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    Transcript-Specific Cytoplasmic Degradation of YRA1 Pre-mRNA Mediated by the Yeast EDC3 Protein: A Dissertation

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    Authors
    Dong, Shuyun
    Faculty Advisor
    Allan Jacobson, Ph.D.
    Academic Program
    Molecular Genetics and Microbiology
    UMass Chan Affiliations
    Microbiology and Physiological Systems
    Document Type
    Doctoral Dissertation
    Publication Date
    2007-12-17
    Keywords
    Gene Expression
    Cell Nucleus
    Feedback
    Biochemical
    Nuclear Proteins
    RNA Stability
    RNA Precursors
    RNA-Binding Proteins
    Saccharomyces cerevisiae
    Amino Acids, Peptides, and Proteins
    Biochemistry
    Bioinformatics
    Cells
    Computational Biology
    Fungi
    Genetic Phenomena
    Genetics
    Genetics and Genomics
    Genomics
    Molecular Biology
    Molecular Genetics
    Nucleic Acids, Nucleotides, and Nucleosides
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    Abstract
    mRNA degradation is a fundamental process that controls both the level and the fidelity of gene expression. Using a combination of bioinformatic, genomic, genetic, and molecular biology approaches, we have shown that Edc3p, a yeast mRNA decay factor, controls the stability of the intron-containing YRA1 pre-mRNA. We found that Edc3p-mediated degradation of YRA1 pre-mRNA: 1) is a component of a negative feedback loop involved in the autoregulation of YRA1, 2) takes place in the cytoplasm, 3) is independent of translation, 4) occurs through a deadenylation-independent decapping and 5΄ to 3΄ exonucleotic decay mechanism, and 5) is controlled by specific cis-acting elements and trans-regulatory factors. Cis-regulation of YRA1 pre-mRNA degradation is complicated and precise. Sequences in exon1 inhibit YRA1 pre-mRNA splicing and/or promote pre-mRNA export in a size-dependent but sequence-independent manner. Sequences in the intron dictate the substrate specificity for Edc3p-mediated decay. Five structurally different but functionally interdependent modules were identified in the YRA1 intron. Two modules, designated Edc3p-responsive elements (EREs), are required for triggering an Edc3p-response. Three other modules, designated translational repression elements (TREs), are required for repressing translation of YRA1 pre-mRNA. TREs enhance the efficiency of the response of the EREs to Edc3p by inhibiting translation-dependent nonsense-mediated mRNA decay (NMD). Trans-regulation of YRA1 pre-mRNA is governed by Yra1p, which inhibits YRA1 pre-mRNA splicing and commits the pre-mRNA to nuclear export, and the RNP export factors, Mex67p and Crm1p, which jointly promote YRA1 pre-mRNA export. Mex67p also appears to interact with sequences in the YRA1 intron to promote translational repression and to enhance the Edc3p response of YRA1 pre-mRNA. These results illustrate how common steps in the nuclear processing, export, and degradation of a transcript can be uniquely combined to control the expression of a specific gene and suggest that Edc3p-mediated decay may have additional regulatory functions in eukaryotic cells.
    DOI
    10.13028/ckcv-mt21
    Permanent Link to this Item
    http://hdl.handle.net/20.500.14038/31671
    Rights
    Copyright is held by the author, with all rights reserved.
    ae974a485f413a2113503eed53cd6c53
    10.13028/ckcv-mt21
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