Genome-Wide DNA Methylation Profiling: The mDIP-Chip Technology

  • Yin Shen
  • Shaun D. Fouse
  • Guoping Fan
Part of the Methods in Molecular Biology book series (MIMB, volume 568)


Aberrant DNA methylation is one of the major characteristics of tumor cells in addition to genetic and other epigenetic alterations. Evidence shows that both regional hypermethylation and global hypomethylation can occur in cancer cells. Increased DNA methylation can be found at select tumor-suppressor gene promoters, causing the silencing of these genes in tumorigenic cells. At the same time, a global decrease in DNA methylation is frequently observed in cancer cells, which may contribute to genome instability. Unlike genetic mutations, hypermethylation at tumor-suppressor gene promoters can be reversed with epigenetic therapy by using DNA demethylating agents.

To better understand the mechanisms of cancer initiation and progression, and to better assess the effects of epigenetic therapy, a reliable high-throughput method for genome-wide DNA methylation analysis is needed. Recently, the process of coupling methylated DNA immunoprecipitation (mDIP) with microarray hybridization has been proven to be a successful strategy to map genome-wide DNA methylation patterns in different cell types.

Key words

DNA methylation CpG island Immunoprecipitation Microarray Cancer 



We thank Dr. Howard Cedar at Hebrew University and Drs. Xiaoyu Zhang and Steve Jacobsen at UCLA for sharing with us their technical notes. Funding support for this work is from National Institutes of Health.


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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Yin Shen
    • 1
  • Shaun D. Fouse
    • 1
  • Guoping Fan
    • 1
  1. 1.Department of Human Genetics and Institute of Stem Cell Biology and MedicineDavid Geffen School of Medicine, UCLALos AngelesUSA

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