Regulation of translation initiation by the epitranscriptome

Project Summary/Abstract My research program investigates how the epitranscriptome regulates protein synthesis and how this interplay affects cell fate decisions under normal homeostasis and stress conditions. The epitranscriptome is the collection of more than 150 chemical modifications that occur on RNA molecules and influence all steps of gene expression. One such step is the translation of mRNAs - the process by which the information stored in DNA is converted into functional proteins. Though translation typically initiates at an optimal 'AUG' start codon, the 5' untranslated region (5'UTR) can harbor cryptic initiation sites. These cryptic sites result in upstream Open Reading Frames (uORFs) that generally regulate the expression of canonical proteins but can also produce new minipeptides with diverse biological functions. Importantly, these uORFs are not merely errors in translation but serve as regulatory mechanisms typically co-opted by cells when exposed to stress conditions. Hence, understanding how cells harness the noncanonical mechanisms of translation to their advantage remains a fundamental question in biology. My published and preliminary studies demonstrate that different RNA modifications and their cognate RNA- modifying enzyme dynamically regulate translation initiation. Under this MIRA award, my research program will integrate RNA biochemistry, chemical biology, transcriptomics, and cell biology to fill gaps in our understanding of how RNA modifications regulate uORF expression and the adaptability of eukaryotic cells to stress conditions. We will also investigate how genetic and physical interactions between RNA-modifying enzymes and translation factors influence the noncanonical mechanism of translation initiation. Lastly, we will implement synthetic biology strategies to modulate the expression of aberrant uORFs in transcript-specific manners. Overall, this research program will provide new insights on how the epitranscriptome is harnessed to diversify the coding potential of the genome. Our long-term goal is to pioneer conceptual leaps and technological innovations to comprehend and manipulate the epitranscriptome for the benefit of human health.