Single-cell genomics profiling of the endoderm of the mouse embryonic pharynx

Maldevelopment of the pharyngeal endoderm, an embryonic tissue critical for patterning of the pharyngeal region and ensuing organogenesis, ultimately contributes to several classes of human developmental syndromes and disorders. Such syndromes are characterized by a spectrum of phenotypes that currently cannot be fully explained by known mutations or genetic variants due to gaps in characterization of critical drivers of normal and dysfunctional development. Despite the disease-relevance of pharyngeal endoderm, we still lack a comprehensive and integrative view of the molecular basis and gene regulatory networks (GRNs) driving pharyngeal endoderm development. To close this gap, we applied transcriptomic and chromatin accessibility single-cell sequencing technologies to generate a multi-omic developmental resource spanning pharyngeal endoderm patterning to the emergence of organ-specific epithelia in the developing mouse embryo. We identify novel cell-type specific gene regulation, distill GRN models that define developing organ domains, and characterize the role of an immunodeficiency-associated forkhead box transcription factor. Overall design: Single-cell RNA profiling of Foxn1 knockout and heterozygous control mouse embryonic pharyngeal endoderm. On embryonic day 12.5, pharyngeal endoderm was isolated by a combination of dissection (mechanical isolation of the whole pharynx) and cell sorting (purification of viable, Pax9+ epithelia). Data include two samples per genotype (biological replicates).