An overview of the analysis of DNA methylation in mammalian genomes

Biological Chemistry

Volumn 383, Issue 6, 2002, Pages 893-906

  Shiraishi, Masahiko ^a   Oates, Adam J ^a   Sekiya, Takao ^a  

^a Nat'l Cancer Center Research Inst   (Japan)

Author keywords

Bisulfite modification; Denaturing gradient gel electrophoresis; DNA methyltransferase; Methyl CpG binding protein; Restriction endonucleases; Zinc finger protein

Indexed keywords

5 METHYLCYTOSINE; BINDING PROTEIN; CYTOSINE; PYRIMIDINE;

ANALYTIC METHOD; CARCINOGENESIS; CHEMICAL REACTION; CHROMOSOME ANALYSIS; CONTROLLED STUDY; CPG ISLAND; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA METHYLATION; GENE SILENCING; GENOME; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; IN VIVO STUDY; MAMMAL; MASS SPECTROMETRY; MEDICAL RESEARCH; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DNA BINDING; RESTRICTION MAPPING; REVIEW; SINGLE STRAND CONFORMATION POLYMORPHISM;

ANIMALS; CYTOSINE; DNA METHYLATION; GENOME; HUMANS; MAMMALS; MODELS, MOLECULAR; NUCLEIC ACID DENATURATION;

MAMMALIA;

EID: 0036340020     PISSN: 14316730     EISSN: None     Source Type: Journal    
DOI: 10.1515/BC.2002.096     Document Type: Review

References (119)

1. Use of denaturing gradient gel electrophoresis to study conformational transition in nucleic acids
2. INK4B methylation in acute myeloid leukemia
3. Organization and control of imprinted genes: The common features
4. A novel MSP/DHPLC method for the investigation of the methylation status of imprinted genes enables the molecular detection of low cell mosaicisms
5. A mammalian protein with specific demethylase activity for mCpG DNA
6. Methylation-sensitive, single-strand conformation analysis (MS-SSCA): A rapid method to screen for and analyze methylation
7. Use of restriction endonucleases to detect and isolate genes from mammalian genomes
8. CpG-rich islands and the function of DNA methylation
9. Use of restriction enzyme to study eukaryotic DNA methylation: I. The methylation pattern in ribosomal DNA from Xenopus laevis
10. Transcriptional silencing in yeast is assoiated with reduced nucleosome acetylation
11. Selective degradation of thymidine and thymine deoxynucleosides
12. The degradation of DNA by hydrazine: A critical study of the suitability of the reaction for the quantitative determination of purine nucleotide sequences
13. Reduced rates of gene loss, gene silencing, and gene mutation in Dnmt1-deficient embryonic stem cells
14. Mutational separation of DNA binding from catalysis in a DNA cytosine methyltransferase
15. DNA hypomethylation leads to elevated mutation rates
16. Crystal structure of the Hhal DNA methyltransferase complexed with S-adenosyl-L-methionine
17. AdoMet-dependent methylation, DNA methyltransferases, and base pairing
18. Recognition of DNA methylation by zinc fingers
19. DNA binding site of the growth factor-induced protein Zif268
20. Genomic sequencing
21. Alterations in DNA helix stability due to base modifications can be evaluated using denaturing gradient gel electrophoresis
22. Aberrant CpG-island methylation has non-random and tumor-type-specific patterns
23. Inhibition of DNA methyltransferase and induction of Friend erythroleukemia cell differentiation by 5-azacytidine and 5-aza-2'-deoxycytidine
24. Purification of CpG islands using a methylated DNA binding column
25. MethyLight: A high-throughput assay to measure DNA methylation
26. Unusual properties of the DNA from Xanthomonas phage XP-12 in which 5-methylcytosine completely replaces cytosine
27. DNA methylation through a locally unpaired intermediate
28. Length-independent separation of DNA restriction fragments in two-dimensional gel electrophoresis
29. DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: Correspondence with melting theory
30. The use of permanganate as a sequencing reagent for identification of 5-methylcytosine residues in DNA
31. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands
32. CpG methylation has differential effects on the binding of YY1 and ETS proteins to the bi-directional promoter of the Surf-1 and Surf-2 genes
33. CpG methylation and the binding of YY1 and ETS proteins to the Surf-1/Surf-2 bidirectional promoter
34. Physical studies on synthetic DNAs containing 5-methylcytosine
35. Rapid quantitation of methylation differences at specific sites using methylation-sensitive single nuclectice primer extension (Ms-SNuPE)
36. DNA methylation is linked to deacetylation of histone H3, but not H4, on the imprinted genes Snrpn and U2af1-rs1
37. Bisulfite genomic sequencing: Systematic investigation of critical experimental parameters
38. A genomic scanning method for higher organisms using restriction sites as landmarks
39. A new imprinted gene cloned by a methylation-sensitive genome scanning method
40. Bisulfite modification of nucleic acids and their constituents
41. The selective degradation of pyrimidines in nucleic acids by permanganate oxidation
42. The addition of sodium bisulfite to uracil and to cytosine
43. Reaction of sodium bisulfite with uracil, cytosine, and their derivatives
44. Identification and characterization of a family of mammalian methyl-CpG binding proteins
45. Promoter-region hypermethylation and gene silencing in human cancer
46. Methylation-specific PCR: A novel PCR Assay for methylation status of CpG islands
47. Sp1 transcription factor binds DNA and activates transcription even when the binding site is CpG methylated
48. High-resolution methylation analysis of the human hypoxanthine phosphoribosyltransferase gene 5' region on the active and inactive X chromosomes: Correlation with binding sites for transcription factors
49. The permanganate oxidation of thymine
50. The permanganate oxidation of thymidine and thymidylic acid
51. The permanganate oxidation of deoxyribonucleic acids
52. Engineered zinc finger proteins that respond to DNA modification by Haelll and Hhal methyltransferase enzymes
53. Mutagenicity of 5-aza-2′-deoxycytidine is mediated by the mammalian DNA methyltransferase
54. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription
55. Toxicity of 5-aza-2′-deoxycytidine to mammalian cells is mediated primarily by covalent trapping of DNA methyltransferase rather than DNA demethylation
56. Screening hypermethylated regions by methylation-sensitive single-strand conformational polymorphism
57. Hhal methyltransferase flips its target base out of the DNA helix
58. Dynamic models of the flipped-out cytosine during Hhal methyltransferase-DNA interactions in solution
59. Sequence-determined DNA separations
60. Purification, sequence, and cellular localization of a novel chromosomal protein that binds to methylated DNA
61. DNA methylation analysis using bisulfite treatment and PCR-single-strand conformation polymorphism in colorectal cancer showing microsatellite instability
62. Selective association of the methyl-CpG binding protein MBD2 with the silent p14/pl6 locus in human neoplasia
63. A new method for sequencing DNA
64. Sequencing end-labeled DNA with base-specific chemical cleavages
65. Characterization of MeCP2, a vertebrate DNA binding protein with affinity for methylated DNA
66. Differential nuclear protein binding to 5-azacytosine-containing DNA as a potential mechanism for 5-aza-2′-deoxycytidine resistance
67. Detection of single base substitutions in total genomic DNA
68. Detection and localization of single base changes by denaturing gradient gel electrophoresis
69. In vivo footprinting of a muscle specific enhancer by ligation mediated PCR
70. Dissection of methyl-CpG binding domain from the chromosomal protein MeCP2
71. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a hi-stone deacetylase complex
72. Altered chromatin structure associated with methylation-induced gene silencing in cancer cells: Correlation of accessibility, methylation, MeCP2 binding and acetylation
73. DNA methylation analysis: A review of current methodologies
74. The quantitation of 5-methylcytosine in DNA by the chloroacetaldehyde reaction
75. Enzymatic C5-cytosine methylation of DNA: Mechanistic implications of new crystal structures for Hhal methyltransferase-DNA-AdoHcy complexes
76. Solution structure of the methyl-CpG-binding domain of the methylation-dependent transcriptional repressor MBD1
77. Solution structutre of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA
78. Detection of 5-methylcytosine in DNA sequence
79. Zinc finger-DNA recognition: Crystal structure of a Zif268-DNA complex at 2.1 Å
80. Genomic sequencing and methylation analysis by ligation-mediated PCR
81. Mutation hotspots and DNA methylation
82. The p120 catenin partner Kaiso is a DNA methylation-dependent transcriptional repressor
83. DNA methylation is a reversible biological signal
84. Identifying 5-methylcytosine and related modifications in DNA genomes
85. The crystal structure of Haelll methyltransferase covalently complexed to DNA: An extrahelical cytosine and rearranged base pairing
86. X-chromosome inactivation and epigenetic mechanism
87. On base flipping
88. Base flipping
89. Covalent bond formation between a DNA-cytosine methyltransferase and DNA containing 5-azacytosine
90. Recent progress in the biology, chemistry and structural biology of DNA glycosylases
91. Reactions of uracil and cytosine derivatives with sodium bisulfite: A specific deamination method
92. Establishment of imprinted methylation patterns during development
93. Formation of diastereomers of 5,6-dihydrothymine-6-sulfonate by deamination of 5-methylcytosine with bisulfite
94. Preferential isolation of DNA fragments associated with CpG islands
95. The isolation of CpG islands from human chromosomal regions 11q13 and Xp22 by segregation of partly melted molecules
96. Isolation of DNA fragments associated with methylated CpG islands in human adenocarcinomas of the lung using a methylated DNA binding column and denaturing gradient gel electrophoresis
97. Tight interaction between densely methylated DNA fragments and the methyl-CpG binding domain of the rat MeCP2 protein attached to a solid support
98. Heterogeneity in the methylation status of genomic DNA fragments demonstrating similar elution profiles in methyl-CpG binding domain column chromatography
99. Quantitative DNA methylation analysis by fluorescent polymerase chain reaction single-strand conformation polymorphism using an automated DNA sequencer
100. Analysis of putative RNase sensitivity and protease insensitivity of demethylation activity in extracts from rat myoblast
101. The structure of poly-5-methyl-cyticlylic acid and its twin-stranded complex with poly-inosinic acid
102. Studies on the nucleotide arrangement in nucleic acids. IX. Selective degradation of pyrimidine deoxyribonucleotides
103. Identification of 5-methylcytosine in complex genomes
104. Changes in methylation patterns identified by two-dimensional DNA fingerprinting
105. The flip side of DNA methylation
106. The solution structure of the domain from MeCP2 that binds to methylated DNA
107. Comparison of bisulfite modification of 5-methyldeoxycytidine and deoxycytidine residues
108. Detection and measurement of PCR bias in quantitative methylation analysis of bisulfite-treated DNA
109. DNA demethylation in vitro: Involvement of RNA
110. 2 zinc finger proteins
111. In-tube DNA methylation profiling by fluorescence melting curve analysis
112. Kinetic and catalytic mechanism of Hhal methyltransferase
113. COBRA: A sensitive and quantitative DNA methylation assay
114. CpG island arrays: An application toward deciphering epigenetic signatures of breast cancer
115. Dissecting complex epigenetic alterations in breast cancer using CpG island microarrays
116. Cytosine methylation and the ecology of intragenomic parasites
117. Effect of DNA cytosine methylation upon deamination-induced mutagenesis in a natural target sequence in duplex DNA
118. 5-Methylcytosine-DNA glycosylase activity is present in a cloned G/T mismatch DNA glycosylase associated with the chicken embryo DNA demethylation complex
119. 5-Methylcytosine DNA glycosylase activity is also present in the human MBD4 (G/T mismatch glycosylase) and in a related avian sequence