatic cancer genome. Mol Oncol 3:425-438.
94. Taylor KH, Kramer RS,Davis JW, Guo J, DuffDJ, Xu D, CaldwellCW, ShiH. 2007. Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Res 67:8511-8518.
95. Thu KL, Vucic EA, Kennett JY, Heryet C, Brown CJ, Lam WL,Wilson IM. 2009. Methylated DNA immunoprecipitation. J Vis Exp 23.
96. Voelkerding KV, Dames SA, Durtschi JD. 2009. Next-generation sequencing: From basic research to diagnostics. Clin Chem 55:641-658.
97. Vucic EA, Wilson IM, Campbell JM, Lam WL. 2009. Methylation Analysis by DNA Immunoprecipitation (MeDIP). Methods Mol Biol 556:141-153.
98. Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL, Schubeler D. 2005. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37:853-862.
99. Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, Rebhan M, Schubeler D. 2007. Distribution, silencing potential and evolutionary impact of promoterDNAmethylation in the human genome. Nat Genet 39:457-466.
100. Wen B, Wu H, Bjornsson H, Green RD, Irizarry R, Feinberg AP. 2008. Overlapping euchromatin/heterochromatin-associated marks are enriched in imprinted gene regions and predict allele-specific modification. Genome Res 18:1806-1813.
101. Wheelan SJ, Martinez Murillo F, Boeke JD. 2008. The incredible shrinking world of DNA microarrays. Mol Biosyst 4:726-732.
102. Wilson IM, Davies JJ, Weber M, Brown CJ, Alvarez CE, MacAulay C, Schubeler D, LamWL. 2006. Epigenomics: Mapping the methylome. Cell Cycle 5:155-158.
103. Xiong Z, Laird PW. 1997. COBRA: A sensitive and quantitative DNA methylation assay. Nucleic Acids Res 25:2532-2534.
104. Yamashita S, Hosoya K, Gyobu K, Takeshima H, Ushijima T. 2009. Development of a novel output value for quantitative assessment in methylated DNA immunoprecipitation-CpG island microarray analysis. DNA Res 10:275-286.
105. Yan PS, Chen CM, Shi H, Rahmatpanah F, Wei SH, CaldwellCW, Huang TH. 2001. Dissecting complex epigenetic alterations in breast cancer using CpG island microarrays. Cancer Res 61:8375-8380.
106. Zilberman D, Henikoff S. 2007. Genome-wide analysis of DNA methylation patterns. Development 134:3959-3965.