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theses

Small non-coding RNAs are a diverse class of molecules with wide biological importance, including regulatory roles, implications for evolution and possible medical therapeutics. The advent of next generation sequencing technology and various computational tools has aided in increasing the throughput and methods of discovery for these molecules. In this thesis we utilize and expand upon the most current methodologies of computational discovery, sequencing analysis and visualization for non-coding RNA, particularly microRNA (miRNA), in the Antarctic midge, Belgica antarctica and Drosophila melanogaster. These methods and the unique properties of B. antarctica’s genome lead to discoveries of evolutionary and functional importance, especially for a class of miRNA called mirtrons. We show that mirtrons within the B. antarctica can relocate to an alternative gene loci, or are lost from their host gene. This relocation and loss of mirtrons is based on computational discovery and predictions, but is supported and validated by other examples in literature covering a wide range of taxa. The data and results suggest a re-examination of the mechanisms that birth miRNA, specifically in terms of evolutionary duplication events. Additionally we describe and expand upon a tool for the in silico visualization of small non-coding RNA sequencing data, Genome Navigator. This tool can be used interactively to visualize concepts generated from high-throughput DNA and RNA sequencing data. We applied the new functionalities of Genome Navigator to elucidate biogenesis properties of another class of small non-coding RNA, called tRNA-derived fragments (tRFs). These properties strikingly resemble the canonical biogenesis cleavage patterns of miRNA.

ETD_6543

M.S.

Includes bibliographical references

by Karl Swanson

doi:10.7282/T3VD718N

ETD graduate

The author owns the copyright to this work.