Dissection of a CTCF insulator and its impact on chromosome topology and oncogene expression in gastrointestinal stromal tumor (RNA-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 in SDH-intact cells, we established derivatives of the GIST-T1 cell line. We then performed gene expression profiling analysis between WT and insulator KO cell lines using data obtained from RNA-seq.