Fig. 4

The role of CTCF and CTCFL zinc fingers and N/C terminals in site-specific binding. a Schematic showing the doxycycline-inducible parent (Ctcf, Ctcfl) and chimeric (CTCFL N terminus - CTCF ZFs - CTCFL C terminus (LCL) and CTCF N terminus - CTCFL ZFs - CTCF C terminus (CLC) transgenes knocked into the Tigre locus. All transgenes contain an N terminal 3 × FLAG, C terminal mRUBY2, and TetO-3G and rtTA3G for doxycycline-induced expression. b Western blot using FLAG antibody shows that the level of expression of transgenes is comparable across cell types as well as experimental conditions (D versus ID). Histone H3 serves as loading control. c Heatmaps of CTCF, CTCFL, LCL, and CLC ChIP-seq signals at regions where they bind in the presence of endogenous CTCF (D). The heatmaps are divided into CTCF only, CTCF+CTCFL overlapping, and CTCFL-only regions. Cohesin peaks (RAD21 ChIP) are shown for the corresponding conditions. Peaks are ranked by FLAG ChIP using cells expressing the CTCF transgene. Average profiles are shown above the corresponding heatmaps. d–f IgV tracks showing ChIP-seq for CTCF, CTCFL, LCL, and CLC at Ctcfl, Prss50, Gal3st1 (d), Zbtb45, Stat2, Mrps33 (e), Hoxb, and Clasp1 (f) using a FLAG antibody in cells harboring the respective transgenes in the absence of CTCF. g Binding site motifs at CTCF and CTCFL-only sites, as well as CTCF and CTCFL overlapping sites. Motifs for CLC and LCL were identified in the presence of endogenous CTCF. The zinc fingers and the corresponding bases to which they bind are marked. h Annotation of the genomic locations of peaks bound at CTCF and CTCFL-only sites, as well as CTCF and CTCFL overlapping sites. Motifs for CLC and LCL were identified in the presence of endogenous CTCF. The locations of UTR, promoter (+/−  3 kb around TSS), intron, exon, downstream (3 kb), and distal intergenic regions are marked