Fig. 4: Osmotic shock reveals genome-wide correlation of Top2 activity and transcription.
From: Osmotic disruption of chromatin induces Topoisomerase 2 activity at sites of transcriptional stress
A 100 bp binned CC-seq-v2 map of Top2ccs across chromosome 1 in untreated cells (UT), and minutes following osmotic shock with 0.6 M sorbitol. Arrows highlight regions of change. The log2 ratio between 0.5 min sorbitol and untreated cells (1 kb smoothed; bottom) reveals regions of relatively greater Top2ccs in each condition overlapping highly expressed regions revealed by RNA-seq smoothed with a 10 kb Hann window (dark red track). B Violin plot of CC-seq-v2 density in 10 kb bins, in untreated cells and following osmotic shock. Each timepoint was tested for significant difference vs untreated by two-sided KS test. Bonferroni-adjusted P values are indicated above each timepoint. C–E Log2 fold change in CC-seq-v2 maps of Top2ccs in minutes following osmotic shock relative to untreated cells (UT) across chromosome 5 (C), 6 (D), and 7 (E), smoothed with a 10 kb Hann window, revealing regions of relatively greater Top2ccs in each comparison and how this changes during the 30 min osmotic shock period (coloured tracks). Black arrows highlight correlation of induced Top2ccs with highly transcribed loci, indicated by RNA-seq smoothed with a 10 kb Hann window (top dark red track). F Pearson correlation between CC-seq-v2 signals in untreated cells and in cells shocked for increasing times at three binning resolutions (solid lines). As a control, the inter-replicate Pearson correlation for the untreated condition is also plotted (dotted line). G Pearson correlation between CC-seq-v2 and RNA-seq signals at each time point at three resolutions (solid lines). H Cross-correlation function (CCF) of 1 kb-binned stranded CC-seq-v2 and RNA-seq signals at displacements of −25 to +25 kb for all timepoints (coloured lines). The arrow indicates the 5′ → 3′ direction of transcription. At positive displacements, RNA-seq signals are positively correlated with 3′-ward CC-seq signals. Dotted lines indicate the 95% confidence interval. Source data are provided as a Source Data file.
