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Enrichment of Short interspersed transposable elements (SINEs) in hypomethylated genic regions in embryonic stem cells
Author(s) -
Muramoto Hiroki,
Yagi Shintaro,
Hirabayashi Keiji,
Sato Shinya,
Ohgane Jun,
Tanaka Satoshi,
Shiota Kunio
Publication year - 2010
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.24.1_supplement.459.2
Subject(s) - differentially methylated regions , dna methylation , biology , transposable element , methylation , cpg site , genome , genetics , somatic cell , gene , embryonic stem cell , microbiology and biotechnology , gene expression
Genome‐wide studies of DNA methylation modification of embryonic stem cells (ESCs) and somatic cells have revealed that there are numerous tissue‐dependently and differentially methylated regions (T‐DMRs). Combination of methylation status of each T‐DMR, called DNA methylation profile, is specific to ESCs. Transposable elements (TEs) occupy about the half of the mammalian genome. In general, DNA methylation modification repressed transposition of TEs. In this study, we examined whether there exist genomic sequence features, focusing on TE distributions, around genes that have T‐DMRs differentially methylated between ESCs and somatic cells. We first identified T‐DMRs hypo/hypermethylated in ESCs in promoter regions by comparing genome‐wide methylation status of ESCs with liver, and explored the TE proportions in flanking region over 100 kb. We found that genes with hypomethylated T‐DMRs in ESCs showed significantly higher SINE and lower LINE proportions. The enriched SINEs had a CpG‐rich property and were of specific subfamilies. These results demonstrated that SINE enrichment in the flanking regions is a distinctive characteristics of genes with hypomethylated T‐DMRs and further suggest that SINEs play a role in the formation of ESC DNA mehtylation profile. This work was supported by the grants from NEDO, NIBIO, and JSPS Research Fellowship for Young Scientists.