Fig. 1

Loss of Rnf40 alters gene expression on genes displaying low or moderate levels of H2Bub1. a SmoothScatter plot analysis displays the relationship between H2Bub1 occupancy on the gene body compared to the mRNA levels of the corresponding gene. Gene density is indicated on the right. The correlation coefficient is calculated with the “Pearson” method. b Correlation plot shows the heatmap with the Pearson correlation coefficients for H2Bub1, H3K4me3, H3K27me3, H3K27ac, GRO-Seq, and EZH2 on the region 1 kb downstream of the TSS of all genes. c The heatmaps show H2Bub1, H3K4me3, H3K27me3, H3K27ac, and GRO-seq levels surrounding the TSS (±5 kb) of all genes in wild-type (Rnf40 ^+/+) MEFs. TSSs are sorted according to H2Bub1 level in descending order. The color key is shown on the right. According to H2Bub1 occupancy, genes are grouped into high (“H”) displaying genes ranked in the upper 25th percentile, moderate (“M”) in the 50th to 75th percentile of ranked genes, low (“L”) in the 25th to 50th of ranked genes, and the lowest 25th percentile (“No”) of ranked genes. d Western blot analysis for RNF40 and H2Bub1 levels in Rnf40 ^+/+ and Rnf40-null (Rnf40 ^–/–) MEFs. HSC70 and H2B are shown as loading controls. To induce Rnf40 knockout, cells were treated with 250 nM of (Z)-4-Hydroxytamoxifen (4-OHT) for five days. e Boxplot compares the absolute value of log₂-fold changes in gene expression for the defined groups. p values were calculated by unpaired Wilcoxon-Mann-Whitney-Test. f Correlation plot compares the log₂-normalized counts of gene expression between Rnf40 ^+/+ and Rnf40 ^–/– MEFs. Differentially regulated genes following Rnf40 deletion were defined as upregulated genes (red, baseMean > 15, p value < 0.05, log₂-fold change > 1) and downregulated genes (green, baseMean > 15, p value < 0.05, log₂-fold change < –1)