Fig. 1: Analyses of genome wide RNA-seq and ChIP-seq data identify transcription factors whose expression is MAP3K4, CBP, HDAC6, and H2BK5Ac dependent.
From: Coordinated regulation of Rel expression by MAP3K4, CBP, and HDAC6 controls phenotypic switching
a Bioinformatics analyses of RNA-seq and anti-H2BK5Ac ChIP-seq data from TSWT cells or TSKI4 cells expressing control shRNA, TSWT cells expressing Crebbp shRNA (TSWTCBPsh) or TSKI4 cells expressing Hdac6 shRNA (TSKI4H6sh). Venn diagram shows 756 genes whose expression is MAP3K4, CBP, and HDAC6 dependent. Of these 756 genes, 183 genes are H2BK5Ac dependent. The cutoff fold-change value for differentially expressed genes was ≤ 0.75 for TSKI4/TSWT and TSWTCBPsh/TSWT and ≥ 1.5 for TSKI4H6sh/TSKI4. b Enrichment of genes encoding DNA-binding proteins. Pie chart depicts the Gene Ontology for the molecular function annotation of the 183 co-regulated genes. Twelve percent of these genes are transcription factors (TFs) categorized under sequence-specific DNA binding. c Table shows differential expression of MAP3K4, CBP, HDAC6, and H2BK5Ac dependent TFs identified in (b). TFs with ≥ 0.5 reads per kilobase of transcript per million mapped reads (RPKM) in TSWT cells are shown. RNA-seq RPKM values for each sample were expressed as ratios. For example, RPKM values in TSKI4 cells were divided by those for TSWT cells. Anti-H2BK5Ac ChIP-seq values determined using EpiCenter were also expressed as a ratio dividing values in TSKI4 cells by those for TSWT cells52. TFs were prioritized using the Wilcoxon rank sum test of TSKI4/TSWT H2BK5Ac ChIP-seq and RNA-seq ratios. See also Supplementary Fig. 1.
