Fig. 2: Loss of cohesin regulator PDS5A results in de-repression of canonical PRC1/PRC2 target genes.
From: Loss of cohesin regulator PDS5A reveals repressive role of Polycomb loops
a Western blot of cohesin, PcG proteins and histone modifications in Pds5aGT KO and Pds5aGT WT ESCs and in Pds5a KO and wild-type ESCs. b Volcano plots show gene expression changes in Pds5aGT KO vs. Pds5aGT WT ESCs (top) and Pds5a KO vs. wild-type ESCs (bottom) (n = three replicates). Number of significantly up- or downregulated genes (black) (adjusted P value ≤ 0.05; LFC ≥ 0.5). Number of significantly up- and downregulated PRC1/PRC2 target genes (red). c Violin plots compare expression changes of all DEGs with different gene classes in Pds5aGT KO ESCs and Pds5a KO ESCs. In the middle of each density curve is a small box plot, with the rectangle showing the ends of the first and third quartiles and central dot the median. Significance was determined by Wilcoxon rank-sum test. Asterisks indicate significant differences between groups (**** p < 1 × 10−5; n.s. – not significant). d Dot plots show expression changes of selected PRC1/PRC2 target genes in Pds5aGT KO ESCs and Pds5a KO ESCs. e Heatmap shows cluster analysis of common upregulated (red) and downregulated (blue) DEGs in Pds5aGT KO ESCs and Pds5a KO ESCs. Most enriched gene ontology (GO) terms and corresponding significance are indicated for each cluster (right).
