The study of the factors that control RNA expression to give rise to diverse cell types, from the same genome, has occupied scientists for more than 50 years. However, transcriptional regulation is just the beginning. Each expressed RNA can potentially adopt a new purpose as a function of its spatial position within a cell. RNA localization has been analyzed one RNA at a time because assaying RNA spatial organization on a systems-level is currently not possible. This Innovator proposal is focused on developing the methods to produce the first ever view of RNA localization on a transcriptome-wide level within cells. We will develop a novel methodology to seek and find the cellular localization of every RNA within specific cellular locations. These methods are designed to be applicable to any cell type. By merging our technology with RNA sequencing we will construct RNA Localization Heatmaps to identify sites where certain RNAs are localized to. We will then integrate our data with existing datasets to understand how RNA-binding proteins direct RNAs to their cellular destinations. Our ultimate goal is to not only find where RNAs are, but also how they get there. Deciphering the molecular code for RNA organization will have broad impact on the biomedical community. Such knowledge could be used to better understand RNA-guided cellular reprogramming, design better RNA therapeutics, and further our understanding of how RNA localization contributes to normal and diseased phenotypes. This proposal is highly suitable for the New Innovator Award mechanism. Planned experiments will develop novel tools and methods to radically transform our understanding of cellular and RNA organization, while at the same time discovering an extended set of molecular codes that researchers could employ for RNA design.

Public Health Relevance

RNA localization is a hallmark of essentially every biological process: from development to the onset of cancer. However, a comprehensive understanding of RNA localization is presently lacking. Understanding the breadth of RNA localization and how RNA spatial organization and function is controlled would dramatically increase our understanding of how it controls biology and disease, and potentially lead to optimized design of RNA-based therapies.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
NIH Director’s New Innovator Awards (DP2)
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Special Emphasis Panel ()
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Ainsztein, Alexandra M
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University of California Irvine
Schools of Pharmacy
United States
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