Transcriptome profiles of engineered isogenic HEK293T cells. A Four-way Venn diagram of differentially expressed genes (DEGs) in biallelic loss-of function (LoF/LoF) AFF3 lines and biallelic KINSSHIP/KINSSHIP (DN (dominant negative)/DN) AFF3 lines upon comparison with unmutated wild-type lines. DEG counts are stratified in genes up- (UP) and downregulated (DOWN). B Volcano plots of DEGs in biallelic loss-of function (LoF/LoF) AFF3 lines (left panel) and biallelic KINSSHIP/KINSSHIP (DN/DN) AFF3 KINSSHIP lines (right panel) upon comparison with unmutated wild-type lines. The top 30 most significant DEGs in LoF/LoF that are dysregulated in an opposite manner in KINSSHIP/KINSSHIP (DN/DN) are indicated, together with some of the most differentially expressed genes (-log10(Padj) > 20 and abs(log2FoldChange) > 0.5). C Gene set enrichment analysis (GSEA) for hallmark pathways of DEGs in biallelic loss-of function (LoF/LoF) AFF3 lines (left panel) and biallelic dominant-negative KINSSHIP/KINSSHIP (DN/DN) AFF3 KINSSHIP lines (right panel) upon comparison with unmutated wild-type lines. D Four-way Venn diagram of differentially expressed genes (DEGs) in biallelic loss-of function (LoF/LoF) AFF3 lines and biallelic KINSSHIP/KINSSHIP (DN/DN) AFF3 KINSSHIP lines upon comparison with unmutated wild-type lines and AFF3 ChIP-seq peaks identified in HEK293T cells (HEK293T) and in Mus musculus ES cells (mmES). DEGs bound by AFF3 discussed in the text are indicated. E Examples of DEGs NRC31 (top) and DDX17 (bottom) loci bound by AFF3. UCSC genome browser snapshot showing from to top to bottom AFF3 ChIP-seq HEK293T results, UCSC and REFSeq curated gene structure and vertebrate PhyloP conservation scores (left panels). Expression level of NRC31 (top) and DDX17 (bottom) in + / + (blue), LoF/LoF (yellow), and KINSSHIP/KINSSHIP (DN/DN; green) HEK293T engineered lines (right panels)
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