Hematopoietic stem cells (HSCs) rely on complex regulatory networks to preserve stemness. Due to the scarcity of HSCs, technical challenges have limited our insights into the interplay between metabolites, transcription, and the epigenome. In this study, we generated low-input metabolomics, transcriptomics, chromatin accessibility, and chromatin immunoprecipitation data, revealing distinct metabolic hubs that are enriched in HSCs and their downstream multipotent progenitors. Mechanistically, we uncover a non-classical retinoic acid (RA) signaling axis that regulates HSC function. We show that HSCs rely on Cyp26b1, an enzyme conventionally considered to limit RA effects in the cell. In contrast to the traditional view, we demonstrate that Cyp26b1 is indispensable for production of the active metabolite 4-oxo-RA. Further, RA receptor beta (Rarb) is required for complete transmission of 4-oxo-RA-mediated signaling to maintain stem cells. Our findings emphasize that a single metabolite controls stem cell fate by instructing epigenetic and transcriptional attributes.

造血干细胞 (HSC) 依靠复杂的调控网络来保持干性。由于 HSC 的稀缺性，技术挑战限制了我们对代谢物、转录和表观基因组之间相互作用的了解。在这项研究中，我们生成了低输入代谢组学、转录组学、染色质可及性和染色质免疫沉淀数据，揭示了 HSC 及其下游多能祖细胞中富集的独特代谢中心。从机制上讲，我们发现了调节 HSC 功能的非经典视黄酸 (RA) 信号轴。我们证明 HSC 依赖 Cyp26b1，这种酶通常被认为可以限制细胞中的 RA 效应。与传统观点相反，我们证明 Cyp26b1 对于活性代谢物 4-oxo-RA 的产生是不可或缺的。此外，RA 受体 β (Rarb) 是 4-oxo-RA 介导的信号传导的完整传递以维持干细胞所必需的。我们的研究结果强调，单一代谢物通过指示表观遗传和转录属性来控制干细胞的命运。