Fig. 1

Acute CTCF depletion alters chromatin accessibility. A Schematic diagram of the auxin-inducible degron model for tagging endogenous CTCF in MLL-rearranged B-ALL SEM cells [19]. SEM cells were transduced with a lentivirus expressing a transgene encoding doxycycline-inducible OsTIR1. The miniAID-mClover3 cassette was inserted in both endogenous alleles in frame with CTCF. In the presence of doxycycline and auxin (IAA), forced expression of OsTIR1 combines with Skp1/Culin/F-box ubiquitin ligase components to form a functional SCF/OsTIR1 E3 ubiquitin ligase complex that rapidly degrades miniAID-mClover3 fusion proteins. B CTCF immunoblots confirmed successful degradation of the CTCF-miniAID-mClover3 fusion protein translated from the knockin samples. C Heatmap centered at ATAC-seq nucleosome-free peak summits for differential accessibility regions (DARs). CTCF Cut&Run data indicate that the increased DARs have the strongest CTCF binding, whereas the decreased DARs have weaker overall CTCF binding with double summits (yellow average profile curve denoted in the enlarged area). ATAC-seq profiling of USF1/2 double-knockout SEM cells served as negative controls. D Boxplots of ATAC-seq peak intensities (fragments per kb of peaks per million reads mapped, FPKM) at control NFRs, decreased DARs, and increased DARs (DARs were FDR-corrected p value < 0.05 and |log2fold change| > 1. E Violin plots of the overall distance of the closest CTCF motif to decreased DARs increased DARs, or control regions. The physical distance at the y-axis was calculated by log₁₀ (distance + 1 bp). **** p value < 0.0001 in Wilcox test