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Fig. 3 | Epigenetics & Chromatin

Fig. 3

From: PDS5A and PDS5B differentially affect gene expression without altering cohesin localization across the genome

Fig. 3

PDS5A and PDS5B display partially overlapping and distinct effects on gene expression. A Overlap of differentially expressed genes (DEGs) in Pds5a−/− and Pds5b−/− mESCs relative to WT mESCs. All cells treated with siGLO as a transfection control. B Correlation plot of log2 fold change in expression of Common DEGs (2866) in Pds5a−/− and Pds5b−/− mESCs. Axes cropped, removing one outlier. C Heatmap of log2 fold change in expression for all DEGs in both Pds5a−/− and Pds5b−/− mESCs. ChIP-seq signal of PDS5A in WT and Pds5b−/− mESCs and PDS5B signal in WT and Pds5a−/− mESCs is shown at the promoters of these DEGs. D Violin plot of log2 fold change in expression for all DEGs, those within Super-enhancer Domains, and those within Polycomb Domains in Pds5a−/− and Pds5b−/− mESCs. Significance was determined using a Kruskal–Wallis test followed by Dunn’s multiple comparisons test. Asterisks indicate significant differences between groups (** p < 0.01, **** 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−/− and Pds5b−/− mESCs, relative to WT mESCs. Asterisks indicate significant differences from WT determined using DESeq2 (padj < 0.01). F Overlap of differentially expressed genes in Pds5a−/− siGLO, Pds5b−/− siGLO, and Pds5a−/− siPds5b mESCs. Common and Redundant gene classes are highlighted. G Clustered heatmap of log2 fold change in expression for a combined list of DEGs in WT siPds5b, Pds5a−/− siGLO, and Pds5a−/− siPds5b mESCs all relative to WT siGLO mESCs. H Gene Ontology (GO) analysis for biological processes correlated with DEGs that are Pds5a−/− specific, Pds5b−/− specific, Common, or Redundant upon loss of PDS5 proteins. I Average signal plots of PDS5A, PDS5B, and RAD21 ChIP-seq signal in WT (solid line) and knockout (dotted) mESCs at Pds5a−/− specific, Pds5b−/− specific, Common, or Redundant DEG promoters (Z-score normalized). J Percentages of promoters in Pds5a−/− specific, Pds5b−/− specific, Common, Redundant, or Non-DEG gene classes that overlap with WT cohesin ChIA–PET high-confidence interaction anchors [46]

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