non-CG mega-DMRs tend to be partially methylated in the CG context in non-pluripotent cells (99.5% of non-CG mega-DMR bases are partially methylated in ADS cells; Fig. 5d). Taken together, these data indicate that specific large regions of somatic cell genomes proximal to centromeres and telomeres that are in the partially methylated mCG state, and that bear the heterochromatin modification H3K9me3, may often be resistant to complete reprogramming of non-CG methylation to the embryonic state, remaining in a somatic configuration after induction of pluripotency (exemplified for one DMR in Fig. 5e).
