Fig. 5: Analysis of KAT5 target genes, gene expression changes, and epigenetic patterning associated with KAT5on and KAT5off states in GSC-0827 tumors.
From: KAT5 regulates neurodevelopmental states associated with G0-like populations in glioblastoma
a KAT5 binding associated with transcription start sites in GSC-0827 tumors. An antibody recognizing the V5 epitope tag was used to perform CUT&TAG on KAT5-V5 ectopically expressed in C13 Dox + /KAT5on tumors. Dox-/KAT5off tumors (6 days Dox0-) were used as a control. K-mean clustering for KAT5on was used to define separate cluster classes shown (Supplementary Data 11). b Gene set enrichment analysis for KAT5 bound genes from clusters 2, 3, and 4 from (a). c Comparisons of KAT5 bound genes with common essential genes (depmap.org) and essential transcription factors in GSC-0827s. d Fold change of cells in each scRNA-seq cluster for KAT5off tumors. e Violin plots of gene expression module scores for each cell from scRNA-seq data of Dox+ vs. Dox- GSC-0827 C13 tumors. Each data point = single cell. KS test was used to test significance (p < 0.0001)(4951 Dox+ cells; 5507 Dox- cells). Genes associated with each model are available in Supplementary Fig. 12 and Supplementary Data 5. f ChromHMM analysis of genomic regions in KAT5on C13 tumor cells showing 8 possible chromatin states (i.e., emission states) for H3K4me2, H3K27ac, and H3K27me3, the associated number of genes, and emission state region genomic annotations. Genome% = intergenic space; TES = transcription end sites; TSS = transcription start sites. The darker blue color corresponds to a greater probability of observing the mark in the state. The full data set is available in Supplementary Data 12. g, h Overlap of genes associated with emission state E4 from (f), which display both activating and repressive chromatin marks, and those with significant changes H3K27ac and H3K27me3 after loss of KAT5 activity in GSC-0827 tumors. DiffBind and DESeq2 were used to score significant changes in chromatin marks (Supplementary Data 13,14, 15) from KAT5on and KAT5off C13 tumor samples (n = 2). Note: DiffBind could not be performed on H3K4me2 marks for C13 tumor samples because one replicate failed to produce sufficient quality data. i Enrichment for genes associated with expression of human transcription factors (TFs). Left panel: genes enriched for H3K27ac regions after loss of KAT5 activity. Right panel: genes depleted for H3K27me3 regions after loss of KAT5 activity. The analysis was performed using the Enrichr pipeline (Kelshov et al., 2016) using the hypergeometric test by comparing the top 300 genes associated with specific human transcription factors in the ARCHS4 database (Lachmann, et al. 2018). j Examples of multivalent genes in KAT5on C13 tumors that upon Dox withdrawal gain H3K27ac and lose H3K27me3 marks (i.e., overlapping genes from h). Additional examples including GNG7, SLIT1, and SOX8 are shown in Supplementary Fig. 12.
