Figure 5

Global changes in genomic levels of H3K9ac and H3K4me3 with loss of H3f3b suggest a moderate role for H3.3 in euchromatin. (A) Immunostaining in wildtype (WT) 63 versus knockout (KO) 56 indicates a modest decrease in global histone 3 lysine 4 tri-methylation (H3K4me3) levels in KO nuclei. Scale bar = 10 um. (B) ChIP-seq analysis of H3K4me3 and histone 3 lysine 9 acetylation (H3K9ac) marks was performed, normalizing samples to input for peak calling. Venn diagrams show the number of total and overlapping peaks in WT and KO samples. Note, that for each condition the data presented are total peak numbers from merged biological duplicates of WT1 and WT2 versus KO1 and KO2. The number and percentage of overlapping peaks are indicated in the middle of each diagram. (C) Binding affinity clustering heatmap of H3K9ac (left) and H3K4me3 (right) peaks in two biological replicates of WT and KO MEFs. Correlation color codes are shown above each plot. Clustering was performed using R package DiffBind, which clusters the samples based on the normalized read counts for each sample at each putative histone mark peak.