Fig. 4: Ybx1 suppresses H3K27me3 levels.
From: Ybx1 fine-tunes PRC2 activities to control embryonic brain development
a Heat maps indicate the binding intensity of H3K27me3, H3K4me3, and Ybx1, with low (white) or high (dark color) intensity, within 2 kb of all Ybx1 CUT&RUN-seq peaks. Average binding profiles from five different categories (cat.) are presented. In all five categories, H3K27me3 levels increased in Ybx1-KO NPCs. Cat. 1, H3K4me3 peaks to the left of Ybx1 peaks; 2, H3K4me3 peaks to the right of Ybx1 peaks; 3, H3K4me3 peaks at Ybx1-bound peak center; 4, high H3K4me3 increase in Ybx1-KO; 5, no H3K4me3. b Proportion of differentially expressed genes in Ybx1-KO vs. WT NPCs bound by Ybx1 protein in control NPCs. P values were calculated by two-tailed Fisher’s exact test. c H3K27me3 and H3K4me3 ChIP-seq and Ybx1 CUT&RUN-seq tracks at Foxg1, Neurod2, and Satb2 gene loci in Ybx1-KO and sibling control NPCs. d MA plot of LOG2(H3K27me3 fold-changes of Ybx1-KO/WT NPCs) versus mean H3K27me3 levels at individual genes. Blue indicates downregulated genes and black indicates upregulated genes in Ybx1-KO NPCs. e GSEA of genes containing significantly increased H3K27me3 levels at promoters with differentially expressed genes in Ybx1-KO versus control NPCs. P values were calculated by one-tailed Kolmogorov–Smirnov statistic test. f MA plot is similar to d, but shows H3K4me3 levels.
