Enrichment of short interspersed transposable elements to embryonic stem cell-specific hypomethylated gene regions
Enrichment of short interspersed transposable elements to embryonic stem cell-specific hypomethylated gene regions
复制标题
将短散布转座元件富集到胚胎干细胞特异性低甲基化基因区域
DOI：
10.1111/j.1365-2443.2010.01423.x
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发表时间：
2010
期刊：
影响因子：
2.1
通讯作者：
Shiota K
中科院分区：
文献类型：
--
作者：
Muramoto H;Yagi S;Hirabayashi K;Sato S;Ohgane J;Tanaka S;Shiota K
胚胎干细胞（ESC）具有独特的表观基因组，包括其全基因组DNA甲基化修饰状态，如Pou 5 f1和Nanog的组织依赖性和差异甲基化区域（T-DMR）的ESC特异性低甲基化。在这里，我们通过关注转座因子，包括短散置因子（西内斯），长散置因子（LINES）和长末端重复序列（LTR），对与ESC和体细胞之间差异甲基化的T-DMR相关的序列特征进行了全基因组研究。我们发现低甲基化T-DMR主要存在于富含SINE/缺乏LINE的基因组位点中。西内斯的富集分布在300 kb切口上，并且存在连续分布在1 Mb上的富含SINE的基因组结构域，其包含多个低甲基化的T-DMR。 序列信息分析表明，富集的西内斯中含有丰富的CpG序列，属于特定的亚家族。富集的西内斯的一个子集是Dppa 3基因座处ESC中的低甲基化T-DMR，尽管西内斯在ESC和肝脏中总体上是甲基化的。总之，我们提出SINE富集是ESC中含有低甲基化T-DMR的区域的基因组特性，这是ESC特异性表观基因组信息的一个新方面。
Embryonic stem cells (ESCs) have a distinctive epigenome, which includes their genome‐wide DNA methylation modification status, as represented by the ESC‐specific hypomethylation of tissue‐dependent and differentially methylated regions (T‐DMRs) ofPou5f1andNanog. Here, we conducted a genome‐wide investigation of sequence characteristics associated with T‐DMRs that were differentially methylated between ESCs and somatic cells, by focusing on transposable elements including short interspersed elements (SINEs), long interspersed elements (LINEs) and long terminal repeats (LTRs). We found that hypomethylated T‐DMRs were predominantly present in SINE‐rich/LINE‐poor genomic loci. The enrichment for SINEs spread over 300 kb incisand there existed SINE‐rich genomic domains spreading continuously over 1 Mb, which contained multiple hypomethylated T‐DMRs. The characterization of sequence information showed that the enriched SINEs were relatively CpG rich and belonged to specific subfamilies. A subset of the enriched SINEs were hypomethylated T‐DMRs in ESCs atDppa3gene locus, although SINEs are overall methylated in both ESCs and the liver. In conclusion, we propose that SINE enrichment is the genomic property of regions harboring hypomethylated T‐DMRs in ESCs, which is a novel aspect of the ESC‐specific epigenomic information.