Genetic variation modulates aberrant DNA hypomethylation in naïve pluripotent stem cells

Naïve pluripotent stem cells (nPSC) frequently undergo pathological and not readily reversible loss of DNA methylation marks at imprinted gene loci. This abnormality poses a hurdle for the use of pluripotent cell lines in biomedical applications and underscores the need to identify the causes underlying imprint instability in these cells. Here, we show that nPSCs from inbred mouse strains exhibit pronounced strain-specific susceptibility to locus-specific deregulation of imprinting marks during reprogramming to pluripotency and upon culture with MAP kinase inhibitors, the most common approach to maintain naïve pluripotency. Analysis of genetically highly diverse nPSCs from the Diversity Outbred (DO) stock confirms that genetic variation is a major determinant of epigenome stability in pluripotent cells. We leverage the variable DNA hypomethylation in DO lines to identify several trans-acting quantitative trait loci (QTLs) that determine epigenome stability at either specific target loci or genome-wide. Candidate factors encoded by two multi-target QTLs on chromosomes 4 and 17 suggest specific transcriptional regulators that contribute to methylation maintenance in nPSCs. We propose that genetic variants represent candidate biomarkers to identify pluripotent cell lines with desirable properties and might serve as entry points for the targeting engineering of nPSCs with stable epigenomes. We performed EM-seq + targeted enrichment to measure DNA methylation at a panel of ~400 genomic regions in naïve pluripotent stem cells. Our goal was to evaluate the variability in DNA methylation levels present among 80 naïve pluripotent stem cell lines derived from Diversity Outbred mouse stock