Fig. 6

BPTF shares functional genomic targets with Set1. A) Profile plot comparing ATAC-seq data from control(RNAi) and bptf(RNAi) stem cells at Set1 (left) and MLL1/2 (right) gene targets. The shaded area represents the standard error. B) Quantitation and statistical analysis of ATAC-seq data in A; statistical significance was determined using a Wilcoxon test (p-value with Bonferroni correction). * = p ≤ 0.05, ** = p ≤ 0.01, *** = p ≤ 0.001, **** = p ≤ 0.0001). C) Venn diagram comparing genes identified as likely targets of Set1, MLL1/2, and BPTF in X1 stem cells. Targets = genes with loss of H3K4me3 or ATAC-seq at promoters (+/- 1 kb of TSS) in their respective RNAi conditions. p-val = 8.65e-74 for BPTF targets overlap with Set1 targets; p-val = 1.04e-75 for BPTF targets overlap with MLL1/2. D) Venn diagrams comparing common Set1 and BPTF targets (217 genes) with DEGs at day 12 (left) as well as common MLL1/2 and BPTF targets with DEGs at day 12 (right). P-values were calculated using a hypergeometric test. E) Plots comparing differential changes in chromatin accessibility (ATAC-seq) with differential changes in gene expression (RNA-seq) in bptf(RNAi) stem cells at Set1 versus MLL1/2 target genes (from C, D). Data points shown have pAdj < 0.05 in both datasets. Correlation coefficients (R) and p-values were calculated using Spearman Rank correlation. The grey shaded areas around the regression lines represent 95% confidence intervals. F) GO Term enrichment analysis for genes with reduced chromatin accessibility in bptf(RNAi) X1 stem cells (“BPTF-dependent loci”), reduced H3K4me3 in set1(RNAi) X1 stem cells (“Set1-dependent loci”), and reduced H3K4me3 in mll1/2(RNAi) X1 stem cells (“MLL1/2-dependent loci”)