Fig. 4: A significant fraction of target genes shared by DCAF1 and EZH2.

a Heat map of genes differentially regulated in control, DCAF1-depleted, or EZH2-depleted SW620 colon cancer cells. Data show three biological replicates. (See also Supplementary Fig. 8). b Venn diagram showing genes that were upregulated or downregulated (>1.5 fold; FDR < 0.05) in DCAF1-depleted or EZH2-depleted SW620 cells compared to mock-depleted control cells. c Gene ontology analysis of genes that were commonly activated in DCAF1-depleted and EZH2-depleted SW620 cells using Qiagen Ingenuity Pathway Analysis software. d RNA-seq data were validated by RT-qPCR using primers specific for the 8 genes that were upregulated and the 1 gene that was unaffected following DCAF1 knockdown. Also included in this analysis was mRNA extracted from DCAF1-rescued SW620 cells. The values are expressed as fold changes from the mRNA levels in mock-depleted control cells. Primer sequences are listed in Supplementary Table 4. Data represent the mean ± SEM of three independent experiments. P values were calculated using two-way ANOVA with post-hoc Tukey’s test for multiple comparisons. *P < 0.05, **P < 0.01 and ***P < 0.001 versus Ctrl sh. (See also Supplementary Fig. 11a). e RT-qPCR assays were carried out as in (d), but using EZH2-depleted SW620 cells. For rescue experiments, EZH2-depleted cells were transfected with shRNA-resistant EZH2 wild type, T367A mutant, or T367D mutant. Data are represented as mean ± SEM of three independent experiments. P values were calculated using two-way ANOVA with post-hoc Tukey’s test for multiple comparisons. **P < 0.01 and ***P < 0.001 versus Ctrl sh. (See also Supplementary Fig. 11b). f ChIP assays were performed in mock-depleted (Ctrl sh) and DCAF1-depleted (DCAF1 sh) SW620 cells using antibodies against DCAF1, EZH2, EZH2T367p and H3K27me3 as indicated. To rescue the effects of DCAF1 knockdown, shRNA-resistant DCAF1 was expressed. Precipitation efficiencies relative to non-enriched input samples were determined for the three locations across the ARL14 locus by qPCR with primers listed in Supplementary Table 5. Percent input is determined as the amount of immunoprecipitated DNA relative to input DNA. Data are represented as mean ± SEM of three independent experiments. (See also Supplementary Figs. 12a, c). g ChIP assays were as described in (F), but using EZH2-depleted SW620 cells transfected with shRNA-resistant EZH2 wild type, T367A mutant, or T367D mutant. Data are represented as mean ± SEM of three independent experiments. (See also Supplementary Figs. 12b, d) (c–g) Source data are provided as a Source Data file.