We discovered previously that 40% of the genome of IMR90 fibroblasts was in a partially methylated state, termed partially methylated domains (PMDs)18. The DNA methylomes of the primary somatic cell lines we have profiled here also contain PMDs in a similar proportion of the genome to IMR90 cells (Fig. 2a). As observed previously in IMR90 cells, the transcript abundance associated with genes located within PMDs was lower than the average for all other genes (Fig. 2b). Notably, these PMDs were transformed to a fully methylated state in the CG context by induction of a pluripotent state (Fig. 2a and Supplementary Fig. 7). Lastly, the reprogramming process was able to reverse the transcriptional repression associated with the PMD state (Fig. 2b).
