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Regulatory Patterns of Histone Modifications to Control the DNA Methylation Status at CpG Islands
Inkyung Jung1 and Dongsup Kim1,2,*
1Department of Bio and Brain Engineering, KAIST, Daejeon 305-701, Republic of Korea
2KAIST Institute for BioCentury, KAIST, Daejeon 305-701, Republic of Korea
*Corresponding author
  Received : March 24, 2009
  Accepted : March 30, 2009
  Published : March 30, 2009
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Introduction: Histone modifications and DNA methylation are the major factors in epigenetic gene regulation. Especially, revealing how histone modifications are related to DNA methylation is one of the challenging problems in this field. In this paper, we address this issue and propose several plausible mechanisms for precise controlling of DNA methylation status at CpG islands.
Materials and Methods: To establish the regulatory relationships, we used 38 histone modification types including H2A.Z and CTCF, and DNA methylation status at CpG islands across chromosome 6, 20, and 22 of human CD4+ T cell. We utilized Bayesian network to construct regulatory network.
Results and Discussion: We found several meaningful relationships supported by previous studies. In addition, our results show that histone modifications can be clustered into several groups with different regulatory properties. Based on those findings we predicted the status of methylation level at CpG islands with high accuracy, and suggested core-regulatory network to control DNA methylation status.

Keyword: histone modification, epigenetics, DNA methylation
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