Detection method for methylation density on microarray using methyl-CpG-binding domain protein

Analytical Biochemistry

Volumn 387, Issue 2, 2009, Pages 143-149

  Luo, Junfeng ^a   Zheng, Wenli ^a   Wang, Yan ^a   Wu, Zhixiang ^a   Bai, Yunfei ^a   Lu, Zuhong ^a  

^a SOUTHEAST UNIVERSITY   (China)

Author keywords

DNA methylation; Methyl CpG binding domain (MBD); Microarray

Indexed keywords

CELL CULTURE; FLUORESCENCE; GENES; METHYLATION; MICROARRAYS; POLYMERASE CHAIN REACTION; RECOMBINANT PROTEINS;

BISULFITE-SEQUENCING; CANCER CELL LINES; DETECTION METHODS; DNA METHYLATION; FLUORESCENCE SIGNALS; METHYL-CPG-BINDING; METHYLTRANSFERASES; TUMOR SUPPRESSOR GENES;

ALKYLATION;

ANTIBODY; BACTERIAL ENZYME; BISULFITE; CARBOXYTETRAMETHYLRHODAMINE; CYCLIN DEPENDENT KINASE INHIBITOR 2A; CYCLIN DEPENDENT KINASE INHIBITOR 2B; FLUORESCENT DYE; GENOMIC DNA; METHYL CPG BINDING PROTEIN; METHYLTRANSFERASE; RHODAMINE; SSSI METHYLASE; UNCLASSIFIED DRUG;

ARTICLE; CDKN 2A GENE; CDKN 2B GENE; CELL LINE; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; DNA MICROARRAY; DNA SEQUENCE; FLUORESCENCE ANALYSIS; HUMAN; HUMAN CELL; METHYLATION DENSITY; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN EXPRESSION; QUANTITATIVE ANALYSIS; SENSITIVITY AND SPECIFICITY; TUMOR SUPPRESSOR GENE; VALIDATION PROCESS;

EID: 61849094247     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2008.11.020     Document Type: Article

References (37)

1. Ferguson-Smith A.C., and Surani M.A. Imprinting and the epigenetic asymmetry between parental genomes. Science 293 (2001) 1086-1089
2. Lee J.T. Molecular links between X-inactivation and autosomal imprinting: X-inactivation as a driving force for the evolution of imprinting?. Curr. Biol. 13 (2003) R242-R254
3. Issa J.P. Age-related epigenetic changes and the immune system. Clin. Immunol. 109 (2003) 103-108
4. Robertson K.D. DNA methylation and human disease. Nat. Rev. Genet. 6 (2005) 597-610
5. Jones P.A., and Laird P.W. Cancer epigenetics comes of age. Nat. Genet. 21 (1999) 163-167
6. Hsieh C.L. Dependence of transcriptional repression on CpG methylation density. Mol. Cell Biol. 14 (1994) 5487-5494
7. Bachman K.E., Herman J.G., Corn P.G., Merlo A., Costello J.F., Cavenee W.K., Baylin S.B., and Graff J.R. Methylation-associated silencing of the tissue inhibitor of metalloproteinase-3 gene suggests a suppressor role in kidney, brain, and other human cancers. Cancer Res. 59 (1999) 798-802
8. Cameron E.E., Baylin S.B., and Herman J.G. p15(INK4B) CpG island methylation in primary acute leukemia is heterogeneous and suggests density as a critical factor for transcriptional silencing. Blood 94 (1999) 2445-2451
9. Yan P.S., Shi H., Rahmatpanah F., Hsiau T.H., Hsiau A.H., Leu Y.W., Liu J.C., and Huang T.H. Differential distribution of DNA methylation within the RASSF1A CpG island in breast cancer. Cancer Res. 63 (2003) 6178-6186
10. Dodge J.E., List A.F., and Futscher B.W. Selective variegated methylation of the p15 CpG island in acute myeloid leukemia. Int. J. Cancer 78 (1998) 561-567
11. Esteller M., Corn P.G., Baylin S.B., and Herman J.G. A gene hypermethylation profile of human cancer. Cancer Res. 61 (2001) 3225-3229
12. Willemze R., Suciu S., Archimbaud E., Muus P., Stryckmans P., Louwagie E.A., Berneman Z., Tjean M., Wijermans P., Dohner H., Jehn U., Labar B., Jaksic B., Dardenne M., and Zittoun R. A randomized phase II study on the effects of 5-aza-2'-deoxycytidine combined with either amsacrine or idarubicin in patients with relapsed acute leukemia: an EORTC Leukemia Cooperative Group phase II study (06893). Leukemia 11 suppl. 1 (1997) S24-S27
13. Wijermans P., Lubbert M., Verhoef G., Bosly A., Ravoet C., Andre M., and Ferrant A. Low-dose 5-aza-2'-deoxycytidine, a DNA hypomethylating agent, for the treatment of high-risk myelodysplastic syndrome: a multicenter phase II study in elderly patients. J. Clin. Oncol. 18 (2000) 956-962
14. Wijermans P., and Lübbert M. Epigenetic therapy with decitabine for myelodysplasia and leukemia. Fut, Oncol 1 (2005) 585-591
15. Chim S.S., Tong Y.K., Chiu R.W., Lau T.K., Leung T.N., Chan L.Y., Oudejans C.B., Ding C., and Lo Y.M. Detection of the placental epigenetic signature of the maspin gene in maternal plasma. Proc. Natl. Acad. Sci. USA 102 (2005) 14753-14758
16. Ballestar E., and Wolffe A.P. Methyl-CpG-binding proteins: targeting specific gene repression. Eur. J. Biochem. 268 (2001) 1-6
17. 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
18. Brock G.J., Huang T.H., Chen C.M., and Johnson K.J. A novel technique for the identification of CpG islands exhibiting altered methylation patterns (ICEAMP). Nucleic Acids Res. 29 (2001) e123
19. Rauch T., and Pfeifer G.P. Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated-CpG islands in cancer. Lab. Invest. 85 (2005) 1172-1180
20. Rauch T., Li H., Wu X., and Pfeifer G.P. MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells. Cancer Res. 66 (2006) 7939-7947
21. Ballestar E., Paz M.F., Valle L., Wei S., Fraga M.F., Espada J., Cigudosa J.C., Huang T.H., and Esteller M. Methyl-CpG binding proteins identify novel sites of epigenetic inactivation in human cancer. EMBO J. 22 (2003) 6335-6345
22. Gebhard C., Schwarzfischer L., Pham T.H., Schilling E., Klug M., Andreesen R., and Rehli M. Genome-wide profiling of CpG methylation identifies novel targets of aberrant hypermethylation in myeloid leukemia. Cancer Res. 66 (2006) 6118-6128
23. Agrawal S., Hofmann W.K., Tidow N., Ehrich M., van den Boom D., Koschmieder S., Berdel W.E., Serve H., and Muller-Tidow C. The C/EBPdelta tumor suppressor is silenced by hypermethylation in acute myeloid leukemia. Blood 109 (2007) 3895-3905
24. Rauch T., Wang Z., Zhang X., Zhong X., Wu X., Lau S.K., Kernstine K.H., Riggs A.D., and Pfeifer G.P. Homeobox gene methylation in lung cancer studied by genome-wide analysis with a microarray-based methylated CpG island recovery assay. Proc. Natl. Acad. Sci. USA 104 (2007) 5527-5532
25. van Steensel B. Mapping of genetic and epigenetic regulatory networks using microarrays. Nat. Genet. 37 (2005) S18-S24
26. Fan Y., Nikitina T., Zhao J., Fleury T.J., Bhattacharyya R., Bouhassira E.E., Stein A., Woodcock C.L., and Skoultchi A.I. Histone H1 depletion in mammals alters global chromatin structure but causes specific changes in gene regulation. Cell 123 (2005) 1199-1212
27. Takai D., and Jones P.A. Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc. Natl. Acad. Sci. USA 99 (2002) 3740-3745
28. Frommer M., McDonald L.E., Millar D.S., Collis C.M., Watt F., Grigg G.W., Molloy P.L., and Paul C.L. 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
29. Clark S.J., Harrison J., Paul C.L., and Frommer M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res. 22 (1994) 2990-2997
30. Sambrook J., Fritsch E.F., and Maniatis T. Molecular Cloning: A Laboratory Manual (1989), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
31. Silverton E.W., Navia M.A., and Davies D.R. Three-dimensional structure of an intact human immunoglobulin. Proc. Natl. Acad. Sci. USA 74 (1977) 5140-5144
32. Nan X., Meehan R.R., and Bird A. Dissection of the methyl-CpG binding domain from the chromosomal protein MeCP2. Nucleic Acids Res. 21 (1993) 4886-4892
33. Proll J., Fodermayr M., Wechselberger C., Pammer P., Sonnleitner M., Zach O., and Lutz D. Ultra-sensitive immunodetection of 5' methyl cytosine for DNA methylation analysis on oligonucleotide microarrays. DNA Res. 13 (2006) 37-42
34. Iolascon A., Giordani L., Moretti A., Basso G., Borriello A., and Della Ragione F. Analysis of CDKN2A, CDKN2B, CDKN2C, and cyclin Ds gene status in hepatoblastoma. Hepatology 27 (1998) 989-995
35. Shao J., Li Y., Li H., Wu Q., Hou J., and Liew C. Deletion of chromosomes 9p and 17 associated with abnormal expression of p53, p16/MTS1, and p15/MTS2 gene protein in hepatocellular carcinomas. Chin. Med. J. (Engl.) 113 (2000) 817-822
36. Zhang D., Wang Y., Bai Y., Ge Q., Qiao Y., Luo J., Jia C., and Lu Z. A novel method to quantify local CpG methylation density by regional methylation elongation assay on microarray. BMC Genomics 9 (2008) 59
37. Galm O., Rountree M.R., Bachman K.E., Jair K.W., Baylin S.B., and Herman J.G. Enzymatic regional methylation assay: a novel method to quantify regional CpG methylation density. Genome Res. 12 (2002) 153-157