Date of Award
5-2013
Document Type
Dissertation
Degree Name
Doctor of Philosophy (PhD)
Legacy Department
Genetics
Committee Chair/Advisor
Feltus, Alex
Committee Member
Lawton-Rauh , Amy
Committee Member
Frugoli , Julia
Committee Member
Liang , Haiying
Abstract
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 (&alpha event), there remain 11,452 conserved noncoding sequences (CNSs) that have been retained proximal to &alpha 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 &alpha duplicate pairs is correlated with changes in average expression intensity (AEI), &alpha 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.
Recommended Citation
Spangler, Jacob, "CONSERVED NONCODING SEQUENCES REGULATE STEADY-STATE mRNA LEVELS IN Arabidopsis thaliana" (2013). All Dissertations. 1103.
https://tigerprints.clemson.edu/all_dissertations/1103
Spangler_Supplemental_File_2.xlsx (7027 kB)
Spangler_Supplemental_File_3.xlsx (111 kB)