Pluripotency Factors Regulate Definitive Endoderm Specification through Eomesodermin. Homo sapiens

Understanding the molecular mechanisms controlling early cell fate decisions in mammals is a major objective towards the development of robust methods for the differentiation of human pluripotent stem cells into clinically relevant cell types. Here, we used human embryonic stem cells (hESCs) to study specification of definitive endoderm in vitro. Using a combination of whole genome expression and ChIP-seq analyses, we established a hierarchy of transcription factors regulating endoderm specification. Importantly, pluripotency factors, namely NANOG, OCT4 and SOX2 have an essential function in this network by actively directing differentiation. Indeed, these transcription factors control the expression of EOMES, which marks the onset of endoderm specification. In turn, EOMES interacts with SMAD2/3 to initiate the transcriptional network governing endoderm formation. Together, these results provide for the first time a comprehensive molecular model connecting the transition from pluripotency to endoderm specification during mammalian development. Overall design: ChIP-Seq of Eomesodermin binding in human embyonic stem cells, differentiated towards an endodermal fate for 48h in chemically-defined culture media. Includes an input DNA control. Supplementary file GSE26097_README.txt contains descriptions of the raw data files and processed data files.阐明调控哺乳动物早期细胞命运决定的分子机制，是开发稳健高效的人多能干细胞（human pluripotent stem cells）定向分化为临床相关细胞类型技术的核心研究目标。本研究利用人胚胎干细胞（human embryonic stem cells, hESCs）体外研究定形内胚层（definitive endoderm）的定向分化过程。通过全基因组表达谱分析与染色质免疫沉淀测序（ChIP-seq）的联合应用，本研究构建了调控内胚层定向分化的转录因子层级调控网络。值得关注的是，多能性因子NANOG、OCT4与SOX2可通过主动调控分化进程，在该调控网络中发挥不可或缺的核心功能。具体而言，这些转录因子可调控EOMES的表达，而EOMES的表达正是内胚层定向分化起始的标志性事件。后续EOMES可与SMAD2/3相互作用，启动调控内胚层形成的转录调控网络。综上，本研究首次建立了哺乳动物发育过程中从多能状态向定形内胚层定向分化转变的完整分子模型。实验整体设计：针对经化学成分限定培养基定向诱导分化48小时的人胚胎干细胞，开展Eomesodermin结合位点的ChIP-seq分析，同时设置DNA输入对照样本。补充文件GSE26097_README.txt包含原始数据文件与经处理后数据文件的详细说明。