Fig. 6
Mediator complex and its interactors at promoters. a Predominant Gene Ontology terms for genes with broad H3k4me3 promoters and for active genes nearest to SEs (SE genes) in NSCs. Numbers of genes in each category are indicated between brackets. b Overlap of genes with broad H3K4me3 promoters and SE genes in NSCs. Venn diagram with the two categories of genes, their overlap and their predominant Gene Ontology terms is shown. Numbers of genes in each category are indicated between brackets. c Distribution of mRNA levels in NSCs of the different categories of active genes. Box plots based on RNA-seq triplicate data are shown. Broad-SE, broad H3K4me3 promoter genes not nearest to SE. SE-Broad, SE genes without broad H3K4me3 promoter. SE + Broad, SE genes with broad H3K4me3 promoter. Typical, genes nearest to a typical enhancer but not nearest to an SE and without a broad H3K4me3 promoter. mRNA levels of all genes and top 100 genes within each category are shown. Statistically significant differences between groups are indicated as separate letters above the box plots, as assessed by Student t-tests comparing all gene subsets (lower case letters) or top 100 subsets (upper case letters). p < 0.001 except for B, p < 0.05. If the letters are the same, the difference between these groups is not significant. Source data are provided as a Source Data file. d ChIP-seq density plots around promoters of the different categories of genes for the indicated factors and histone modifications. Mean ChIP-seq density (y-axis) and distance to TSS (x-axis) are shown. e Overlap of binding sites of Med1 with binding sites of Mediator interactors at the Trim8 broad H3K4me3 promotor area in NSCs. ChIP-seq tracks for the indicated proteins and histone modifications at the Trim8 gene are shown. Range of reads per million per base pair is indicated on the y-axis. Scale bar is indicated
