Fig. 5: Deregulation of inducible genes in the absence of cohesin is due primarily to a reduced probability of transcription.

a Loss of cohesin alters the expression of inducible genes at the transcriptional level. One hour LPS for GRO-seq, 2 h LPS for RNA-seq. r Pearson correlation. Two-sided Pearson's product-moment correlation (null hypothesis: correlation = 0). Three biological replicates for RNA-seq and two biological replicates for GRO-seq. b The fraction of cells expressing Il12b by smRNA-FISH (top left) and the number of transcripts per cell (bottom left) are plotted for cells expressing at least five transcripts at the indicated time points after LPS activation of wild-type and Rad21^−/− macrophages. Numbers represent adjusted P values. Wilcoxon signed-rank test with Bonferroni correction for multiple testing. Example images are shown on the right. N = 40,941 cells, four independent biological replicates. c Left: heatmap of inducible macrophage genes³⁰ detected by scRNA-seq in at least 20% of wild-type (grey) or Rad21^−/− macrophages (red). Middle: Fraction of cells with detectable transcripts for inducible genes. Right: The expression level of LPS-inducible transcripts in cells with detectable transcripts is plotted as ln(CPM +1). Numbers represent adjusted P values. Two-sided Wilcoxon signed-rank test with Bonferroni correction for multiple testing. N = 1362 cells. d Burst fraction and burst intensity measurements for inducible immune genes in wild-type (black) and Rad21^−/− macrophages (red). N = 11,8058 cells, 3–7 independent biological replicates.