Unravelling the chromatin landscape and enhancer logic mediating spatiotemporal patterning of early cardiovascular progenitors [ChIP-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: ChIP-seq samples targeting 3HA-tagged Mesp1, 3-HA tagged Zic3 and H3K27Ac

哺乳动物心脏起源于多个表达Mesp1的心血管祖细胞（cardiovascular progenitors，CPs）群体，这些细胞在原肠胚形成早期阶段被特化。Mesp1作为心血管祖细胞特化与分化的主控调控因子发挥作用，但目前尚不清楚Mesp1如何调控新生中胚层细胞的染色质景观，以明确不同心血管祖细胞群体的时空分布模式。本研究结合小鼠多能干细胞分化过程中的染色质免疫共沉淀测序（ChIP-seq）、RNA测序（RNA-seq）及转座酶可及性测序（ATAC-seq），解析了Mesp1介导的染色质景观时序重塑过程。我们鉴定出受时序调控的不同增强子，这些增强子可清除细胞的多能状态，并特化介导心脏发育的心血管祖细胞池。研究发现，Mesp1作为先锋转录因子（transcription factor，TF）行使功能，并鉴定出Zic转录因子（TFs）作为关键辅因子，可在关键中胚层增强子位点调控Mesp1的先锋活性，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分化为介导心脏发育的不同心血管祖细胞群体过程中，染色质景观与增强子重塑的动态变化规律。整体实验设计：针对3HA标记的Mesp1、3HA标记的Zic3及H3K27乙酰化修饰（H3K27Ac）的ChIP-seq样本。