Fig. 3: Characterization of dynamic histone modifications around primed chromatin.

a Ten chromatin markers were used to train the chromatin states in primary hepatic stellate cells by chromHMM. The different shades of the same color were used to distinguish the chromatin state. The middle section displaying a heatmap of the emission parameters, in which each row corresponds to a different state, and each column corresponds to a different mark defined on the basis of the observed data. The right heatmap displays the fold enrichment for the eight chromatin accessibility clusters in epigenomic-marked chromatin states. A darker blue color corresponds to a greater fold enrichment, and there is one color scale for the entire heatmap. b Profiles of H3K4me3, H3K27me3, and H3K27ac signals surrounding different chromatin clusters as defined in Fig. 2a. Rows correspond to ±3 kb regions across the midpoint of each primed chromatin site. c Normalized H3K4me3, H3K27me3, and H3K27ac signal profiles at a locus in TIMP4 are shown together with a normalized ATAC-seq profile. The vertical yellow boxes highlight the transcription start sites. d Representative immunofluorescence images of cells cultured on different matrices for two days. Anti-H3K27ac (yellow), anti-H3K4me3 (red), and anti-H3K27ac (green). Scale bar, 10 µm.