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Volumn 4, Issue 4, 2003, Pages 233-250

DNA methylation analysis techniques

Author keywords

5 methylcytosine; Bisulfite; DNA methylation; PCR; Review

Indexed keywords

DNA;

EID: 0042386500     PISSN: 13895729     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1025103319328     Document Type: Review
Times cited : (146)

References (60)
  • 1
    • 0026807035 scopus 로고
    • Use of denaturing gradient gel electrophoresis to study conformational transitions in nucleic acids
    • Abrams ES and Stanton VP (1992) Use of denaturing gradient gel electrophoresis to study conformational transitions in nucleic acids. Methods Enzymol 212: 71-104
    • (1992) Methods Enzymol. , vol.212 , pp. 71-104
    • Abrams, E.S.1    Stanton, V.P.2
  • 4
    • 0033913645 scopus 로고    scopus 로고
    • Aging, methylation and cancer
    • Ahuja N and Issa JP (2000) Aging, methylation and cancer. Histol Histopathol 15: 835-842
    • (2000) Histol. Histopathol. , vol.15 , pp. 835-842
    • Ahuja, N.1    Issa, J.P.2
  • 5
    • 0032830639 scopus 로고    scopus 로고
    • Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2
    • Amir RE, Van Den Veyver IB, Wan M, Tran CQ, Francke U and Zoghbi HY (1999) Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2. Nat Genet 23: 185-188
    • (1999) Nat. Genet. , vol.23 , pp. 185-188
    • Amir, R.E.1    Van Den Veyver, I.B.2    Wan, M.3    Tran, C.Q.4    Francke, U.5    Zoghbi, H.Y.6
  • 6
    • 0035041886 scopus 로고    scopus 로고
    • A novel MSP/DHPLC method for the investigation of the methylation status of imprinted genes enables the molecular detection of low cell mosaicisms
    • Baumer A, Wiedemann U, Hergersberg M and Schinzel A (2001) A novel MSP/DHPLC method for the investigation of the methylation status of imprinted genes enables the molecular detection of low cell mosaicisms. Hum Mutat 17: 423-430
    • (2001) Hum. Mutat. , vol.17 , pp. 423-430
    • Baumer, A.1    Wiedemann, U.2    Hergersberg, M.3    Schinzel, A.4
  • 8
    • 0033753779 scopus 로고    scopus 로고
    • The DNA methyltransferases of mammals
    • Bestor TH (2000) The DNA methyltransferases of mammals. Hum Mol Genet 9: 2395-2402
    • (2000) Hum. Mol. Genet. , vol.9 , pp. 2395-2402
    • Bestor, T.H.1
  • 9
    • 0032836903 scopus 로고    scopus 로고
    • Methylation-sensitive, single-strand conformation analysis (MS-SSCA): A rapid method to screen for and analyze methylation
    • Bianco T, Hussey D and Dobrovic A (1999) Methylation-sensitive, single-strand conformation analysis (MS-SSCA): a rapid method to screen for and analyze methylation. Hum Mutat 14: 289-293
    • (1999) Hum. Mutat. , vol.14 , pp. 289-293
    • Bianco, T.1    Hussey, D.2    Dobrovic, A.3
  • 10
    • 0032966262 scopus 로고    scopus 로고
    • Complex methylation patterns analyzed by single-strand conformation polymorphism
    • Burri N and Chaubert P (1999) Complex methylation patterns analyzed by single-strand conformation polymorphism. Biotechniques 26: 232-234
    • (1999) Biotechniques , vol.26 , pp. 232-234
    • Burri, N.1    Chaubert, P.2
  • 14
    • 0030704336 scopus 로고    scopus 로고
    • Genome methylation of the marine annelid worm Chaetopterus variopedatus: Methylation of a CpG in an expressed H1 histone gene
    • del Gaudio R, Di Giaimo R and Geraci G (1997) Genome methylation of the marine annelid worm Chaetopterus variopedatus: methylation of a CpG in an expressed H1 histone gene. FEBS Lett 417: 48-52
    • (1997) FEBS Lett. , vol.417 , pp. 48-52
    • del Gaudio, R.1    Di Giaimo, R.2    Geraci, G.3
  • 15
    • 0033784719 scopus 로고    scopus 로고
    • Detection of CpG methylations in human mismatch repair gene HMLH1 promoter by denaturing high-performance liquid chromatography (DHPLC)
    • 171
    • Deng D, Deng G, Zhou J and Xin H (2000) Detection of CpG methylations in human mismatch repair gene HMLH1 promoter by denaturing high-performance liquid chromatography (DHPLC). Chin J Cancer Res 12: 171, 191
    • (2000) Chin. J. Cancer Res. , vol.12 , pp. 191
    • Deng, D.1    Deng, G.2    Zhou, J.3    Xin, H.4
  • 17
    • 0041719983 scopus 로고    scopus 로고
    • A rapid, quantitative, non-radioactive bisulfite-SNuPE-IP RP HPLC assay for methylation analysis at specific CpG sites
    • El Maarri O, Herbiniaux U, Walter J and Oldenburg J (2002) A rapid, quantitative, non-radioactive bisulfite-SNuPE-IP RP HPLC assay for methylation analysis at specific CpG sites. Nucleic Acids Res 30: e25
    • (2002) Nucleic Acids Res. , vol.30
    • El Maarri, O.1    Herbiniaux, U.2    Walter, J.3    Oldenburg, J.4
  • 18
    • 0036301150 scopus 로고    scopus 로고
    • High-performance capillary electrophoretic method for the quantification of 5-methyl 2′-deoxycytidine in genomic DNA: Application to plant, animal and human cancer tissues
    • Fraga MF, Uriol E, Borja DL, Berdasco M, Esteller M, Canal MJ and Rodriguez R (2002) High-performance capillary electrophoretic method for the quantification of 5-methyl 2′-deoxycytidine in genomic DNA: application to plant, animal and human cancer tissues. Electrophoresis 23: 1677-1681
    • (2002) Electrophoresis , vol.23 , pp. 1677-1681
    • Fraga, M.F.1    Uriol, E.2    Borja, D.L.3    Berdasco, M.4    Esteller, M.5    Canal, M.J.6    Rodriguez, R.7
  • 20
    • 0036144883 scopus 로고    scopus 로고
    • Methylation-specific oligonucleotide microarray: A new potential for high-throughput methylation analysis
    • Gitan RS, Shi H, Chen CM, Yan PS and Huang TH (2002) Methylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis. Genome Res 12: 158-164
    • (2002) Genome Res. , vol.12 , pp. 158-164
    • Gitan, R.S.1    Shi, H.2    Chen, C.M.3    Yan, P.S.4    Huang, T.H.5
  • 21
    • 0030738231 scopus 로고    scopus 로고
    • Rapid quantitation of methylation differences at specific sites using methylation-sensitive single nucleotide primer extension (Ms-SNuPE)
    • Gonzalgo ML and Jones PA (1997) Rapid quantitation of methylation differences at specific sites using methylation-sensitive single nucleotide primer extension (Ms-SNuPE). Nucleic Acids Res 25: 2529-2531
    • (1997) Nucleic Acids Res. , vol.25 , pp. 2529-2531
    • Gonzalgo, M.L.1    Jones, P.A.2
  • 22
    • 0031050736 scopus 로고    scopus 로고
    • Identification and characterization of differentially methylated regions of genomic DNA by methylation-sensitive arbitrarily primed PCR
    • Gonzalgo ML, Liang G, Spruck CH, Zingg JM, Rideout WM and Jones PA (1997) Identification and characterization of differentially methylated regions of genomic DNA by methylation-sensitive arbitrarily primed PCR. Cancer Res 57: 594-599
    • (1997) Cancer Res. , vol.57 , pp. 594-599
    • Gonzalgo, M.L.1    Liang, G.2    Spruck, C.H.3    Zingg, J.M.4    Rideout, W.M.5    Jones, P.A.6
  • 24
    • 0033047813 scopus 로고    scopus 로고
    • Methylation profiling of CpG islands in human breast cancer cells
    • Huang TH, Perry MR and Laux DE (1999) Methylation profiling of CpG islands in human breast cancer cells. Hum Mol Genet 8: 459-470
    • (1999) Hum. Mol. Genet. , vol.8 , pp. 459-470
    • Huang, T.H.1    Perry, M.R.2    Laux, D.E.3
  • 25
    • 0030888263 scopus 로고    scopus 로고
    • Identification of DNA methylation markers for human breast carcinomas using the methylation-sensitive restriction fingerprinting technique
    • Huang THM, Laux DE, Hamlin BC, Tran P, Tran H and Lubhan DB (1997) Identification of DNA methylation markers for human breast carcinomas using the methylation-sensitive restriction fingerprinting technique. Cancer Res 57: 1030-1034
    • (1997) Cancer Res. , vol.57 , pp. 1030-1034
    • Huang, T.H.M.1    Laux, D.E.2    Hamlin, B.C.3    Tran, P.4    Tran, H.5    Lubhan, D.B.6
  • 26
    • 0032960181 scopus 로고    scopus 로고
    • Cancer epigenetics comes of age
    • Jones PA and Laird PW (1999) Cancer epigenetics comes of age. Nat Genet 21: 163-167
    • (1999) Nat. Genet. , vol.21 , pp. 163-167
    • Jones, P.A.1    Laird, P.W.2
  • 28
    • 0019202657 scopus 로고
    • Quantitative reversed-phase high performance liquid chromatographic determination of major and modified deoxyribonucleosides in DNA
    • Kuo KC, McCune RA, Gehrke CW, Midgett R and Ehrlich M (1980) Quantitative reversed-phase high performance liquid chromatographic determination of major and modified deoxyribonucleosides in DNA. Nucleic Acids Res 8: 4763-4776
    • (1980) Nucleic Acids Res. , vol.8 , pp. 4763-4776
    • Kuo, K.C.1    McCune, R.A.2    Gehrke, C.W.3    Midgett, R.4    Ehrlich, M.5
  • 29
    • 0026099668 scopus 로고
    • Single nucleotide primer extension to detect genetic diseases: Experimental application to hemophilia B (factor IX) and cystic fibrosis genes
    • Kuppuswamy MN, Hoffmann JW, Kasper CK, Spitzer SG, Groce SL and Bajaj SP (1991) Single nucleotide primer extension to detect genetic diseases: experimental application to hemophilia B (factor IX) and cystic fibrosis genes. Proc Natl Acad Sci USA 88: 1143-1147
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 1143-1147
    • Kuppuswamy, M.N.1    Hoffmann, J.W.2    Kasper, C.K.3    Spitzer, S.G.4    Groce, S.L.5    Bajaj, S.P.6
  • 30
    • 0023476284 scopus 로고
    • Computational simulation of DNA melting and its application to denaturing gradient gel electrophoresis
    • Lerman LS and Silverstein K (1987) Computational simulation of DNA melting and its application to denaturing gradient gel electrophoresis. Methods Enzymol 155: 482-501
    • (1987) Methods Enzymol. , vol.155 , pp. 482-501
    • Lerman, L.S.1    Silverstein, K.2
  • 31
    • 0026708177 scopus 로고
    • Targeted mutation of the DNA methyltransferase gene results in embryonic lethality
    • Li E, Bestor TH and Jaenisch R (1992) Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69: 915-926
    • (1992) Cell , vol.69 , pp. 915-926
    • Li, E.1    Bestor, T.H.2    Jaenisch, R.3
  • 32
    • 0036856355 scopus 로고    scopus 로고
    • MethPrimer: Designing primers for methylation PCRs
    • Li LC and Dahiya R (2002) MethPrimer: designing primers for methylation PCRs. Bioinformatics 18: 1427-1431
    • (2002) Bioinformatics , vol.18 , pp. 1427-1431
    • Li, L.C.1    Dahiya, R.2
  • 33
    • 0027468779 scopus 로고
    • Cloning the differences between two complex genomes
    • Lisitsyn N, Lisitsyn N and Wigler M (1993) Cloning the differences between two complex genomes. Science 259: 946-951
    • (1993) Science , vol.259 , pp. 946-951
    • Lisitsyn, N.1    Lisitsyn, N.2    Wigler, M.3
  • 34
    • 0033533552 scopus 로고    scopus 로고
    • DNA methylation analysis using bisulfite treatment and PCR-single-strand conformation polymorphism in colorectal cancer showing microsatellite instability
    • Maekawa M, Sugano K, Kashiwabara H, Ushiama M, Fujita S, Yoshimori M and Kakizoe T (1999) DNA methylation analysis using bisulfite treatment and PCR-single-strand conformation polymorphism in colorectal cancer showing microsatellite instability. Biochem Biophys Res Common 262: 671-676
    • (1999) Biochem. Biophys. Res. Common. , vol.262 , pp. 671-676
    • Maekawa, M.1    Sugano, K.2    Kashiwabara, H.3    Ushiama, M.4    Fujita, S.5    Yoshimori, M.6    Kakizoe, T.7
  • 35
    • 0036311221 scopus 로고    scopus 로고
    • Methylation sequencing from limiting DNA: Embryonic, fixed, and microdissected cells
    • Millar DS, Warnecke PM, Melki JR and Clark SJ (2002) Methylation sequencing from limiting DNA: embryonic, fixed, and microdissected cells. Methods 27: 108-113
    • (2002) Methods , vol.27 , pp. 108-113
    • Millar, D.S.1    Warnecke, P.M.2    Melki, J.R.3    Clark, S.J.4
  • 36
    • 0032585866 scopus 로고    scopus 로고
    • DNA methylation analysis: A review of current methodologies
    • Oakeley EJ (1999) DNA methylation analysis: a review of current methodologies. Pharmacol Ther 84: 389-400
    • (1999) Pharmacol. Ther. , vol.84 , pp. 389-400
    • Oakeley, E.J.1
  • 37
    • 0030851819 scopus 로고    scopus 로고
    • Developmental changes in DNA methylation of the two tobacco pollen nuclei during maturation
    • Oakeley EJ, Podesta A and Jost JP (1997) Developmental changes in DNA methylation of the two tobacco pollen nuclei during maturation. Proc Natl Acad Sci USA 94: 11721-11725
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 11721-11725
    • Oakeley, E.J.1    Podesta, A.2    Jost, J.P.3
  • 38
    • 0032881723 scopus 로고    scopus 로고
    • Quantification of 5-methylcytosine in DNA by the chloroacetaldehyde reaction
    • 752
    • Oakeley EJ, Schmitt F and Jost JP (1999) Quantification of 5-methylcytosine in DNA by the chloroacetaldehyde reaction. Biotechniques 27: 744-50, 752
    • (1999) Biotechniques , vol.27 , pp. 744-750
    • Oakeley, E.J.1    Schmitt, F.2    Jost, J.P.3
  • 39
    • 0033615717 scopus 로고    scopus 로고
    • DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development
    • Okano M, Bell DW, Haber DA and Li E (1999) DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99: 247-257
    • (1999) Cell , vol.99 , pp. 247-257
    • Okano, M.1    Bell, D.W.2    Haber, D.A.3    Li, E.4
  • 40
    • 0030471926 scopus 로고    scopus 로고
    • A modified and improved method for bisulphite based cytosine methylation analysis
    • Olek A, Oswald J and Walter J (1996) A modified and improved method for bisulphite based cytosine methylation analysis. Nucleic Acids Res 24: 5064-5066
    • (1996) Nucleic Acids Res. , vol.24 , pp. 5064-5066
    • Olek, A.1    Oswald, J.2    Walter, J.3
  • 41
    • 0024595101 scopus 로고
    • Detection of polymorphisms of human DNA by gel as single-strand conformation polymorphisms
    • Orita M, Iwahana H, Kanazawa H, Hayashi K and Sekiya T (1989) Detection of polymorphisms of human DNA by gel as single-strand conformation polymorphisms. Proc Natl Acad Sci USA 86: 2766-2770
    • (1989) Proc. Natl. Acad. Sci. USA , vol.86 , pp. 2766-2770
    • Orita, M.1    Iwahana, H.2    Kanazawa, H.3    Hayashi, K.4    Sekiya, T.5
  • 42
    • 0032212130 scopus 로고    scopus 로고
    • Urea improves efficiency of bisulphite-mediated sequencing of 5′-methylcytosine in genomic DNA
    • Paulin R, Grigg GW, Davey MW and Piper AA (1998) Urea improves efficiency of bisulphite-mediated sequencing of 5′-methylcytosine in genomic DNA. Nucleic Acids Res 26: 5009-5010
    • (1998) Nucleic Acids Res. , vol.26 , pp. 5009-5010
    • Paulin, R.1    Grigg, G.W.2    Davey, M.W.3    Piper, A.A.4
  • 43
    • 0034801809 scopus 로고    scopus 로고
    • DNA methylation in genomic imprinting, development, and disease
    • Paulsen M and Ferguson-Smith AC (2001) DNA methylation in genomic imprinting, development, and disease. J Pathol 195: 97-110
    • (2001) J. Pathol. , vol.195 , pp. 97-110
    • Paulsen, M.1    Ferguson-Smith, A.C.2
  • 44
    • 0028961759 scopus 로고
    • A bisulfite method of 5-methylcytosine mapping that minimizes template degradation
    • Raizis AM, Schmitt F and Jost JP (1995) A bisulfite method of 5-methylcytosine mapping that minimizes template degradation. Anal Biochem 226: 161-166
    • (1995) Anal. Biochem. , vol.226 , pp. 161-166
    • Raizis, A.M.1    Schmitt, F.2    Jost, J.P.3
  • 45
    • 0031024587 scopus 로고    scopus 로고
    • Active mammalian replication origins are associated with a high-density cluster of mCpG dinucleotides
    • Rein T, Zorbas H and DePamphilis ML (1997) Active mammalian replication origins are associated with a high-density cluster of mCpG dinucleotides. Mol Cell Biol 17: 416-426
    • (1997) Mol. Cell Biol. , vol.17 , pp. 416-426
    • Rein, T.1    Zorbas, H.2    DePamphilis, M.L.3
  • 46
    • 0032524437 scopus 로고    scopus 로고
    • Identifying 5-methylcytosine and related modifications in DNA genomes
    • Rein T, DePamphilis ML and Zorbas H (1998) Identifying 5-methylcytosine and related modifications in DNA genomes. Nucleic Acids Res 26: 2255-2264
    • (1998) Nucleic Acids Res. , vol.26 , pp. 2255-2264
    • Rein, T.1    DePamphilis, M.L.2    Zorbas, H.3
  • 47
    • 0037068372 scopus 로고    scopus 로고
    • DNA methylation and chromatin - Unraveling the tangled web
    • Robertson KD (2002) DNA methylation and chromatin - unraveling the tangled web. Oncogene 21: 5361-5379
    • (2002) Oncogene , vol.21 , pp. 5361-5379
    • Robertson, K.D.1
  • 48
    • 0031019988 scopus 로고    scopus 로고
    • Antibiotics induce genome-wide hypermethylation in cultured Nicotiana tabacum plants
    • Schmitt F, Oakeley EJ and Jost JP (1997) Antibiotics induce genome-wide hypermethylation in cultured Nicotiana tabacum plants. J Biol Chem 272: 1534-1540
    • (1997) J. Biol. Chem. , vol.272 , pp. 1534-1540
    • Schmitt, F.1    Oakeley, E.J.2    Jost, J.P.3
  • 49
    • 0000023099 scopus 로고
    • Attachment of a 40-base-pair G+C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction in improved detection of single-base changes
    • Sheffield VC, Cox DR, Lerman LS and Myers RM (1989) Attachment of a 40-base-pair G+C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction in improved detection of single-base changes. Proc Natl Acad Sci USA 86: 232-236
    • (1989) Proc. Natl. Acad. Sci. USA , vol.86 , pp. 232-236
    • Sheffield, V.C.1    Cox, D.R.2    Lerman, L.S.3    Myers, R.M.4
  • 50
    • 0025060989 scopus 로고
    • A quantitative HpaII-PCR assay to measure methylation of DNA from a small number of cells
    • Singer-Sam J, LeBon JM, Tanguay RL and Riggs AD (1990) A quantitative HpaII-PCR assay to measure methylation of DNA from a small number of cells. Nucleic Acids Res 18: 687
    • (1990) Nucleic Acids Res. , vol.18 , pp. 687
    • Singer-Sam, J.1    LeBon, J.M.2    Tanguay, R.L.3    Riggs, A.D.4
  • 51
    • 0016700864 scopus 로고
    • Detection of specific sequences among DNA fragments separated by gel electrophoresis
    • Southern EM (1975) Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 98: 503-517
    • (1975) J. Mol. Biol. , vol.98 , pp. 503-517
    • Southern, E.M.1
  • 52
    • 0033563165 scopus 로고    scopus 로고
    • Identification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification
    • Toyota M, Ho C, Ahuja N, Jair KW, Li Q, Ohe-Toyota M, Baylin SB and Issa JP (1999) Identification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification. Cancer Res 59: 2307-2312
    • (1999) Cancer Res. , vol.59 , pp. 2307-2312
    • Toyota, M.1    Ho, C.2    Ahuja, N.3    Jair, K.W.4    Li, Q.5    Ohe-Toyota, M.6    Baylin, S.B.7    Issa, J.P.8
  • 53
    • 0035962668 scopus 로고    scopus 로고
    • Methyl CpG binding proteins: Coupling chromatin architecture to gene regulation
    • Wade PA (2001) Methyl CpG binding proteins: coupling chromatin architecture to gene regulation. Oncogene 20: 3166-3173
    • (2001) Oncogene , vol.20 , pp. 3166-3173
    • Wade, P.A.1
  • 54
    • 0030697141 scopus 로고    scopus 로고
    • Detection and measurement of PCR bias in quantitative methylation analysis of bisulphite-treated DNA
    • Warnecke PM, Stirzaker C, Melki JR, Millar DS, Paul CL and Clark SJ (1997) Detection and measurement of PCR bias in quantitative methylation analysis of bisulphite-treated DNA. Nucleic Acids Res 25: 4422-4426
    • (1997) Nucleic Acids Res. , vol.25 , pp. 4422-4426
    • Warnecke, P.M.1    Stirzaker, C.2    Melki, J.R.3    Millar, D.S.4    Paul, C.L.5    Clark, S.J.6
  • 56
    • 0034949862 scopus 로고    scopus 로고
    • In-tube DNA methylation profiling by fluorescence melting curve analysis
    • Worm J, Aggerholm A and Guldberg P (2001) In-tube DNA methylation profiling by fluorescence melting curve analysis. Clin Chem 47: 1183-1189
    • (2001) Clin. Chem. , vol.47 , pp. 1183-1189
    • Worm, J.1    Aggerholm, A.2    Guldberg, P.3
  • 58
    • 0034999807 scopus 로고    scopus 로고
    • Denaturing high-performance liquid chromatography: A review
    • Xiao W and Oefner PJ (2001) Denaturing high-performance liquid chromatography: A review. Hum Mutat 17: 439-474
    • (2001) Hum. Mutat. , vol.17 , pp. 439-474
    • Xiao, W.1    Oefner, P.J.2
  • 59
    • 0030825309 scopus 로고    scopus 로고
    • COBRA: A sensitive and quantitative DNA methylation assay
    • Xiong Z and Laird PW (1997) COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res 25: 2532-2534
    • (1997) Nucleic Acids Res. , vol.25 , pp. 2532-2534
    • Xiong, Z.1    Laird, P.W.2


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