Fig. 5

H3K4me3 concentrates chromatin accessibility at promoters. A) Pie chart showing the distribution of mapped H3K4me3 peaks in control(RNAi) stem cells. B) Profile plot comparing H3K4me3 signal in control(RNAi) and bptf(RNAi) stem cells averaged across all genes. The shaded area represents the standard error. C) Venn diagram showing the number of promoters in planarian stem cells with an H3K4me3 peak, an ATAC-seq peak, or both. Overlap p-value was calculated using the hypergeometric test. D) Profile plot comparing H3K4me3 signal in control(RNAi) and bptf(RNAi) stem cells at the gene promoters in each group of the Venn in C (H3K4me3 only, H3K4me3 + ATAC peak, and ATAC peak only). The shaded area represents the standard error. E) Profile plot comparing ATAC-seq signal in control(RNAi) and bptf(RNAi) stem cells for gene promoters in each group of the Venn shown in C. The shaded area represents the standard error. F) Box plots measuring changes in ATAC-seq signal at the promoters of genes in each group in E. Statistical significance was determined using a Wilcoxon test (p-value with Bonferroni correction, **** = p ≤ 0.0001). G) Scatter plots comparing changes in chromatin accessibility (ATAC-seq; csaw) with changes in gene expression (RNA-seq; DESeq2) in bptf(RNAi) X1 stem cells at loci with an H3K4me3 peak at their promoters (left plot) versus those without an H3K4me3 peak (right plot). 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