Regulation of mRNA translation by cis-acting sequences and trans-acting factors

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While the regulation of gene expression is well recognized as being important to human disease, there is a fundamental gap in understanding the role of post-transcriptional processes. Because post-transcriptional processes are critical for the regulation of protein production, addressing this knowledge gap will facilitate better models of the relationship between genotype and phenotype. Like transcription, mRNA translation is regulated by cis-acting sequences and trans-acting factors. upstream Open Reading Frames (uORFs) are cis-acting regulatory element found in most human genes, and some disease-linked mutations appear to alter the presence of uORFs. The primary focus of my laboratory is to determine how cis-acting sequences and trans-acting factors control translation. Our goal for the next funding period is to determine the functions of human uORFs and evaluate their regulation by trans-acting RNA binding proteins (RBPs). To accomplish this, we have adapted our yeast Massively Parallel Reporter Assays (MPRAs) for use in human tissue culture. In addition, our computational analysis has identified thousands of primate-conserved human uORFs, many of which have conserved RBP binding sites downstream of their start codons. The vast majority of these uORFs have not been functionally studied. Our innovative approach combines exquisite systems biology tools with cutting-edge computational modeling to investigate the functions of these ubiquitous cis-regulatory elements. The proposed research is significant because it is expected to fundamentally advance our understanding of human gene regulation.