Three-dimensional genome architectural CCCTC-binding factor makes choice in duplicated enhancers at Pcdh alpha locus
Three-dimensional genome architectural CCCTC-binding factor makes choice in duplicated enhancers at Pcdh alpha locus
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三维基因组结构 CCCTC 结合因子在 Pcdh α 基因座的重复增强子中做出选择
DOI：
10.1007/s11427-019-1598-4
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发表时间：
2020
期刊：
影响因子：
--
通讯作者：
Wu Qiang
中科院分区：
文献类型：
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作者：
Wu Yonghu;Jia Zhilian;Ge Xiao;Wu Qiang
在发育过程中，基因表达受远端增强子和靶启动子之间的长距离染色质相互作用的时空调控。然而，增强子和启动子之间的相互作用的特异性如何实现在很大程度上仍然未知。由于哺乳动物基因组中增强子的数量远远多于启动子，因此基因调控过程中增强子选择的复杂性仍然不清楚。CTCF是CCCTC结合因子，可定向结合广泛的基因组位点（称为CBS（CTCF结合位点）），介导大量远端增强子和靶启动子之间的定向染色质循环。为了研究CTCF参与增强子选择的机制，我们使用基于CRISPR/Cas9的DNA片段编辑来复制聚簇Pcdh α基因的天然基因组位点中含有CBS的增强子和启动子。我们发现，启动子的调控是由近端的一个重复的增强子，这种选择是依赖于CTCF介导的定向增强子启动子循环。此外，基因表达在增强子切换时不变。此外，启动子复制后，只有近端启动子被CTCF介导的定向染色质环选择与远端增强子接触。最后，我们证明了增强子激活和染色质与启动子的成环对于基因表达是必不可少的。这些发现对于CTCF在增强子和启动子之间的特异性相互作用以及通过增强子转换对基因表达的发育调节中的作用具有重要意义。
During development, gene expression is spatiotemporally regulated by long-distance chromatin interactions between distal enhancers and target promoters. However, how specificity of the interactions between enhancers and promoters is achieved remains largely unknown. As there are far more enhancers than promoters in mammalian genomes, the complexities of enhancer choice during gene regulation remain obscure. CTCF, the CCCTC-binding factor that directionally binds to a vast range of genomic sites known as CBSs (CTCF-binding sites), mediates oriented chromatin looping between a substantial set of distal enhancers and target promoters. To investigate mechanisms by which CTCF engages in enhancer choice, we used CRISPR/Cas9-based DNA-fragment editing to duplicate CBS-containing enhancers and promoters in the native genomic locus of the clusteredPcdhαgenes. We found that the promoter is regulated by the proximal one among duplicated enhancers and that this choice is dependent on CTCF-mediated directional enhancer-promoter looping. In addition, gene expression is unaltered upon the switch of enhancers. Moreover, after promoter duplication, only the proximal promoter is chosen by CTCF-mediated directional chromatin looping to contact with the distal enhancer. Finally, we demonstrated that both enhancer activation and chromatin looping with the promoter are essential for gene expression. These findings have important implications regarding the role of CTCF in specific interactions between enhancers and promoters as well as developmental regulation of gene expression by enhancer switching.