Single-cell epigenomics reveals mechanisms of human cortical development

During mammalian development, differences in chromatin state coincide with cellular differentiation and reflect changes in the gene regulatory landscap

Individual human cortical progenitors can produce excitatory and inhibitory neurons

The cerebral cortex is a cellularly complex structure comprising a rich diversity of neuronal and glial cell types. Cortical neurons can be broadly categorized into two classes-excitatory neurons that use the neurotransmitter glutamate, and inhibitory interneurons that use γ-aminobutyric acid (GABA). Previous developmental studies in rodents have led to a prevailing model in which excitatory neurons are born from progenitors located in the cortex, whereas cortical interneurons are born from a separate population of progenitors located outside the developing cortex in the ganglionic eminences1-5. However, the developmental potential of human cortical progenitors has not been thoroughly explored. Here we show that, in addition to excitatory neurons and glia, human cortical progenitors are also capable of producing GABAergic neurons with the transcriptional characteristics and morphologies of cortical interneurons. By developing a cellular barcoding tool called 'single-cell-RNA-sequencing-compatible tracer for identifying clonal relationships' (STICR), we were able to carry out clonal lineage tracing of 1,912 primary human cortical progenitors from six specimens, and to capture both the transcriptional identities and the clonal relationships of their progeny. A subpopulation of cortically born GABAergic neurons was transcriptionally similar to cortical interneurons born from the caudal ganglionic eminence, and these cells were frequently related to excitatory neurons and glia. Our results show that individual human cortical progenitors can generate both excitatory neurons and cortical interneurons, providing a new framework for understanding the origins of neuronal diversity in the human cortex

Single-cell epigenomics reveals mechanisms of human cortical development.

During mammalian development, differences in chromatin state coincide with cellular differentiation and reflect changes in the gene regulatory landscape1. In the developing brain, cell fate specification and topographic identity are important for defining cell identity2 and confer selective vulnerabilities to neurodevelopmental disorders3. Here, 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 tissue samples from the human forebrain. 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 that are found in vivo. Systematic comparison of chromatin accessibility across brain regions revealed unexpected diversity among neural progenitor cells in the cerebral cortex and implicated retinoic acid signalling in the specification of neuronal lineage identity in the prefrontal cortex. 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

lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements.

Massively parallel reporter assays (MPRAs) can simultaneously measure the function of thousands of candidate regulatory sequences (CRSs) in a quantitative manner. In this method, CRSs are cloned upstream of a minimal promoter and reporter gene, alongside a unique barcode, and introduced into cells. If the CRS is a functional regulatory element, it will lead to the transcription of the barcode sequence, which is measured via RNA sequencing and normalized for cellular integration via DNA sequencing of the barcode. This technology has been used to test thousands of sequences and their variants for regulatory activity, to decipher the regulatory code and its evolution, and to develop genetic switches. Lentivirus-based MPRA (lentiMPRA) produces 'in-genome' readouts and enables the use of this technique in hard-to-transfect cells. Here, we provide a detailed protocol for lentiMPRA, along with a user-friendly Nextflow-based computational pipeline-MPRAflow-for quantifying CRS activity from different MPRA designs. The lentiMPRA protocol takes ~2 months, which includes sequencing turnaround time and data processing with MPRAflow

Temporally distinct 3D multi-omic dynamics in the developing human brain

The human hippocampus and prefrontal cortex play critical roles in learning and cognition1,2, yet the dynamic molecular characteristics of their development remain enigmatic. Here we investigated the epigenomic and three-dimensional chromatin conformational reorganization during the development of the hippocampus and prefrontal cortex, using more than 53,000 joint single-nucleus profiles of chromatin conformation and DNA methylation generated by single-nucleus methyl-3C sequencing (snm3C-seq3)3. The remodelling of DNA methylation is temporally separated from chromatin conformation dynamics. Using single-cell profiling and multimodal single-molecule imaging approaches, we have found that short-range chromatin interactions are enriched in neurons, whereas long-range interactions are enriched in glial cells and non-brain tissues. We reconstructed the regulatory programs of cell-type development and differentiation, finding putatively causal common variants for schizophrenia strongly overlapping with chromatin loop-connected, cell-type-specific regulatory regions. Our data provide multimodal resources for studying gene regulatory dynamics in brain development and demonstrate that single-cell three-dimensional multi-omics is a powerful approach for dissecting neuropsychiatric risk loci

Massively parallel characterization of regulatory elements in the developing human cortex

Nucleotide changes in gene regulatory elements are important determinants of neuronal development and diseases. Using massively parallel reporter assays in primary human cells from mid-gestation cortex and cerebral organoids, we interrogated the cis-regulatory activity of 102,767 open chromatin regions, including thousands of sequences with cell type-specific accessibility and variants associated with brain gene regulation. In primary cells, we identified 46,802 active enhancer sequences and 164 variants that alter enhancer activity. Activity was comparable in organoids and primary cells, suggesting that organoids provide an adequate model for the developing cortex. Using deep learning we decoded the sequence basis and upstream regulators of enhancer activity. This work establishes a comprehensive catalog of functional gene regulatory elements and variants in human neuronal development

Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain

INTRODUCTION Genome-wide association studies (GWASs) have identified thousands of loci associated with neurodevelopmental and psychiatric disorders, yet our lack of understanding of the target genes and biological mechanisms underlying these associations remains a major challenge. GWAS signals for many neuropsychiatric disorders, including autism spectrum disorder, schizophrenia, and bipolar disorder, are particularly enriched for gene-regulatory elements active during human brain development. However, the lack of a unified population-scale, ancestrally diverse gene-regulatory atlas of human brain development has been a major obstacle for the functional assessment of top loci and post-GWAS integrative analyses. RATIONALE To address this critical gap in knowledge, we have uniformly processed and systematically characterized gene, isoform, and splicing quantitative trait loci (cumulatively referred to as xQTLs) in the developing human brain across 672 unique samples from 4 to 39 postconception weeks spanning European, African-American, and Latino/admixed American ancestries). With this expanded atlas, we sought to specifically localize the timing and molecular features mediating the greatest proportion of neuropsychiatric GWAS heritability, to prioritize candidate risk genes and mechanisms for top loci, and to compare with analogous results using larger adult brain functional genomic reference panels. RESULTS In total, we identified 15,752 genes harboring a gene, isoform and/or splicing cis-xQTL, including 49 genes associated with four large, recurrent inversions. Highly concordant effect sizes were observed across populations, and our diverse reference panel improved resolution to fine-map underlying candidate causal regulatory variants. Substantially more genes were found to harbor QTLs in the first versus second trimester of brain development, with a notable drop in gene expression and splicing heritability observed from 10 to 18 weeks coinciding with a period of rapidly increasing cellular heterogeneity in the developing brain. Isoform-level regulation, particularly in the second trimester, mediated a greater proportion of heritability across multiple psychiatric GWASs compared with gene expression regulation. Through colocalization and transcriptome-wide association studies, we prioritized biological mechanisms for ~60% of GWAS loci across five neuropsychiatric disorders, with >2-fold more colocalizations observed compared with larger adult brain functional genomic reference panels. We observed convergence between common and rare-variant associations, including a cryptic splicing event in the high-confidence schizophrenia risk gene SP4. Finally, we constructed a comprehensive set of developmentally regulated gene and isoform coexpression networks harboring unique cell-type specificity and genetic enrichments. Leveraging this cell-type specificity, we identified >8000 module interaction QTLs, many of which exhibited additional GWAS colocalizations. Overall, neuropsychiatric GWASs and rare variant signals localized more strongly within maturing excitatory- and interneuron-associated modules compared with those enriched for neural progenitor cell types. Results can be visualized at devbrainhub.gandallab.org. CONCLUSION We have generated a large-scale, cross-population resource of gene, isoform, and splicing regulation in the developing human brain, providing comprehensive developmental and cell-type-informed mechanistic insights into the genetic underpinnings of complex neurodevelopmental and psychiatric disorders