SLC CRISPR drop-out screen to identify essential SLCs in pluripotency maintenance and exit

Early embryos and stem cells remodel their metabolic networks during key developmental transitions, adapting to dynamically changing environments and energetic demands. However, how metabolic rewiring is mediated and contributes to large-scale epigenetic remodelling and cell identity are poorly understood. Here, we investigate the role of solute carrier (SLC) - mediated metabolite uptake and compartmentalisation in this metabolic–epigenetic interface. We perform an unbiased SLC CRISPR dropout screen in mouse embryonic stem cells (ESCs) and identify a subset of SLCs essential for naïve pluripotency. We observe a strong enrichment for mitochondrial- and endoplasmic reticulum-localised SLCs, suggesting that intracellular metabolite compartmentalisation could be as critical as, if not more than, the regulation of exogenous nutrient uptake. Focusing on the mitochondrial NAD? transporter SLC25A51, we show that its loss selectively impairs naïve ESC viability, disrupts mitochondrial respiration and leads to extensive TCA cycle rewiring. Remarkably, we discover that SLC25A51 loss also perturbs ESC nuclear metabolism, induces histone hyperacetylation, and triggers aberrant hypertranscription. Accordingly, SLC25A51 knockouts fail to downregulate naïve pluripotency factors and to exit pluripotency when induced to differentiate. Collectively, our findings reveal that select mitochondrial SLCs are rate-limiting to metabolism and viability in naïve ESCs, and that SLC25A51's transport function is coupled to epigenetic programming that preserves a naïve chromatin state competent for differentiation.