GSBS Dissertations and Theses
ORCID ID
0000-0002-7288-1527
Publication Date
2017-12-18
Document Type
Doctoral Dissertation
Academic Program
Neuroscience
Department
RNA Therapeutics Institute
First Thesis Advisor
Melissa J. Moore
Keywords
biochemistry, deep-sequencing, neurodegenerative disease, quality control, ribosome, RNA biology, RNA damage, RNA-Seq, structural biology, translation, yeast
Abstract
The translation of mRNA into functional proteins is essential for all life. In eukaryotes, aberrant RNAs containing sequence features that stall or severely slow down ribosomes are subject to translation-dependent quality control. Targets include mRNAs encoding a strong secondary structure (No-Go Decay; NGD) or stretches of positively-charged amino acids (Peptide-dependent Translation Arrest/Ribosome Quality Control; PDTA/RQC), mRNAs lacking an in-frame stop codon (Non-Stop Decay; NSD), or defective 18S rRNAs (18S Nonfunctional rRNA Decay; 18S NRD). Previous work from our lab showed that the S. cerevisiae NGD factors DOM34 and HBS1, and PDTA/RQC factor ASC1, all participate in the kinetics of 18S NRD. Upon further investigation of 18S NRD, our research revealed the critical role of ribosomal protein S3 (RPS3), thus adding to the emerging evidence that the ribosome senses its own translational status.
While aberrant mRNAs mentioned above can occur endogenously, damaging agents, such as oxidative stress or UV irradiation, can negatively affect the chemical integrity of RNA. Such lesions could lead to translation errors and ribosome stalling. However, current tools to monitor the fate of damaged RNA are quite limited and only provide a low-resolution picture. Therefore, we sought to develop a deep-sequencing method to detect damaged RNA, taking advantage of reverse transcriptase's ability to insert a mutation across a damaged site. Using oxidized RNA as a model damaged RNA, our preliminary data showed increased G>T mutations in oxidized RNA. This method provides the foundation for future work aimed at understanding how cells deal with damaged RNA.
Repository Citation
Limoncelli KA. (2017). Identification of Factors Involved in 18S Nonfunctional Ribosomal RNA Decay and a Method for Detecting 8-oxoguanosine by RNA-Seq. GSBS Dissertations and Theses. https://doi.org/10.13028/M2MM5T. Retrieved from https://escholarship.umassmed.edu/gsbs_diss/945
DOI
10.13028/M2MM5T
DOI Link
Rights and Permissions
Licensed under a Creative Commons license
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.
Included in
Biochemistry Commons, Bioinformatics Commons, Genetics Commons, Molecular Biology Commons, Nucleic Acids, Nucleotides, and Nucleosides Commons, Structural Biology Commons