Fig. 3: Ezh2Y641F induces complex changes in the transcriptome and its response to PRC2 inhibition.
a Comparative gene expression between Ezh2Y641F/WT and WT iMEFs highlighting significantly up-regulated (red) and down-regulated (blue) genes. FC, fold change. b Top, Overlap between genes up-regulated in Ezh2Y641F/WT versus WT iMEFs and those up-regulated in 2-µM-UNC1999-treated WT iMEFs. Bottom, Overlap between genes down-regulated in Ezh2Y641F/WT versus WT iMEFs and those up-regulated in 2-µM-UNC1999-treated Ezh2Y641F/WT iMEFs. c Overlap between genes up-regulated in WT and Ezh2Y641F/WT iMEFs treated with 0.25 µM (top) or 2 µM (bottom) UNC1999. d PCA of variance among RNA-seq of WT and Ezh2Y641F/WT iMEFs in the indicated treatment conditions. e Heatmap representing RNA-seq expression z-scores for all genes up-regulated in either WT or Ezh2Y641F/WT iMEFs upon 2-µM UNC1999 treatment. Genes are ordered in clusters according to genotype-specific expression level and up-regulation. f Box plots showing gene-length-normalized average H3K27me3 enrichment in untreated WT and Ezh2Y641F/WT iMEFs for each cluster shown in (e) (n = 92, 175, 140, and 134 genes, respectively). Boxes represent median and first and third quartiles, while whiskers show minimum and maximum. RPK, read per kilobase. g Left, results of MEME motif enrichment analysis over promoters of genes differentially expressed in Ezh2Y641F/WT versus WT iMEFs focusing on TFs whose expression is up-regulated. Right, heatmap representing RNA-seq expression z-scores for the genes encoding these TFs. TF, transcription factor. TSS, transcription start site. h Protein-protein interaction network built from the TFs identified in (g) with STRING and Cytoscape, with the thickness of each edge reflecting the degree of evidence for interaction. i Bubble plots showing GO terms significantly enriched among genes up-regulated in 2-µM-UNC1999-treated WT and Ezh2Y641F iMEFs. GO, gene ontology. j Heatmap representing RNA-seq expression z-scores for genes corresponding to GO:0019886, the most highly enriched GO term among genes up-regulated in 2-µM-UNC1999-treated Ezh2Y641F iMEFs.
