Single cell epigenomics reveals mechanisms of human cortical development

During mammalian development, chromatin state differences coincide with cellular differentiation and reflect changes in the gene regulatory landscape. In the developing brain, cell fate specification and topographic identity play important roles in defining cell identity and confer selective vulnerabilities to neurodevelopmental disorders. To identify cell type specific chromatin accessibility patterns in the developing human brain, we used a single cell assay for transposase accessibility by sequencing (scATAC-seq) in primary human forebrain tissue samples. We applied unbiased analyses to identify genomic loci that undergo extensive cell type- and brain region-specific changes in accessibility during neurogenesis and an integrative analysis to predict cell type specific candidate regulatory elements. We found that cerebral organoids recapitulate most putative cell type-specific enhancer accessibility patterns but lack many cell type specific open chromatin regions found in vivo. Systematic comparison of chromatin accessibility across brain regions revealed an unexpected diversity among neural progenitor cells in the cerebral cortex and implicate retinoic acid signaling in the specification of prefrontal cortex neuronal lineage identity. Together, our results reveal the important contribution of chromatin state to the emerging patterns of cell type diversity and cell fate specification and provide a blueprint for evaluating the fidelity and robustness of cerebral organoids as a model for cortical development. We performed scATAC-seq and scRNA-seq on cortical organoids derived from 3 human pluripotent stem cell lines (13234, H28126, H1) at three different timepoints of differentiation using the 10x Genomics Chromium Gene Expression and ATAC solutions. We performed a separate experiment with 13234-derived cerebral organoids in which 3 different treatment condiitons were used (Vitamin A treatment, no Vitamin A, and DEAB). These organoids were processed at 10 weeks for scRNA-seq using the 10x Genomics Chromium Gene Expression solution.