High-throughput method for analyzing methylation of CpGs in targeted genomic regions

Proceedings of the National Academy of Sciences of the United States of America

Volumn 107, Issue 28, 2010, Pages 12587-12592

  Nautiyal, Shivani ^a   Carlton, Victoria E H ^a   Lu, Yontao ^a   Ireland, James S ^a   Flaucher, Diane ^a   Moorhead, Martin ^a   Gray, Joe W ^b   Spellman, Paul ^b   Mindrinos, Michael ^c   Berg, Paul ^d   Faham, Malek ^a  

^a Thermo Fisher Scientific   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d STANFORD UNIVERSITY   (United States)

Author keywords

Array; Technology; Tumor

Indexed keywords

ARTICLE; CELL DIFFERENTIATION; CPG ISLAND; DNA METHYLATION; DNA SEQUENCE; GENETIC ANALYSIS; GENOMIC ISLAND; HIGH THROUGHPUT SCREENING; HOUSEKEEPING GENE; HUMAN; METHYLATION; MICROARRAY ANALYSIS; NONHUMAN; PRIORITY JOURNAL; TUMOR CELL;

CELL DIFFERENTIATION; DINUCLEOSIDE PHOSPHATES; DNA; DNA METHYLATION; GENOME; HUMANS; METHYLATION;

EID: 77955458087     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1005173107     Document Type: Article

References (27)

1. Li E, Bestor TH, Jaenisch R (1992) Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69:915-926.
2. Ideraabdullah FY, Vigneau S, Bartolomei MS (2008) Genomic imprinting mechanisms in mammals. Mutat Res 647:77-85.
3. Tost J (2009) DNA methylation: An introduction to the biology and the diseaseassociated changes of a promising biomarker. Methods Mol Biol 507:3-20.
4. Lopez J, Percharde M, Coley HM, Webb A, Crook T (2009) The context and potential of epigenetics in oncology. Br J Cancer 100:571-577.
5. Iacobuzio-Donahue CA (2009) Epigenetic changes in cancer. Annu Rev Pathol 4: 229-249.
6. Huang TH, Perry MR, Laux DE (1999) Methylation profiling of CpG islands in human breast cancer cells. Hum Mol Genet 8:459-470.
7. Lippman Z, Gendrel AV, Colot V, Martienssen R (2005) Profiling DNA methylation patterns using genomic tiling microarrays. Nat Methods 2:219-224. (Pubitemid 41122130)
8. Waalwijk C, Flavell RA (1978) MspI, an isoschizomer of hpaII which cleaves both unmethylated and methylated hpaII sites. Nucleic Acids Res 5:3231-3236. (Pubitemid 9016996)
9. 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.
10. Yan PS, Potter D, Deatherage DE, Huang TH, Lin S (2009) Differential methylation hybridization: Profiling DNA methylation with a high-density CpG island microarray. Methods Mol Biol 507:89-106.
11. Weber M, et al. (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39:457-466.
12. Mohn F, Weber M, Schübeler D, Roloff TC (2009) Methylated DNA immunoprecipitation (MeDIP). Methods Mol Biol 507:55-64.
13. Frommer M, et al. (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.
14. Cokus SJ, et al. (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452:215-219.
15. Meissner A, et al. (2008) Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454:766-770.
16. Ball MP, et al. (2009) Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol 27:361-368.
17. Deng J, et al. (2009) Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotechnol 27:353-360.
18. Bibikova M, et al. (2006) High-throughput DNA methylation profiling using universal bead arrays. Genome Res 16:383-393.
19. Bibikova M, et al. (2009) Genome-wide DNA methylation profiling using Infinium® assay. Epigenomics 1:177-200.
20. Nosho K, et al. (2008) Comprehensive biostatistical analysis of CpG island methylator phenotype in colorectal cancer using a large population-based sample. PLoS ONE 3: e3698.
21. Eads CA, et al. (2000) MethyLight: A high-throughput assay to measure DNA methylation. Nucleic Acids Res 28:E32.
22. Shelton BP, Misso NL, Shaw OM, Arthaningtyas E, Bhoola KD (2008) Epigenetic regulation of human epithelial cell cancers. Curr Opin Mol Ther 10:568-578.
23. Subramaniam MM, et al. (2009) RUNX3 inactivation in colorectal polyps arising through different pathways of colonic carcinogenesis. Am J Gastroenterol 104: 426-436.
24. Ashburner M, et al.; The Gene Ontology Consortium (2000) Gene ontology: Tool for the unification of biology. Nat Genet 25:25-29.
25. Saxonov S, Berg P, Brutlag DL (2006) A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci USA 103:1412-1417. (Pubitemid 43191179)
26. Tian J, et al. (2004) Accurate multiplex gene synthesis from programmable DNA microchips. Nature 432:1050-1054.
27. Doi A, et al. (2009) Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat Genet 41:1350-1353.