The cerebral cortex is responsible for higher-order functions in the nervous system and has undergone substantial expansion in size in primates. The development of the forebrain, including the assembly of the expanded human cerebral cortex, is a lengthy process that involves the diversification and expansion of neural progenitors, the generation and positioning of layer-specific glutamatergic neurons, the cellular migration of γ-aminobutyric acid (GABA)–ergic neurons, and the formation and maturation of glial cells. Disruption of these cellular events by either genetic or environmental factors can lead to neurodevelopmental disease, including autism spectrum disorders and intellectual disability.

Human forebrain development is, to a large extent, inaccessible for cellular-level study, direct functional investigation, or manipulation. The lack of availability of primary brain tissue samples—in particular, at later stages—as well as the limitations of conventional in vitro cellular models have precluded a detailed mechanistic understanding of corticogenesis in healthy and disease states. Therefore, tracking epigenetic changes in specific forebrain cell lineages over long time periods, has the potential to unravel the molecular programs that underlie cell specification in the human cerebral cortex and, by temporally mapping disease risk onto these changes, to identify cell types and periods of increased disease susceptibility.

We used three-dimensional (3D) directed differentiation of human pluripotent stem cells into dorsal and ventral forebrain domains and applied the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) in combination with RNA-sequencing (RNA-seq) to map the epigenetic and gene expression signatures of neuronal and glial cell lineages over 20 months in vitro. We show, through direct comparison with primary brain tissue from our study and several epigenetic datasets, that human stem cell–derived 3D forebrain organoids recapitulated in vivo chromatin accessibility patterns over time. We then integrated these data to discover putative enhancer-gene linkages and lineage-specific transcription factor regulators, including a diverse repertoire of factors that may control cortical specification. We validated protein expression of some of these transcription factors using immunofluorescence, confirming cellular and temporal dynamics in both primary tissue and forebrain organoids. Next, we used this resource to map genes and genetic variants associated with schizophrenia and autism spectrum disorders to distinct accessibility patterns to reveal cell types and periods of susceptibility. Last, we identified a wave of chromatin remodeling during cortical neurogenesis, during which a quarter of regulatory regions are active, and then highlighted transcription factors that may drive these developmental changes.

Using long-term 3D neural differentiation of stem cells as well as primary brain tissue samples, we found that organoids intrinsically undergo chromatin state transitions in vitro that are closely related to human forebrain development in vivo. Leveraging this platform, we identified epigenetic alterations putatively driven by specific transcription factors and discovered a dynamic period of chromatin remodeling during human cortical neurogenesis. Finally, we nominated several key transcription factors that may coordinate over time to drive these changes and mapped cell type–specific disease-associated variation over time and in specific cell types.

ATAC-seq and …