Fig. 5: Longer and more frequent R-loops are formed in regions of H2A.Z eviction. | Nature Communications

Fig. 5: Longer and more frequent R-loops are formed in regions of H2A.Z eviction.

From: ANP32E drives vulnerability to ATR inhibitors by inducing R-loops-dependent transcription replication conflicts in triple negative breast cancer

Fig. 5

a DRIP-seq peak counts per cell line representing R-loops abundance. Individual replicate values are shown as mean ± s.d.; mean indicated above each sample. b Cumulative DRIP-seq signal at RNaseH1-sensitive tIMEC-A R-loop peaks (n = 47,940), aligned at peak start and shown from –500 to +800 bp. c Pie chart showing the percentage of ANP32E-induced R-loops that are RNaseH1-sensitive or -resistant. d Tukey boxplots (25th to 75th percentile and median) of R-loop peak lengths (bp) per cell line. Peaks present in three biological replicates: tIMEC = 34,125; tIMEC-A = 82,494; tIMEC-A-H1 = 90,009. P values from a two-tailed Wilcoxon test. e Density plot of R-loop lengths overlapping H2A.Z-loss regions in tIMEC vs tIMEC-A. Dashed line marks the 75th percentile; shaded for tIMEC-A. f Density plot of R-loop lengths intersecting regions of chromatin accessibility loss in tIMEC vs tIMEC-A. Dashed 75th percentile marked as in (e). g Pie charts showing number of R-loop-associated genes with upregulated (UP), downregulated (DOWN), or unchanged (NO) expression in tIMEC vs tIMEC-A (based on RNA-seq). h Cumulative CUT&RUN signal for H2A.Z at TSS (top) and gene body (bottom) of genes stratified by expression (High, Medium, Low) from RNA-seq. i Tukey Boxplot (25th to 75th percentile and median) of gene expression values (log2TPM) in R-loop-forming genes in tIMEC-A vs other cell lines. n: tIMEC = 4092, tIMEC-A = 5387, tIMEC-A-H1 = 6055; four replicates/conditions. P values from a two-tailed unpaired t-test. j Barplot showing mean ± s.d. log2FC of R-loop length between tIMEC and tIMEC-A, grouped by gene expression pattern retrieved from four biological replicates: Low (n = 2293/4271), Mid (n = 2963/5773), High (n = 2364/4456). Two-tailed Wilcoxon test p values reported. k Left: Tukey boxplot Boxplot (25th to 75th percentile and median) of differential pausing index (PI) sites (log2FC tIMEC-A vs tIMEC), representative data from three biological replicates. Horizontal lines define Faster, Equivalent, or Slower pS5RNApol II release in tIMEC-A vs tIMEC. Right: Barplot of H2A.Z FRiP (fraction of reads in peak) values at regions with faster pS5RNApol II release in tIMEC-A (n = 12,660).

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