Fig. 4

Comparative gene expression analysis of histone writers and erasers across the cell lines from the melanoma progression model. Gene expression levels were assessed by quantitative polymerase reaction (qPCR) analysis of the cell lines melan-a, 4C, 4C11−, and 4C11+. a Gene expression analysis for the lysine acetyltransferases Hat1, Ep300, Kat2a, and Kat5. Hat1 showed the highest expression in melan-a cells and then exhibited progressive lower expression in the 4C, 4C11−, and 4C11+ cell lines. Ep300 showed statistically significant upregulation in the mesenchymal-like cell lines 4C and 4C11−. Kat5 was significantly upregulated in 4C cells in comparison to melan-a cells but returned to melan-a levels in 4C11− and 4C11+ cells. b Gene expression analysis for the lysine methyltransferases NSD1 and SET2. The gene expression of Nsd1 was significantly downregulated in 4C11+ cells in comparison to the other cell lines. Setd2 expression was the highest in melan-a and 4C11− cells, showing intermediate values in 4C cells and the lowest expression in 4C11+ cells. c Gene expression analysis for the histone deacetylases HDAC1, HDAC3, HDAC6, and HDAC11. The expression levels of Hdac1, Hdac3, and Hdac6 were progressively reduced in the cell lines, with 4C11+ cells showing the lowest expression levels. In contrast, the expression levels of Hdac11 were higher in both mesenchymal-like cell lines 4C and 4C11−. d Gene expression analysis for the histone demethylases Kdm2a and Kdm2b. The expression of Kdm2a was significantly reduced in 4C11− cells. Kdm2b expression was significantly increased in 4C cells compared to melan-a cells and decreased in 4C11− and 4C11+ cells. Statistical analyses were made by comparing the expression levels of each gene across the cell lines using one-way ANOVA followed by the Tukey’s multiple comparison test. *p < 0.05, **p < 0.01, and ***p < 0.001. Genes were considered to be differentially expressed when the multiplicity adjusted p values in the pairwise comparisons were lower than 0.05