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Dissertation/Thesis Abstract

Conserved noncoding sequences regulate steady-state mRNA levels in Arabidopsis thaliana
by Spangler, Jacob Brian, Ph.D., Clemson University, 2013, 163; 3565242
Abstract (Summary)

Arabidopsis thaliana has undergone three whole genome duplications within its ancestry, and these events have dramatically affected its gene complement. Of the most recent whole genome duplication events (α event), there remain 11,452 conserved noncoding sequences (CNSs) that have been retained proximal to α duplicate gene pairs. As functional DNA elements are expected to diverge in sequence at a slower rate than nonfunctional DNA elements, the retained CNSs likely encode gene regulatory function. Within this dissertation I provide evidence for the regulatory role of CNSs within Arabidopsis thaliana. Using a collection of over 5,000 microarray RNA expression profiling datasets, I demonstrate that the presence of CNSs near α duplicate pairs is correlated with changes in average expression intensity (AEI), α duplicate pair co-expression, mRNA stability, and breadth of gene expression. The effects of CNSs on AEI, co-expression, and mRNA stability vary relative to their subgene position, because they are located in nontranscribed (5’-upstream and 3’-downstream) and transcribed (5’- UTR, intronic and 3’-UTR) regions. Modeling gene interactions through the generation of co-expression networks, I also demonstrate that a portion of CNSs participate in known gene regulatory networks. Collectively, this body of work demonstrates that CNSs regulate steady-state mRNA levels within Arabidopsis thailiana through both transcriptional and post-transcriptional mechanisms.

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Indexing (document details)
Advisor: Feltus, Alex
Commitee: Frugoli, Julia, Lawton-Rauh, Amy, Liang, Haiying
School: Clemson University
Department: Genetics and Biochemistry
School Location: United States -- South Carolina
Source: DAI-B 74/10(E), Dissertation Abstracts International
Subjects: Genetics, Evolution and Development
Keywords: Arabidopsis, Conserved noncoding sequence, Steady-state mRNA
Publication Number: 3565242
ISBN: 978-1-303-14796-8
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