Supplementary Figure 3: Epigenomic analysis of cellular insulin resistance

(a) Trypsinized histone fragments from Dex- and TNF-treated cells were subjected to mass spectrometry. Depicted is a heat map displaying changes in histone 3 marks (n = 2). (b) ChIP-Seq was performed using antibodies directed against the indicated histone modifications at different time points after Dex and TNF treatment. Shown are the total number of called peaks for each modification and time point. (c) Heat maps for model parameters from ChromHMM model learned from x-axis labelled ChIP-seq data sets across control and all Dex and TNF time points. The columns indicate the relative percentage of the genome represented by each chromatin state. WCE = whole-cell extract. (d) Heat maps for enrichment of each state for various annotated functional genomic elements e. Heat maps for enrichment of each state as a function of distance from TSS. (f) Numbers of promoters and enhancers during adipocyte differentiation (compared to Day 7 adipocytes), or at each time point after Dex and TNF treatment (compared to untreated) are indicated. The percentages of nonoverlapping promoters or enhancers that change with differentiation or drug treatment are shown at right.