Characterization of CTCFL and CTCF binding. A A large fraction of CTCFL-binding sites is located close to promoters. We determined for each CTCFL-only-binding site the distance to the nearest transcriptional start site (TSS) and plotted the frequencies of binding sites in the depicted window from −40 kb to +40 kb around the center of CTCFL-binding sites. CTCF is plotted as comparison. B Comparison of the genomic distribution of CTCF- and CTCFL-binding sites. Sites are separated into CTCF-only, CTCFL-only and (CTCF + CTCF). The entire genome is also plotted (all). The binding location is separated into exon, intron, intergenic, transcription start site (TSS) and transcriptional end sites (TES), and plotted as frequencies of total (Y ax). C Clustered heatmap representation of the three different classes of CTCF/CTCFL-binding sites with respect to chromatin context. We compared CTCF and CTCFL binding to published ChIP-sequencing data sets for the cohesin complex subunit Smc1, H3K4me3, a phosphorylated form (serine 5) of RNA PolII, (PolIISer5P) and histone H3 [8, 42, 43]. D Cumulative profiles across the three different classes of CTCF/CTCFL-binding sites with respect to chromatin context. The average ChIP-sequencing profiles are shown for the same data sets as in (C). E Cumulative profiles across the three different classes of CTCF/CTCFL-binding sites with respect to H3.3.