RNAs are remarkable because they can be both information carriers and structured functional macromolecules. They play a wide variety of roles in biology, including in gene expression regulation by riboswitches. Riboswitches are metabolite-dependent functional RNAs composed of aptamer domains and expression platforms, which bind small-molecule targets and regulate gene expression, respectively. Most riboswitches have been found in bacteria, with a single example known in plants, fungi, and algae, where it regulates alternative splicing and transcript stability. To discover more eukaryotic riboswitches, small-molecule aptamers need to be mapped out and tested for regulatory functions. Recently, adenosine aptamers were discovered in the human genome and preliminary results indicate that they sense ATP through a kinetic mechanism. The objective of this project is to measure the distribution of a variety of metabolite aptamers in genetic model eukaryotes. The aptamers will be detected using in vitro selections from a metagenomic genomic library and tested for potential roles as riboswitches. Adenosine aptamers, together with new aptamers found using SELEX will be tested for gene regulatory functions. Altogether, this research will contribute to the fundamental understanding of eukaryotic RNA biology and help define the roles that non-coding functional RNAs play in gene regulation and other cellular mechanisms.
Broader impacts This project will enhance our understanding of regulatory roles that RNAs play in eukaryotic model organisms, including plants. Throughout the project period undergraduate and graduate students will be trained in molecular and cellular biosciences, providing them with sets of broadly applicable problem-solving skills on both in both experimental and computational biology. In addition, a large numbers of young students from local middle schools, many of them from backgrounds that do not emphasize education and from schools that lack the resources for laboratory experimentation, will be exposed to the thrill of molecular biology to encourage them to consider higher education in the sciences
