Cell-type-specific effects of genetic variation on chromatin accessibility during human neuronal differentiation

Abstract

Common genetic risk for neuropsychiatric disorders is enriched in regulatory elements active during cortical neurogenesis. However, the mechanisms mediating the effects of genetic variants on gene regulation are poorly understood. To determine the functional impact of common genetic variation on the non-coding genome longitudinally during human cortical development, we performed a chromatin accessibility quantitative trait loci (caQTL) analysis in neural progenitor cells and their differentiated neuronal progeny from 92 donors. We identified 8,111 caQTLs in progenitors and 3,676 caQTLs in neurons, with highly temporal, cell-type specific effects. A subset (~20%) of caQTLs were also associated with changes in gene expression. Motif-disrupting alleles of transcriptional activators generally led to decreases in chromatin accessibility, whereas motif-disrupting alleles of repressors led to increases in chromatin accessibility. By integrating cell-type specific caQTLs and brain-relevant genome-wide association data, we were able to fine-map loci and identify regulatory mechanisms underlying non-coding neuropsychiatric disorder risk variants.

Inference of cell-type specific imprinted regulatory elements and genes during human neuronal differentiation

“…We utilized primary human neural progenitor (phNPC) chromatin accessibility and expression quantitative trait loci (QTL) datasets described in our previous work (Liang et al 2021; to infer imprinted genes and REs. phNPCs were cultured in vitro as progenitor cells and also differentiated for 8 weeks, virally labeled, and sorted to obtain a homogeneous population of neurons.…”

“…phNPCs were cultured in vitro as progenitor cells and also differentiated for 8 weeks, virally labeled, and sorted to obtain a homogeneous population of neurons. We then performed ATAC-seq and RNA-seq to obtain chromatin accessibility profiles (Liang et al 2021) (N_Progenitor=76 and N_Neuron=61) and gene expression profiles ) (N_Progenitor=85 and N_Neuron=74) in both cell types (Figure 1A). We identified heterozygous genetic variants using imputed genotype data for all donors in progenitors and neurons in order to distinguish the two chromosomes, though we are unable to classify maternal or paternal origin.…”

“…We cultured and differentiated the phNPCs into neurons following the same methods in our previous work (Stein et al 2014;Liang et al 2021).…”

“…ATAC-seq libraries were prepared immediately following cellular dissociation described in our previous methods (Buenrostro et al 2015;Liang et al 2021). All libraries were sequenced on an Illumina HiSeq2500 or MiSeq machine using 50 bp paired-end sequencing.…”

“…Raw ATAC-seq and RNA-seq data were quality controlled and aligned to the human genome (GRCh38/hg38) using WASP to prevent mapping bias as previously described (Liang et al 2021;Aygün et al 2021). Genotype data were preprocessed and imputed as previously described (Liang et al 2021).…”