Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
Nucleic Acids Res. 2021 Jan 25;49(2):726-744. doi: 10.1093/nar/gkaa1204.
The establishment of the small intestinal (SI) lineage during human embryogenesis ensures functional integrity of the intestine after birth. The chromatin dynamics that drive SI lineage formation and regional patterning in humans are essentially unknown. To fill this knowledge void, we apply a cutting-edge genomic technology to a state-of-the-art human model of early SI development. Specifically, we leverage chromatin run-on sequencing (ChRO-seq) to define the landscape of active promoters, enhancers and gene bodies across distinct stages of directed differentiation of human pluripotent stem cells into SI spheroids with regional specification. Through comprehensive ChRO-seq analysis we identify candidate stage-specific chromatin activity states, novel markers and enhancer hotspots during the directed differentiation. Moreover, we propose a detailed transcriptional network associated with SI lineage formation or regional patterning. Our ChRO-seq analyses uncover a previously undescribed pattern of enhancer activity and transcription at HOX gene loci underlying SI regional patterning. We also validated this unique HOX dynamics by the analysis of single cell RNA-seq data from human fetal SI. Overall, the results lead to a new proposed working model for the regulatory underpinnings of human SI development, thereby adding a novel dimension to the literature that has relied almost exclusively on non-human models.
人类胚胎发生过程中小肠（SI）谱系的建立确保了出生后肠道的功能完整性。驱动 SI 谱系形成和区域模式形成的染色质动力学在人类中基本上是未知的。为了填补这一知识空白，我们将一项前沿的基因组技术应用于早期 SI 发育的最先进的人类模型中。具体来说，我们利用染色质运行测序（ChRO-seq）来定义在人类多能干细胞定向分化为具有区域特异性的 SI 球体的不同阶段中，活跃启动子、增强子和基因体的景观。通过全面的 ChRO-seq 分析，我们在定向分化过程中确定了候选的阶段特异性染色质活性状态、新型标记和增强子热点。此外，我们提出了一个与 SI 谱系形成或区域模式形成相关的详细转录网络。我们的 ChRO-seq 分析揭示了在 SI 区域模式形成中，HOX 基因座上增强子活性和转录的先前未描述的模式。我们还通过分析来自人胎儿 SI 的单细胞 RNA-seq 数据验证了这种独特的 HOX 动力学。总的来说，这些结果提出了一个新的工作模型，用于解释人类 SI 发育的调控基础，从而为几乎完全依赖非人类模型的文献增加了一个新的维度。
