Progress of Bioinformatics Study in DNA Methylation

Progress in Biochemistry and Biophysics

Volumn 36, Issue 2, 2009, Pages 143-150

  Fan, Shi Cai ^a,b   Zhang, Xue Gong ^a  

^a TSINGHUA UNIVERSITY   (China)

^b UNIVERSITY OF ELECTRONIC SCIENCE AND TECHNOLOGY OF CHINA   (China)

Author keywords

Bioinformatics study; Cpg island; Dna methylation; Epigenetics; Prediction, mechanism

Indexed keywords

EID: 67649517031     PISSN: 10003282     EISSN: None     Source Type: Journal    
DOI: 10.3724/SP.J.1206.2008.00426     Document Type: Review

References (58)

1. Goldberg A D, Allis C D, Bernstein E. Epigenetics: a landscape takes shape. Cell, 2007, 128(4): 635-638
2. Bird A P. CpG islands as gene markers in the vertebrate nucleus. Trends Genet, 1987, 3: 342-347 (Pubitemid 18001851)
3. Reik W, Santos F, Dean W. Mammalian epigenomics: reprogramming the genome for development and therapy. Theriogenology, 2003, 59(1): 21-32
4. Bird A. DNA methylation patterns and epigenetic memory. Genes Dev, 2002, 16(1): 6-21 (Pubitemid 34049633)
5. Bird A P, Wolffe A P. Methylation-induced repression - belts, braces, and chromatin. Cell, 1999,99(5): 451-454
6. Kim J, Kollhoff A, Bergmann A, et al. Methylation-sensitive binding of transcription factor YY1 to an insulator sequence within the paternally expressed imprinted gene, Peg3. Hum Mol Genet, 2003, 12(3): 233-245
7. Bradbury J. Human epigenome project - up and running. PLoS Biol, 2003, 1(3): E82 (Pubitemid 39112125)
8. Eckhardt F, Lewin J, Cortese R, et al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet, 2006, 38(12): 1378- 1385
9. Ehrlich M, Gama-Sosa M A, Huang L H, et al. Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells. Nucleic Acids Res, 1982,10(8): 2709-2721
10. Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol, 1987, 196(2): 261-282
11. Takai D, Jones P A. Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci USA, 2002, 99 (6): 3740-3745
12. Wang Y, Leung F C. An evaluation of new criteria for CpG islands in the human genome as gene markers. Bioinformatics, 2004, 20(7): 1170-1177 (Pubitemid 38660354)
13. Larsen F, Gundersen G, Lopez R, et al. CpG islands as gene markers in the human genome. Genomics, 1992, 13(4): 1095-1107
14. Hansen R S, Stoger R, Wijmenga C, et al. Escape from gene silencing in ICF syndrome: evidence for advanced replication time as a major determinant. Hum Mol Genet, 2000, 9(18): 2575-2587
15. Yamada Y, Watanabe H, Miura F, et al. A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 21q. Genome Res, 2004, 14(2): 247-266
16. Hanahan D, Weinberg R A. The hallmarks of cancer. Cell, 2000, 100(1): 57-70
17. Rakyan V K, Hildmann T, Novik K L, et al. DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project. PLoS Biol, 2004, 2(12): e405
18. Cokus S J, Feng S, Zhang X, et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature, 2008, 452(7184): 215-219
19. Bibikova M, Lin Z, Zhou L, et al. High-throughput DNA methylation profiling using universal bead arrays. Genome Res, 2006, 16(3): 383-393
20. Zhang D, Wang Y, Bai Y, et al. A novel method to quantify local CpG methylation density by regional methylation elongation assay on microarray. BMC Genomics, 2008, 9: 59
21. Rollins R A, Haghighi F, Edwards J R, et al. Large-scale structure of genomic methylation patterns. Genome Res, 2006, 16(2): 157-163
22. Weber M, Davies J J, Wittig D, et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet, 2005, 37(8): 853-862
23. Schumacher A, Kapranov P, Kaminsky Z, et al. Microarray-based DNA methylation profiling: technology and applications. Nucleic Acids Res, 2006, 34(2): 528-542
24. Weber M, Hellmann I, Stadler M B, et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet, 2007, 39(4): 457-466
25. Carr I M, Valleley E M, Cordery S F, et al. Sequence analysis and editing for bisulphite genomic sequencing projects. Nucleic Acids Res, 2007, 35(10): e79
26. Grunau C, Renault E, Rosenthal A, et al. MethDB - a public database for DNA methylation data. Nucleic Acids Res, 2001, 29(1): 270-274
27. He X, Chang S, Zhang J, et al. MethyCancer: the database of human DNA methylation and cancer. Nucleic Acids Res, 2008, 36 (Database issue): D836-841
28. Ongenaert M, Van Neste L, De Meyer T, et al. PubMeth: a cancer methylation database combining text-mining and expert annotation. Nucleic Acids Res, 2008, 36(Database issue): D842-846
29. Lauss M, Visne I, Weinhaeusel A, et al. MethCancerDB - aberrant DNA methylation in human cancer. Br J Cancer, 2008, 98 (4): 816-817
30. Bhasin M, Zhang H, Reinherz E L, et al. Prediction of methylated CpGs in DNA sequences using a support vector machine. FEBS Lett, 2005, 579(20): 4302-4308
31. Amoreira C, Hindermann W, Grunau C. An improved version of the DNA methylation database (MethDB). Nucleic Acids Res, 2003, 31 (1): 75-77
32. Das R, Dimitrova N, Xuan Z, et al. Computational prediction of methylation status in human genomic sequences. Proc Natl Acad Sci USA, 2006, 103(28): 10713-10716
33. Fang F, Fan S, Zhang X, et al. Predicting methylation status of CpG islands in the human brain. Bioinformatics, 2006, 22(18): 2204 - 2209
34. Feltus F A, Lee E K, Costello J F, et al. Predicting aberrant CpG island methylation. Proc Natl Acad Sci USA, 2003, 100 (21): 12253-12258
35. Bock C, Paulsen M, Tierling S, et al. CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure. PLoS Genet, 2006, 2(3): e26
36. Bock C, Walter J, Paulsen M, et al. CpG island mapping by epigenome prediction. PLoS Comput Biol, 2007, 3(6): e110
37. Barski A, Cuddapah S, Cui K, et al. High-resolution profiling of histone methylations in the human genome. Cell, 2007, 129 (4): 823-837
38. Fan S, Zhang M Q, Zhang X. Histone methylation marks play important roles in predicting the methylation status of CpG islands. Biochem Biophys Res Commun, 2008, 374(3): 559-564
39. Brandeis M, Frank D, Keshet I, et al. Sp1 elements protect a CpG island from de novo methylation. Nature, 1994, 371(6496): 435 - 438
40. Butcher DT, Mancini-DiNardo DN, Archer TK, et al. DNA binding sites for putative methylation boundaries in the unmethylated region of the BRCA1 promoter. Int J Cancer, 2004, 111(5): 669-678
41. Turker M S. The establishment and maintenance of DNA methylation patterns in mouse somatic cells. Semin Cancer Biol, 1999, 9(5): 329-337 (Pubitemid 29532859)
42. Turker M S. Gene silencing in mammalian cells and the spread of DNA methylation. Oncogene, 2002, 21(35): 5388-5393
43. Mummaneni P, Yates P, Simpson J, et al. The primary function of a redundant Sp1 binding site in the mouse aprt gene promoter is to block epigenetic gene inactivation. Nucleic Acids Res, 1998, 26(22): 5163-5169
44. Fan S, Fang F, Zhang X, et al. Putative zinc finger protein binding sites are over-represented in the boundaries of methylation-resistant CpG islands in the human genome. PLoS ONE, 2007, 2(11): e1 184
45. Issa J P. Aging, DNA methylation and cancer. Crit Rev Oncol Hematol, 1999, 32(1): 31-43 (Pubitemid 29486762)
46. 46JonesPA,BaylinSB.Thefundamentalroleofepigeneticeventsincancer. NatRevGenet,2002,3(6):415-428(Pubitemid34587077)
47. Ordway J M, Budiman M A, Korshunova Y, et al. Identification of novel high-frequency DNA methylation changes in breast cancer. PLoS ONE, 2007, 2(12): e1314
48. Piotrowski A, Benetkiewicz M, Menzel U, et al. Microarray-based survey of CpG islands identifies concurrent hyper- and hypomethylation patterns in tissues derived from patients with breast cancer. Genes Chromosomes Cancer, 2006, 45(7): 656-667
49. Keshet I, Schlesinger Y, Farkash S, et al. Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat Genet, 2006, 38(2): 149-153
50. Gebhard C, Schwarzfischer L, Pham T H, et al. Genome-wide profiling of CpG methylation identifies novel targets of aberrant hypermethylation in myeloid leukemia. Cancer Res, 2006, 66(12): 6118-6128
51. Yu J, Zhang H Y, Ma Z Z, et al. Methylation profiling of twenty four genes and the concordant methylation behaviours of nineteen genes that may contribute to hepatocellular carcinogenesis. Cell Res, 2003, 13(5): 319-333
52. Zhang C Y, Mao L, Li L, et al. Promoter methylation as a common mechanism for inactivating E-cadherin in human salivary gland adenoid cystic carcinoma. Cancer, 2007, 110(1): 87-95
53. Yang H J, Liu V W, Wang Y, et al. Differential DNA methylation profiles in gynecological cancers and correlation with clinico- pathological data. BMC Cancer, 2006, 6: 212
54. Tamaru H, Selker E U. A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature, 2001, 414(6861): 277-283
55. Jackson J P, Lindroth A M, Cao X, et al. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature, 2002, 416(6880): 556-560
56. Jaenisch R, Bird A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet, 2003, 33(Suppl): 245-254
57. Lehnertz B, Ueda Y, Derijck A A, et al. Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr Biol, 2003, 13 (14): 1192-1200
58. Li X, Wang X, He K, et al. High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression. Plant Cell, 2008, 20(2): 259-276