MicroRNAs (miRNAs) have essential functions during embryonic development, and their dysregulation causes cancer^1,2. Altered global miRNA abundance is found in different tissues and tumours, which implies that precise control of miRNA dosage is important^1,3,4, but the underlying mechanism(s) of this control remain unknown. The protein complex Microprocessor, which comprises one DROSHA and two DGCR8 proteins, is essential for miRNA biogenesis^5,6,7. Here we identify a developmentally regulated miRNA dosage control mechanism that involves alternative transcription initiation (ATI) of DGCR8. ATI occurs downstream of a stem-loop in DGCR8 mRNA to bypass an autoregulatory feedback loop during mouse embryonic stem (mES) cell differentiation. Deletion of the stem-loop causes imbalanced DGCR8:DROSHA protein stoichiometry that drives irreversible Microprocessor aggregation, reduced primary miRNA processing, decreased mature miRNA abundance, and widespread de-repression of lipid metabolic mRNA targets. Although global miRNA dosage control is not essential for mES cells to exit from pluripotency, its dysregulation alters lipid metabolic pathways and interferes with embryonic development by disrupting germ layer specification in vitro and in vivo. This miRNA dosage control mechanism is conserved in humans. Our results identify a promoter switch that balances Microprocessor autoregulation and aggregation to precisely control global miRNA dosage and govern stem cell fate decisions during early embryonic development.

MicroRNAs (miRNAs) 在胚胎发育过程中具有重要功能，它们的失调会导致癌症^1,2。在不同的组织和肿瘤中发现了改变的全局 miRNA 丰度，这意味着精确控制 miRNA 剂量很重要^1,3,4，但这种控制的潜在机制仍然未知。蛋白质复合物微处理器由一个 DROSHA 和两个 DGCR8 蛋白质组成，对 miRNA 生物发生至关重要^5,6,7。在这里，我们确定了一种发育调节的 miRNA 剂量控制机制，该机制涉及DGCR8的替代转录起始 (ATI) 。ATI 发生在DGCR8的茎环下游mRNA 在小鼠胚胎干 (mES) 细胞分化过程中绕过自动调节反馈回路。茎环的缺失导致 DGCR8:DROSHA 蛋白质化学计量不平衡，导致不可逆的微处理器聚集、初级 miRNA 加工减少、成熟 miRNA 丰度降低以及脂质代谢 mRNA 靶点的广泛去抑制。尽管全局 miRNA 剂量控制对于 mES 细胞退出多能性并不是必需的，但其失调会改变脂质代谢途径并通过在体外和体内破坏胚层规范来干扰胚胎发育。这种 miRNA 剂量控制机制在人类中是保守的。