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Fig. 1 | Genome Biology

Fig. 1

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

Fig. 1

Genomic profiling of CTCF and BORIS occupancy in human cancer cells. a Schematic representation of CTCF and BORIS zinc fingers (ZF) shows the four essential amino acids involved in DNA recognition for each ZF. The amino acids of BORIS that differ from CTCF are highlighted in red. The numbers between ZFs show linker length. b Electrophoretic mobility shift assay (EMSA) with increasing amount of full-length BORIS protein (left panel) and unprogrammed TNT (right panel) on the background of a constant level of full-length CTCF protein. The fourth CTCF binding site out of seven mapped in the H19-IGF2 imprinting control region (ICR) was used as the labeled probe. c, d Gene tracks show the distribution of CTCF (red) and BORIS (blue) bound regions in the K562 cell line (c) and in cell lines K562, Delta47, OVCAR8, and normal human dermal fibroblasts (NHDFs) (d). The molecules against which antibodies were directed and cell lines used in ChIP-seq are shown on the left. The number of tags per one million of mapped reads is indicated. The gray frames and arrows show CTCF-only, CTCF&BORIS and BORIS-only bound regions. eh Heatmaps depict CTCF (red) and BORIS (blue) occupancy in NHDFs (e), K562 (f), OVCAR8 (g) and Delta47 (h) cells. e Heatmap shows the absence of BORIS occupancy at CTCF bound regions mapped in BORIS-negative NHDFs. f The genome-wide overlapping of CTCF- and BORIS-bound regions mapped in K562 cells is shown on the left side of the heatmap. The overlapping of CTCF and BORIS occupancy was done independently for each cell type. The tag density of CTCF and BORIS ChIP-seq data was collected within a 10-kb window around the summit of CTCF (CTCF&BORIS and CTCF-only) and BORIS peaks (BORIS-only). The collected data were subjected to k-means clustering using linear normalization based on similar tag density profiles. The molecules against which antibodies were directed in ChIP-seq are listed on top of the heat map. i Heatmap shows the enrichment of ChIP-Re-ChIP tag density at CTCF&BORIS-bound regions. ChIP-Re-ChIP occupancy (purple) is presented in comparison with CTCF (red) and BORIS (blue) ChIP-seq data for Delta47 cells. The tag density was subjected to k-means ranked clustering with two clusters expected

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