Fig. 1

Topoisomerase 1 depletion instigates R-loop changes genome wide. a Western blot verifying Top1 depletion upon specific siRNA transfection compared to control β-actin. b Dot blot analysis of R-loop formation: two-fold serial dilutions of genomic DNA starting at 7.5 micrograms were arrayed on a membrane and probed using the S9.6 antibody. c Distribution of DRIPc peaks gains (left) and loss (right) upon Top1 depletion across several genomic compartments depicted below. Numbers indicate the percentage occupied by each compartment. The total genomic space covered by R-loop gains and losses is indicated. (TSS) transcription start site; (PAS) poly-adenylation site. d Top; total number of uniquely mapped reads overlapping with peaks of R-loop gains (left) and losses (right) in control and Top1-depleted samples. Bottom, the relative difference in reads between gains and losses indicates that gains predominate over losses. e DRIPc-seq signal profiles for control and Top1-depleted cells over rDNA region. Average signal over two replicates is shown as solid line with standard error (shaded). Structural features of the rDNA region are on top. The 5’ETS region shows significant R-loop increase (grey shade)