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Journal of Biochemistry 2006 139(3):503-515; doi:10.1093/jb/mvj044
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© 2006 The Japanese Biochemical Society.

Regular Paper

Distinct DNA Methylation Activity of Dnmt3a and Dnmt3b towards Naked and Nucleosomal DNA

Hideyuki Takeshima1, Isao Suetake1, Hideto Shimahara2, Kiyoe Ura3, Shin-ichi Tate1 and Shoji Tajima1,*

1 Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871; 2 Center for Nano Materials and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292; and 3 Division of Gene Therapy Science, Osaka University School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0871

* To whom correspondence should be addressed. Tel: +81-6-6879-8627, Fax: +81-6-6879-8629, E-mail: tajima{at}protein.osaka-u.ac.jp

In mammals, the resetting of DNA methylation patterns in early embryos and germ cells is crucial for development. De novo type DNA methyltransferases Dnmt3a and Dnmt3b are responsible for creating DNA methylation patterns during embryogenesis and in germ cells. Although their in vitro DNA methylation properties are similar, Dnmt3a and Dnmt3b methylate different genomic DNA regions in vivo. In the present study, we have examined the DNA methylation activity of Dnmt3a and Dnmt3b towards nucleosomes reconstituted from recombinant histones and DNAs, and compared it to that of the corresponding naked DNAs. Dnmt3a showed higher DNA methylation activity than Dnmt3b towards naked DNA and the naked part of nucleosomal DNA. On the other hand, Dnmt3a scarcely methylated the DNA within the nucleosome core region, while Dnmt3b significantly did, although the activity was low. We propose that the preferential DNA methylation activity of Dnmt3a towards the naked part of nucleosomal DNA and the significant methylation activity of Dnmt3b towards the nucleosome core region contribute to their distinct methylation of genomic DNA in vivo.


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