The availability of robust protocols to differentiate induced pluripotent stem cells (iPSCs) into many human cell lineages has transformed research into the origins of human disease. The efficacy of differentiating iPSCs into specific cellular models is influenced by many factors including both intrinsic and extrinsic features. Among the most challenging models is the generation of human bronchial epithelium at air‐liquid interface (HBE‐ALI), which is the gold standard for many studies of respiratory diseases including cystic fibrosis. Here, we perform open chromatin mapping by ATAC‐seq and transcriptomics by RNA‐seq in parallel, to define the functional genomics of key stages of the iPSC to HBE‐ALI differentiation. Within open chromatin peaks, the overrepresented motifs include the architectural protein CTCF at all stages, while motifs for the FOXA pioneer and GATA factor families are seen more often at early stages, and those regulating key airway epithelial functions, such as EHF, are limited to later stages. The RNA‐seq data illustrate dynamic pathways during the iPSC to HBE‐ALI differentiation, and also the marked functional divergence of different iPSC lines at the ALI stages of differentiation. Moreover, a comparison of iPSC‐derived and lung donor‐derived HBE‐ALI cultures reveals substantial differences between these models.

中文翻译：

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一种功能基因组学方法，用于研究 iPSC 在气液界面向肺上皮的分化。

将诱导多能干细胞 (iPSC) 分化为许多人类细胞谱系的强大方案的可用性已将研究转变为人类疾病的起源。将 iPSC 区分为特定细胞模型的功效受到许多因素的影响，包括内在和外在特征。其中最具挑战性的模型是气液界面（HBE-ALI）人支气管上皮的生成，这是包括囊性纤维化在内的许多呼吸系统疾病研究的金标准。在这里，我们通过 ATAC-seq 进行开放染色质映射和通过 RNA-seq 进行转录组学并行，以定义 iPSC 到 HBE-ALI 分化关键阶段的功能基因组学。在开放的染色质峰内，过度表达的基序包括所有阶段的结构蛋白 CTCF，而 FOXA 先驱和 GATA 因子家族的基序在早期更常见，而那些调节关键气道上皮功能的基序，如 EHF，则仅限于后期。RNA-seq 数据说明了 iPSC 到 HBE-ALI 分化过程中的动态途径，以及不同 iPSC 系在 ALI 分化阶段的显着功能差异。此外，iPSC 衍生和肺供体衍生的 HBE-ALI 培养物的比较揭示了这些模型之间的实质性差异。以及不同 iPSC 系在 ALI 分化阶段的显着功能差异。此外，iPSC 衍生和肺供体衍生的 HBE-ALI 培养物的比较揭示了这些模型之间的实质性差异。以及不同 iPSC 系在 ALI 分化阶段的显着功能差异。此外，iPSC 衍生和肺供体衍生的 HBE-ALI 培养物的比较揭示了这些模型之间的实质性差异。