Dissection of a CTCF insulator and its impact on chromosome topology and oncogene expression in gastrointestinal stromal tumor (ChIP-Seq). Dissection of a CTCF insulator and its impact on chromosome topology and oncogene expression in gastrointestinal stromal tumor (ChIP-Seq)

Enhancer-Promoter communication is dependent on the topological organization of genomic DNA, including topologically-associated domains (TADs) and boundaries enforced by the CTCF insulator protein. Here, we characterized the structure and function of the FGF3/4 locus and the boundary element that insulates the region from an enhancer in the adjacent TAD. Overall design: To investigate the impact of CTCF insulator disruptions, we established derivatives of the GIST-T1 cell line. We then performed chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for CTCF, H3K27ac and H3K27me3 in GIST-T1 WT and insulator KO cell lines.

增强子-启动子调控通讯（Enhancer-Promoter communication）依赖于基因组DNA的拓扑组织结构，包括拓扑关联结构域（topologically-associated domains, TADs）以及由CTCF绝缘子蛋白（CTCF insulator protein）所维系的边界区域。本研究针对FGF3/4基因座的结构与功能，以及将该区域与相邻TAD内增强子绝缘的边界元件展开了表征分析。
实验设计概述：为探究CTCF绝缘子功能破坏的影响，我们构建了GIST-T1细胞系的衍生株系。随后，我们分别对野生型（WT）及绝缘子敲除（KO）的GIST-T1细胞系，开展了针对CTCF、H3K27ac与H3K27me3的染色质免疫共沉淀测序（chromatin immunoprecipitation DNA-sequencing, ChIP-seq）实验。