Figure 2

MITF binds and represses genes of extracellular matrix (ECM) and focal adhesion genes. (a) Volcano plot showing 2136 DEGs with qval <0.5 among which 1516 genes with log2FC≥|1| fold change in expression ∆MITF-X6 vs. EV-SkMel28. (b) GO BP analysis of the 1284 induced and 852 reduced DEGs between ∆MITF-X6 vs. EV-SkMel28 cells presented in dot plot; adjusted p-value is red lowest to blue highest; gene ratio is the ratio between DEGs and all genes in the GO category. (c) Dot plot of enrichment analysis showing the enrichment of gene signatures from the literature in reduced and induced DEGs of ∆MITF-X6 vs. EV-SkMel28. p Value is red lowest to blue highest; gene ratio is the ratio between genes and all genes in the GO category; reduced: genes reduced in expression in ∆MITF-X6 compared to EV-SkMel28; induced: genes induced in expression in the ∆MITF-X6 compared to EV-SkMel28. (d) GO BP analysis of MITF CUT and RUN peaks associated genes were plotted using Clusterprofiler (Yu et al., 2012) in R; All: MITF CUT and RUN peak-associated genes, induced and reduced: Induced or reduced DEGs of ∆MITF-X6 vs. EV-SkMel28 cells based on MITF CUT and RUN peak presence on their gene promoter or distal region binding. (e) Venn diagram showing the overlap between MITF targets identified from MITF CUT and RUN with induced, reduced, ECM and focal adhesion DEGs of ∆MITF-X6 vs. EV-SkMel28 cells. (f) Venn diagram displaying the common overlap between MITF ChIP-seq targets in different cell lines and differentially expressed ECM and focal adhesion genes in ∆MITF-X6 vs. EV-SkMel28 cells. (g) Heatmap showing the differentially expressed ECM genes in ∆MITF-X6 vs. EV-SkMel28 cells that are commonly bound by MITF across different MITF CUT and RUN data sets. Zcore converted TPM value from RNA-seq data was used for plotting. (h) Motif analysis of MITF CUT-and-RUN targets of induced and reduced genes in ∆MITF-X6 vs. EV-SkMel28 cells.