Genome-wide profiling of DNA methylation in human cancer cells

Genomics

Volumn 98, Issue 4, 2011, Pages 280-287

  Ogoshi, Katsumi ^a   Hashimoto, Shin ichi ^a,b   Nakatani, Yoichiro ^b   Qu, Wei ^b   Oshima, Kenshiro ^b   Tokunaga, Katsushi ^a   Sugano, Sumio ^b   Hattori, Masahira ^b   Morishita, Shinichi ^b   Matsushima, Kouji ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

Colon cancer; Differentially methylated regions; DNA methylation; Second generation sequencing technology

Indexed keywords

ARTICLE; CELL STRAIN HCT116; CELL STRAIN HT29; CLDN1 GENE; COLON CANCER; CPG ISLAND; DNA METHYLATION; DNA SEQUENCE; GENE EXPRESSION; GENE STRUCTURE; HUMAN; HUMAN CELL; METHYLATION SPECIFIC DIGITAL SEQUENCING; ONCOGENE; PLEKHC1 GENE; PRIORITY JOURNAL; TACC1 GENE; TRANSCRIPTION INITIATION SITE;

COLONIC NEOPLASMS; CPG ISLANDS; DNA METHYLATION; DNA RESTRICTION ENZYMES; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOME, HUMAN; GENOMIC INSTABILITY; HCT116 CELLS; HT29 CELLS; HUMANS; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION INITIATION SITE;

EID: 84860389965     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2011.07.003     Document Type: Article

References (48)

1. Bestor T.H. The DNA methyltransferases of mammals. Hum. Mol. Genet. 2000, 9:2395-2402.
2. Bird A. DNA methylation patterns and epigenetic memory. Genes Dev. 2002, 16:6-21.
3. Reik W. Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 2007, 447:425-432.
4. Laird P.W. The power and the promise of DNA methylation markers. Nat. Rev. Cancer 2003, 3:253-266.
5. Feinberg A.P. The epigenetics of cancer etiology. Semin. Cancer Biol. 2004, 14:427-432.
6. Ozanne S.E., Constancia M. Mechanisms of disease: the developmental origins of disease and the role of the epigenotype. Nat. Clin. Pract. Endocrinol. Metab. 2007, 3:539-546.
7. Jones P.A., Baylin S.B. The epigenomics of cancer. Cell 2007, 128:683-692.
8. Esteller M. Epigenetics in cancer. N. Engl. J. Med. 2008, 358:1148-1159.
9. Keshet I., et al. Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat. Genet. 2006, 38:149-153.
10. Cross S.H., Charlton J.A., Nan X., Bird A.P. Purification of CpG islands using a methylated DNA binding column. Nat. Genet. 1994, 6:236-244.
11. Rauch T.A., Wu X., Zhong X., Riggs A.D., Pfeifer G.P. A human B cell methylome at 100-base pair resolution. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:671-678.
12. Frommer M., et al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl. Acad. Sci. U. S. A. 1992, 89:1827-1831.
13. Clark S.J., Harrison J., Paul C.L., Frommer M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res. 1994, 22:2990-2997.
14. Bird A.P., Southern E.M. Use of restriction enzymes to study eukaryotic DNA methylation: I. The methylation pattern in ribosomal DNA from Xenopus laevis. J. Mol. Biol. 1978, 118:27-47.
15. Hu M., et al. Distinct epigenetic changes in the stromal cells of breast cancers. Nat. Genet. 2005, 37:899-905.
16. Hellman A., Chess A. Gene body-specific methylation on the active X chromosome. Science 2007, 315:1141-1143.
17. Khulan B., et al. Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res. 2006, 16:1046-1055.
18. Zhang X., et al. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell 2006, 126:1189-1201.
19. Zilberman D., Gehring M., Tran R.K., Ballinger T., Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat. Genet. 2007, 39:61-69.
20. Bibikova M., et al. High-throughput DNA methylation profiling using universal bead arrays. Genome Res. 2006, 16:383-393.
21. Irizarry R.A., et al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat. Genet. 2009, 41:178-186.
22. Meissner A., et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 2008, 454:766-770.
23. Lister R., et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 2008, 133:523-536.
24. Cokus S.J., et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 2008, 452:215-219.
25. Li J., et al. An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines. BMC Genomics 2009, 10:223.
26. Barski A., et al. High-resolution profiling of histone methylations in the human genome. Cell 2007, 129:823-837.
27. Hillier L.W., et al. Whole-genome sequencing and variant discovery in C. elegans. Nat. Methods 2008, 5:183-188.
28. Hashimoto S., et al. High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer. PLoS One 2009, 4:e4108.
29. Marioni J.C., Mason C.E., Mane S.M., Stephens M., Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 2008, 18:1509-1517.
30. Hafner M., et al. Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods 2008, 44:3-12.
31. Holt K.E., et al. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat. Genet. 2008, 40:987-993.
32. McGhee J.D., et al. ELT-2 is the predominant transcription factor controlling differentiation and function of the C. elegans intestine, from embryo to adult. Dev. Biol. 2009, 327:551-565.
33. Yagi S., et al. DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression. Genome Res. 2008, 18:1969-1978.
34. Shann Y.J., et al. Genome-wide mapping and characterization of hypomethylated sites in human tissues and breast cancer cell lines. Genome Res. 2008, 18:791-801.
35. Ball M.P., et al. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat. Biotechnol. 2009, 27:361-368.
36. Maunakea A.K., et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 2010, 466:253-257.
37. Lister R., et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009, 462:315-322.
38. Eckhardt F., et al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat. Genet. 2006, 38:1378-1385.
39. Demircan B., et al. Comparative epigenomics of human and mouse mammary tumors. Genes Chromosomes Cancer 2009, 48:83-97.
40. Lu C., et al. Regulation of tumor angiogenesis by EZH2. Cancer Cell 2010, 18:185-197.
41. Fukasawa M., et al. Microarray analysis of promoter methylation in lung cancers. J. Hum. Genet. 2006, 51:368-374.
42. Yamashita S., Tsujino Y., Moriguchi K., Tatematsu M., Ushijima T. Chemical genomic screening for methylation-silenced genes in gastric cancer cell lines using 5-aza-2'-deoxycytidine treatment and oligonucleotide microarray. Cancer Sci. 2006, 97:64-71.
43. Mori Y., et al. A genome-wide search identifies epigenetic silencing of somatostatin, tachykinin-1, and 5 other genes in colon cancer. Gastroenterology 2006, 131:797-808.
44. Jin Z., et al. Hypermethylation of the nel-like 1 gene is a common and early event and is associated with poor prognosis in early-stage esophageal adenocarcinoma. Oncogene 2007, 26:6332-6340.
45. Dallol A., et al. Tumour specific promoter region methylation of the human homologue of the Drosophila Roundabout gene DUTT1 (ROBO1) in human cancers. Oncogene 2002, 21:3020-3028.
46. Xian J., et al. Targeted disruption of the 3p12 gene, Dutt1/Robo1, predisposes mice to lung adenocarcinomas and lymphomas with methylation of the gene promoter. Cancer Res. 2004, 64:6432-6437.
47. Ghosh S., et al. Alterations of ROBO1/DUTT1 and ROBO2 loci in early dysplastic lesions of head and neck: clinical and prognostic implications. Hum. Genet. 2009, 125:189-198.
48. Wong V.C., et al. Identification of an invasion and tumor-suppressing gene, Endoglin (ENG), silenced by both epigenetic inactivation and allelic loss in esophageal squamous cell carcinoma. Int. J. Cancer 2008, 123:2816-2823.