Date of Award




Document Type


Degree Name

Doctor of Philosophy (PhD)


Department of Nanoscale Science and Engineering


Nanoscale Sciences

Content Description

1 online resource (xiv, 201 pages) : color illustrations.

Dissertation/Thesis Chair

Thomas J. Begley

Committee Members

J. Andres Melendez, Xinxin Ding, Qing-Yu Zhang, JoEllen Welsh


Alkbh8, Alkylation Repair Homolog 8, Codon Bias, Environmental Stress Response, Epitranscriptomics, Selenoproteins, Stress (Physiology), Transfer RNA, Genetic translation, Genetic regulation, Naphthalene

Subject Categories

Molecular Biology | Toxicology


Epitranscriptomic marks in the form of enzyme-catalyzed modifications to RNA nucleosides can be important regulators of translation and play integral roles in the response to stress. Dynamic changes in tRNA modification status can regulate the translation of stress response proteins whose transcripts have distinct codon biases. The epitranscriptomic writer Alkylation repair homolog 8 (ALKBH8) plays a crucial part in the translation of codon biased transcripts, as it regulates stop codon recoding, which is a specialized form of translation used to generate selenoproteins. ALKBH8 modifies the wobble uridine of selenocysteine tRNA (tRNASec) to promote the decoding of an internal UGA codon on transcripts that have at least 2X as many stop codons compared to most transcripts, with selenoproteins used to detoxify reactive oxygen species (ROS). In my thesis I present evidence that lungs from the Alkbh8def mice display markers of oxidative stress, DNA damage, and inflammation under normal growth conditions. Using the environmental toxicant naphthalene (NA), I have demonstrated that lungs from Alkbh8def mice are more sensitive to NA exposures than WT, showing higher susceptibility to lung damage. Furthermore, Alkbh8def mice display broad selenoprotein deficiency in response to NA-induced stress, which we predict is a result of a translational defect due to decreased ALKBH8-catalyzed wobble uridine modifications on tRNASec. I further show that Alkbh8def mice do not develop tolerance and do not survive the exposures. My data supports a model in which the ALKBH8 writer and epitranscriptomic marks allow cells to develop tolerance and adapt to chronic stress. In an effort to identify other stress response transcripts with codon biases I helped develop the CUT database. CUT provides codon usage data for all yeast, mouse and rat genes/transcripts, enabling insights into codon patterns with possible regulatory functions. I developed a search method to identify all UGA-containing transcripts in the mouse genome which not only identified all selenoproteins but also identified other readthrough targets, many of which serve stress-response functions. This study revealed a diverse set of new transcripts which may undergo translational recoding of a stop codon. My studies provide specific examples and support the idea that epitranscriptomic writers and codon bias play important roles in environmental responses.