Figure 3
Factors promoting R-loop formation in NSPCs. (A) Box-and-whiskers plot showing gene length of active genes with (n = 8430) or without (n = 7093) R-loop peaks in NSPCs and all RefSeq genes (n = 22,735), for comparison. P values were determined by one-way ANOVA with Tukey’s post hoc correction. (B) Comparison of gene length of transcription rate-matched genes (n = 3255) with or without R-loop peaks in NSPCs (P < 0.0001; ns, not significant; Mann–Whitney U test). (C) Transcriptional activity of active genes with (n = 8430) or without (n = 7093) R-loops in NSPCs. P < 0.0001, Mann–Whitney U test. (D) Pie charts showing distribution of genes with R-loop peaks in NSPCs (top) or ESCs (bottom) across the indicated classes of GC skew, showing that most genes with R-loops exhibit GC skew. (E) Metaplot analysis of RPKM-normalized raw DRIP-seq signal across the TSS, gene body, and TES of active NSPC genes with (blue, n = 7079) or without GC skew (yellow, n = 8449) in the promoter region.
