In addition to carrying genetic information, the linear sequence of RNA can fold into higher order structures capable of interacting with other molecules and directly catalyzing biochemical reactions. These dual properties have led to the hypothesis that RNA constitutes the primordial molecule that gave rise to all current life forms.
Decades of research in model organisms have shown that specific messenger RNA (mRNA) structures are critical for embryonic development and that altered mRNA structures are sufficient to cause a variety of pathologies. Despite the known importance of RNA structures in regulating gene expression, the catalog of functional RNA structures is limited. Our understanding of the roles of RNA structure is derived largely from a handful of cases that have been examined through painstaking years of molecular biology and in vitro biochemistry.
The immediate goals of our research are to: 1) develop methods to simultaneously measure the structures of all mRNAs in vivo, even when a given mRNA might fold into alternate or competing conformations 2) use these methods to identify biologically relevant changes in mRNA structure in a model system for embryonic development, and 3) determine whether these structures act alone or in concert with other RNAs or RNA binding proteins. The long-term goal of our research is to understand the principles of RNA folding in vivo, how RNA structure regulates gene expression in normal cells, and what aspects go awry in the onset of disease states such as neurodegeneration and cancer.
We use a small molecule called DMS (dimethyl sulfate) that enters cells rapidly and modifies unpaired adenine and cytosine bases in the RNA. This assay is coupled with high-throughput sequencing such that the DMS-modified bases can be detected either transcriptome-wide or for a selected population of RNA molecules. We use Drosophila melanogaster to determine the distribution and changes of mRNA structures during oogenesis and embryogenesis as well as to investigate how functional RNA structures regulate mRNA localization and translation. The methods we develop in the process are widely universal and aimed at determining basic principles through which the chemical properties of RNA have a profound effect on gene expression.
- Harold M. Weintraub Award (2015)