A panel of CpG methylation sites distinguishes human embryonic stem cells and induced pluripotent stem cells

Kevin Huang, Yin Shen, Zhigang Xue, Marina Bibikova, Craig April, Zhenshan Liu, Linzhao Cheng, Andras Nagy, Matteo Pellegrini, Jian Bing Fan, Guoping Fan

Research output: Contribution to journalArticleResearchpeer-review

Abstract

Whether human induced pluripotent stem cells (hiPSCs) are epigenetically identical to human embryonic stem cells (hESCs) has been debated in the stem cell field. In this study, we analyzed DNA methylation patterns in a large number of hiPSCs (n = 114) and hESCs (n = 155), and identified a panel of 82 CpG methylation sites that can distinguish hiPSCs from hESCs with high accuracy. We show that 12 out of the 82 CpG sites were subject to hypermethylation in part by DNMT3B. Notably, DNMT3B contributes directly to aberrant hypermethylation and silencing of the signature gene, TCERG1L. Overall, we conclude that DNMT3B is involved in a wave of de novo methylation during reprogramming, a portion of which contributes to the unique hiPSC methylation signature. These 82 CpG methylation sites may be useful as biomarkers to distinguish between hiPSCs and hESCs.

Original languageEnglish
Pages (from-to)36-43
Number of pages8
JournalStem Cell Reports
Volume2
Issue number1
DOIs
Publication statusPublished - 14 Jan 2014
Externally publishedYes

Cite this

Huang, Kevin ; Shen, Yin ; Xue, Zhigang ; Bibikova, Marina ; April, Craig ; Liu, Zhenshan ; Cheng, Linzhao ; Nagy, Andras ; Pellegrini, Matteo ; Fan, Jian Bing ; Fan, Guoping. / A panel of CpG methylation sites distinguishes human embryonic stem cells and induced pluripotent stem cells. In: Stem Cell Reports. 2014 ; Vol. 2, No. 1. pp. 36-43.
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abstract = "Whether human induced pluripotent stem cells (hiPSCs) are epigenetically identical to human embryonic stem cells (hESCs) has been debated in the stem cell field. In this study, we analyzed DNA methylation patterns in a large number of hiPSCs (n = 114) and hESCs (n = 155), and identified a panel of 82 CpG methylation sites that can distinguish hiPSCs from hESCs with high accuracy. We show that 12 out of the 82 CpG sites were subject to hypermethylation in part by DNMT3B. Notably, DNMT3B contributes directly to aberrant hypermethylation and silencing of the signature gene, TCERG1L. Overall, we conclude that DNMT3B is involved in a wave of de novo methylation during reprogramming, a portion of which contributes to the unique hiPSC methylation signature. These 82 CpG methylation sites may be useful as biomarkers to distinguish between hiPSCs and hESCs.",
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Huang, K, Shen, Y, Xue, Z, Bibikova, M, April, C, Liu, Z, Cheng, L, Nagy, A, Pellegrini, M, Fan, JB & Fan, G 2014, 'A panel of CpG methylation sites distinguishes human embryonic stem cells and induced pluripotent stem cells' Stem Cell Reports, vol. 2, no. 1, pp. 36-43. https://doi.org/10.1016/j.stemcr.2013.11.003

A panel of CpG methylation sites distinguishes human embryonic stem cells and induced pluripotent stem cells. / Huang, Kevin; Shen, Yin; Xue, Zhigang; Bibikova, Marina; April, Craig; Liu, Zhenshan; Cheng, Linzhao; Nagy, Andras; Pellegrini, Matteo; Fan, Jian Bing; Fan, Guoping.

In: Stem Cell Reports, Vol. 2, No. 1, 14.01.2014, p. 36-43.

Research output: Contribution to journalArticleResearchpeer-review

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AU - Cheng, Linzhao

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AU - Fan, Guoping

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