Extended Data Fig. 3: Genome-wide analysis of R-loop accumulation upon BRG1 depletion.
a, DRIP-seq mean coverage over gene bodies (±2kb) from control samples (n = 2). b, DRIP-qPCR in control K562 cells. Immunoprecipitation values normalized to untreated samples. Data are mean + SEM (n = 3). (Paired Student’s t-test, one-tailed). c, DRIP-seq mean-coverage over DRIPc-seq peaks (n = 2). d, Length of siC DRIPc-seq peaks (n = 2). e, Genome annotation of DRIPc peaks of siC and R loop-gain peaks siBRG1 K562 cells. f, Vulcano plot of DRIPc-seq differential analysis between siC (blue) and siBRG1 (vermillion) K562 cells (n = 2). Dots represent peaks. g, Absolute numbers of de novo and increasing DRIPc-seq peaks of siBRG1 cells (n = 2). h, Representative screenshot comparing siC and siBRG1 DRIPc-seq profiles considering or discarding Alu-containing reads. Watson-Crick strand reads shown together (n = 2). i, Metagenomic analysis of DRIPc-seq mean coverages along gene bodies (n = 2). j, BRG1 ChIP-seq average coverage (n = 2) over genes presenting R-loop-gain peaks distributed in quartiles according to the R loop-gaining rate of DRIPc-seq. Dots represent genes. Regression line in red. k, Venn diagram with BRG1-bound and R-loop-gain genes after siBRG1 (Hypergeometric test). l, Gene lengths of entire genome and R-loop-gain genes (Mann-Whitney U-test, two-tailed). m, Expression of R-loop-gain genes in siC and BRG1-depleted cells (Mann-Whitney U-test, two-tailed). n, Box-plot of GC-content. Details as in (l). o, Metaplot of GC-skew along gene body over gene sets of (l). Dark and light-colored lines represent genes from each strand. p, Box-plot of expression values. Details as in (l). q, Metaplot of DRIPc-seq mean coverage increase (ΔDRIPc-seq) upon BRG1-depletion over chromosomes or rDNA (n = 2). r, Venn diagram showing R-loop-forming genes in siC cells and R-loop-gain genes in siBRG1 and siUAP56 K562 cells. Other details as in Figs. 1–3.
