Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection
Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection
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串联 CTCF 位点作为绝缘子来平衡空间染色质接触和拓扑增强子-启动子选择
DOI：
10.1186/s13059-020-01984-7
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发表时间：
2020-03-23
期刊：
影响因子：
12.3
通讯作者：
Wu, Qiang
中科院分区：
文献类型：
--
作者：
Jia, Zhilian;Li, Jingwei;Wu, Qiang
CTCF是一种关键的绝缘体结合蛋白，哺乳动物基因组包含许多CTCF位点，其中许多位点是串联组织的。使用CRISPR dna片段编辑，结合染色体构象捕获，我们发现CTCF位点，如果位于原钙粘蛋白（Pcdh）和β -珠蛋白簇中的增强子和启动子之间，通过形成不同的定向染色质环，作为增强子阻断绝缘子，而不管增强子是否含有CTCF位点。此外，计算机模拟和体内基因缺失以及体外dCas9阻断显示，通过Pcdh和免疫球蛋白重链（Igh）簇中串联CTCF位点的大阵列，启动子在细胞群体中的平衡使用和单细胞中随机单等位基因的表达。此外，与直觉相反，CTCF绝缘体促进远端定向CTCF位点的远程染色质相互作用，这与内聚蛋白“环挤压”模型一致。最后，基因表达水平与位于增强子和启动子之间的CTCF绝缘子在全基因组范围内呈负相关。因此，单个CTCF绝缘子确保适当的增强子绝缘和启动子激活，而串联CTCF拓扑绝缘子决定平衡的空间接触和启动子选择。这些发现对拓扑染色质绝缘子在三维基因组折叠和发育基因调控中的作用具有重要意义。
Background CTCF is a key insulator-binding protein, and mammalian genomes contain numerous CTCF sites, many of which are organized in tandem. Results Using CRISPR DNA-fragment editing, in conjunction with chromosome conformation capture, we find that CTCF sites, if located between enhancers and promoters in the protocadherin (Pcdh) and beta-globin clusters, function as an enhancer-blocking insulator by forming distinct directional chromatin loops, regardless whether enhancers contain CTCF sites or not. Moreover, computational simulation in silico and genetic deletions in vivo as well as dCas9 blocking in vitro revealed balanced promoter usage in cell populations and stochastic monoallelic expression in single cells by large arrays of tandem CTCF sites in the Pcdh and immunoglobulin heavy chain (Igh) clusters. Furthermore, CTCF insulators promote, counter-intuitively, long-range chromatin interactions with distal directional CTCF sites, consistent with the cohesin "loop extrusion" model. Finally, gene expression levels are negatively correlated with CTCF insulators located between enhancers and promoters on a genome-wide scale. Thus, single CTCF insulators ensure proper enhancer insulation and promoter activation while tandem CTCF topological insulators determine balanced spatial contacts and promoter choice. Conclusions These findings have interesting implications on the role of topological chromatin insulators in 3D genome folding and developmental gene regulation.