Persistent Link:
http://hdl.handle.net/10150/196006
Title:
Post-Transcriptional Gene Regulation in Plants
Author:
Hayden, Celine
Issue Date:
2006
Publisher:
The University of Arizona.
Rights:
Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.
Abstract:
Many elements contribute to the regulation of protein expression in eukaryotes. One such element, the upstream open reading frame (uORF), is the focus of this dissertation because it has not previously been well-characterized on a genome-wide scale. To undertake this project, an evaluation and improvement of full-length cDNA collections was implemented (Chapter 2). Most uORF amino acid sequences are not conserved in evolution, but those that are conserved seem likely to play sequence-specific roles in translational control of downstream, or major, open reading frames (mORF). By comparing full-length cDNA sequence libraries from Arabidopsis and rice we identified 26 homology groups of conserved peptide uORFs, only two of which had been reported previously. The conserved uORF amino acid sequences of each homology group were distinct from those of any other homology group, and within each uORF homology group mORFs always code for similar proteins in Arabidopsis and rice. Essentially all uORFs and their associated mORFs have been subject to purifying selection as determined by Ka/Ks analysis. The mORFs of conserved uORF transcripts encode transcription factors at a much higher frequency than expected (31% vs. 6% for the genome as a whole, p=10-7); a variety of different types of transcription factors are represented among these mORFs. Duplicate copies of conserved uORF-possessing genes that were created by whole genome duplication in an Arabidopsis ancestor are much more likely to have been retained in extant Arabidopsis than duplicates of the average gene (39% vs. 14%, p=5x10-3). Two of the 26 uORF homology groups were also found to be present in animals, indicating a high degree of sequence conservation and an ancient origin for these groups. The evolutionary history of one of these groups suggests that some uORFs arise by a 'transcriptional fusion' model.
Type:
text; Electronic Dissertation
Degree Name:
PhD
Degree Level:
doctoral
Degree Program:
Plant Science; Graduate College
Degree Grantor:
University of Arizona
Advisor:
Jorgensen, Richard
Committee Chair:
Jorgensen, Richard

Full metadata record

DC FieldValue Language
dc.language.isoENen_US
dc.titlePost-Transcriptional Gene Regulation in Plantsen_US
dc.creatorHayden, Celineen_US
dc.contributor.authorHayden, Celineen_US
dc.date.issued2006en_US
dc.publisherThe University of Arizona.en_US
dc.rightsCopyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.en_US
dc.description.abstractMany elements contribute to the regulation of protein expression in eukaryotes. One such element, the upstream open reading frame (uORF), is the focus of this dissertation because it has not previously been well-characterized on a genome-wide scale. To undertake this project, an evaluation and improvement of full-length cDNA collections was implemented (Chapter 2). Most uORF amino acid sequences are not conserved in evolution, but those that are conserved seem likely to play sequence-specific roles in translational control of downstream, or major, open reading frames (mORF). By comparing full-length cDNA sequence libraries from Arabidopsis and rice we identified 26 homology groups of conserved peptide uORFs, only two of which had been reported previously. The conserved uORF amino acid sequences of each homology group were distinct from those of any other homology group, and within each uORF homology group mORFs always code for similar proteins in Arabidopsis and rice. Essentially all uORFs and their associated mORFs have been subject to purifying selection as determined by Ka/Ks analysis. The mORFs of conserved uORF transcripts encode transcription factors at a much higher frequency than expected (31% vs. 6% for the genome as a whole, p=10-7); a variety of different types of transcription factors are represented among these mORFs. Duplicate copies of conserved uORF-possessing genes that were created by whole genome duplication in an Arabidopsis ancestor are much more likely to have been retained in extant Arabidopsis than duplicates of the average gene (39% vs. 14%, p=5x10-3). Two of the 26 uORF homology groups were also found to be present in animals, indicating a high degree of sequence conservation and an ancient origin for these groups. The evolutionary history of one of these groups suggests that some uORFs arise by a 'transcriptional fusion' model.en_US
dc.typetexten_US
dc.typeElectronic Dissertationen_US
thesis.degree.namePhDen_US
thesis.degree.leveldoctoralen_US
thesis.degree.disciplinePlant Scienceen_US
thesis.degree.disciplineGraduate Collegeen_US
thesis.degree.grantorUniversity of Arizonaen_US
dc.contributor.advisorJorgensen, Richarden_US
dc.contributor.chairJorgensen, Richarden_US
dc.contributor.committeememberChandler, Vickien_US
dc.contributor.committeememberParker, Royen_US
dc.contributor.committeememberXiong, Zhongguoen_US
dc.identifier.proquest1684en_US
dc.identifier.oclc137356735en_US
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