Fig. 5: TUG1 resolves (CA)n/(TG)n containing R-loops.

a Scatter plots comparing the mean log2 concentration of DRIP-seq signals. HeLa/Fucci2 cells transfected with Ctrl ASO or TUG1#1 for 4 h were treated with or without 10 μM CPT for the last 2 h. TUG1#1-treated cells (left) and CPT-treated cells (right) against control samples. Peaks with false discovery rate (FDR) < 0.1 are colored magenta, and the number above and below the diagonal line represents up- and down-regulated peaks after the treatment, respectively. DRIP-seq signals were normalized based on library size. b Venn diagram showing the overlap between TUG1-sensitive and CPT-sensitive peaks. c Metaplot of mean input-subtracted DRIP-seq signals in 4 kb window around the TUG1-sensitive (left) and CPT-sensitive (right) peak centers. d A snapshot of representative locus of DRIP-seq peaks enhanced by TUG1 KD in chr22:49,973,028-49,975,721 (C22orf34). (CA)n repeat-containing sequence is indicated below with CA dinucleotide colored gray. e Metaplot of γ-H2AX accumulation in 4 kb window around the TUG1-sensitive (red) and CPT-sensitive (green) peak centers. f Genomic annotation of peaks differentially altered by TUG1 KD or CPT treatment, defined by homer. Percentages of repeat types (>1%) are detailed in the plot. g Simple repeat enrichment analysis in TUG1-sensitive (left) or CPT-sensitive (right) peaks. The x axis shows the fraction of TUG1- or CPT-sensitive peaks overlapping with the indicated repeat types and sequences in RepeatMasker. The y-axis shows negative log10 P-values of enrichment or depletion of indicated repeat types and sequences above background. P-values were estimated by comparison with GC%-matched background regions for TUG1- or CPT-sensitive peaks using two-sided Fisher’s exact-test and adjusted using the Benjamini–Hochberg method.