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.