Fig. 6: The RUVBL1/2 complex is required for the precise expression of genes, but does account for the specific binding of transcription factors.

a Cell growth analyses after RUVBL2 depletion (n = 3 biological replicates), error bar indicates the mean + /− SD. b Diagram showing the experimental design for the treatment of RUVBL2-degron cells. c Western blot analyses of RUVBL2 protein levels at different time points during RUVBL2 degradation. d Snapshots of poly(A) RNA-Seq signals on the c-Myc, Ccnd1, Chop, and Atf4 loci at different time points during RUVBL2 degradation. e Cluster analyses of RNA-Seq expression signals after RUVBL2 degradation at different time points. The enriched GO terms and the motifs were shown accordingly. f The results of the metagene analyses of RUVBL1 and RUVBL2 ChIP-Seq signals at the gene promoters of each cluster are shown in e. g Pie charts showing the distribution of target genes corresponding to specific transcription factors peak belonging to the clusters in e. The “other” cluster indicates the targeted genes that did not belong to any other cluster. “Random” indicates the distribution of 8000 genes randomly selected from the genome. h The numbers of genes in each cluster shown in e that were simultaneously affected by UPF1 knockdown⁸⁰ are plotted in a bar graph. The percentages in the bracket were the ratio of the number of genes in each cluster as shown in e. i Cluster analyses of the percentage splicing index (PSI) after RUVBL2 degradation at different time points. The corresponding enriched GO terms are shown. j The PSI of Smg1 exon 2 is shown on bar graphs. Error bars indicate the mean + /− SDs. rMATS were used to calculate the significance difference of PSI (n = 2, *p < 0.05, **p < 0.01, ***p < 0.001). The position of the exon and the splicing event are illustrated in the upper panel. The FDR are extracted from rMATS by adjusting p-values with BH method.