Fig. 5

Overexpression of IGF2BPs globally upregulates target gene expression and R-loop levels in promoter regions. A R-loop enrichments in randomized regions are shown as the purple (Scramble), blue (OE IGF2BP1), green (OE IGF2BP2) and orange (OE IGF2BP3) lines. B Distribution of the S9.6 peaks at the indicated genomic features in PC-3 cells. C Nine quadrant chart of mRNA expression ratios and R-loop density [Purple dots, significantly upregulate in both R-loop and mRNA; blue dots, significantly downregulate in both R-loop and mRNA; green dots, significantly downregulate in mRNA and upregulate in R-loop; green dots, significantly upregulate in mRNA and downregulate in R-loop], Correlation of mRNA expression ratios and R-loop density determined by Pearson coefficient. D The list of genes included in the DRIP-seq results and published m⁶A-DIP-seq results were compared using Venn diagram. E The coverage plots of S9.6 DRIP densities in the promoter region of the indicated gene (SEMA3F). F Compared to the median levels of all genes annotated in RefSeq, the SEMA3F promoter is GC rich and G-skewed. 50-bp sliding windows were used to compute GC% = [(G + C)/(G + C + A + T)]%, and GC skew = (G − C)/(G + C). The GC% and GC skew at the SEMA3F promoter (in red), and the median level for all gene promoters (in green) are shown. G R-loop levels of SEMA3F promoter in IGF2BPs overexpression DU-145 and PC-3 cells compared to control by DRIP-qPCR, Data are presented as means ± SD, two-tailed unpaired t-test. *p-value < 0.05, **p-value < 0.01, ***p-value < 0.001, ****p-value < 0.0001