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Preference of DNA Methyltransferases for CpG Islands in Mouse Embryonic Stem Cells

2004; Cold Spring Harbor Laboratory Press; Volume: 14; Issue: 9 Linguagem: Inglês

10.1101/gr.2431504

1549-5469

Naka Hattori, Tetsuya Abe, Naoko Hattori, Masako Suzuki, Tomoki Matsuyama, Shigeo Yoshida, En Li, Kunio Shiota,

Genomics and Chromatin Dynamics

Many CpG islands have tissue-dependent and differentially methylated regions (T-DMRs) in normal cells and tissues. To elucidate how DNA methyltransferases (Dnmts) participate in methylation of the genomic components, we investigated the genome-wide DNA methylation pattern of the T-DMRs with Dnmt1 -, Dnmt3a -, and/or Dnmt3b -deficient ES cells by restriction landmark genomic scanning (RLGS). Approximately 1300 spots were detected in wild-type ES cells. In Dnmt1 -/- ES cells, additional 236 spots emerged, indicating that the corresponding loci are methylated by Dnmt1 in wild-type ES cells. Intriguingly, in Dnmt3a -/- Dnmt3b -/- ES cells, the same 236 spots also emerged, and no additional spots appeared differentially. Therefore, Dnmt1 and Dnmt3a/3b share targets in CpG islands. Cloning and virtual image RLGS revealed that 81% of the RLGS spots were associated with genes, and 62% of the loci were in CpG islands. By contrast to the previous reports that demethylation at repeated sequences was severe in Dnmt1 -/- cells compared with Dnmt3a -/- Dnmt3b -/- cells, a complete loss of methylation was observed at RLGS loci in Dnmt3a -/- Dnmt3b -/- cells, whereas methylation levels only decreased to 16% to 48% in the Dnmt1 -/- cells. We concluded that there are CpG islands with T-DMR as targets shared by Dnmt1 and Dnmt3a/3b and that each Dnmt has target preferences depending on the genomic components.