Aberrant DNA Methylation in Human iPSCs Associates with MYC-Binding Motifs in a Clone-Specific Manner Independent of Genetics

Cell Stem Cell. 2017 Apr 6;20(4):505-517.e6. doi: 10.1016/j.stem.2017.03.010.


Induced pluripotent stem cells (iPSCs) show variable methylation patterns between lines, some of which reflect aberrant differences relative to embryonic stem cells (ESCs). To examine whether this aberrant methylation results from genetic variation or non-genetic mechanisms, we generated human iPSCs from monozygotic twins to investigate how genetic background, clone, and passage number contribute. We found that aberrantly methylated CpGs are enriched in regulatory regions associated with MYC protein motifs and affect gene expression. We classified differentially methylated CpGs as being associated with genetic and/or non-genetic factors (clone and passage), and we found that aberrant methylation preferentially occurs at CpGs associated with clone-specific effects. We further found that clone-specific effects play a strong role in recurrent aberrant methylation at specific CpG sites across different studies. Our results argue that a non-genetic biological mechanism underlies aberrant methylation in iPSCs and that it is likely based on a probabilistic process involving MYC that takes place during or shortly after reprogramming.

Keywords: MYC binding motifs; NHLBI NextGen; aberrant methylation; genetic background; iPSC; iPSCORE; induced pluripotent stem cells; methylation variation; reprogramming.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Clone Cells
  • CpG Islands / genetics
  • DNA Methylation / genetics*
  • Fibroblasts / metabolism
  • Gene Expression Regulation
  • Genetic Variation
  • Genome-Wide Association Study
  • Humans
  • Induced Pluripotent Stem Cells / metabolism*
  • Nucleotide Motifs / genetics*
  • Proto-Oncogene Proteins c-myc / metabolism*
  • Sequence Analysis, RNA
  • Transcription Factors / metabolism
  • Twins, Monozygotic / genetics


  • Proto-Oncogene Proteins c-myc
  • Transcription Factors