Edited by Xiao-Fan WangProper neural commitment is essential for ensuring the appropriate development of the human brain and for preventing neurodevelopmental diseases such as autism spectrum disorders, schizophrenia, and intellectual disorders. However, the molecular mechanisms underlying the neural commitment in humans remain elusive. Here, we report the establishment of a neural differentiation system based on human embryonic stem cells (hESCs) and on comprehensive RNA sequencing analysis of transcriptome dynamics during early hESC differentiation. Using weighted gene co-expression network analysis, we reveal that the hESC neurodevelopmental trajectory has five stages: pluripotency (day 0); differentiation initiation (days 2, 4, and 6); neural commitment (days 8 -10); neural progenitor cell proliferation (days 12, 14, and 16); and neuronal differentiation (days 18, 20, and 22). These stages were characterized by unique module genes, which may recapitulate the early human cortical development. Moreover, a comparison of our RNA-sequencing data with several other transcriptome profiling datasets from mice and humans indicated that Module 3 associated with the day 8 -10 stage is a critical window of fate switch from the pluripotency to the neural lineage. Interestingly, at this stage, no key extrinsic signals were activated. In contrast, using CRISPR/ Cas9 -mediated gene knockouts, we also found that intrinsic hub transcription factors, including the schizophrenia-associated SIX3 gene and septo-optic dysplasia-related HESX1 gene, are required to program hESC neural determination. Our results improve the understanding of the mechanism of neural commitment in the human brain and may help elucidate the etiology of human mental disorders and advance therapies for managing these conditions. Brain development is one of the most complicated and hierarchical events in mammals. A series of temporal processes, including neural commitment, patterning and sub-regionalization, neurogenesis, and neuronal network formation, are required to generate a functional brain (1-4). Defects in any of these processes will lead to neurodevelopmental diseases such as autism spectrum disorders, schizophrenia, depression, and epilepsy. Neural commitment occurs after gastrulation and initiates the program to form neural epithelium (5-7). Many studies on amphibians and rodents reveal that the inhibition of BMP 3 signaling is an evolutionally conserved mechanism for neural induction; in addition, intrinsic factors play pivotal roles to direct fate transition from pluripotency to neural lineage (8 -11). Nonetheless, how the neural commitment is ensured in human brain has not been clearly elucidated. Systematically understanding the critical role of signaling pathways and transcriptional factors in modulating and shaping human brain development is hindered by limited accessibility to early embryos and inadequate amounts of stage-specific and cell type-specific materials. These problems may now be solved by the use of human embryonic stem cells (h...