Defense: Comparative genomics and regulation of tRNAs and tRNA fragments

Speaker Name: 
Andrew Holmes
Speaker Title: 
PhD Candidate
Speaker Organization: 
Biomolecular Engineering & Bioinformatics
Start Time: 
Tuesday, August 7, 2018 - 2:00pm
End Time: 
Tuesday, August 7, 2018 - 3:30pm
Biomed 200
Todd Lowe

Abstract:  I report on two different forms of whole-genome analysis of tRNA gene regulation. The first is analysis of tRNA fragments using RNA-sequencing. I develop a computational method to analyze changes in RNA sequencing data from tRNAs and tRNA fragments and use this method to analyze changes in RNA-sequencing results from the use of demethylase treatment, PNK end treatment, and RNA sequencing kit to determine how RNA-sequencing results of tRNA can change from experiment to experiment. I also analyze tRNA sequencing on a chromatin level using previously published genome-wide chromatin data. Here, I categorize tRNAs based on their expression and compare these tRNAs to examine what the determinants of expression are. Using this data, I also build a method to compare tRNAs across related species and find how tRNA conservation varies with expression.