Preference of DNA methyltransferases for CpG islands in mouse embryonic stem cells.
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.
Laboratory of Cellular Biochemistry, Animal Resource Sciences/Veterinary Medical Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan.
Naka
N
Hattori
Tetsuya
T
Abe
Naoko
N
Hattori
Masako
M
Suzuki
Tomoki
T
Matsuyama
Shigeo
S
Yoshida
En
E
Li
Kunio
K
Shiota
D000818:Animals; D002478:Cells, Cultured; D018899:CpG Islands; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000172:deficiency* / Q000235:genetics*; D019175:DNA Methylation; D004622:Embryo, Mammalian / Q000166:cytology*; D006720:Homozygote; D051379:Mice; D018345:Mice, Knockout; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013234:Stem Cells / Q000201:enzymology*
D004248:DNA (Cytosine-5-)-Methyltransferases