Fig. 2

Distinct characteristics of CTCF and CTCFL and their binding sites. a IgV tracks show RNA-seq in cells harboring the CTCFL transgene in U, I, D, and ID conditions. FLAG ChIP-seq to detect CTCFL and CTCF in cells with the respective transgenic knock-ins. The protein whose binding is being assessed is underlined. Expression of Ctcfl, Prss50, and Stra8 are also shown. b Heatmaps showing CTCF and CTCFL ChIP-seq signals at regions where they bind alone or together in CTCF D, CTCFL D, and ID conditions. The heatmaps are divided into CTCF only, CTCF+CTCFL overlapping, and CTCFL-only sites. Cohesin binding profiles (RAD21 ChIP) are shown for the corresponding conditions. Peaks are ranked by FLAG ChIP in cells expressing the CTCF transgene. Average profiles are shown below the corresponding heatmaps. c Venn diagrams showing the numbers of unique and overlapping CTCF and CTCFL binding sites (D condition). d Binding site motifs for unique and overlapping CTCF and CTCFL binding sites. Zinc fingers and the corresponding bases to which they bind are marked. e Annotation of the genomic locations of peaks for unique and overlapping CTCF and CTCFL binding sites in D condition. The locations of UTR, promoters (+/− 3 kb around TSS), introns, exons, downstream (3 kb), and distal intergenic regions are marked. f Volcano plot highlighting DEGs in wild-type versus CTCFL expressing mESCs in the presence of endogenous CTCF. Red and blue points identify genes with significantly increased or decreased expression, respectively (FDR < 0.01). The number of genes that are significantly up- or downregulated is indicated in either case. g Heatmaps showing the inhibition of chromatin binding of CTCF, but not CTCFL, after RNaseA treatment. The heatmaps are divided into CTCF only, CTCF+CTCFL overlapping, and CTCFL-only sites. Peaks are ranked by FLAG ChIP in cells expressing the CTCF transgene (CTCF ID). Average profiles are shown below the corresponding heatmaps