Hippo-YAP signaling controls lineage differentiation of mouse embryonic stem cell through super-enhancers [RNA-seq]

Hippo-YAP signaling pathway is a highly conserved pathway during evolution. It involves in a broad spectrum of physiological and pathological procedure. It also functions in early lineage differentiation of pluripotent stem cells, but the detailed mechanisms remain elusive. Our previous research revealed that knockout of Mst1 and Mst2, the key components of Hippo signaling in mouse embryonic stem cells (ESCs), led ESCs preferentially differentiate into ectoderm lineage, and the differentiation to mesoderm and endoderm lineage was disturbed. To uncover the underlying regulatory mechanisms, we performed ChIP-seq experiments with antibodies against Yap, master transcription factors and some characterized histone modification markers. Combined with RNA-seq assays of wild type and Mst KO ESCs and day 4 embryoid bodies (EBs), we found that YAP is preferentially enriched at Nanog, Sox2, Oct4 and H3K27Ac co-marked super-enhancers (SEs) in ESCs. The upregulation of YAP in Mst KO ESCs resulted in the formation of new super-enhancers on lineage associated genes, leading to the upregulation of these genes and the distortion of ESC differentiation. Hence, our study revealed a super-enhancer related ESC lineage differentiation mechanism which can be shaped by Hippo-YAP signaling. Overall design: Examination of ES and EB in 2 cell types.

Hippo-YAP信号通路（Hippo-YAP signaling pathway）是一条进化过程中高度保守的信号通路，广泛参与生理与病理过程，同时调控多能干细胞的早期谱系分化，但其具体调控机制仍不明确。我们此前的研究发现，在小鼠胚胎干细胞（ESCs）中敲除Hippo信号通路的关键组分Mst1与Mst2后，ESCs会优先向外胚层谱系分化，而向中胚层与内胚层谱系的分化则受到干扰。为揭示潜在的调控机制，我们使用针对Yap、核心转录因子以及部分已表征的组蛋白修饰标记物的抗体，开展了染色质免疫共沉淀测序（ChIP-seq）实验；结合野生型、Mst基因敲除ESCs以及第4天拟胚体（EBs）的RNA测序（RNA-seq）检测，我们发现，在ESCs中，YAP优先富集于由Nanog、Sox2、Oct4与H3K27Ac共同标记的超级增强子（super-enhancers, SEs）区域。在Mst基因敲除的ESCs中，YAP的表达上调会诱导谱系相关基因区域形成全新的超级增强子，进而推动这些基因的表达上调并引发ESCs分化异常。综上，本研究揭示了一种可由Hippo-YAP信号通路调控的、与超级增强子相关的ESCs谱系分化机制。实验整体设计：对两种细胞类型（ES和EB）进行检测分析。