Fig. 7: Identification of direct target genes of the RUVBL2-Pol II axis.

a Workflow of the process used to identify the genes directly targeted by RUVBL2. The FDR are extracted from DESeq2 by adjusting p-values using BH method. b Heatmap analyses of RUVBL2 direct target genes based on PRO-Seq expression. c Snapshots showing the RUVBL1 and RUVBL2 ChIP-Seq signals and nascent RNA (PRO-Seq) signals at the Bmp4 and c-Myc loci after RUVBL2 degradation. d ChIP-Seq signals in the promoter regions of 45 genes directly targeted by RUVBL2 and 45 nontargeted genes in 153 datasets obtained from the Cistrome DB (Supplementary Data 5). e The 10 factors with the largest and smallest coefficients in the elastic net were selected. The heatmap shows the relative occupancy of these 10 factors in the 45 genes directly targeted by RUVBL2 and in 45 nontarget genes. f Pie chart indicating the percentage of C-MYC or CXXC1 ChIP-Seq-determined target genes that overlap the RUVBL2-affected genes as determined by the RNA-Seq data shown in Fig. 6g. g Profiles of PRO-Seq signals at the gene regions of directly targeted genes (n = 45), all genes (n = 36821) and posttranscriptional early response genes (n = 41) after RUVBL2 degradation. The profile above 0 indicates the signal on the sense strand, the profile below 0 indicates the signal on the antisense strand. Two-tailed Wilcoxon tests was performed to calculate the significance (*p < 0.05, **p < 0.01, ***p < 0.001). The center line of boxplot represents median, the box limits represent upper and lower quartiles, and the whiskers represents 1.5x interquartile range or maximum/minimum value. h The RUVBL2 direct target gene Bmp4 was examined by single-molecule RNA FISH combined with RPB1 immunofluorescence. Representative images are shown, scale bar is 3 μm. i The signals of the Pol ll (RPB1 IF) cluster that overlap with nascent RNA foci were measured, the boxplot indicated median (middle line), 25th and 75th percentile (box) and 5th and 95th percentile (whiskers), as well as outliers (single black points). Statistically analyzed (two-tailed Student’s t test) from at least 10 different fields of each condition (Auxin 0 h n = 61, Auxin 1 h n = 38). **p < 0.01.