Fig. 4

H3K18la in human muscle marks active promoters and enhancers. A Correlation heatmap of hPTM levels in genome-wide quantified peaks from human muscle. Pearson’s correlation coefficient R is displayed as color gradient. B Distribution of all hPTMs across genomic features. C Peak fold enrichment adjusted for genome-wide feature size. D Venn diagram depicting the promoter overlaps marked by the active hPTMs. Overlaps are colored according to the absolute number of promoters marked by various combinations of active hPTMs. Percentages indicate the fraction of actively marked promoters belonging to each group. E Scatterplots showing pairwise correlation of promoter H3K18la levels with other hPTM levels (log₂CPM) highlighting the promoters of genes with highest (red, n = 2000) or lowest (cyan, n = 2000) normalized gene expression (RPKM). Pearson’s correlation coefficient R and p-values are indicated. F Normalized gene expression (log₂RPKM) per gene category is depicted as boxplots. Gene categories are defined by the combination of active hPTMs as in D. G ChromHMM analysis based on 5 hPTMs profiled in human muscle. The color scale shows the emission parameter of each mark for each state. Fold enrichment of ChromHMM states for total genomic fraction coverage, published skeletal muscle enhancers [57], different genomic features, and ENCODE cCREs, scaled from −2 to 2. H Venn diagrams depicting the overlap of dELS and pELS as marked by the different combination of the active hPTMs. Overlaps are colored according to the absolute number of ELS marked by various combinations of active hPTMs. Percentages indicate the fraction of actively marked ELS belonging to each group. I Heatmap showing the fold enrichment of hPTM peaks in cCREs (ENCODE); Σ (bp overlap)/[Σ (bp PTM peak)*Σ (bp cCRE)], scaled from −2 to 2. J Bar plots depicting the fraction of published human muscle enhancers [57] overlapping with the human hPTM peaks. K Top 10 GO terms (category “Biological Process”) resulting from a GO analysis of the corresponding closest genes to the 2000 dELS with highest H3K18la peaks (see the “Materials and methods” section for details on how enhancer and gene were linked)