Department of Reproductive Biology, National Institute for Child Health and Development, Tokyo, Japan.
PLoS One. 2010 Sep 27;5(9):e13017. doi: 10.1371/journal.pone.0013017.
Human induced pluripotent stem (iPS) cells are currently used as powerful resources in regenerative medicine. During very early developmental stages, DNA methylation decreases to an overall low level at the blastocyst stage, from which embryonic stem cells are derived. Therefore, pluripotent stem cells, such as ES and iPS cells, are considered to have hypo-methylated status compared to differentiated cells. However, epigenetic mechanisms of "stemness" remain unknown in iPS cells derived from extra-embryonic and embryonic cells.
METHODOLOGY/PRINCIPAL FINDINGS: We examined genome-wide DNA methylation (24,949 CpG sites covering 1,3862 genes, mostly selected from promoter regions) with six human iPS cell lines derived from human amniotic cells and fetal lung fibroblasts as well as two human ES cell lines, and eight human differentiated cell lines using Illumina's Infinium HumanMethylation27. A considerable fraction (807 sites) exhibited a distinct difference in the methylation level between the iPS/ES cells and differentiated cells, with 87.6% hyper-methylation seen in iPS/ES cells. However, a limited fraction of CpG sites with hypo-methylation was found in promoters of genes encoding transcription factors. Thus, a group of genes becomes active through a decrease of methylation in their promoters. Twenty-three genes including SOX15, SALL4, TDGF1, PPP1R16B and SOX10 as well as POU5F1 were defined as genes with hypo-methylated SS-DMR (Stem cell-Specific Differentially Methylated Region) and highly expression in iPS/ES cells.
CONCLUSIONS/SIGNIFICANCE: We show that DNA methylation profile of human amniotic iPS cells as well as fibroblast iPS cells, and defined the SS-DMRs. Knowledge of epigenetic information across iPS cells derived from different cell types can be used as a signature for "stemness" and may allow us to screen for optimum iPS/ES cells and to validate and monitor iPS/ES cell derivatives for human therapeutic applications.
人类诱导多能干细胞（iPS）目前被用作再生医学中的强大资源。在囊胚阶段，DNA 甲基化程度降低到整体低水平，胚胎干细胞就来源于这个阶段。因此，与分化细胞相比，多能干细胞，如 ES 和 iPS 细胞，被认为具有低甲基化状态。然而，在源自胚胎外和胚胎细胞的 iPS 细胞中，“干性”的表观遗传机制仍不清楚。
方法/主要发现：我们使用 Illumina 的 Infinium HumanMethylation27 检查了来自人羊膜细胞和胎儿肺成纤维细胞的六个人类 iPS 细胞系以及两个人类 ES 细胞系和八个人类分化细胞系的全基因组 DNA 甲基化（覆盖 13862 个基因的 24949 个 CpG 位点，主要从启动子区域选择）。iPS/ES 细胞和分化细胞之间的甲基化水平存在显著差异（807 个位点），iPS/ES 细胞中观察到 87.6%的高甲基化。然而，在编码转录因子的基因启动子中发现了有限数量的低甲基化 CpG 位点。因此，通过降低启动子中的甲基化，一组基因变得活跃。包括 SOX15、SALL4、TDGF1、PPP1R16B 和 SOX10 以及 POU5F1 在内的 23 个基因被定义为具有低甲基化 SS-DMR（干细胞特异性差异甲基化区域）和在 iPS/ES 细胞中高表达的基因。
结论/意义：我们表明人羊膜 iPS 细胞以及成纤维 iPS 细胞的 DNA 甲基化谱，并定义了 SS-DMR。来自不同细胞类型的 iPS 细胞的表观遗传信息知识可作为“干性”的特征，并可用于筛选最佳的 iPS/ES 细胞，并验证和监测 iPS/ES 细胞衍生物在人类治疗应用中的应用。
Zotero 插件
