Date of Award

2020

Degree Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Graduate Group

Cell & Molecular Biology

First Advisor

Brian D. Gregory

Abstract

After transcription, RNAs are tightly regulated through many post-transcriptional processing steps to allow for proper gene expression in a context-specific manner and have a multitude of functions both in their abilities to encode for proteins or function as non-coding RNAs. The coordination of the myriad of post-transcriptional gene regulatory steps in a stress-dependent manner is poorly understood. Specifically, while the role of RNA secondary structure, covalent RNA modifications and RNA-RNA binding protein interactions on regulating RNA fate has been linked to a plant’s response to stress, their coordination has yet to be studied. Additionally, RNAs can function in a non-protein-coding capacity. These non-coding RNAs function in a developmental- and stress-dependent manner to affect essential organismal processes but are still poorly understood and merit additional analyses.This dissertation examines the role of several post-transcriptional regulatory processes during stress response in Arabidopsis and examines the function and biogenesis of two classes of non-protein-coding RNAs. I first demonstrate large rearrangements of RNA secondary structure during an agriculturally relevant salt stress and describe a link between the role of RNA modifications in regulating RNA secondary structure and ultimately the stability and translation of proteins required for proper stress response. I then examine a group of non-protein-coding RNAs (long non-coding RNAs (lncRNAs)), focusing on a previously unstudied lncRNA termed COBRA1 and characterize its essential function during plant development. Finally, I explore a mechanism to generate a class of non-canonical non-coding RNAs that are linked at their 5’ and 3’ ends, forming a circular RNA (circRNA), and generate a molecular tool to permit further study of these obscure molecules. Overall, I use a combination of molecular, biochemical, and bioinformatic approaches to better understand the regulation of gene expression at the RNA level and examine the formation and function of non-protein-coding RNAs. Together, these studies have raised many questions for future studies to address that will ultimately explore novel mechanisms that mediate plant resistance to stress as well as lead to a better understanding of the biogenesis and the roles of non-coding RNAs during development.

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