ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry [HiChIP]. ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry [HiChIP]

The transcription factor ZNF143 contains seven tandem zinc fingers and is involved in 3D genome construction; however, the mechanism by which ZNF143 functions in chromatin looping remains unclear. Here, we show that ZNF143 directionally recognizes diverse genomic sites and is required for chromatin looping between these sites. In addition, ZNF143 is located between CTCF and cohesin at numerous CTCF sites and ZNF143 removal narrows the space between CTCF and cohesin. Moreover, genetic deletion of ZNF143, in conjunction with acute CTCF depletion, revealed that ZNF143 and CTCF collaborate to regulate higher-order genome organization. Thus, ZNF143 is recruited by CTCF to the CTCF sites to regulate TAD formation and genome compartmentalization whereas directional recognition of DNA motifs directly by ZNF143 itself regulates promoter activity via chromatin looping. Overall design: HiChIP for ZNF143, CTCF, and RAD21 in wild type HEC-1-B cells, ZNF143KO cells, or in CTCF-AID cell that treated with auxin for 0h or 24h.

转录因子ZNF143含有7个串联锌指结构域，参与三维基因组构建，但其在染色质环化中的作用机制仍未明确。
本研究证实，ZNF143可定向识别多样化的基因组位点，并对这些位点间的染色质环化不可或缺。此外，在大量CCCTC结合因子（CCCTC-binding factor, CTCF）结合位点处，ZNF143定位于CTCF与黏连蛋白（cohesin）之间；敲除ZNF143会缩小CTCF与黏连蛋白之间的空间间距。进一步实验显示，联合遗传敲除ZNF143与急性耗竭CTCF，证实二者可协同调控高阶基因组组织结构。
综上，ZNF143可被CTCF招募至CTCF结合位点，以调控拓扑关联结构域（Topologically Associating Domain, TAD）形成与基因组区室化；而ZNF143自身直接定向识别DNA基序，则通过染色质环化调控启动子活性。
整体实验设计：针对野生型HEC-1-B细胞、ZNF143敲除（ZNF143KO）细胞，以及经生长素处理0小时或24小时的CTCF-AID细胞，开展针对ZNF143、CTCF及RAD21的HiChIP实验。