TCA cycle rewiring underpins histone acetylation sourcing and cell-fate transitions during exit from naive pluripotency

Metabolism shapes stem cell differentiation and epigenome regulation, especially during the exit from naive pluripotency in vitro . Yet how metabolic networks reorganize at implantation remains unclear. Here, we map metabolite routing in pre- and post-implantation mouse embryos and across dynamic pluripotency transitions in stem cells, revealing that the tricarboxylic acid (TCA) cycle undergoes spatio-temporal rewiring rather than a simple shutdown. Pyruvate emerges as a central metabolic nexus, where pyruvate carboxylase and malic enzyme activities create a cyclical carbon flow essential for balanced metabolic and transcriptional states, timely exit from naive pluripotency, and differentiation. As cells leave naive pluripotency, glutamine increasingly fuels the TCA cycle; unexpectedly, it is also the dominant carbon source for histone acetylation. The necessary acetyl-CoA is generated via IDH1-mediated reductive glutamine carboxylation and is coupled to pyruvate cycling, sustaining histone acetylation. These findings uncover a metabolically rewired, route-specific nutrient utilization program that links metabolism to epigenomic regulation and pluripotency transitions at implantation. • TCA cycle rewiring underpins embryo implantation and exit from naive pluripotency • Pyruvate cycling enables a timely exit from naive pluripotency and differentiation • Glutamine is the primary metabolic source for histone acetylation in pluripotency • Pyruvate cycling and reductive glutamine carboxylation sustain histone acetylation Using carbon tracing and functional experiments, Kafkia, Pladevall-Morera, et al. show that TCA cycle rewiring underlies mouse embryo implantation and the exit from naive pluripotency. In this context, pyruvate cycling enables timely cell-state transitions, while, coupled to it, reductive glutamine metabolism fuels the histone acetylation backbone.