An unbiased genome-wide screen reveals that mouse metastable epialleles are extremely rare

Metastable epialleles (MEs) are genomic loci at which epigenetic marks are established stochastically during early embryonic development and maintained during subsequent differentiation and throughout life, leading to stable epigenetic and phenotypic variation amongst genetically identical individuals. Although MEs were first described in mice over 20 years ago, the extent of epigenetic metastability in the mouse genome remains unknown. We present the first unbiased genome-wide screen for MEs in mice. Using deep whole-genome bisulfite sequencing across tissues derived from the three embryonic germ layers in isogenic C57BL/6J mice, we identified only 30 MEs, documenting their rarity and precisely localizing them. In line with recent findings, our results showed no effects of maternal dietary methyl donor supplementation on ME methylation, challenging previous findings linking epigenetic metastability with developmental plasticity. Not all MEs are associated with intracisternal A-particle (IAP) elements; the vast majority of those that are, however, localize at the 5' end of the IAP. Additionally, we discovered autosomal regions at which systemic interindividual variation in DNA methylation is associated with sex. These findings advance our understanding of MEs' epigenetic regulation in embryonic development and provide insights into sex-associated epigenetic development that apparently precedes sexual differentiation.