Aberrant DNA methylation reprogramming during induced pluripotent stem cell generation is dependent on the choice of reprogramming factors.
Aberrant DNA methylation reprogramming during induced pluripotent stem cell generation is dependent on the choice of reprogramming factors.
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DOI：
10.1186/2045-9769-3-4
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发表时间：
2014
期刊：
影响因子：
--
通讯作者：
Batada NN
中科院分区：
文献类型：
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作者：
Planello AC;Ji J;Sharma V;Singhania R;Mbabaali F;Müller F;Alfaro JA;Bock C;De Carvalho DD;Batada NN
体细胞通过过表达重编程因子转化为多能干细胞涉及表观遗传重塑。诱导多能干细胞（iPSCs）与胚胎干细胞（ESCs）在CpG位点的DNA甲基化比例显著不同。不同的重编程因子是否对iPSCs中异常DNA甲基化的类型和程度有不同的影响尚不清楚。为了帮助解决这个关键问题，我们使用Yamanaka因子（OCT4, SOX2， KLF4和cMYC）或Thomson因子（OCT4, SOX2， NANOG和LIN28）从一个常见的成纤维细胞来源生成了人类iPSCs，并确定了它们的全基因组DNA甲基化谱。除了所有ipsc中存在的共享DNA甲基化畸变外，我们还鉴定了Yamanaka-iPSC （Y-iPSC）特异性和Thomson-iPSC （T-iPSC）特异性复发畸变。引人注目的是，不仅基因组畸变的位置不同，而且畸变的类型也不同：用Yamanaka因子重编程主要导致CpGs去甲基化失败，而用Thomson因子重编程主要导致CpGs甲基化失败。Y-iPSCs和T-iPSCs之间编码DNMT3b和TET3转录本水平的差异可能部分促成了不同类型的畸变。最后，Y-iPSCs中新的异常甲基化基因在NANOG靶点上富集，这些靶点在某些癌症中也异常甲基化。因此，我们的研究揭示了重编程因子的选择会影响iPSCs中DNA甲基化畸变的数量、位置和类别。这些发现可能为如何产生DNA甲基化异常较少的人类iPSCs提供线索。本文的在线版本（doi:10.1186/2045-9769-3-4）包含补充材料，可供授权用户使用。
The conversion of somatic cells into pluripotent stem cells via overexpression of reprogramming factors involves epigenetic remodeling. DNA methylation at a significant proportion of CpG sites in induced pluripotent stem cells (iPSCs) differs from that of embryonic stem cells (ESCs). Whether different sets of reprogramming factors influence the type and extent of aberrant DNA methylation in iPSCs differently remains unknown. In order to help resolve this critical question, we generated human iPSCs from a common fibroblast cell source using either the Yamanaka factors (OCT4, SOX2, KLF4 and cMYC) or the Thomson factors (OCT4, SOX2, NANOG and LIN28), and determined their genome-wide DNA methylation profiles. In addition to shared DNA methylation aberrations present in all our iPSCs, we identified Yamanaka-iPSC (Y-iPSC)-specific and Thomson-iPSC (T-iPSC)-specific recurrent aberrations. Strikingly, not only were the genomic locations of the aberrations different but also their types: reprogramming with Yamanaka factors mainly resulted in failure to demethylate CpGs, whereas reprogramming with Thomson factors mainly resulted in failure to methylate CpGs. Differences in the level of transcripts encoding DNMT3b and TET3 between Y-iPSCs and T-iPSCs may contribute partially to the distinct types of aberrations. Finally, de novo aberrantly methylated genes in Y-iPSCs were enriched for NANOG targets that are also aberrantly methylated in some cancers. Our study thus reveals that the choice of reprogramming factors influences the amount, location, and class of DNA methylation aberrations in iPSCs. These findings may provide clues into how to produce human iPSCs with fewer DNA methylation abnormalities. The online version of this article (doi:10.1186/2045-9769-3-4) contains supplementary material, which is available to authorized users.