Abstract
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.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 1-11 |
| Number of pages | 11 |
| Journal | Genes to Cells |
| Volume | 12 |
| Issue number | 1 |
| DOIs | |
| State | Published - Jan 2007 |
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ASJC Scopus subject areas
- Genetics
- Cell Biology
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Genome-wide and locus-specific DNA hypomethylation in G9a deficient mouse embryonic stem cells. / Ikegami, Kohta; Iwatani, Misa; Suzuki, Masako; Tachibana, Makoto; Shinkai, Yoichi; Tanaka, Satoshi; Greally, John M.; Yagi, Shintaro; Hattori, Naka; Shiota, Kunio.
In: Genes to Cells, Vol. 12, No. 1, 01.2007, p. 1-11.Research output: Contribution to journal › Article
}
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
VL - 12
SP - 1
EP - 11
JO - Genes to Cells
JF - Genes to Cells
SN - 1356-9597
IS - 1
ER -