Fig. 4: Chromatin immunoprecipitation (ChIP) and ChIP-seq analysis on the H3K4me2 mark following transforming growth factor beta (TGFβ)/tumor necrosis factor alpha (TGFβ/TNFα) treatment.
From: EMT is associated with an epigenetic signature of ECM remodeling genes
a Volcano plot of the 42,076 H3K4me2 merged islands. In red, the regions significantly enriched in TGFβ-/TNFα-treated cells versus non-treated cells. FC: fold change treated versus non-treated. fdr: false discovery rate treated versus non-treated. b Activating and/or repressive function prediction of H3K4me2 in A549 cells. BETA-basic integrates H3K4me2 differentially enriched regions and transcriptome data on TGFβ/TNFα treated cells and non-treated conditions to identify upregulated (red) and downregulated (purple) genes. The dashed line indicates the non-differentially expressed genes as background. Genes are cumulated by the rank on the basis of the regulatory potential score from high to low. p Values represent the significance of difference in the upregulated or downregulated groups compared with the non-differentially expressed group by Kolmogorov–Smirnov test. c Integration of transcriptome and ChIP-seq data for the A549 cell line. Top: heat maps of read coverage from −5 kb to +5 kb around the transcription start site for TGFβ-/TNFα-treated (left) and non-treated (right) conditions. Each line represents an upregulated gene identified by BETA. Genes are ordered according to their increasing rank product. Upper panels: read coverage density plots. Bottom: Corresponding gene expression heat map for treated (n = 4) and non-treated conditions (n = 4). Black lines indicate differentially expressed genes. d Increase expression of ADAM19 and MMP9 and decrease expression of SCNN1A in A549 cells treated with TGFβ/TNFα (mean ± SD of at least 3 independent experiments). e Ratio of fold change (epithelial–mesenchymal transition: TGFβ/TNFα treated A549 versus NT: untreated A549 cells) following ChIP against H3K4me2 and H3K27me3 marks on MMP9, ADAM19, and SCNN1A promoters. Dotted line = 1 (mean ± SEM of at least 3 independent experiments) *p < 0.05
