Fig. 4

PDS5 proteins localize to the same genomic sites as STAG proteins. A Clustered heatmaps of PDS5A, PDS5B, STAG1, STAG2, and RAD21 ChIP-seq signal at a union list of PDS5A, PDS5B, STAG1, and STAG2 peaks, ordered by RAD21 signal (k-means = 2) (Z-score normalized). B Western blot analysis following co-immunoprecipitation of IgG (negative control), PDS5A, PDS5B, and RAD21 in WT nuclear lysates, under low and high stringency conditions. Control blots for this experiment are in Fig. 1E. C Clustered heatmap of log2 fold change in expression for a combined list of DEGs in Pds5a^−/− siGLO, Pds5a^−/− siStag1, Pds5a^−/− siStag2, and Pds5a^−/− siPds5b mESCs relative to WT siGLO mESCs. D Violin plot of log2 fold change in expression for all DEGs, those within Super-enhancer Domains, and those within Polycomb Domains for Pds5a^−/− siGLO, Pds5a^−/− siStag1, Pds5a^−/− siStag2, and Pds5a^−/− siPds5b mESCs relative to WT siGLO mESCs. Significance was determined using a Kruskal–Wallis test followed by Dunn’s multiple comparisons test. Asterisks indicate significant differences between groups (* p < 0.05, **** p < 0.0001). E Bar graphs of log2 fold change in expression of pluripotency genes (Pou5f1, Sox2, Nanog), ectodermal lineage genes (Pax6 and Nestin), and endodermal lineage genes (Gata6 and Sox17) in Pds5a^−/− siGLO, Pds5a^−/− siStag1, Pds5a^−/− siStag2, and Pds5a^−/− siPds5b mESCs. Asterisks indicate significant differences from WT siGLO mESCs determined using DESeq2 (padj < 0.01)