RNA functions as the central conduit of information exchange in all cells, a role encapsulated in two critical observations. First, a large fraction of emerging infectious diseases are caused by RNA viruses including Ebola, Chikungunya, Zika, and Dengue. Second, a much larger fraction of the mammalian genome is transcribed into diverse kinds of non-coding RNAs (~70%) than is translated into protein (1- 2%). The functions of messenger, non-coding, and viral RNAs are governed by the linear sequence, base-paired secondary structure, higher-order tertiary structure, and quaternary interactions involving proteins and small molecules. Overall, our understanding of the number and complexity of RNA structures and how RNA structure drives diverse biological functions is very limited. Most methods developed to date for analyzing RNA structure in high-throughput ways do not measure structure in a definitive and accurate way, making it difficult to define broad principles for interrelationships between RNA structure and function. We seek to understand the fundamental roles of RNA structure in all areas of biology by pursuing a two-pronged approach involving (1) inventing, developing, and rigorously validating highly accurate chemistry-based technologies for discovery of novel RNA structures and the networks of interactions between RNAs and proteins and then (2) applying these technologies to problems of broad importance. Here we propose to interrogate the structures and interaction partners of the pathogenic Dengue RNA virus and the Xist long non-coding RNA. Throughout this work, we will focus on in-cell analysis of native viral and endogenous RNAs. This work is expected to have long-term impact for three broad reasons. First, RNA elements with higher-order folds and extensive protein networks are likely to be harbingers of function. Second, there are likely to be structural folds that are different from the relatively limited classes of structures that have been analyzed to date. Third, RNA elements with higher-order folds also contain clefts and crevices that are ideal targets for small- molecule ligands ? and novel drugs ? that modulate biological function by targeting RNA.

Public Health Relevance

This proposal focuses on the broad visions of (i) creating novel technologies for rigorous, quantitative, and experimentally concise analysis of higher-order RNA structures and (ii) applying these technologies to the compelling challenges of discovering novel tertiary structures and protein regulatory networks in the genomes of pathogenic viruses and in non-coding RNAs. This project will create new technologies for analysis of RNA structure and function, ultimately driving both basic biological discovery and novel, RNA-targeted, small-molecule drug development.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Unknown (R35)
Project #
5R35GM122532-03
Application #
9754843
Study Section
Special Emphasis Panel (ZGM1)
Program Officer
Sakalian, Michael
Project Start
2017-06-09
Project End
2022-05-31
Budget Start
2019-06-01
Budget End
2020-05-31
Support Year
3
Fiscal Year
2019
Total Cost
Indirect Cost
Name
University of North Carolina Chapel Hill
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
608195277
City
Chapel Hill
State
NC
Country
United States
Zip Code
27599
Dethoff, Elizabeth A; Boerneke, Mark A; Gokhale, Nandan S et al. (2018) Pervasive tertiary structure in the dengue virus RNA genome. Proc Natl Acad Sci U S A 115:11513-11518
Mustoe, Anthony M; Busan, Steven; Rice, Greggory M et al. (2018) Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing. Cell 173:181-195.e18
Langdon, Erin M; Qiu, Yupeng; Ghanbari Niaki, Amirhossein et al. (2018) mRNA structure determines specificity of a polyQ-driven phase separation. Science 360:922-927
Kirk, Jessime M; Kim, Susan O; Inoue, Kaoru et al. (2018) Functional classification of long non-coding RNAs by k-mer content. Nat Genet 50:1474-1482
Williams 2nd, Benfeard; Zhao, Bo; Tandon, Arpit et al. (2017) Structure modeling of RNA using sparse NMR constraints. Nucleic Acids Res 45:12638-12647
Corley, Meredith; Solem, Amanda; Phillips, Gabriela et al. (2017) An RNA structure-mediated, posttranscriptional model of human ?-1-antitrypsin expression. Proc Natl Acad Sci U S A 114:E10244-E10253