RNAs play key roles in maintenance and expression of genetic information and provide potential targets and reagents for therapeutic intervention in pathological states associated with infectious diseases and hereditary disorders. Assembly of precise RNA structures and RNA-ligand complexes is essential to virtually all RNA-mediated processes. Our goal is to understand how RNAs fold into functional structures in living cells. Direct analysis of RNA folding steps in biological processes is challenging because numerous components interact in complex pathways and many steps intervene between assembly of an RNA structure and execution of its biological function. Catalytic RNAs provide useful model systems for probing folding mechanisms because catalytic activity reports directly and quantitatively on assembly of functional RNA structures. The foundation of our program is a system we developed using RNA catalysis to monitor intracellular assembly of RNA structures that integrates molecular biology and genetics with kinetics and thermodynamics. So far, this unique approach has enabled us to show that some kinetic and equilibrium parameters of intracellular RNA folding reactions agree remarkably well with parameters measured for the same reactions in vitro, provided that in vitro reactions approximate intracellular ionic conditions. On the other hand, we found that competition between alternative RNA secondary structures produces dramatically different outcomes in vitro and in vivo. The discrepancy between in vitro and in vivo RNA folding behavior highlights the importance of investigating RNA folding directly and quantitatively in a biological context. We propose to elaborate upon this approach by incorporating metabolomics and fluorescence methodologies and apply it to study new areas of intracellular RNA folding. These areas include the interplay between kinetics and thermodynamics during mRNA remodeling after transit through the ribosome, the influence of RNA-binding proteins and small ligands on RNA folding during transcription, and the mechanisms through which regulatory RNAs integrate information from multiple chemical signals to regulate gene expression. The proposed studies will generate fundamental insights into folding of the RNA structures that are central to normal growth and development and the assembly of RNA complexes with intracellular ligands that mediate gene regulation. The results of this work will also provide a framework for developing technical and therapeutic applications that involve RNAs as targets and reagents.

Public Health Relevance

RNAs play key roles in maintenance and expression of genetic information and provide potential targets and agents for therapeutic intervention. The proposed studies of intracellular RNA folding and interactions with chemical signals will contribute basic insight into RNA-mediated processes in growth, development, and disease and provide a framework for the rational design of RNA-based therapeutics.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM062277-11
Application #
8462989
Study Section
Macromolecular Structure and Function B Study Section (MSFB)
Program Officer
Preusch, Peter C
Project Start
2001-03-01
Project End
2015-04-30
Budget Start
2013-05-01
Budget End
2014-04-30
Support Year
11
Fiscal Year
2013
Total Cost
$370,245
Indirect Cost
$174,865
Name
Scripps Research Institute
Department
Type
DUNS #
781613492
City
La Jolla
State
CA
Country
United States
Zip Code
92037
Ruminski, Dana J; Watson, Peter Y; Mahen, Elisabeth M et al. (2016) A DEAD-box RNA helicase promotes thermodynamic equilibration of kinetically trapped RNA structures in vivo. RNA 22:416-27
Watson, Peter Y; Fedor, Martha J (2011) The glmS riboswitch integrates signals from activating and inhibitory metabolites in vivo. Nat Struct Mol Biol 18:359-63
Mahen, Elisabeth M; Watson, Peter Y; Cottrell, Joseph W et al. (2010) mRNA secondary structures fold sequentially but exchange rapidly in vivo. PLoS Biol 8:e1000307
Watson, Peter Y; Fedor, Martha J (2009) Determination of intracellular RNA folding rates using self-cleaving RNAs. Methods Enzymol 468:259-86
Fedor, Martha J (2008) Alternative splicing minireview series: combinatorial control facilitates splicing regulation of gene expression and enhances genome diversity. J Biol Chem 283:1209-10
Mahen, Elisabeth M; Harger, Jason W; Calderon, Elise M et al. (2005) Kinetics and thermodynamics make different contributions to RNA folding in vitro and in yeast. Mol Cell 19:27-37
Yadava, Ramesh S; Mahen, Elisabeth M; Fedor, Martha J (2004) Kinetic analysis of ribozyme-substrate complex formation in yeast. RNA 10:863-79
Fedor, Martha J (2004) Determination of kinetic parameters for hammerhead and hairpin ribozymes. Methods Mol Biol 252:19-32