Fig. 1: CC-seq-v2 maps physiological Top2 activity in etoposide-unchallenged cells.
From: Osmotic disruption of chromatin induces Topoisomerase 2 activity at sites of transcriptional stress
A Nucleotide-resolution CC-seq-v2 maps of physiological Top2ccs in G1-arrested S. cerevisiae over a 20 kb range. Red and blue traces indicate Top2-linked 5′ DNA termini on the top and bottom strands, respectively. Arrows and rectangles indicate positions of genes and Ty elements, respectively. Circles indicate positions of nucleosome midpoints, with grayscale intensity indicating nucleosome centre positioning score56. B CC-seq-v2 maps of physiological Top2ccs in TOP2+ and top2-td strains, under degron-inducing conditions (see methods). C Pearson correlation (R) of CC-seq-v2 signals on top and bottom strands, after displacement (Top-Bottom) by the indicated distance. Positive values indicate bottom strand displacements leftwards relative to the top strand. D Average DNA base composition over a 32 bp window centred on random genomic loci (top), physiological Top2 sites mapped by CC-seq-v2 (middle), or VP16-stabilised Top2cc sites mapped by CC-seq-v1 (bottom)23. Values reported are for the top strand only. Absolute log2 fold nucleotide base deviation between the v2 untreated and v1 VP16 patterns is plotted as a grayscale track, highlighting the greatest difference at the −3 and +3 positions. E Violin plot of genome-wide CC-seq-v2 Top2cc signal densities in specific genome compartments. Dotted lines highlight difference between median density in promoter-containing IGRs and genic regions. F Average (pileup) of CC-seq-v2 signals around 67548 nucleosome midpoints, smoothed with a 100 bp sliding Hann window. Grey circles indicate inferred positions of nucleosomes. G CC-seq-v2 maps of physiological Top2ccs (top) and stranded RNA-seq maps of transcription (bottom) in G1-arrested W303 S. cerevisiae cells. Both data sets are binned at 10 kb resolution, and plotted across whole chromosome 4. The P value of a Pearson’s product-moment correlation two-sided t-test is reported. H Violin plot of genome-wide RNA-seq and CC-seq-v2 Top2cc signal densities, binned at three resolutions. Source data are provided as a Source Data file.
