Gardiner-Garden M, Frommer M: CpG islands in vertebrate genomes. J Mol Biol. 1987, 196: 261-282. 10.1016/0022-2836(87)90689-9.
Article
CAS
PubMed
Google Scholar
Clark SJ, Melki J: DNA methylation and gene silencing in cancer: which is the guilty party?. Oncogene. 2002, 21: 5380-5387. 10.1038/sj.onc.1205598.
Article
CAS
PubMed
Google Scholar
Li E, Bestor TH, Jaenisch R: Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell. 1992, 69: 915-926. 10.1016/0092-8674(92)90611-F.
Article
CAS
PubMed
Google Scholar
Li E, Beard C, Jaenisch R: Role for DNA methylation in genomic imprinting. Nature. 1993, 366: 362-365. 10.1038/366362a0.
Article
CAS
PubMed
Google Scholar
Migeon BR: Concerning the role of X-inactivation and DNA methylation in fragile X syndrome. Am J Med Genet. 1992, 43: 182-187. 10.1002/ajmg.1320430145.
Article
Google Scholar
Feinberg AP, Tycko B: The history of cancer epigenetics. Nat Rev Cancer. 2004, 4: 143-153. 10.1038/nrc1279.
Article
CAS
PubMed
Google Scholar
Hu M, Yao J, Cai L, Bachman KE, Brûle van den F, Velculescu V, Polyak K: Distinct epigenetic changes in the stromal cells of breast cancers. Nat Genet. 2005, 37: 899-905. 10.1038/ng1596.
Article
CAS
PubMed
Google Scholar
Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL, Schübeler D: Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet. 2005, 37: 853-862. 10.1038/ng1598.
Article
CAS
PubMed
Google Scholar
Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M, Ji H, Potash JB, Sabunciyan S, Feinberg AP: The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet. 2009, 41: 178-186. 10.1038/ng.298.
Article
CAS
PubMed Central
PubMed
Google Scholar
Weber M, Hellmann I, Stadler MB, Ramos L, Pääbo S, Rebhan M, Schübeler D: Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet. 2007, 39: 457-466. 10.1038/ng1990.
Article
CAS
PubMed
Google Scholar
Herman JG, Baylin SB: Gene silencing in cancer in association with promoter hypermethylation. N Engl J Med. 2003, 349: 2042-2054. 10.1056/NEJMra023075.
Article
CAS
PubMed
Google Scholar
Esteller M: Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet. 2007, 8: 286-298. 10.1038/nrg2005.
Article
CAS
PubMed
Google Scholar
Komashko VM, Acevedo LG, Squazzo SL, Iyengar SS, Rabinovich A, O'Geen H, Green R, Farnham PJ: Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells. Genome Res. 2008, 18: 521-532. 10.1101/gr.074609.107.
Article
CAS
PubMed Central
PubMed
Google Scholar
Pomraning KR, Smith KM, Freitag M: Genome-wide high throughput analysis of DNA methylation in eukaryotes. Methods. 2009, 47: 142-150. 10.1016/j.ymeth.2008.09.022.
Article
CAS
PubMed
Google Scholar
Pelizzola M, Koga Y, Urban AE, Krauthammer M, Weissman S, Halaban R, Molinaro AM: MEDME: an experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment. Genome Res. 2008, 18: 1652-1659. 10.1101/gr.080721.108.
Article
CAS
PubMed Central
PubMed
Google Scholar
Irizarry RA, Ladd-Acosta C, Carvalho B, Wu H, Brandenburg SA, Jeddeloh JA, Wen B, Feinberg AP: Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res. 2008, 18: 780-790. 10.1101/gr.7301508.
Article
CAS
PubMed Central
PubMed
Google Scholar
Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Briney E, Hubbard TJ, Drubin R, Tavaré S, Beck S: A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol. 2008, 26: 779-785. 10.1038/nbt1414.
Article
CAS
PubMed Central
PubMed
Google Scholar
Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR: Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 2008, 133: 523-536. 10.1016/j.cell.2008.03.029.
Article
CAS
PubMed Central
PubMed
Google Scholar
Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE: Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008, 452: 215-219. 10.1038/nature06745.
Article
CAS
PubMed Central
PubMed
Google Scholar
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: Human DNA methylomes at base resolution show widewpread epigenomic differences. Nature. 2009, 462: 315-322. 10.1038/nature08514.
Article
CAS
PubMed Central
PubMed
Google Scholar
Wu GJ, Sinclair CS, Paape J, Ingle JN, Roche PC, James CD, Couch FJ: 17q23 amplifications in breast cancer involve the PAT1, RAD51C, PS6K, and SIGma1B genes. Cancer Res. 2000, 60: 5371-5375.
CAS
PubMed
Google Scholar
Bärlund M, Monni O, Weaver JD, Kauraniemi P, Sauter G, Heiskanen M, Kallioniemi OP, Kallioniemi A: Cloning of BCAS3 (17q23) and BCAS4 (20q13) genes that undergo amplification, overexpression, and fusion in breast cancer. Genes Ghromosomes Cancer. 2002, 35: 311-317. 10.1002/gcc.10121.
Article
Google Scholar
Jackson K, Yu MC, Arakawa K, Fiala E, Youn B, Fiegl H, Müller-Holzner E, Widschwendter M, Ehrlich M: DNA hypomethylation is prevalent even in low-grade breast cancers. Cancer Biol Ther. 2004, 3: 1225-1231.
Article
CAS
PubMed
Google Scholar
Tommasi S, Karm DL, Wu X, Yen Y, Pfeifer GP: Methylation of homeobox genes is a frequent and early epigenetic event in breast cancer. Breast Cancer Res. 2009, 11: R14-10.1186/bcr2233.
Article
PubMed Central
PubMed
Google Scholar
Laux DE, Curran EM, Welshons WV, Lubahn DB, Huang TH: Hypermethylation of the Wilms' tumor suppressor gene CpG island in human breast carcinomas. Breast Cancer Res. 1999, 56: 35-43. 10.1023/A:1006222803788.
Article
CAS
Google Scholar
Novak P, Jensen T, Oshiro MM, Wozniak RJ, Nouzova M, Watts GS, Klimecki WT, Kim C, Futscher BW: Epigenetic inactivation of the HOXA gene cluster in breast cancer. Cancer Res. 2006, 66: 10664-10670. 10.1158/0008-5472.CAN-06-2761.
Article
CAS
PubMed
Google Scholar
Hoeflich KP, O'Brien C, Boyd Z, Cavet G, Guerrero S, Jung K, Januario T, Savage H, Punnoose E, Truong T, Zhou W, Berry L, Murray L, Amler L, Belvin M, Friedman LS, Lackner MR: In vivo antitumor activity of MEK and phosphatidylinositol 3-kinase inhibitors in basal-like breast cancer models. Clin Cancer Res. 2009, 15: 4649-64. 10.1158/1078-0432.CCR-09-0317.
Article
CAS
PubMed
Google Scholar
Saxonov S, Berg P, Brutlag DL: A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci USA. 2006, 103: 1412-1417. 10.1073/pnas.0510310103.
Article
CAS
PubMed Central
PubMed
Google Scholar
Lacroix M, Leclercq G: Relevance of breast cancer cell lines as models for breast tumours: an update. Breast Cancer Res Treat. 2004, 83: 249-289. 10.1023/B:BREA.0000014042.54925.cc.
Article
CAS
PubMed
Google Scholar
Lombaerts M, van Wezel T, Philippo K, Dierssen JW, Zimmerman RM, Oosting J, van Eijk R, Eilers PH, Water van de B, Cornelisse CJ, Cleton-Jansen AM: E-cadherin transcriptional downregulation by promoter methylation but not mutation is related to epithelial-to-mesenchymal transition in breast cancer cell lines. Br J Cancer. 2006, 94: 661-671.
CAS
PubMed Central
PubMed
Google Scholar
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: Epithelial progeny of estrogen-exposed breast progenitor cells display a cancer-like methylome. Cancer Res. 2008, 68: 1786-1796. 10.1158/0008-5472.CAN-07-5547.
Article
CAS
PubMed Central
PubMed
Google Scholar
Dumont N, Wilson MB, Crawford YG, Reynolds PA, Sigaroudinia M, Tlsty TD: Sustained induction of epithelial to mesenchymal transition activates DNA methylation of genes silenced in basal-like breast cancers. Proc Natl Acad Sci USA. 2008, 105: 14867-14872. 10.1073/pnas.0807146105.
Article
CAS
PubMed Central
PubMed
Google Scholar
Jones PA: The DNA methylation paradox. Trends Genet. 1999, 15: 34-37. 10.1016/S0168-9525(98)01636-9.
Article
CAS
PubMed
Google Scholar
Burk U, Schubert J, Wellner U, Schmalhofer O, Vincan E, Spaderna S, Brabletz T: A reciprocal repression between ZEB1 and members of the miR-200 family promotes EMT and invasion in cancer cells. EMBO Rep. 2008, 9: 582-589. 10.1038/embor.2008.74.
Article
CAS
PubMed Central
PubMed
Google Scholar