Global analysis of post-transcriptional gene regulatory mechanisms

Post-transcriptional regulation of gene expression is complicated and multi-leveled and essential for the final phenotype of a cell or tissue in disease and in health. RNA binding proteins (RBPs) are associated with mRNA transcripts throughout their life cycles and regulate many post-transcriptional processes including, but not limited to, mRNA stability, localization, and translation and have the ability to couple multiple of these processes. Aberrant regulation by RBPs can frequently result in malignancies like cancer. Alternative splicing, a co- and post-transcriptional process, has diverse impacts on different levels of regulation of gene expression including the diversity of protein sequence, mRNA stability, and subcellular transcript localization as well. Previously, the Sanford Lab and others discovered that alternative splicing may also influence translation by identifying mRNA transcripts from the same gene with distinct polyribosome association patterns in human cell lines. Here, I present data that shows that the coupling of alternative splicing with translational control is a conserved mechanism of gene regulation in higher primates and that specific mRNA sequences altered through alternative splicing seem responsible for this regulatory coupling. Subsequently, I explored the changes in cis- and transregulatory landscape of these mRNAs that could be connected to the isoform-specific polysome association and translation: I investigated the effect of single nucleotide variants on RNA binding protein (RBP) binding, mRNA secondary structure, and codon optimality in relation to isoform-specific polysome association. While I found multiple candidate RBPs worth investigating, I only found a modest correlation between mRNA secondary structure or codon optimality and isoform specific translation. In addition, I explored the interaction of RNA binding proteins with microRNAs and was able to find a strong binding preference for RBPs binding to (which area) of microRNAs. Further, I investigated the role of a specific RBP and a known marker for malignancy, IGF2BP3 in multiple oncogenic environments. In the context of B-cell acute lymphoblastic leukemia, I was able to identify high confidence targets of IGF2BP3 involved in leukemogenesis. Taken together, these projects elucidate the complexity of protein/RNA interactions and their multifaceted abilities to regulate post-transcriptional processes both in healthy and disease phenotypes. Finally, I am presenting BiocSwirl, a novel platform for teaching R based bioinformatics to students and scientists of all levels of computational understanding. The courses are interactive with live feedback and provide a rich and new learning experience in bioinformatics