To determine if the non-CG mega-DMRs affected disruption of transcriptional activity, we compared the transcript abundance between ADS-iPSCs and H1 ES cells of genes located within these regions (Fig. 5f). Of the 50 RefSeq genes within the non-CG mega-DMRs, 33 showed ≥ 2-fold lower transcript abundance in ADS-iPSCs compared to H1 ES cells (Supplementary Table 7). This indicates that non-CG mega-DMRs are associated with transcriptional disruption in the iPSCs (Fig. 5g). Notably, 10 of the 11 iDMRs that were consistently hypermethylated in every iPSC line (Fig. 4a, b) were located within the non-CG mega-DMRs (P = 8.5 × 10−39), but this was not true of any of the common hypomethylated CG-DMRs. Further, 9 of these 10 consistently hypermethylated iDMRs located in non-CG mega-DMRs were transmitted to the trophoblast cells derived from the FF-iPSC 19.11 line. Lastly, 64% of genes with lower transcript abundance in ADS-iPSCs in non-CG mega-DMRs also showed dense CG hypermethylation at the transcriptional start site (Fig. 5f, red circles), a subset of which were consistently hypermethylated at the transcriptional start site in all iPSC lines analysed and
