Analyzing Regulation of tRNAs, tRNA Fragments, and mRNAs in Whole Genomes

Rather than focus on individual pathways or genes, whole-genome analysis of regulation allows for the discovery of the biological processes that drive cells decisions and fate in single-celled and multicellular organisms. I report on three different forms of whole-genome analysis of 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 expression data, I also build a method to compare tRNAs across related species and find how tRNA conservation varies with expression. Finally, I examine cis-regulatory structural mRNA elements in archaea. I find that the known types of cis-regulatory element in bacteria are conserved, and then I use a combination of RNA sequencing data and methods for finding conserved RNA structure to predict these elements in three archaeal species. I build a list of candidate structural elements including new ribosomal autoregulatory elements in each species