Biological Sciences, School of


Date of this Version

Spring 4-8-2016


Krista D. Patefield, 2016. No Nonsense: The Protection of Wild-Type mRNAs From Nonsense-Mediated mRNA Decay in Saccharomyces cerevisiae. PhD Dissertation. University of Nebraska-Lincoln


A DISSERTATION Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Doctor of Philosophy, Major: Biological Sciences (Genetics, Cellular and Molecular Biology), Under the Supervision of Professor Audrey L. Atkin. Lincoln, Nebraska: April, 2016

Copyright © 2016 Krista D. Patefield


Gene regulation in eukaryotes is tightly controlled at multiple levels to ensure proper expression and cellular homeostasis. Misregulation of gene expression is a common source of genetic disease. One mechanism by which cells are able to control gene expression is through the synthesis and degradation of the mRNA molecules encoding the genes. The transcription and degradation of mRNA molecules controls the pool mRNAs that are available to the translational machinery. One of the well-studied mRNA decay pathways is the Nonsense-Mediated mRNA Decay pathway (NMD). Originally, NMD was discovered as a posttranscriptional mRNA surveillance mechanism responsible for the deadenylation-independent decapping and rapid 5’à3’ degradation of mRNAs that harbor premature termination codons (PTCs). Approximately one-third of all inherited genetic disease and cancers are related to NMD. It is now known that NMD plays a much larger role in the stability and expression of wild-type mRNAs as well. Wild-type mRNAs with NMD-targeting signals, which include 1) a translated uORF, 2) a long 3’ UTR, 3) leaky scanning leading to out-of-frame initiation of translation, 3) programmed ribosome frameshift sites, and 5) regulated alternative splicing variants, are rapidly destabilized by NMD. It has also been observed that some wild-type mRNAs contain NMD targeting signals but are not degraded by NMD due to protecting mechanism. Here we show that the SSY5 mRNA in Saccharomyces cerevisiae is a wild-type mRNA with multiple NMD targeting signals but is not degraded by NMD. None of the current models for NMD protection explain the SSY5 mRNA stability so the mechanism of protection is likely to be novel. Additionally, we show the SSY5 mRNA is primarily degraded 5’à3’. We also explore two additional mRNAs, YAP1 and GCN4, in S. cerevisiae that also contain at least one NMD-targeting signal but are not degraded by NMD. Elucidating the mechanism of protection from NMD of these three mRNAs will provide valuable insight to the underlying molecular mechanisms of NMD, which despite thorough investigation remain unclear. Understanding the molecular intricacies of the NMD pathway will allow for the efficient development of NMD-related disease therapies with minimal risks and side-effects.

Advisor: Audrey L. Atkin