Bisulphite differential denaturation PCR for analysis of DNA methylation

Epigenetics

Volumn 1, Issue 2, 2006, Pages 94-100

  Rand, Keith N ^a   Mitchell, Susan M ^a   Clark, Susan J ^b   Molloy, Peter L ^a  

^a CSIRO   (Australia)

^b GARVAN INSTITUTE OF MEDICAL RESEARCH   (Australia)

Author keywords

Denaturation temperature; DNA methylation; Hypomethylation; Polymerase chain reaction; Sodium bisulphite

Indexed keywords

BRCA1 PROTEIN; BRCA1 PROTEIN, HUMAN; DNA; GLUTATHIONE TRANSFERASE P1; GSTP1 PROTEIN, HUMAN; HYDROGEN SULFITE; PRIMER DNA; SULFITE; UNCLASSIFIED DRUG;

ARTICLE; CHEMISTRY; DNA DENATURATION; DNA METHYLATION; EVALUATION; FEMALE; GENETICS; GENOME; HUMAN; METABOLISM; METHODOLOGY; POLYMERASE CHAIN REACTION; TEMPERATURE;

BRCA1 PROTEIN; DNA; DNA METHYLATION; DNA PRIMERS; FEMALE; GENOME, HUMAN; GLUTATHIONE S-TRANSFERASE PI; HUMANS; NUCLEIC ACID DENATURATION; POLYMERASE CHAIN REACTION; SULFITES; TEMPERATURE;

EID: 34648864301     PISSN: 15592294     EISSN: 15592308     Source Type: Journal    
DOI: 10.4161/epi.1.2.2680     Document Type: Article

References (23)

1. Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA. Primer directed amplification of DNA with a thermostable DNA polymerase. Science 1988; 2329:487-91.
2. Bartlett JMS, Stirling D. PCR Protocols. 2nd ed. Totowa, New Jersey, USA: Humana Press, 2003.
3. Lipsky RH, Mazzanti CM, Rudolph JG, Xu K, Vyas G, Bozak D, Radel MQ, Goldman D. DNA melting analysis for detection of single nucleotide polymorphisms. Clin Chem 2001; 47:635-44.
4. Guildberg P, Worm J, Gronbaek K. Profiling DNA methylation by melting analysis. Methods 2002; 27:121-7.
5. Betz B, Florl AR, Seifert HH, Dall P, Schulz WA, Niederacher D. Denaturing highperformance liquid chromatography (DHPLC) as a reliable high-throughput prescreening method for aberrant promoter methylation in cancer. Human Mutat 2004; 23:612-20.
6. Yap EP, McGee JO. Short PCR product yields improved by lower denaturation temperatures. Nucleic Acids Res 1991; 19:1713.
7. Masny A, Plucienniczak A. Ligation mediated PCR performed at low denaturation temperatures-PCR melting profiles. Nucleic Acids Res 2003; 31:e114.
8. Suspene R, Henry M, Guillot S, Wain-Hobson S, Vartarian JP. Recovery of APOBEC3-edited human immunodeficiency virus G->A hypermutants by differential DNA denaturation PCR. J Gen Virol 2005; 86:125-129.
9. Clark SJ, Harrison J, Frommer M. CpNpG methylation in mammalian cells. Nature Genet 1995; 10:20-27.
10. Ramsahoye BH, Biniszkiewicz D, Lyko F, Clark V, Bird AP, Jaenisch R. Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc Natl Acad Sci USA 2000; 97:5237-42.
11. Grace Goll M, Bestor T. Eukaryotic cytosine methyltransferases. Annu Rev Biochem 2005; 74:481-514.
12. Ehrlich M. Expression of various genes is controlled by DNA methylation during mammalian development. J Cell Biochem 2003; 88:899-910.
13. Dunn BC. Hypomethylation: One side of a larger picture. Ann NY Acad Sci 2003; 983:28-42.
14. de Smet C, Lurquin C, Lethe B, Mertelange V, Boon T. DNA methylation is the primary silencing mechanism for a set of germ line-and tumor-specific genes with a CpG rich promoter. Molec Cell Biol 1999; 19:7327-35.
15. de Smet C, Loriot A, Boon T. Promoter-dependent mechanism leading to selective hypomethylation within the 5′ region of gene MAGE-A1 in tumour cells. Molec Cell Biol 2004; 24:4781-90.
16. Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, Paul CL. A genomic sequencing protocol which yields a positive display of 5-methyl cytosine residues in individual DNA strands. Proc Natl Acad Sci USA 1992; 89:1827-31.
17. Clark SJ, Harrison J, Paul CL, Frommer M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res 1994; 22:2990-7.
18. Millar DS, Ow KK, Paul CL, Russell PJ, Molloy PL, Clark SJ. Detailed methylation analysis of the glutathione S-transferase oo(GSTP1) gene in prostate cancer. Oncogene 1999; 18:1313-24.
19. Rand KN, Qu W, Ho T, Clark SJ, Molloy PL. Conversion-specific detection of DNA methylation using real-time polymerase chain reaction (ConLight-MSP) to avoid false positives. Methods 2002; 27:114-20.
20. Warnecke PM, Stirzaker C, Song J. Grunau C, Melki JR, Clark SJ. Identification and resolution of artifacts in bisulfite sequencing. Methods 2002; 27:101-7.
21. Herman JG, Graff JR, Myohanen S, Nelkin BD, Baylin, SB. Methylation-specific PCR: A novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci USA 1996; 93:9821-6.
22. Rand KN, Ho T, Qu W, Mitchell SM, White R, Clark SJ, Molloy PL. Headloop suppression PCR and its application to selective amplification of methylated DNA sequences. Nucleic Acids Res 2005; 33:e127.
23. Cottrell SE, Distler J, Goodman NS, Mooney SH, Kluth A, Olek A, Schwope I, Tetzner R, Ziebarth H, Berlin K. A real-time PCR assay for DNA-methylation using methylationspecific blockers. Nucleic Acids Res 2004; 32:e10.