Figure 5. EZH2 is a transcriptional repressor in ASC.

RNA-seq was performed on enriched splenic ASC from tamoxifen treated Ezh2^fl/fl (Ctl) and Ezh2^fl/flRosa26^CreERT2/+ (KO) mice three days post LPS inoculation. (A) Volcano plot summarizing differentially expressed genes (DEG) (FDR < 0.05, log2FC > 1) between Ctl and KO ASC. RNA-seq data represents three biological replicates of Ctl and KO ASC. (B) Top GSEA gene sets. (C) The log2FC for DEG was plotted versus the log2 fold change in promoter H3K27me3 enrichment between nB and ASC. (D) Heatmap of H3K27me3 enrichment for 2 kb surrounding promoters of 1,498 upregulated DEG. Data were ranked by the change in H3K27me3 in ASC versus nB. Color bars map distinct clusters of genes from C. ATAC-seq was performed on Ctl and KO nB and ASC from tamoxifen treated bone marrow chimeras three days following LPS inoculation (See Figure 4). (E) Promoter accessibility (ATAC-seq) Heatmap for genes in D was categorized using K-means clustering (k = 3). Three independent replicates of Ctl nB, Ctl ASC, and KO ASC, and two replicates of KO nB are shown. (F) ATAC-seq derived volcano plot showing differentially accessible regions (DAR) (FDR < 0.05, log2FC > 1) comparing KO and Ctl ASC. (G) For the indicated genes, the change in expression by RNA-seq are plotted with a genome plot depicting chromatin accessibility and H3K27me3 enrichment data for each locus. ATAC-seq data is summarized as mean of three biological replicates for Ctl nB, Ctl ASC, and KO ASC, and two replicates for KO nB. H3K27me3 ChIP-seq data represents the mean of two biological replicates for nB and ASC. Promoter regions are highlighted. FPKM, fragments per kilobase per million; rpm, reads per million; rppm, reads per peak per million. (See also Supplemental Figure 4)