Transcriptional and Epigenomic Landscapes of CNS and non-CNS Vascular Endothelial Cells

Vascular endothelial cell (EC) function depends on appropriate organ-specific molecular and cellular specializations. To explore genomic mechanisms that control this specialization, we have analyzed and compared the transcriptome, accessible chromatin, and DNA methylome landscapes from mouse brain, liver, lung, and kidney ECs. Analysis of transcription factor (TF) motifs at candidate cis-regulatory elements together with TF gene expression reveals both shared and organ-specific EC TFs. In the embryo, only those ECs that are adjacent to or within the developing CNS exhibit canonical Wnt signaling, which correlates precisely with blood-brain barrier (BBB) differentiation and Zic3 expression. In acutely cultured brain ECs, the rapid loss of BBB markers is closely correlated with down-regulation of canonical Wnt signaling. In the early postnatal brain, single cell RNA-seq of purified ECs reveals close relationships between veins and mitotic cells and between arteries and tip cells, and a division of capillary ECs into vein-like and artery-like classes. RNA-seq and MethylC-seq of postnatal day 7 (P7) vascular endothelial cells (ECs) from brain, liver, lung, and kidney of Tie2-GFP mice; RNA-seq and ATAC-seq of primary brain EC culture; single cell RNA-seq of P7 mouse brain ECs血管内皮细胞（Vascular endothelial cell，EC）的功能依赖于器官特异性的分子与细胞特化。为探究调控该特化过程的基因组学机制，本研究对小鼠脑、肝、肺、肾来源的血管内皮细胞的转录组、开放染色质组以及DNA甲基化组图谱进行了分析与比较。通过对候选顺式调控元件处的转录因子（transcription factor，TF）基序与转录因子基因表达情况开展联合分析，本研究同时揭示了血管内皮细胞中既共享又具有器官特异性的转录因子。在胚胎发育阶段，唯有紧邻发育中的中枢神经系统（central nervous system，CNS）或位于其内的血管内皮细胞可呈现经典Wnt信号通路活化，该通路活性与血脑屏障（blood-brain barrier，BBB）分化以及Zic3基因的表达精准相关。在急性分离培养的脑源性血管内皮细胞中，血脑屏障标志物的快速丢失与经典Wnt信号通路的下调呈现显著相关性。在出生早期的脑组织中，对纯化后的血管内皮细胞进行单细胞RNA测序（single cell RNA-seq）分析后发现，静脉与有丝分裂细胞、动脉与尖端细胞之间存在紧密的表达关联，同时毛细血管内皮细胞可划分为静脉样与动脉样两个亚类。针对Tie2-GFP转基因小鼠出生后第7天（postnatal day 7，P7）的脑、肝、肺、肾组织来源的血管内皮细胞开展RNA测序（RNA-seq）与MethylC-seq测序；针对原代脑源性血管内皮细胞培养物开展RNA测序与转座酶可及性染色质测序（ATAC-seq）；以及针对出生后第7天小鼠脑组织来源的血管内皮细胞开展单细胞RNA测序。