DNA methylation: Bisulphite modification and analysis (original) (raw)

References

  1. Warnecke, P.M. & Clark, S.J. DNA methylation profile of the mouse skeletal alpha-actin promoter during development and differentiation. Mol. Cell. Biol. 19, 164–172 (1999).
    Article CAS Google Scholar
  2. Jones, P.A. Overview of cancer epigenetics. Semin. Hematol. 42, S3–S8 (2005).
    Article CAS Google Scholar
  3. Grigg, G. & Clark, S. Sequencing 5-methylcytosine residues in genomic DNA. Bioessays 16, 431–436 (1994).
    Article CAS Google Scholar
  4. Clark, S.J. & Frommer, M. in DNA and Nucleoprotein Structure In Vivo Springer-Verlag (eds. Saluz, H.P. & Wiebauer, K.) 123–132 (R.G. Landes Company, Austin, Texas, 1995).
    Google Scholar
  5. Clark, S.J. & Frommer, M. in Laboratory Methods for the Detection of Mutations and Polymorphisms in DNA (ed. Taylor, G.) 151–162 (CRC Press, New York, 1997).
    Google Scholar
  6. Frommer, M. et al. 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 (1992).
    Article CAS Google Scholar
  7. Clark, S.J., Harrison, J., Paul, C.L. & Frommer, M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res. 22, 2990–2997 (1994).
    Article CAS Google Scholar
  8. Rakyan, V.K. et al. DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project. PLoS Biol. 2, e405 (2004).
    Article Google Scholar
  9. Rauscher, F.J. It is time for a Human Epigenome Project. Cancer Res. 65, 11229 (2005).
    Article CAS Google Scholar
  10. Murrell, A., Rakyan, V.K. & Beck, S. From genome to epigenome. Hum. Mol. Genet. 14 (Spec No. 1): R3–R10 (2005).
    Article CAS Google Scholar
  11. Jones, P.A. & Martienssen, R. A blueprint for a Human Epigenome Project: the AACR Human Epigenome Workshop. Cancer Res. 65, 11241–11246 (2005).
    Article CAS Google Scholar
  12. Callinan, P.A. & Feinberg, A.P. The emerging science of epigenomics. Hum. Mol. Genet. 15 (Spec No. 1): R95–R101 (2006).
    Article CAS Google Scholar
  13. Garber, K. Momentum building for human epigenome project. J. Natl. Cancer Inst. 98, 84–86 (2006).
    Article Google Scholar
  14. Esteller, M. The necessity of a human epigenome project. Carcinogenesis 27, 1121–1125 (2006).
    Article CAS Google Scholar
  15. Singal, R. & Grimes, S.R. Microsoft Word macro for analysis of cytosine methylation by the bisulfite deamination reaction. Biotechniques 30, 116–120 (2001).
    Article CAS Google Scholar
  16. Li, L.C. & Dahiya, R. MethPrimer: designing primers for methylation PCRs. Bioinformatics 18, 1427–1431 (2002).
    Article CAS Google Scholar
  17. Tusnady, G.E., Simon, I., Varadi, A. & Aranyi, T. BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes. Nucleic Acids Res. 33, e9 (2005).
    Article Google Scholar
  18. Warnecke, P.M. et al. Identification and resolution of artifacts in bisulfite sequencing. Methods 27, 101–107 (2002).
    Article CAS Google Scholar
  19. Grunau, C., Clark, S.J. & Rosenthal, A. Bisulfite genomic sequencing: systematic investigation of critical experimental parameters. Nucleic Acids Res. 29, E65–5 (2001).
    Article CAS Google Scholar
  20. Paul, C.L. & Clark, S.J. Cytosine methylation: quantitation by automated genomic sequencing and GENESCAN analysis. Biotechniques 21, 126–133 (1996).
    Article CAS Google Scholar
  21. Boyd, V.L. & Zon, G. Bisulfite conversion of genomic DNA for methylation analysis: protocol simplification with higher recovery applicable to limited samples and increased throughput. Anal. Biochem. 326, 278–280 (2004).
    Article CAS Google Scholar
  22. Lewin, J., Schmitt, A.O., Adorjan, P., Hildmann, T. & Piepenbrock, C. Quantitative DNA methylation analysis based on four-dye trace data from direct sequencing of PCR amplificates. Bioinformatics 20, 3005–3012 (2004).
    Article CAS Google Scholar
  23. Han, W., Cauchi, S., Herman, J.G. & Spivack, S.D. DNA methylation mapping by tag-modified bisulfite genomic sequencing. Anal. Biochem. 355, 50–61 (2006).
    Article CAS Google Scholar
  24. Tost, J., Dunker, J. & Gut, I.G. Analysis and quantification of multiple methylation variable positions in CpG islands by Pyrosequencing. Biotechniques 35, 152–156 (2003).
    Article CAS Google Scholar
  25. Colella, S., Shen, L., Baggerly, K.A., Issa, J.P. & Krahe, R. Sensitive and quantitative universal Pyrosequencing methylation analysis of CpG sites. Biotechniques 35, 146–150 (2003).
    Article CAS Google Scholar
  26. Laird, C.D. et al. Hairpin-bisulfite PCR: assessing epigenetic methylation patterns on complementary strands of individual DNA molecules. Proc. Natl. Acad. Sci. USA 101, 204–209 (2004).
    Article CAS Google Scholar
  27. Schatz, P., Dietrich, D. & Schuster, M. Rapid analysis of CpG methylation patterns using RNase T1 cleavage and MALDI-TOF. Nucleic Acids Res. 32, e167 (2004).
    Article Google Scholar
  28. Ehrich, M. et al. Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc. Natl. Acad. Sci. USA 102, 15785–15790 (2005).
    Article CAS Google Scholar
  29. Worm, J., Aggerholm, A. & Guldberg, P. In-tube DNA methylation profiling by fluorescence melting curve analysis. Clin. Chem. 47, 1183–1189 (2001).
    CAS PubMed Google Scholar
  30. Guldberg, P., Worm, J. & Gronbaek, K. Profiling DNA methylation by melting analysis. Methods 27, 121–127 (2002).
    Article CAS Google Scholar
  31. Yang, I. et al. Rapid quantification of DNA methylation through dNMP analysis following bisulfite-PCR. Nucleic Acids Res. 34, e61 (2006).
    Article Google Scholar
  32. Yamamoto, T. et al. Methylation assay by nucleotide incorporation: a quantitative assay for regional CpG methylation density. Biotechniques 36, 846–50 852, 854 (2004).
    Article CAS Google Scholar
  33. Maekawa, M. et al. DNA methylation analysis using bisulfite treatment and PCR-single-strand conformation polymorphism in colorectal cancer showing microsatellite instability. Biochem. Biophys. Res. Commun. 262, 671–676 (1999).
    Article CAS Google Scholar
  34. Bianco, T., Hussey, D. & Dobrovic, A. Methylation-sensitive, single-strand conformation analysis (MS-SSCA): A rapid method to screen for and analyze methylation. Hum. Mutat. 14, 289–293 (1999).
    Article CAS Google Scholar
  35. Baumer, A., Wiedemann, U., Hergersberg, M. & Schinzel, A. 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).
    Article CAS Google Scholar
  36. Sadri, R. & Hornsby, P.J. Rapid analysis of DNA methylation using new restriction enzyme sites created by bisulfite modification. Nucleic Acids Res. 24, 5058–5059 (1996).
    Article CAS Google Scholar
  37. Xiong, Z. & Laird, P.W. COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res. 25, 2532–2534 (1997).
    Article CAS Google Scholar
  38. Eads, C.A. & Laird, P.W. Combined bisulfite restriction analysis (COBRA). Methods Mol. Biol. 200, 71–85 (2002).
    CAS PubMed Google Scholar
  39. Gonzalgo, M.L. & Jones, P.A. Quantitative methylation analysis using methylation-sensitive single-nucleotide primer extension (Ms-SNuPE). Methods 27, 128–133 (2002).
    Article CAS Google Scholar
  40. Kaminsky, Z.A., Assadzadeh, A., Flanagan, J. & Petronis, A. Single nucleotide extension technology for quantitative site-specific evaluation of metC/C in GC-rich regions. Nucleic Acids Res. 33, e95 (2005).
    Article Google Scholar
  41. El-Maarri, O., Herbiniaux, U., Walter, J. & Oldenburg, J. A rapid, quantitative, non-radioactive bisulfite-SNuPE- IP RP HPLC assay for methylation analysis at specific CpG sites. Nucleic Acids Res. 30, e25 (2002).
    Article Google Scholar
  42. Gitan, R.S., Shi, H., Chen, C.M., Yan, P.S. & Huang, T.H. Methylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis. Genome Res. 12, 158–164 (2002).
    Article CAS Google Scholar
  43. Adorjan, P. et al. Tumour class prediction and discovery by microarray-based DNA methylation analysis. Nucleic Acids Res. 30, e21 (2002).
    Article Google Scholar
  44. Thomassin, H., Kress, C. & Grange, T. MethylQuant: a sensitive method for quantifying methylation of specific cytosines within the genome. Nucleic Acids Res. 32, e168 (2004).
    Article Google Scholar
  45. Bibikova, M. et al. High-throughput DNA methylation profiling using universal bead arrays. Genome Res. 16, 383–393 (2006).
    Article CAS Google Scholar
  46. Herman, J.G., Graff, J.R., Myohanen, S., Nelkin, B.D. & Baylin, S.B. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc. Natl. Acad. Sci. USA 93, 9821–9826 (1996).
    Article CAS Google Scholar
  47. Eads, C.A. et al. MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res. 28, E32 (2000).
    Article CAS Google Scholar
  48. Rand, K., Qu, W., Ho, T., Clark, S.J. & Molloy, P. Conversion-specific detection of DNA methylation using real-time polymerase chain reaction (ConLight-MSP) to avoid false positives. Methods 27, 114–120 (2002).
    Article CAS Google Scholar
  49. Zeschnigk, M. et al. A novel real-time PCR assay for quantitative analysis of methylated alleles (QAMA): analysis of the retinoblastoma locus. Nucleic Acids Res. 32, e125 (2004).
    Article Google Scholar
  50. Cottrell, S.E. et al. A real-time PCR assay for DNA-methylation using methylation-specific blockers. Nucleic Acids Res. 32, e10 (2004).
    Article Google Scholar
  51. Rand, K.N. et al. Headloop suppression PCR and its application to selective amplification of methylated DNA sequences. Nucleic Acids Res. 33, e127 (2005).
    Article Google Scholar
  52. Shaw, R.J., Akufo-Tetteh, E.K., Risk, J.M., Field, J.K. & Liloglou, T. Methylation enrichment pyrosequencing: combining the specificity of MSP with validation by pyrosequencing. Nucleic Acids Res. 34, e78 (2006).
    Article Google Scholar
  53. Rand, K., Mitchell, S., Clark, S. & Molloy, P. Bisulphite differential denaturation PCR for analysis of DNA methylation. Epigenetics 1, 94–100 (2006).
    Article Google Scholar
  54. Warnecke, P.M. et al. Detection and measurement of PCR bias in quantitative methylation analysis of bisulphite-treated DNA. Nucleic Acids Res. 25, 4422–4426 (1997).
    Article CAS Google Scholar

Download references