Additional file 1 of TP63–TRIM29 axis regulates enhancer methylation and chromosomal instability in prostate cancer

Additional file 1: Table S1. related to Figure 1. Data sets used in the study. Sheet1—List of all datasets used in the study. Sheet2—List of PRAD sample IDs used in the study. Table S2 related to Figure 2. TP63 regulates the gene cluster associated with epigenetic variability and chromosomal instability in PRAD. Sheet1—list of genes from TP63 cluster. Sheet2—Ontology analysis of the TP63 cluster genes. Gene Ontology (GO) terms related to biological process. Sheet3—Ontology analysis of the TP63 cluster genes. Gene Ontology (GO) terms related to cellular components. Table S3 related to Figure 3. CpG sites associated with TP63 cluster belong to TP63-dependent enhancers and super-enhancer. Sheet1—list of CpG sites associated with TP63 cluster. Sheet2—Ontology analysis of genes located near the TP63 CpG sites. Gene Ontology (GO) terms related to biological process. Sheet3—Ontology analysis of genes located near the TP63 CpG sites. Disease ontology. Table S4 related to Figure 4. TRIM29 interacts with TP63 and regulates expression of the TP63 cluster. Sheet1—Ontology analysis of the TP63 cluster genes under TP63 and TRIM29 simultaneously regulation. Gene Ontology (GO) terms related to biological process. Table S5 related to Figure 5. TRIM29 promotes decrease of chromosomal instability in PRAD. Sheet1—Partners of TRIM29 in RWPE-1 cells. Sheet2—Association between the TP63 cluster and the response to genotoxic stress. Figure S1. related to Figure 2. A GSEA plots evaluating the TP63 cluster signatures upon differential expressing genes between cancer and normal samples in TCGA dataset. B Boxenplot represents expression level of TP63 in TCGA PRAD samples. Each successive level outward 50%-percentile contains half of the remaining data. C Expression of TP63 in PRAD and normal prostate epithelium cell lines. D Immunoblot (IB) analysis of overexpression (OE) of TP63 in PC3 cells and knockdown (KD) of TP63 in the RWPE-1 cells. Figure S2. related to Figure 3. A Representation of DNA methylation level of 1645 TP63 CpG sites in normal and PRAD cell lines. B Overexpression of TP63 in PC3 promotes decreased methylation of two CpG sites (MRSE-qPCR) compared to an empty vector control. Error bar = SD. N = 3 C TP63 knockdown in the RWPE-1 cell line promotes increased methylation of two CpG-sites (MRSE-qPCR) compared to control. Error Bar = SD. N = 3. Figure S3. related to Figure 4. A GSEA plots evaluating the TP63 cluster signature upon TRIM29 knockdown in MCF10A (breast basal epithelium, GSE26238). B TP63 ChIP in RWPE-1 and PC3 cells with TP63 overexpression demonstrates enrichment of TRIM29 enhancer 1. All samples were done in triplicate. Error Bars = SEM IP - immunoprecipitation. Figure S4. Molecular mapping of TRIM29 and TP63 interactions. A Outline of the constructs of full length TRIM29 and of its truncated mutants. Immunoblotting (IB) of purified FLAG-tagged TRIM29 with anti-TP63 antibodies. B. Outline of the constructs of full length TP63 and of its truncated mutants. Immunoblotting (IB) of purified FLAG-tagged TP63 with anti-GFP antibodies. Figure S5. Violin plots of the γH2AX foci number per nucleus in RWPE-1 and RWPE-1 with knockdown of TRIM29 cells before and after TNFα (100 ng/mL) treatment. “***” stands for p-value<1e-8. ns non significant