Spatial Organization of tRNAs

Name of Research Sponsor: Dr. David Engelke

Dates of Involvement: Fall 2009- Spring 2010

Abstract

The 274 tRNA genes in Saccharomyces cerevisiae are scattered throughout the linear maps of the 16 chromosomes, but the genes are clustered together in the nucleolus in 3-demensional space. Until recently, the approaches used have not been able to show the how individual tRNA genes are organized. Knowing individual location is important because tRNAs are retrotransposon-like elements that occur multiple times within a genome. Moreover, spatial arrangement of tRNA genes contributes to tRNA gene-mediated (tgm) silencing of RNA polymerase II transcription adjacent to tRNA genes. Recently, our work suggests that this clustering is not random. A technique entitled chromosome conformation capture (3C) is used to determine physical interactions between individual loci in the nucleus. The basis of the 3C procedure is cross-linking segments of DNA with other, nearby segments. A collaborating laboratory characterized approximately 200 million junctions across the genome to identify what segments of DNA are near tRNA genes in the nucleus. From this data, 260 tRNA genes were found to interact strongly with other tRNAs. Specific interactions between tRNA genes occur with significantly high frequency. These interactions were analyzed for patterns. Identical tRNA genes show a strong preference to localize with each other regardless of where they are localized in the linear genome. To explain this, a hypothesis has been posed that during evolution, tRNA genes duplicated and integrated into a nearby chromosomal location. Further experiments will delve further into this hypothesis. Together these experiments will further the understanding of how eukaryotic genomes are organized.