Novel imprinted single CpG sites found by global DNA methylation analysis in human parthenogenetic induced pluripotent stem cells

Genomic imprinting is the process of epigenetic modification whereby genes are expressed in a parent-of-origin dependent manner; it plays an important role in normal growth and development. Parthenogenetic embryos contain only the maternal genome. Parthenogenetic embryonic stem cells could be useful for studying imprinted genes. In humans, mature cystic ovarian teratomas originate from parthenogenetic activation of oocytes; they are composed of highly differentiated mature tissues containing all three germ layers. To establish human parthenogenetic induced pluripotent stem cell lines (PgHiPSCs), we generated parthenogenetic fibroblasts from ovarian teratoma tissues. We compared global DNA methylation status of PgHiPSCs with that of biparental human induced pluripotent stem cells by using Illumina Infinium HumanMethylation450 BeadChip array. This analysis identified novel single imprinted CpG sites. We further tested DNA methylation patterns of two of these sites using bisulfite sequencing and described novel candidate imprinted CpG sites. These results confirm that PgHiPSCs are a powerful tool for identifying imprinted genes and investigating their roles in human development and diseases.

基因组印记（Genomic imprinting）是一类表观遗传修饰（epigenetic modification）过程，指基因以亲本起源依赖性方式进行表达，其在正常生长发育中发挥关键调控作用。孤雌生殖胚胎仅包含母本基因组，孤雌胚胎干细胞可用于印记基因（imprinted genes）的相关研究。在人类中，成熟囊性卵巢畸胎瘤（mature cystic ovarian teratomas）起源于卵母细胞（oocytes）的孤雌激活，其由包含全部三胚层的高度分化成熟组织构成。为构建人类孤雌诱导多能干细胞系（PgHiPSCs），我们从卵巢畸胎瘤组织中分离得到孤雌成纤维细胞。我们采用Illumina Infinium HumanMethylation450 BeadChip芯片，比较了PgHiPSCs与双亲本人类诱导多能干细胞的全基因组DNA甲基化状态，该分析鉴定出了全新的单等位印记CpG位点。我们进一步通过亚硫酸氢盐测序（bisulfite sequencing）验证了其中两个位点的DNA甲基化模式，并报道了新型候选印记CpG位点。上述研究结果证实，PgHiPSCs是鉴定印记基因、探究其在人类发育与疾病中功能的高效研究工具。