Fig. 5: Loss of the WDR5-NANOG interaction compromises histone modifications at promoters of pluripotency-associated genes.

Heatmaps showing the genome-wide ChIP-seq binding profiles (merged from n = 2 independent biological replicates per condition) of NANOG (a) and WDR5 (b) at NANOG-specific, WDR5-specific, and shared binding sites in mESCs expressing NANOG^WT or NANOG^R153A (±3 kb from peak center). c Venn diagram summarizing the shared numbers of NANOG and WDR5 ChIP-seq peaks observed in NANOG^WT and NANOG^R153A mESCs. d Venn diagram showing the overlap between genes co-bound by NANOG and WDR5 in WT mESCs (identified by ChIP-seq) and genes differentially expressed in NANOG^R153A mESCs (identified by RNA-seq). e Box plots (related to Fig. 5d) showing the expression levels of WDR5-NANOG target genes in NANOG^WT and NANOG^R153A mESCs. Genes were categorized into groups with increased binding (n = 113 genes), decreased binding (n = 96 genes), no significant change (n = 1878 genes), and housekeeping genes (n = 811 genes). Box plots show the median (center line), with boxes indicating the 25th and 75th percentiles (interquartile range). Whiskers extend to the most extreme data points within 1.5× the interquartile range. Individual data points are overlaid. P values were calculated using unpaired two-sided t-tests. f GO enrichment analysis (related to Fig. 5d) was performed using DAVID. Downregulated and upregulated gene sets were analyzed separately using a one-sided hypergeometric test, with P values adjusted by the Benjamini-Hochberg method (FDR). Dot size indicates gene number and color indicates −log₁₀ (adjusted P value). Heatmaps showing the genome-wide ChIP-seq binding profiles (merged from n = 2 independent biological replicates per condition) of H3K4me3 (g) and H4K16Ac (h) at NANOG-specific, WDR5-specific, and shared binding sites in mESCs expressing NANOG^WT or NANOG^R153A (±3 kb from peak center). i Representative genome browser tracks showing ChIP-seq signals for NANOG, WDR5, H3K4me3, and H4K16ac at the Tcf3 and Dnmt3a loci.