<p> <i>Arabidopsis thaliana</i> 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 <i> Arabidopsis thaliana</i>. 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.</p>
| Identifer | oai:union.ndltd.org:PROQUEST/oai:pqdtoai.proquest.com:3565242 |
| Date | 09 August 2013 |
| Creators | Spangler, Jacob Brian |
| Publisher | Clemson University |
| Source Sets | ProQuest.com |
| Language | English |
| Detected Language | English |
| Type | thesis |
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