Proper expressions of Homeobox A cluster genes (HoxA) are essential for embryonic stem cells (ESC) differentiation and individual development. However, the mechanisms underlying controlling precise spatiotemporal expressions of HoxA during early ESC differentiation remain poorly understood. Herein, we identified a functional CTCF-binding element (CBE+47) closest to the 3'-end of HoxA within the same topologically associated domain (TAD) in ESC. CRISPR-Cas9 mediated the CBE+47 deletion significantly promotes retinoic acid (RA)-induced HoxA expression and early ESC abnormal differentiation. In delineating its underlying mechanisms, we find that CBE+47 can precisely organize chromatin interactions between its adjacent enhancers and HoxA by using chromosome conformation capture assay (Capture-C). Furthermore, we also find that its adjacent enhancers as enhancer-enhancer interaction complex (EEIC) are required for RA-induced HoxA activation. Collectively, these results provide a new insight for RA-induced HoxA expression, also highlight the unique and precise regulatory roles of CBE in ESC differentiation.

中文翻译：

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CTCF结合元件通过协调增强子和HoxA之间的长距离染色质相互作用来调节ESC分化

同源盒A簇基因（HoxA）的正确表达对于胚胎干细胞（ESC）的分化和个体发育至关重要。然而，在早期ESC分化过程中控制HoxA精确时空表达的基本机制仍知之甚少。在本文中，我们在ESC的相同拓扑相关域（TAD）中确定了最接近HoxA 3'-末端的功能性CTCF结合元件（CBE + 47）。CRISPR-Cas9介导的CBE + 47缺失显着促进视黄酸（RA）诱导的HoxA表达和早期ESC异常分化。在描述其潜在机制时，我们发现CBE + 47可以使用染色体构象捕获测定法（Capture-C）精确组织其相邻增强子与HoxA之间的染色质相互作用。此外，我们还发现，RA诱导HoxA激活需要其邻近的增强子，如增强子-增强子相互作用复合物（EEIC）。总的来说，这些结果为RA诱导的HoxA表达提供了新的见解，也突出了CBE在ESC分化中的独特而精确的调节作用。