Recurrent variations in DNA methylation in human pluripotent stem cells and their differentiated derivatives

Kristopher L. Nazor, Gulsah Altun, Candace Lynch, Ha Tran, Julie V. Harness, Ileana Slavin, Ibon Garitaonandia, Franz Josef Müller, Yu Chieh Wang, Francesca S. Boscolo, Eyitayo Fakunle, Biljana Dumevska, Sunray Lee, Hyun Sook Park, Tsaiwei Olee, Darryl D. D'Lima, Ruslan Semechkin, Mana M. Parast, Vasiliy Galat, Andrew L. LaslettUli Schmidt, Hans S. Keirstead, Jeanne F. Loring, Louise C. Laurent*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

312 Scopus citations


Human pluripotent stem cells (hPSCs) are potential sources of cells for modeling disease and development, drug discovery, and regenerative medicine. However, it is important to identify factors that may impact the utility of hPSCs for these applications. In an unbiased analysis of 205 hPSC and 130 somatic samples, we identified hPSC-specific epigenetic and transcriptional aberrations in genes subject to X chromosome inactivation (XCI) and genomic imprinting, which were not corrected during directed differentiation. We also found that specific tissue types were distinguished by unique patterns of DNA hypomethylation, which were recapitulated by DNA demethylation during in vitro directed differentiation. Our results suggest that verification of baseline epigenetic status is critical for hPSC-based disease models in which the observed phenotype depends on proper XCI or imprinting and that tissue-specific DNA methylation patterns can be accurately modeled during directed differentiation of hPSCs, even in the presence of variations in XCI or imprinting.

Original languageEnglish (US)
Pages (from-to)620-634
Number of pages15
JournalCell stem cell
Issue number5
StatePublished - May 4 2012

ASJC Scopus subject areas

  • Genetics
  • Molecular Medicine
  • Cell Biology


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