Advancement: Analysis of tRNA transcription patterns

Speaker Name: 
Bryan Thornlow
Speaker Title: 
PhD Student
Speaker Organization: 
Biomolecular Engineering & Bioinformatics
Start Time: 
Tuesday, May 22, 2018 - 3:00pm
End Time: 
Tuesday, May 22, 2018 - 5:00pm
Biomedical Sciences, Room 200
Assistant Professor Russell Corbett-Detig and Professor Todd Lowe

Abstract:  While tRNAs are well known for their canonical roles in translation, recent studies have shown that tRNAs have diverse secondary functions and extensive variation in their expression. However, tRNA sequencing and subsequent genomic mapping of reads remain difficult due to extensive modifications and sequential redundancy across genes. In spite of deep conservation of tRNA genes at the nucleotide level, the regions flanking these genes show extreme levels of divergence across species and within populations. I propose to use comparative genomics techniques to determine the fundamental cause of this variation, its evolutionary scope, and whether such variation patterns are reflective of the expression of tRNA genes. Then, I will use machine learning to develop a classifier that will use inputs derived from DNA sequencing data alone to infer the transcriptional activity of each tRNA gene in several mammalian genomes. This tool will improve ex! isting tRNA annotations and provide a strong foundation for future studies on tRNA function. Finally, while it has been established that codon preferences are often correlated with the copy number of their corresponding tRNA genes, several Drosophila species have been identified with significant changes in codon preference without accompanying changes in tRNA gene copy number. I propose to sequence tRNAs in these Drosophila species to determine whether changes in codon usage may have been driven by changes in tRNA expression or modification.