Fig. 2: Identification of enhancers by ChIP-seq.

a Overlay of H3K4me1, H3K27ac and promoter-associated H3K4me3 ChIP-seq data from human skeletal myotubes. b, c MDS plot of non-promoter associated H3K27ac (b) and H3K4me1 (c) ChIP-seq data from control (ctrl), palmitate (palm) or TNFα treated cells. Leading log fold-change (logFC) is the mean logFC between the 500 most divergent H3K27ac (b) or H3K4me1 (c) ChIP-seq peaks between each pair of samples. d, e Volcano plot representation of differentially H3K27 acetylated regions among the 62,866 enhancers containing both H3K4me1 and H3K27ac (n = 4 biological replicates, FDR < 0.01) from palmitate (d) or TNFα (e) treated cells. Blue dots represent enhancers that are downregulated and red dots represent enhancers that are upregulated by the respective treatments (n = 4 biological replicates, FDR < 0.01). The ChIP-seq and enhancer analyses are described in detail in the Methods section. f and h, UCSC genome browser (hg38) H3K27ac and RNA-seq tracks from control (ctrl), palmitate (palm) or TNFα treated cells around PDK4 and ANGPTL4 (g) or CCL11 and CXCL8 (i). g and i Quantification of H3K27ac counts pr. million (CPM) at the selected enhancer regions in the individual replicate samples. Values are represented as the mean ± S.D. (n = 4 biological replicates). Asterisks indicate enhancers that are significantly regulated in the ChIP-seq analysis (****FDR < 0.0001, **FDR < 0.01). j, k Quantification of mRNA counts pr. million (CPM) of the indicated genes in the individual replicate samples. Values are represented as the mean ± S.D. (n = 4 biological replicates). Asterisks indicate genes that are significantly regulated in the RNA-seq analysis (**FDR < 0.01, ***FDR < 0.001, ****FDR < 0.0001).