CTCF counter-regulates cardiomyocyte development and maturation programs in the embryonic heart [4C-seq]

Analysis of chromatin architecture suggests that the 3D structure of the genome plays a major role in regulating gene expression, orchestrating the compartmentalization of chromatin and facilitating specific enhancer-promoter interactions. However, the mechanisms that control this structuring of the genome are not fully understood. We have addressed this issue by analyzing the role of CTCF, a major architectural factor in chromatin structure, in the embryonic heart. Loss of CTCF triggered an overall downregulation of the cardiac developmental program, suggesting that CTCF facilitates enhancer-promoter interactions in the developing heart. Detailed analysis of the IrxA gene cluster showed that CTCF loss leads to disruption of the heart-specific regulatory domain that surrounds Irx4, resulting in changes in expression of IrxA cluster genes and neighboring genes. In contrast to the critical role proposed for CTCF in organizing large-scale chromatin domains, our results show that CTCF preferentially mediates local regulatory interactions. Overall design: 4C-seq of E11.5 mouse embryonic hearts using Irx4 and Ndufs6 promoters and a CTCF binding site as as viewpoints. We have two conditions: control and Ctcf heart Knockout染色质高级结构分析表明，基因组三维结构在调控基因表达、协调染色质区室化以及介导特定增强子-启动子相互作用方面发挥核心作用。然而，调控该基因组结构的具体分子机制尚未完全明晰。本研究以胚胎心脏为研究模型，通过分析染色质核心架构因子CTCF（CCCTC结合因子）的功能，对该科学问题展开了探讨。实验结果显示，CTCF缺失会全面下调心脏发育程序的基因表达，提示CTCF可促进发育中心脏内的增强子-启动子相互作用。对IrxA基因簇的详细分析进一步表明，CTCF缺失会破坏Irx4基因周围的心脏特异性调控结构域，进而改变IrxA基因簇及其邻近基因的表达模式。尽管此前研究提出CTCF在大规模染色质结构域组织中发挥关键作用，但本研究结果证实，CTCF更倾向于介导局部调控相互作用。整体实验设计：以Irx4、Ndufs6启动子及一个CTCF结合位点作为锚定视点，对E11.5天小鼠胚胎心脏开展4C-seq测序。实验设置两组处理：对照组与Ctcf心脏敲除组。