Genome-wide and locus-specific DNA hypomethylation in G9a deficient mouse embryonic stem cells.
In the mammalian genome, numerous CpG-rich loci define tissue-dependent and differentially methylated regions (T-DMRs). Euchromatin from different cell types differs in terms of its tissue-specific DNA methylation profile as defined by these T-DMRs. G9a is a euchromatin-localized histone methyltransferase (HMT) and catalyzes methylation of histone H3 at lysines 9 and 27 (H3-K9 and -K27). To test whether HMT activity influences euchromatic cytosine methylation, we analyzed the DNA methylation status of approximately 2000 CpG-rich loci, which are predicted in silico, in G9a(-/-) embryonic stem cells by restriction landmark genomic scanning (RLGS). While the RLGS profile of wild-type cells contained about 1300 spots, 32 new spots indicating DNA demethylation were seen in the profile of G9a(-/-) cells. Virtual-image RLGS (Vi-RLGS) allowed us to identify the genomic source of ten of these spots. These were confirmed to be cytosine demethylated, not just at the Not I site detected by the RLGS but extending over several kilobase pairs in cis. Chromatin immunoprecipitation (ChIP) confirmed these loci to be targets of G9a, with decreased H3-K9 and/or -K27 dimethylation in the G9a(-/-) cells. These data indicate that G9a site-selectively contributes to DNA methylation.
Ikegami
Kohta
K
Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences and Veterinary Medical Sciences, The University of Tokyo, Tokyo 113-8657, Japan.
Iwatani
Misa
M
Suzuki
Masako
M
Tachibana
Makoto
M
Shinkai
Yoichi
Y
Tanaka
Satoshi
S
Greally
John M
JM
Yagi
Shintaro
S
Hattori
Naka
N
Shiota
Kunio
K
D000818:Animals; D047369:Chromatin Immunoprecipitation; D018899:CpG Islands; D003545:Cysteine / Q000378:metabolism; D004247:DNA / Q000378:metabolism; D019175:DNA Methylation; D053595:Embryonic Stem Cells / Q000201:enzymology*; D022041:Euchromatin / Q000201:enzymology / Q000378:metabolism; D017353:Gene Deletion; D016678:Genome; D000076983:Histone Methyltransferases; D011495:Histone-Lysine N-Methyltransferase / Q000235:genetics / Q000378:metabolism*; D006657:Histones / Q000378:metabolism; D051379:Mice; D008957:Models, Genetic; D009707:Nucleosomes / Q000378:metabolism; D016133:Polymerase Chain Reaction; D011496:Protein Methyltransferases
D022041:Euchromatin; D006657:Histones; D009707:Nucleosomes; D004247:DNA; D000076983:Histone Methyltransferases; D011496:Protein Methyltransferases; D011495:Histone-Lysine N-Methyltransferase; D003545:Cysteine