Fig. 3

STAG1 and STAG2 display partially distinct and overlapping roles in gene expression. a Overlap of differentially expressed genes (DEGs) in Stag1^−/− cells compared to wild-type cells and Stag2^−/− cells compared to wild-type cells. Cells were treated with siGLO as a transfection control. b Correlation plot of log2 fold changes of DEGs. DEGs specific to Stag1^−/− are shown in red, DEGS specific to Stag2^−/− are shown in blue, and DEGs sensitive to the loss of either STAG (common) are shown in purple. c Heatmap of log2 fold changes for a combined list of DEGs in Stag1^−/− and Stag2^−/− cells. Heatmap of STAG1 and STAG2 ChIP-seq signal in wild-type cells at the promoters of the combined list of DEGs. d Average signal plots for STAG1, STAG2, and RAD21 ChIP-seq signal in wild-type cells at Stag1^−/− specific, common, and Stag2^−/− specific DEG promoters. e Gene Ontology (GO) terms for biological processes that are Stag1^−/− specific, Stag2^−/− specific, and common to both knockouts. f Violin plot depicting log2 fold changes for all DEGs, and those within Super-enhancer Domains and Polycomb Domains for Stag1^−/− and Stag2^−/− cells. Dotted lines indicate the mean. Asterisks indicate significant differences between groups (****p < 0.0001, **p < 0.01). g Bar graphs with log2 fold change of expression of cell identity genes, including those that represent pluripotency (Pou5f1, Sox2, Nanog), ectoderm (Pax6 and Nestin), and endoderm lineages (Gata6 and Sox17) in Stag1^−/− and Stag2^−/− cells. Asterisks indicate significant differences from wild-type cells (padj < 0.01)