Insights into the functional implications of environmental exposure in RNA modifications



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RNA post-transcriptional modifications are changes to the chemical composition of nucleotides that can reprogram RNA fate and functions. They have critical roles in cellular regulation and gene expression. Preliminary evidence suggests that environmental stressors such as air pollution could impact patterns of these marks. Thus, there is a critical need to identify how environmental stressors are involved in modulating levels and types of RNA modifications and in understanding how these stressors could mis-regulate pathways that lead to adverse health outcomes. However, the lack of large-scale and sensitive technologies to detect and study the role of these marks in low abundant RNAs has limited our understanding of the functional relationship between stress, cellular functions and RNA modifications. My dissertation aims to develop tools to identify mechanisms connecting molecular alterations of specific RNA transcripts to cellular functions underlying environmental stress. To address this, first, we developed a tool to capture RNA modifications in the form of 8-oxo-7,8-dihydroguanosine (8-oxoG), the most predominant modification generated during environmental stress. We applied this tool to profile RNA transcripts in human lung cells exposed to relevant concentrations of air pollution mixtures to identify high-confidence mRNAs that are direct markers of oxidation post exposures to air pollution. Importantly, we identified transcripts that led us to a specific pathway (cholesterol synthesis) that is highly oxidized by air pollution. Overall, these initial studies revealed a novel mechanism that drives abnormal cellular function in steroid metabolism that can be traced to the formation of respiratory diseases. Secondly, we developed a large-scale screening approach, based on MD simulations, that investigates molecular interactions between proteins that modulate RNA activity and stress-induced RNA modifications. We examined four proteins implicated in diseases (PNPase, YTHDF1, NOVA1 and TDP-43). In this work, we found that these proteins share the ability to directly interact with multiple modifications using common RNA-binding domains. From a molecular design perspective, identifying the molecular principles that govern these RNA-protein interactions, provided an opportunity to engineer proteins with higher affinity for RNA modifications. Collectively, these studies support the functional relationship between alterations at the molecular level in RNA molecules and regulation of cellular processes.


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