Fig. 5

TSS-proximal TOP2 activity is strongly correlated with gene transcription. a–d Aggregation of TOP2 CCs in a 10 Kbp window centred on orientated TSSs in human RPE-1 cells. Four example TSSs are shown orientated in the 5′–3′ direction (a). A heatmap of all TSSs in the human genome, with 10 aggregated rows stratified by RPE-1 gene expression level⁴⁸. The colour scale indicates average TOP2 CC density in each 50 bp bin (b). Motifs are also stratified into 4 quartiles of gene expression, and the average TOP2 CC distribution in each quartile plotted at two levels of zoom. Horizontal line is the genome mean. Vertical line is the TSS (c–d). e–h Quantitative correlation between CC-seq signal and transcription rate. Scatterplot of CC-seq (5 Kbp window downstream of TSS) and gene expression (e), or transcription initiation⁴⁹ (f). Scatterplot of CC-seq signal in 5 kb windows directly upstream and downstream of TSS and GRO-seq in 200 bp regions directly upstream and downstream of TSS. Blue line = lowess curve. Pearson r and Spearman r_s values were calculated between CC-seq and log-transformed measures of transcription rate. i–j Aggregate comparison of CC-seq (red line), nucleosome occupancy⁷¹ (grey shading), and strand-specific GRO-seq⁵⁰ centred on TSS at two levels of zoom. MNase-seq data is inverted to emphasise spatial relationship between CC-seq and nucleosome depletion (white). PPP promoter proximal transcriptional pausing, TpM Transcripts per million mapped reads per base pair, HpB Hits per billion mapped reads per base pair, AU arbitrary units