Title

Biochemical and Computational Characterization of Small Regulatory RNAs in the Eastern Oyster, Crassostrea virginica

Date of Award

5-2021

Degree Type

Honors College Thesis

Academic Program

Chemistry BS

Department

Chemistry and Biochemistry

First Advisor

Alex Flynt, Ph.D.

Advisor Department

Biological Sciences

Abstract

RNA interference (RNAi) is a process by which gene expression is regulated using small non-coding RNAs (ncRNAs). Three classes of ncRNAs, including micro-RNA (miRNA), short-interfering RNA (siRNA), and Piwi-interacting RNA (piRNA), are readily distinguishable in eukaryotic systems based on unique characteristics such as read sizes, overlap signatures, and mode of biogenesis. In this study, a method for purification of small RNAs was explored in the eastern oyster, Crassostrea virginica. This method involved the use of Sepharose beads for anion exchange chromatography to enhance purification of Argonaute associated small RNAs. Following RNA extraction and purification, small RNA libraries were created and sequenced on the Illumina platform. The results showed that this approach did not accurately reflect the population of ncRNA in the species as observed in the non-bead-treated total RNAs. However, further improvements to the methodology described here could aid in efficiency in recovering small RNA populations that would minimize the presence of other non-Argonaute associated ncRNAs.

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