Microarray analysis of DNA methylation targets identified by methyl-CpG-binding proteins

Masahiko Shiraishi, Michael W.Y. Chan, Hui-ming Huang

Research output: Chapter in Book/Report/Conference proceedingChapter


We propose the combined use of methyl-CpG-binding domain (MBD) column chromatography and microarray technologies for interrogating cancer genomes. The MBD column chromatograph is based on the affinity binding of methylated CpG island targets to individual MBD proteins and is used to selectively elute bound DNA fragments. The approach is shown to be effective for identifying a large number of methylated loci in the cancer genome. To increase throughput, cloned DNA fragments can further be spotted on microarray slides for differential methylation hybridization. Fluorescently labeled amplicons, which represent different pools of methylated DNA fragments in tumor and control samples, are prepared and cohybridized onto a microarray slide. Methylated loci are identified based on their differential fluorescence intensities in tumors relative to the control samples. Hierarchical clustering algorithms are further employed to segregate tumor subgroups showing similar methylation profiles. Such a microarray-based analysis, which uses cloned methylated loci by the MBD technology, can routinely be used for clinical diagnosis of specific cancer types.

Original languageEnglish (US)
Title of host publicationDNA Methylation
Subtitle of host publicationApproaches, Methods, and Applications
PublisherCRC Press
Number of pages12
ISBN (Electronic)9780203487013
ISBN (Print)9780849320507
StatePublished - Jan 1 2004
Externally publishedYes

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)


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