Figure 4

H4K5ac enrichment in the promoter and CDS. (A) Genes acetylated for H4K5 after CFC are clustered based on acetylation profiles over ±2 kb relative to the TSS. Clusters 3 (green), 4 (blue), and 5 (violet) occur in promoter regions, cluster 1 (red) occurs in the CDS, and cluster 2 (yellow) is unenriched for H4K5ac. (B) Contribution of gene clusters with respect to levels of gene expression show higher contribution of clusters enriched for H4K5ac with higher expression. (C) Clustering of genes acetylated for H4K12ac after CFC generated clusters 2 (yellow) and 5 (violet) in the promoter region, clusters 1 (red) and 3 (green) in the CDS, and cluster 4 (blue) is unenriched for H4K12ac. (D) The contribution of clusters enriched for H4K12ac is also higher with higher gene expression levels. (E) Clustering of genes obtained from IgG-IP controls after CFC result in uniformly distributed clusters including clusters 1 (red), 3 (green), and 5 (blue) in the promoter region, and clusters 2 (yellow) and 4 (blue) in the CDS. (F) IgG clusters show no change in contribution with increasing gene expression levels. (G, H) Custom tracks are shown for G) Sfi1 (chr11:3073466–3095466) and H) Phactr3 (chr2:177908053–177930053), as identified by both MACS and SICER for genes differentially acetylated for H4K5 in FC over control. A gene contiguous to Sfi1 (Pisd-ps1/3) is highlighted in blue, the CDS is highlighted in green, and adjacent intergenic regions in pink. Neighboring genes (Eif4enif1, Drg1, Zfp931, Sycp2, Ppp1r3d, and 9030418K01Rik) are shown to emphasize H4K5ac enrichment in the vicinity of peak-called genes. Splice variants for Phactr3 (Refseq) are annotated below the track. Customized wig tracks were visualized in the UCSC Genome Browser.