TY - JOUR
T1 - Genome-wide and locus-specific DNA hypomethylation in G9a deficient mouse embryonic stem cells
AU - Ikegami, Kohta
AU - Iwatani, Misa
AU - Suzuki, Masako
AU - Tachibana, Makoto
AU - Shinkai, Yoichi
AU - Tanaka, Satoshi
AU - Greally, John M.
AU - Yagi, Shintaro
AU - Hattori, Naka
AU - Shiota, Kunio
PY - 2007/1
Y1 - 2007/1
N2 - 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 locito 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.
AB - 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 locito 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.
UR - http://www.scopus.com/inward/record.url?scp=33845781998&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=33845781998&partnerID=8YFLogxK
U2 - 10.1111/j.1365-2443.2006.01029.x
DO - 10.1111/j.1365-2443.2006.01029.x
M3 - Article
C2 - 17212651
AN - SCOPUS:33845781998
SN - 1356-9597
VL - 12
SP - 1
EP - 11
JO - Genes to Cells
JF - Genes to Cells
IS - 1
ER -