Additional file 1: of DNA methylation at an enhancer of the three prime repair exonuclease 2 gene (TREX2) is linked to gene expression and survival in laryngeal cancer

Figure S1. Differential DNA methylation at the TREX2 locus in the TCGA head and neck squamous cell carcinoma cohort. Figure S2. Correlation of TREX2 mRNA expression and DNA methylation in the TCGA HNSC cohort. Figure S3. Differential DNA methylation and TREX2 expression affect overall survival of laryngeal cancer patients. Figure S4. Identification of the TREX2 gene promoter in luciferase reporter assays. Figure S5. Validation of the identified TREX2 promoter in FANTOM5 CAGE-seq data. Figure S6. Chromatin immunoprecipitation of H3K4me1 at the TREX2 gene locus. Figure S7. Correlation of TREX2 mRNA expression in different cell lines and primary cells (n=15) with mRNA expression of transcription factors with predicted binding motifs at the TREX2 DMR. Figure S8. Induction of TREX2 gene regulatory elements by CEBPB. Figure S9. Luciferase reporter assays for different TREX2 promoter and DMR constructs. Figure S10. Proximity ligation assay for predicted CEBPA binding sites at the TREX2 locus. Table S1A. Genome-wide datasets on transcriptional and epigenetic alterations in cancers from TCGA ( https://portal.gdc.cancer.gov/ ) for 22 cancer types. Table S1B. Differential methylation of two CpG sites located in the differentially methylated TREX2 region for matched pairs of tumor and adjacent normal tissue from TCGA cancer studies. Table S1C. Differential methylation of two CpG sites located in the differentially methylated TREX2 region for all tumor and normal adjacent tissues with DNA methylation values from TCGA cancer studies. Table S2A,B. TREX2 DNA methylation in tumor tissue and overall survival in TCGA cancer studies. Table S3. TREX2 mRNA expression in tumor tissue (given as log2 (normalized expression + 1)) and overall survival in TCGA cancer studies. Table S4. Prediction of transcription factor binding sites at the TREX2 DMR. Table S5. DNA oligonucleotides used for DNA methylation analysis, qRT-PCR, ChIP-qPCR, proximity ligation assay, and molecular cloning. (DOCX 1615 kb