A DNA microarray-based methylation-sensitive (MS)-AFLP hybridization method for genetic and epigenetic analyses

Molecular Genetics and Genomics

Volumn 271, Issue 6, 2004, Pages 678-686

  Yamamoto, F ^a   Yamamoto, M ^a  

^a BURNHAM INSTITUTE   (United States)

Author keywords

Copy number; DNA methylation; DNA Microarray MS AFLP; Methylation sensitive amplified fragment length polymorphism (MS AFLP)

Indexed keywords

GENOMIC DNA;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; BREAST CARCINOMA; CANCER CELL CULTURE; DNA FINGERPRINTING; DNA HYBRIDIZATION; DNA METHYLATION; DNA MICROARRAY; DNA PROBE; EPIGENETICS; FEASIBILITY STUDY; GEL ELECTROPHORESIS; GENETIC ANALYSIS; GENETIC SUSCEPTIBILITY; HUMAN; METHYLATION SENSITIVE AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; PRIORITY JOURNAL; PROSTATE CANCER; SOUTHERN BLOTTING;

EID: 4043086483     PISSN: 16174615     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00438-004-1017-5     Document Type: Article

References (35)

1. Albertson DG, Ylstra B, Segraves R, Collins C, Dairkee SH, Kowbel D, Kuo WL, Gray JW, Pinkel D (2000) Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogene. Nat Genet 25:144-146
2. Baylin S, Bestor TH (2002) Altered methylation patterns in cancer cell genomes: cause or consequence? Cancer Cell 1:299-305
3. Bestor T, Laudano A, Mattaliano R, Ingram V (1988) Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells. The carboxyl-terminal domain of the mammalian enzymes is related to bacterial restriction methyltransferases. J Mol Biol 203:971-983
4. Bird A (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16:6-21
5. 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
6. Clark SJ, Harrison J, Paul CL, Frommer M (1994) High sensitivity mapping of methylated cytosines. Nucleic Acids Res 22:2990-2997
7. Feinberg AP, Vogelstein B (1983) Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301:89-92
8. 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
9. Hansen RS, Wijmenga C, Luo P, Stanek AM, Canfield TK, Weemaes CM, Gartler SM (1999) The DNMT3B DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome. Proc Natl Acad Sci USA 96:14412-14417
10. Hayashizaki Y, Shibata H, Hirotsune S, Sugino H, Okazaki Y, Sasaki N, Hirose K, Imoto H, Okuizumi H, Muramatsu M et al. (1994) Identification of an imprinted U2af binding protein-related sequence on mouse chromosome 11 using the RLGS method. Nat Genet 6:33-40
11. Herman JG, Latif F, Weng Y, Lerman MI, Zbar B, Liu S, Samid D, Duan DS, Gnarra JR, Linehan WM (1994) Silencing of the VHL tumor-suppressor gene by DNA methylation in renal carcinoma. Proc Natl Acad Sci USA 91:9700-9704
12. 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
13. Herman JG, Umar A, Polyak K, Graff JR, Ahuja N, Issa JP, Markowitz S, Willson JK, Hamilton SR, Kinzler KW, Kane MF, Kolodner RD, Vogelstein B, Kunkel TA, Baylin SB (1998) Incidence and functional consequences of hMLH1 promoter hypermethylation in colorectal carcinoma. Proc Natl Acad Sci USA 95:6870-6875
14. Holliday R, Pugh JE (1975) DNA modification mechanisms and gene activity during development. Science 187:226-232
15. Huang TH, Laux DE, Hamlin BC, Tran P, Tran H, Lubahn DB (1997) Identification of DNA methylation markers for human breast carcinomas using the methylation-sensitive restriction fingerprinting technique. Cancer Res 57:1030-1034
16. Huang TH, Perry MR, Laux DE (1999) Methylation profiling of CpG islands in human breast cancer cells. Hum Mol Genet 8:459-470
17. Ji W, Hernandez R, Zhang XY, Qu GZ, Frady A, Varela M, Ehrlich M (1997) DNA demethylation and pericentromeric rearrangements of chromosome 1. Mutat Res 379:33-41
18. Jones PA, Baylin SB (2002) The fundamental role of epigenetic events in cancer. Nat Rev Genet 3:415-428
19. Kallioniemi OP, Kallioniemi A, Sudar D, Rutovitz D, Gray JW, Waldman F, Pinkel D (1993) Comparative genomic hybridization: a rapid new method for detecting and mapping DNA amplification in tumors. Semin Cancer Biol 4:41-46
20. Kane MF, Loda M, Gaida GM, Lipman J, Mishra R, Goldman H, Jessup JM, Kolodner R (1997) Methylation of the hMLH1 promoter correlates with lack of expression of hMLH1 in sporadic colon tumors and mismatch repair-defective human tumor cell lines. Cancer Res 57:808-811
21. Laird PW (2003) The power and the promise of DNA methylation markers. Nat Rev Cancer 3:253-266
22. McGrew MJ, Rosenthal N (1993) Quantitation of genomic methylation using ligation-mediated PCR. Biotechniques 15:722-729
23. Narayan A, Ji W, Zhang XY, Marrogi A, Graff JR, Baylin SB, Ehrlich M (1998) Hypomethylation of pericentromeric DNA in breast adenocarcinomas. Int J Cancer 77:833-838
24. Okano M, Bell DW, Haber DA, Li E (1999) DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99:247-257
25. Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Zhai Y, Dairkee SH, Ljung BM, Gray JW, Albertson DG (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 20:207-211
26. Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO (1999) Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 23:41-46
27. Qu GZ, Grundy PE, Narayan A, Ehrlich M (1999) Frequent hypomethylation in Wilms tumors of pericentromeric DNA in chromosomes 1 and 16. Cancer Genet Cytogenet 109:34-39
28. Riggs AD (1975) X inactivation, differentiation, and DNA methylation. Cytogenet Cell Genet 14:9-25
29. Shi H, Yan PS, Chen CM, Rahmatpanah F, Lofton-Day C, Caldwell CW, Huang TH (2002) Expressed CpG island sequence tag microarray for dual screening of DNA hypermethylation and gene silencing in cancer cells. Cancer Res 62:3214-3220
30. Toyota M, Ho C, Ahuja N, Jair KW, Li Q, Ohe-Toyota M, Baylin SB, Issa JP (1999) Identification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification. Cancer Res 59:2307-2312
31. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407-4414
32. Wigler M, Levy D, Perucho M (1981) The somatic replication of DNA methylation. Cell 24:33-40
33. Xiong Z, Laird PW (1997) COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res 25:2532-2534
34. Xu GL, Bestor TH, Bourc'his D, Hsieh CL, Tommerup N, Bugge M, Hulten M, Qu X, Russo JJ, Viegas-Pequignot E (1999) Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene. Nature 402:187-191
35. Yamamoto F, Yamamoto M, Soto JL, Kojima E, Wang EN, Perucho M, Sekiya T, Yamanaka H (2001) Not 1-Mse 1 methylation-sensitive amplified fragment length polymorhism for DNA methylation analysis of human cancers. Electrophoresis 22:1946-1956