A Susceptibility Locus on Chromosome 13 Profoundly Impacts the Stability of Genomic Imprinting in Mouse Pluripotent Stem Cells

Abstract

Summary: Cultured pluripotent cells accumulate detrimental chromatin alterations, including DNA methylation changes at imprinted genes known as loss of imprinting (LOI). Although the occurrence of LOI is considered a stochastic phenomenon, here we document a genetic determinant that segregates mouse pluripotent cells into stable and unstable cell lines. Unstable lines exhibit hypermethylation at Dlk1-Dio3 and other imprinted loci, in addition to impaired developmental potential. Stimulation of demethylases by ascorbic acid prevents LOI and loss of developmental potential. Susceptibility to LOI greatly differs between commonly used mouse strains, which we use to map a causal region on chromosome 13 with quantitative trait locus (QTL) analysis. Our observations identify a strong genetic determinant of locus-specific chromatin abnormalities in pluripotent cells and provide a non-invasive way to suppress them. This highlights the importance of considering genetics in conjunction with culture conditions for assuring the quality of pluripotent cells for biomedical applications. : The gradual erosion of chromatin marks vital for mammalian development is a problematic feature of pluripotent cell culture. Swanzey et al. provide strong evidence that this instability at imprinted loci is controlled by genetic determinants and map a candidate regulator to a region on mouse chromosome 13. Keywords: genomic imprinting, Dlk1-Dio3, IG-DMR, epigenetic stability, pluripotent stem cells, reprogramming, ascorbic acid, C57BL/6J, quantitative trait locus, DNA methylation