Deciphering the Function of Single Nucleotide Variants in Post-transcriptional Gene Regulation

Single-nucleotide variants (SNVs), such as genetic variants and RNA editing sites, constitute the most prevalent type of sequence variations in the RNA. Genome-wide association studies (GWAS) and global analysis of RNA editing have revealed many genetic variants and RNA editing sites associated with human diseases and complex traits. Yet, the underlying mechanisms of such associations are still missing for most SNVs. In this dissertation, we studied both non-coding and coding SNVs, revealing their functional roles in regulating mRNA abundance and splicing. Understanding the function of non-coding rare genetic variants remains a major challenge. To fill in this gap, we developed a massively parallel reporter assay, allowing functional testing of 3’ UTR variants regulating mRNA abundance in a high-throughput manner. We screened 14,575 rare 3’ UTR genetic variants and identified 5,437 functional ones leading to significant changes in mRNA abundance in at least one human cell line. Supported by TCGA expression outlier analysis and experimental studies, we observed that many rare 3’ UTR variants regulate mRNA abundance of cancer-relevant genes. We next examined a specific set of RNA editing sites that are differentially edited between epithelial and mesenchymal tumors across 7 cancer types in The Cancer Genome Atlas (TCGA). Inspired by the correlations between editing levels and gene expression, we uncovered many 3’ UTR RNA editing sites regulating mRNA abundance. Further, we identified the RNA-binding protein ILF3 as a potential regulator of the editing-dependent gene expression change, especially for immune-relevant genes. We showed that multiple RNA editing sites mediate the ILF3 stabilizing effect on the transcripts encoding Protein Kinase R (PKR), a key player in immune response.In addition to non-coding variants, we further characterized two RNA editing sites in the alternative exon of the gene podocalyxin-like (PODXL), a significant clinical indicator for tumor detection and prognosis. Supported by survival analysis in Kidney Renal Clear Cell Carcinoma (KIRC) patients, we discovered dual roles of RNA editing in promoting the loss of function of PODXL in cancer. We hypothesized that exonic RNA editing sites contribute to proteomic diversity through alternative splicing, a previously overlooked function of RNA editing