Fig. 2. Identification of SOX2 candidate functional enhancers in squamous cancer cells.
a CTCF ChIP-seq signal—signal per million reads (SPMRs) per bp in KYSE140 cells are presented underneath the positions of insulated neighborhoods derived from CTCF ChIA-PET data35. b Averaged ATAC-seq signal from TCGA squamous cancers and H3K27ac ChIP-seq signal (SPMR/bp) from squamous cancer cell lines, AALE and hESC cells are presented at the highlighted SOX2 locus. The super-enhancer region shared by the listed SOX2-high squamous cancer cell lines is highlighted. c H3K27ac HiChIP loops that are connected to the SOX2 promoter in squamous cancer cell lines. HiChIP anchors are defined by the union of H3K27ac peaks identified from the SOX2-high squamous cancer cell lines listed in (b). The color intensity corresponds to the number of PETs supporting each of the loops.