Fig. 5

RNF40 knockdown promotes apoptosis by affecting BCL-2 family members. a Heatmap indicating gene expression levels based on mRNA-seq after siRNA-mediated knockdown of RNF40 in HCT116 cells. RNF40 loss resulted in a deregulated expression of several BCL-2 family members. b Verification of mRNA-seq results in HCT116 cells using qRT-PCR in three independent experiments. RNF40-depleted HCT116 cells display decreased mRNA levels of the anti-apoptotic factors MCL1 and BIRC5 while pro-apoptotic genes BAX and BCL2L11 were upregulated (n = 3); c these findings were confirmed in SW837 cells. Mean ± SEM, Student’s t test. d ChIP-seq profiles show the occupancy of H2Bub1, H3K27ac, and H3K79me3 on the anti-apoptotic genes MCL1 and BIRC5 in SW837 cells. Input signals were subtracted. e In three independent experiments, protein was harvested from HCT116 and SW837 cells and analyzed using Western blot. In both cell lines, RNF40 loss elevated the protein amounts of BIM (encoded by BCL2L11) and the apoptosis marker cleaved PARP