Aberrant DNA methylation reprogramming during iPS generation is dependent on the choice of reprogramming factors

The conversion of somatic cells into pluripotent stem cells via overexpression of reprogramming factors involves epigenome remodeling. DNA methylation at a significant proportion of CpG sites in induced pluripotent stem (iPS) cells differs from that of embryonic stem (ES) cells. Whether different sets of reprogramming factors influence the type and extent of aberrant DNA methylation in iPS cells differently remains unknown. To resolve this critical question, we generate iPS clones from a common fibroblast cell source using either the Yamanaka factors (OCT4, SOX2, KLF4 and MYC) 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 iPS lines, we identify Yamanaka-iPS (Y-iPS)-specific and Thomson-iPS (T-iPS)-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. The differences in the level of transcripts encoding DNMT3b and TET3 between Y-iPS and T-iPS may contribute partially to the distinct types of aberrations. Finally, de novo aberrantly methylated genes in Y-iPS were enriched for NANOG targets which are also aberrantly methylated in some cancers. Our study reveals that the choice of reprogramming factors influences the amount of, the location of and the class of DNA methylation aberrations in iPS cells. The differences in the DNA methylation and demethylation potency of these factors may be exploited to successfully reprogram donor cells with disparate levels of DNA methylation.

Click: HERE to download an Excel file containing normalized and background corrected DNA methylation data for 9 Y-iPS cells, 6 T-iPS cells, 2 parental Fibroblasts and one ES cell.