Fig. 3: Loss of R-loops overlaps intron retention reductions in SF3B1^MUT human primary erythroblasts.

DRIP-sequencing. a Violin plots showing the shared peak numbers in 4 controls, 5 SF3B1^MUT and 6 SF3B1^WT (4 SF^WT, 2 SRSF2^MUT). Two-sided unpaired t-test. Controls versus SF3B1^MUT, P = 0.011; SF3B1^WT versus SF3B1^MUT, P = 0.015. b DRIP-seq profiles ± RNaseH1 (RNH1) of a 50-kb region on chr7 showing the distribution of R-loops in reads per million. c Pie charts representing localizations of shared R-loops at gene features. d Proportion of shared peaks at gene features in SF3B1^MUT samples relative to SF3B1^MUT + SF3B1^WT samples. e DRIP-seq profiles showing R-loops near SUZ12 promoter. f Comparison of the expression of genes with overlapping R-loops at TSS, gene body, TTS and 3’UTR in SF3B1^WT samples and without overlapping R-loops in SF3B1^MUT samples. Violon plots represent the difference of mean expression intensity between SF3B1^WT and SF3B1^MUT samples (d11). Central lines represent the means. Gene numbers in each category are indicated. One sample Wilcoxon signed rank test is used for comparison of actual mean to theorical mean. TSS, P < 0.0001; gene body, P = 0.031; TTS, P = 0.179; 3’UTR, P = 0.118. g Volcano plot representing differential restriction fragments overlapping with peaks between SF3B1^MUT and control samples (left panel) and SF3B1^MUT and SF3B1^WT samples (right panel) with log₂(FC) >|1| using two-sided Wald-test and a BH-adjusted P value < 0.05. h Distribution to gene features of differential R-loops in SF3B1^WT samples and lost in SF3B1^MUT samples. i Venn diagram showing overlap between genes that lost one R-loop and genes with intron retention reduction (IRR) in SF3B1^MUT erythroblasts. j DRIP-seq and RNA-seq overlays at RAD9A and IQGAP3 loci showing R-loop losses and IRR events in SF3B1^MUT erythroblasts. Gene structures using GENCODE GRCh37. k DRIP-qPCR analysis of 4 controls, 3 SF3B1^WT including 1 U2AF1^MUT designated as green dot and 4 SF3B1^MUT samples. Enrichment signals (normalized to input) at specific loci were normalized to EGR1 (no R-loop). RPL13A and TFPT as positive controls. In box plots, central lines represent medians, bounds represent lower and upper quartiles and whiskers correspond to min-max values. Two-sided unpaired t-test for P values (see Suppl informations). b, e, j RPM: reads per million. * P < 0.05; ** P < 0.01; **** P < 0.0001; ns: not significant. Source data are provided as a Source Data file.