Unravelling the chromatin landscape and enhancer logic mediating spatiotemporal patterning of early cardiovascular progenitors [ATAC-seq]. Unravelling the chromatin landscape and enhancer logic mediating spatiotemporal patterning of early cardiovascular progenitors [ATAC-seq]

The mammalian heart arises from various populations of Mesp1-expressing cardiovascular progenitors (CPs) that are specified during the early stages of gastrulation. Mesp1 acts as a master regulator of CP specification and differentiation. However, how Mesp1 regulates the chromatin landscape of nascent mesodermal cells to define the temporal and spatial patterning of the distinct populations of CP remains unknown. Here, by combining ChIP-seq, RNA-seq and ATAC-seq during mouse pluripotent stem cell differentiation, we defined the temporal remodelling of the chromatin landscape mediated by Mesp1. We identified different enhancers that are temporally regulated to erase the pluripotent state and specify the pools of CPs that mediate heart development. We found that Mesp1 acts as a pioneer transcription factor (TF) and identified Zic TFs as essential cofactors that regulate Mesp1 pioneer activity at key mesodermal enhancers, thereby regulating the chromatin remodelling and gene expression associated with the specification of the different populations of CPs in vivo. Our study identifies the dynamics of the chromatin landscape and enhancer remodelling associated with temporal patterning of early mesodermal cells into the distinct populations of CPs that mediate heart development. Overall design: assay for transposase-accessible chromatin using sequencing (ATAC-seq) on differentiating mouse pluripotent stem cells where the expression of Mesp1 is doxycycline-inducible

哺乳动物心脏起源于多群表达Mesp1的心血管祖细胞 (cardiovascular progenitors, CPs)，这些祖细胞在原肠运动早期阶段完成特化。Mesp1作为调控心血管祖细胞特化与分化的主调控因子发挥功能。然而，目前尚不明确Mesp1如何调控新生中胚层细胞的染色质景观，从而界定不同心血管祖细胞群体的时空分布模式。本研究在小鼠多能干细胞 (pluripotent stem cell) 分化过程中，联合运用染色质免疫共沉淀测序 (ChIP-seq)、RNA测序 (RNA-seq) 与转座酶可及性测序 (assay for transposase-accessible chromatin using sequencing, ATAC-seq)，解析了Mesp1介导的染色质景观时序重塑过程。我们鉴定出一批受时序调控的增强子，这些增强子可介导细胞多能状态的清除，并特化出介导心脏发育的心血管祖细胞池。研究发现，Mesp1作为先驱转录因子 (transcription factor, TF) 发挥作用，同时鉴定出Zic家族转录因子为关键辅因子，可在关键中胚层增强子位点调控Mesp1的先驱活性，进而调控体内不同心血管祖细胞群体特化相关的染色质重塑与基因表达程序。本研究阐明了早期中胚层细胞时序模式化为不同心血管祖细胞群体以介导心脏发育过程中，染色质景观与增强子重塑的动态变化规律。
整体实验设计：在可经强力霉素诱导Mesp1表达的分化中小鼠多能干细胞样本中开展转座酶可及性测序 (ATAC-seq) 检测。