Fig. 6
Analysis of global and combinatorial histone modifications (PTMs) during melanoma progression. The acetylation and methylation levels of histone marks were assessed in the cell lines from the melanoma progression model. a Global acetylation and methylation (me1 + me2 + me3) levels were obtained by the sum of the abundance ratios of all peptides containing these modifications. The 4C cell line had a decrease in global acetylation levels and an increase in the dimethylation and global methylation histone marks. b Hierarchical clustering of the samples was based on the relative abundance levels of 245 histone combinatorial PTMs, using the Pearson correlation and the complete linkage method. The 65 histone marks with the highest relative abundance levels are shown. Cell lines with epithelial (4C11+ and MA) and mesenchymal (4C and 4C11−) morphology cluster together. c c-fuzzy means clusters of histone combinatorial PTMs were grouped according to their potential role in melanoma progression, EMT, and metastasis. The clusters 2, 7, and 8 were associated with melanoma progression due to the alteration of their abundance distribution in the 4C, 4C11−, and 4C11+ cell lines. Clusters 1 and 5 were related to epithelial-mesenchymal transition (EMT) due to their relative abundance patterns in epithelial versus mesenchymal cells. Clusters 3, 4, and 6 were associated with metastasis due to the increased or decreased regulation of the histone peptide marks in these clusters in the metastasis-prone 4C11+ cell line. d Heatmaps showing the changes in the relative abundance levels of the combinatorial PTMs grouped in each cluster. Since modifications of the same amino acid residues occur in multiple peptides and clusters, only the average z scores are reported for each histone residue-modification pair in each cluster. The color mapping of the row-wise z scores was made with blue and red colors to represent the down- or upregulation of the corresponding PTMs in each cell line. The row colors on the left side of each heatmap illustrate the clusters in which the combinatorial PTMs are included, whereas the row colors on the right side depict the histones from which the modified amino acid residues belong to