Extended Data Fig. 7: β-catenin and Ikaros factors mediate recruitment of NuRD complex at BENC enhancer.
(a) ChIP-seq analysis for β-catenin, Ikaros factors Ikzf1 and Ikzf3, histone marks H3K27ac and H3K4me3 shown for the Myc locus, including upstream Myc promoter regions and long-range transcriptional enhancers of Myc in B-ALL cells from β-catenin(S33-S45)+/fl mice. Peak density plots show colocalization of β-catenin, Ikzf1 and Ikzf3 peaks and their concentration at BENC enhancer regions. Comparison of changes in H3K27ac active enhancer and H3K4me3 active promoter marks following accumulation of β-catenin (red boxes) or β-catenin baseline (light green boxes), upon Ikaros factor deletion (empty boxes) or Ikaros baseline (dark green boxes) conditions. Ikaros factors and β-catenin show marked enrichment at BENC regions. While accumulation of β-catenin depleted H3K27ac marks at BENC enhancer regions, β-catenin had the opposite effect and increased BENC enhancer activity and H3K27ac signals when Ikaros factors (Ikzf1 and Ikzf3) were deleted. (b) β-catenin binding (mean value of two technical replicates) to BENC enhancer region and other β-catenin targets was measured by ChIP-seq in β-catenin(S33-S45)+/fl B-ALL cells (Ikzf1/3 WT) 1 day after β-catenin stabilization. β-catenin is strongly enriched at BENC enhancer (input n = 11863, Other n = 11857, BENC n = 6 peaks; two-sided unpaired t-test P = 0.0005). Boxplots display boxes at first and third quartile with line at median and whiskers from minimum to maximum datapoints within 1.5x interquartile range. (c) ChIP-qPCR was performed for NuRD complex components (MTA2 and CHD4) at the epithelial Myc enhancer regions as well as lymphoid BENC Myc enhancer region (BENC-D). For each region, MTA2 and CHD4 ChIP were performed for B-ALL cells with induced β-catenin accumulation (red boxes), β-catenin deletion (empty boxes) or intact β-catenin (light green boxes), as well as deletion of Ikaros factors (empty boxes) or intact Ikaros factors (dark green boxes). Data shown represents mean values from 3 independent experiments (n = 3 technical replicates). Two-sided unpaired t-test was used to calculate P values.
