Fig. 3. CTCF N-terminus promotes long-range Igκ loop extrusion by protecting cohesin from WAPL release.

a Representative 3C-HTGTS analysis of Igκ chromatin interaction profile in WT and CTCF-Nm cells using Cer locale as bait. Bait region is indicated by a red star. Zoomed-in views show a representative distal Vκ region (lower left) and a proximal Vκ region (lower right), along with their correlation to E2A and CTCF binding sites. b Quantification of relative chromatin interactions. The relative Cer bait interactions in the indicated Vκ regions in CTCF-Nm cells are presented as a percentage of the WT values. Data represents mean ± SD from three independent replicates. c Analysis of peak interactions at the Vκ region. The relative Cer bait interactions of peaks overlapping with CTCF peaks (purple), E2A peaks (blue) or both (orange) in the indicated Vκ regions in CTCF-Nm cells are shown as a percentage of the WT values. Medians are denoted by the black lines. Each data point represents mean from three independent replicates. d Genome-wide peak analysis of SMC3 ChIP-Seq signal. Heatmaps show signal within ± 1.0 kb region across all peaks, ranked by SMC3 binding intensity. e SMC3 ChIP-Seq profiles at Igκ locus in WT and CTCF-Nm cells. f Quantitative mass spectrometry analysis of the relative abundance of SMC3 immunoprecipitates obtained from chromatin fraction of G1 arrested WT and CTCF-Nm cells. Protein intensities are normalized to the amount of chromatin-bound SMC3 across samples. Data represents mean ± SD from three independent replicates. P values were calculated using unpaired, two-tailed Student’s t test.