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. 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).咽内胚层（pharyngeal endoderm）是对咽部区域模式形成及后续器官发生至关重要的胚胎组织，其发育异常最终会引发多种人类发育综合征与疾病。此类综合征表现出一系列表型，但目前由于对正常与异常发育的关键驱动因素表征存在空白，现有已知突变或遗传变异无法完全解释这些表型。尽管咽内胚层与疾病密切相关，但目前我们仍缺乏对驱动咽内胚层发育的分子基础与基因调控网络（GRNs）的全面整合性认知。为填补这一空白，本研究借助转录组与染色质可及性单细胞测序技术，构建了覆盖发育中小鼠胚胎内咽内胚层模式形成至器官特异性上皮出现过程的多组学发育资源数据集。本研究鉴定出全新的细胞类型特异性基因调控模式，提炼出定义发育中器官区域的基因调控网络（GRNs）模型，并阐明了一种与免疫缺陷相关的叉头框转录因子的功能。对Foxn1敲除与杂合对照的小鼠胚胎咽内胚层进行单细胞RNA测序分析。本研究在胚胎第12.5天，通过解剖分离（机械分离完整咽部）结合细胞分选（纯化活的Pax9阳性上皮细胞）的方法分离咽内胚层；数据集包含每种基因型的两个样本（生物学重复）。