Dynamic regulation of chromatin accessibility and transcription factors underlies distinct organ identity and function

After gut tube closure, different regional domains develop into uniquely functional organs. Our single cell analysis demonstrates that chromatin accessibility predicts lineage fate decisions, reflecting the transcriptional profiles of individual cells. Combining with bulk analyses, we have generated a comprehensive map of epigenetic changes over developmental time, revealing how chromatin accessibility and transcription factor (TF) binding cooperate to control organ identity and differentiation. Loss of the foregut and hindgut lineage-specific TFs, Sox2 and Cdx2, leads to the acquisition of accessibility profiles similar to neighbouring organs, while Sox2 overexpression in early development induces a loss of intestinal identity and pancreatic transformation into foregut fate precursors. Moreover, ectopic expression of Sox2 in normal adult and cancer intestinal and pancreatic tissues leads to lineage alterations, demonstrating its critical role in homeostasis and cancer. Together, these studies define the chromatin and transcriptional mechanisms of organ identity and lineage plasticity in development and disease. We profiled genome-wide chromatin accessibility profile in single cell resolution (scATAC from 10x genomics) in mouse gut endoderm at E9.5. Bulk ATAC-seq and RNA-seq were also generated in mouse gut endoderm at E13.5. Each dataset has two replicates.肠管闭合后，不同的区域亚区会发育为具有独特功能的器官。本研究通过单细胞分析证实，染色质开放性（chromatin accessibility）可预测细胞谱系命运决定，其特征与单个细胞的转录谱相一致。结合批量分析数据，我们构建了发育时序上表观遗传变化的全面图谱，揭示了染色质开放性与转录因子（transcription factor，TF）结合如何协同调控器官特性与细胞分化。 前肠与后肠谱系特异性转录因子Sox2和Cdx2的缺失，会使细胞获得邻近器官的染色质开放性谱特征；而在发育早期过表达Sox2，则会导致肠道细胞特性丧失，并使胰腺细胞转分化为前肠命运前体细胞。 此外，在正常成年及癌变的肠道与胰腺组织中异位表达Sox2，可引发细胞谱系改变，证实其在组织稳态与癌症发生中发挥关键作用。 综上，本系列研究明确了发育与疾病过程中调控器官特性与谱系可塑性的染色质及转录调控机制。我们对胚胎发育第9.5天（E9.5）的小鼠肠内胚层开展了单细胞分辨率的全基因组染色质开放性谱分析（采用10x Genomics平台的单细胞ATAC测序，scATAC）；同时对胚胎发育第13.5天（E13.5）的小鼠肠内胚层进行了批量ATAC测序（Bulk ATAC-seq）与RNA测序（RNA-seq），每个数据集均设置两个生物学重复。