High-throughput sequencing reveals the disruption of methylation of imprinted gene in induced pluripotent stem cells
High-throughput sequencing reveals the disruption of methylation of imprinted gene in induced pluripotent stem cells
复制标题
DOI：
10.1038/cr.2013.173
复制
发表时间：
2014-03-01
期刊：
影响因子：
44.1
通讯作者：
Tian, Jianhui
中科院分区：
文献类型：
--
作者：
Chang, Gang;Gao, Shuai;Tian, Jianhui
诱导性多能干细胞（iPSC）中积累的异常表观遗传修饰是否会最终影响iPSC的多能性仍然存在争议。为了探索这个问题，建立了具有相同遗传背景和前病毒整合位点的iPSC系，并且使用四倍体（4 N）互补测定来表征每个iPSC系的多能性状态。随后，通过mRNA表达、小RNA谱、组蛋白修饰（H3 K27 me 3、H3 K4 me 3和H3 K4 me 2）和DNA甲基化的深度测序分析，比较“4 N-ON”和相应的“4 N-OFF”iPSC系的基因表达和整体表观遗传修饰。我们发现，在多能性降低的iPSC系中，印记基因Zrsr 1的甲基化一直被破坏。此外，破坏的甲基化不能通过改善培养条件或iPSC的亚克隆来挽救。此外，Zrsr 1的低甲基化与iPSC的多能性状态之间的关系在来自其他重编程系统的独立iPSC系中得到进一步验证。
It remains controversial whether the abnormal epigenetic modifications accumulated in the induced pluripotent stem cells (iPSCs) can ultimately affect iPSC pluripotency. To probe this question, iPSC lines with the same genetic background and proviral integration sites were established, and the pluripotency state of each iPSC line was characterized using tetraploid (4N) complementation assay. Subsequently, gene expression and global epigenetic modifications of "4N-ON" and the corresponding "4N-OFF" iPSC lines were compared through deep sequencing analyses of mRNA expression, small RNA profile, histone modifications (H3K27me3, H3K4me3, and H3K4me2), and DNA methylation. We found that methylation of an imprinted gene, Zrsr1, was consistently disrupted in the iPSC lines with reduced pluripotency. Furthermore, the disrupted methylation could not be rescued by improving culture conditions or subcloning of iPSCs. Moreover, the relationship between hypomethylation of Zrsr1 and pluripotency state of iPSCs was further validated in independent iPSC lines derived from other reprogramming systems.