DNA methylation restricts coordinated germline and neural fates in embryonic stem cell differentiation

Abstract

As embryonic stem cells transition from naive to primed pluripotency during early mammalian development, they acquire high DNA methylation levels. During this transition, the germline gets specified and undergoes genome-wide DNA demethylation, while the emergence of the three somatic germ layers is preceded by the acquisition of somatic DNA methylation levels in the primed epiblast. DNA methylation is essential for embryogenesis, but the point at which it becomes critical during differentiation and whether all lineages equally depend on it is unclear. Using culture modeling of cellular transitions, we found that DNA methylation-free mouse embryonic stem cells (ESCs) with a triple DNA methyltransferase knockout (TKO) progressed through the continuum of pluripotency states, but demonstrated skewed differentiation abilities towards neural versus other somatic lineages. More saliently, TKO ESCs were fully competent for establishing primordial germ cell-like cells (PGCLCs), even showing temporally extended and self-sustained capacity for the germline fate. By mapping chromatin states, we found that the neural and germline lineages are linked by a similar enhancer dynamic upon exit from the naive state, defined by common sets of transcription factors-including methyl-sensitive onesthat fail to be decommissioned in absence of DNA methylation. We propose that DNA methylation controls the temporality of a coordinated neural-germline axis of preferred differentiation route during early development.