Developmental cell type specific enhancers in orofacial morphology and disease [human]

The noncoding genome contains sequences called enhancers which facilitate expression of target genes through recruitment and binding of transcription factors. Enhancers are typically active in developmental stage-, tissue-, and cell type-specific patterns, whereby they control the spatiotemporal expression patterns of target genes. Sequence variation within enhancers can alter expression of their target genes where the enhancer is active, causing isolated phenotypes ranging from normal morphological differences to malformations. The role of orofacial enhancers in normal morphology and disease of the orofacial region has previously been established in bulk human assays. However, the conservation of these findings and the cell types contributing to these phenotypes are unknown, limiting work in prevention and treatment of malformations. To uncover cell type-specific enhancers whose sequence variants contribute to normal facial morphology and malformations, we performed single cell multiome (snATAC and snRNA-seq) sequencing on 17 human samples spanning 6 unique stages from 4-8 weeks gestation and 14 mouse samples spanning 6 stages from E9.5-15.5. We identified 15 distinct cell types, for which we leveraged the cell type specific chromatin accessibility and transcriptomic profiles and previously published chromatin conformation data to identify cell type specific enhancer-gene predicted interactions, which we call the ‘enhancerprints’. These enhancerprints revealed a cell type-specific enrichment pattern of common single nucleotide variants for biologically relevant phenotypes such as epithelium in orofacial clefting and mesenchyme in facial variation.