An analytical method for the detection of methylation differences at specific chromosomal loci using primer extension and ion pair reverse phase HPLC

Human Mutation

Volumn 20, Issue 4, 2002, Pages 305-311

  Matin, Maryam M ^a   Baumer, Alessandra ^b   Hornby, David P ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

^b UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

Angelman syndrome; AS; DNA methylation; Epigenetics; Imprinted genes; IP RP HPLC; Prader Willi syndrome; Primer extension; PWS

Indexed keywords

BISULFITE; CYTOSINE; DNA; PRIMER DNA; RESTRICTION ENDONUCLEASE; URACIL;

ALLELE; AMPLICON; ARTICLE; CHROMOSOME; CPG ISLAND; DEAMINATION; DIAGNOSTIC ACCURACY; DISEASE ASSOCIATION; GENE AMPLIFICATION; GENE LOCUS; GENE MUTATION; GENE SEQUENCE; GENE TARGETING; GENETIC ANALYSIS; GENOME; HAPPY PUPPET SYNDROME; INTERMETHOD COMPARISON; ISOTOPE LABELING; MEASUREMENT; METHYLATION; NUCLEOTIDE SEQUENCE; PLASMID; PRADER WILLI SYNDROME; PRIORITY JOURNAL; REVERSED PHASE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; SEQUENCE ANALYSIS;

AMPICILLIN RESISTANCE; ANGELMAN SYNDROME; BASE SEQUENCE; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; CHROMATOGRAPHY, ION EXCHANGE; CPG ISLANDS; CYTOSINE; DEAMINATION; DNA; DNA METHYLATION; DNA PRIMERS; GENETIC MARKERS; GENOMIC IMPRINTING; HUMANS; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; NUCLEIC ACID AMPLIFICATION TECHNIQUES; POLYMERASE CHAIN REACTION; PRADER-WILLI SYNDROME; SULFITES; URACIL;

EID: 0036390019     PISSN: 10597794     EISSN: None     Source Type: Journal    
DOI: 10.1002/humu.10118     Document Type: Article

References (28)

1. Angelman H. 1965. "Puppet children": a report of three cases. Dev Med Child Neurol 7:681-683.
2. Baumer A, Wiedemann U, Hergersberg M, 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.
3. Bestor TH. 2000. The DNA methyltransferases of mammals. Hum Mol Genet 16:2395-2402.
4. Clark SJ, Harrison J, Paul CL, Frommer M. 1994. High sensitivity mapping of methylated cytosines. Nucleic Acids Res 22:2990-2997.
5. Doerfler W. 1983. DNA methylation and gene activity. Ann Rev Biochem 52:93-124.
6. Frommer M, McDonald LE, Millar DS, Collis GM, Watt F, Grigg GW, Molloy PL, Paul CL. 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.
7. Gjerde DT, Hanna CP, Hornby DP. 2002. DNA Chromatography. Weinheim: Wiley-VCH Verlag GmbH. p 228.
8. Gonzalgo M, 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.
9. Herman JG, Graff JR, Myohanen S, Nelkin BD, Baylin SB. 1996. Methylation-specific PCR: a novel assay for methylation status of CpG islands. Proc Natl Acad Sci USA 93:9821-9826.
10. Hoogendoorn B, Owen MJ, Oefner PJ, Williams N, Austin J, O'Donovan MC. 1999. Genotyping single nucleotide polymorphisms by primer extension and high performance liquid chromatography. Hum Genet 104:89-93.
11. Ledbetter DH, Riccardi VM, Airhart SD, Strobel RJ, Keenan BS, Crawford JD. 1981. Deletions of chromosome 15 as a cause of the Prader-Willi syndrome. N Engl J Med 304: 325-329.
12. Matin MM. 2000. Analysis and applications of mutant C5-DNA methyltransferases. Ph.D. thesis, University of Sheffield, Sheffield, UK.
13. Matin MM, Hornby DP. 2000. A positive selection vector combining tetracycline resistance that eliminates the need for bacterial plating. Anal Biochem 278:46-51.
14. Nakao M, Sutcliffe JS, Durtschi B, Mutirangura A, Ledbetter DH, Beaudet AL. 1994. Imprinting analysis of three genes in the Prader-Willi/Angelman region: SNRPN, E6-associated protein, and PAR-2 (D15S225E). Hum Mol Genet 3: 309-315.
15. Nicholls RD, Knoll JH, Butler MG, Karam S, Lalande M. 1989. Genetic imprinting suggested by maternal uniparental heterodisomy in nondeletion Prader-Willi syndrome. Nature 342:281-285.
16. Nicholls RD. 1994. New insights reveal complex mechanisms involved in genomic imprinting. Am J Hum Genet 54: 733-740.
17. Olek A, Oswald J, Walter J. 1996. A modified and improved method for bisulphite based cytosine methylation analysis. Nucleic Acids Res 24:5064-5066.
18. Paul CL, Clark SJ. 1996. Cytosine methylation: quantitation by automated genomic sequencing and GENESCAN analysis. Biotechniques 21:126-133.
19. Prader A, Labhart A, Willi H. 1956. Ein syndrom von adipositas, kleinwuchs, kryptorchismus und oligophrenie nach myatonieartigem zustand im neugeborenenalter: Schweiz Med Wochenschr 86:1260-1261.
20. Reed ML, Leef SE. 1994. Maternal imprinting of human SNRPN, a gene deleted in Prader-Willi syndrome. Nat Genet 6:163-167.
21. Robinson WP, Bottani A, Yagang X, Balakrishman J, Binkert F, Mächler M, Prader A, Schinzel A. 1991. Molecular, cytogenetic, and clinical investigations of Prader-Willi syndrome patients. Am J Hum Genet 49:1219-1234.
22. Shapiro R, Braverman B, Louis JB, Servis RE. 1973. Nucleic acid reactivity and conformation: reaction of cytosine and uracil with sodium bisulfite. J Biol Chem 248:4060-4064.
23. Singer J, Roberts-Ems J, Riggs AD. 1979. Methylation of mouse liver DNA studied by means of the restriction enzymes MspI and HpaII. Science 203:1019-1021.
24. Singer-Sam J, Grant M, LeBon JM, Okuyama K, Chapman V, Monk M, Riggs AD. 1990. Use of a HpaII-polymerase chain reaction assay to study DNA methylation in the Pgk-1 CpG island of mouse embryos at the time of X-chromosome inactivation. Mol Cell Biol 10:4987-4989.
25. Southern EM. 1975. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 98:503-517.
26. Warnecke PM, Bestor TH. 2000. Cytosine methylation and human cancer. Curr Opin Oncol 12:68-73.
27. Xiao W, Oefner PJ. 2001. Denaturing high performance liquid chromatography: a review. Hum Murat 17:439-474.
28. Zeschnigk M, Schmitz B, Dittrich B, Buiting K, Horsthemke B, Doerfler W. 1997. Imprinted segments in the human genome: different DNA methylation patterns in the Prader-Willi/Angelman syndrome region as determined by the genomic sequencing method. Hum Mol Genet 6: 387-395.