Skip to main content
Fig. 6 | Genome Biology

Fig. 6

From: Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions

Fig. 6

CTCF and BORIS interactions are essential for transcriptional regulation in cancers. a Two models are used in the study: K562 cells (BORIS+/+) treated with zinc finger nuclease (ZFN) to knockout/downregulate the BORIS gene (BORIS+/−) and MCF7 cells with stably transfected empty vector (MCF7+EV) or BORIS-expressing vector (MCF7+BORIS). Upon stable change of BORIS expression (western blot) both types of cells showed phenotypic changes. b Western blot analysis of K562 cells (mass culture) upon BORIS depletion by ZFN (before ZFN (wt), 48 h, and two weeks after ZFN). c Number of K562 single-cell clones growing in soft agar after ZFN transfection (ZFN) compared with untransfected cells (Control). d Expression of megakaryocytic lineage markers in three independent single-cell K562 clones after ZFN treatment compared with wild type (wt). e, f Fold changes (log2) in gene expression in response to BORIS depletion in K562 cells (e) and BORIS induction in MCF7 cells (f). Two independent single-cell clones of MCF7 cells with stably expressed BORIS were analyzed (f). Top associated diseases and bio functions (p < 0.0001) are shown for upregulated (red) and downregulated (green) genes on the right (Ingenuity Pathway Analysis). The genes that change expression in a similar way in both independent MCF7 clones with stably transfected BORIS are shown on the heat map (f). g Heat map showing the comparison of genes that changed expression upon BORIS depletion (K562 cells) and BORIS induction (MCF7 cells, clone1) in respect to diseases and bio functions (activation z-score). h Genome browser view of six CTCF&BORIS target genes. The tracks are labeled with the names of molecules against which antibodies were directed and the cell lines used in ChIP-seq, respectively. The red arrows show the beginning and direction of transcription. The schematic occupancy of promoters with either CTCF (red) and BORIS (blue) heterodimers or CTCF homodimer is shown on the right. i Expression of six CTCF&BORIS targets from panel (h) was analyzed by quantitative PCR in cells with upregulated (MCF7+BORIS) and downregulated BORIS (BORIS small interference RNA (si) treatment of K562 cells, mass culture) expression. Asterisk (*) represents p-value <0.05 and double-asterisk (**) represents p-value <0.01 between treated and untreated cells (c, i). Error bars represent standard deviation of the average of triplicate measurements (c, d, i). TSS transcription start site

Back to article page