DNA methylation programming and reprogramming in primate embryonic stem cells

DNA methylation is an important epigenetic mechanism, affecting normal development and playing a key role in reprogramming epigenomes during stem cell derivation. Here we report on DNA methylation patterns in native monkey embryonic stem (ES) cells, fibroblasts and ES cells generated through somatic cell nuclear transfer (SCNT), identifying and comparing epigenome programming and reprogramming. We characterize hundreds of regions that are hyper- or hypo- methylated in fibroblasts compared to native ES cells and show that these are conserved in human cells and tissues. Remarkably, the vast majority of these regions are reprogrammed in SCNT ES cells, leading to almost perfect correlation between the epigenomic profiles of the native and reprogrammed lines. At least 58% of these changes are correlated in cis to transcription changes, Polycomb Repressive Complex-2 occupancy, or binding by the CTCF insulator. We also show that while epigenomic reprogramming is extensive and globally accurate, the efficiency of adding and stripping DNA methylation during reprogramming is regionally variable. In several cases, this variability results in regions that remain methylated in a fibroblast-like pattern even after reprogramming. DNA methylation profiles in rhesus monkey native ES cells (ORMES-22), fibroblasts, and ES cells generated by somatic cell nuclear transfer (CRES-2), as well as a distinctly different native ES line (the homozygous parthenote ORMES-9) to control for ES line specific effects were identified via hybridization to a custom array including a set of human ESC bivalent domains combined with additional methylation related domains and control regions.