Pluripotent stem cells can differentiate into all embryonic germ layers, yet the genes essential for these cell fate transitions in human remain elusive. Here, we mapped the essential genes for the differentiation of human pluripotent stem cells (hPSCs) into the three germ layers by using a genome-wide loss-of-function library established in haploid hPSCs. Strikingly, we observed a high fraction of essential genes associated with plasma membrane, highlighting signaling pathways needed for each lineage differentiation. Interestingly, analysis of all hereditary neurological disorders uncovered high essentiality among microcephaly-causing genes. Furthermore, we demonstrated lineage-specific hierarchies among essential transcription factors and a set of Golgi- and endoplasmic reticulum-related genes needed for the differentiation into all germ layers. Our work sheds light on the gene networks regulating early gastrulation events in human by defining essential drivers of specific embryonic germ layer fates and essential genes for the exit from pluripotency.

多能干细胞可以分化为所有胚芽层，但是人类这些细胞命运转变所必需的基因仍然难以捉摸。在这里，我们通过使用在单倍体hPSC中建立的全基因组功能丧失文库，将用于人类多能干细胞（hPSC）分化为三个胚层的必需基因作图。令人惊讶的是，我们观察到与质膜相关的必需基因的比例很高，突出了每种谱系分化所需的信号通路。有趣的是，对所有遗传性神经系统疾病的分析发现，引起小头畸形的基因具有很高的必要性。此外，我们展示了必需的转录因子以及分化为所有细菌层所需的一组高尔基体和内质网相关基因之间的谱系特异性层次。