DOI
https://doi.org/10.25772/PSB2-6S78
Defense Date
2023
Document Type
Thesis
Degree Name
Master of Science
Department
Bioinformatics
First Advisor
Michael Miles
Abstract
Alcohol use disorder is known to have significant genetic components that contribute to an individual’s susceptibility to the disease. Mouse models are commonly used to study the mechanisms underlying alcohol use disorder, with C57BL/6J (B6) and DBA/2J (D2) being two of the more prominently used inbred strains. Research in the Miles Laboratory has used these two strains, and genetic panels of mice derived from them, to identify potential genes associated with variance in ethanol-related behaviors using quantitative trait loci (QTL) analysis. For example, Ninein (Nin) was identified as a potential candidate gene for the anxiolytic effects of ethanol, discovered because it resides in the confidence interval for a QTL and shows mRNA expression differences between B6 and D2 mice. This differential expression was identified using counts of RNA-Seq reads that have been aligned to a reference genome, specifically the B6 reference genome. Due to the known genetic differences between the two strains, it is possible that the D2 samples could benefit from being aligned to a D2 genome instead of the B6. This would lead to better results overall due to improved read alignment and identification of novel splicing events that might be seen in D2 mice. To test this hypothesis, a dataset consisting of deep (150 million reads) sequencing of RNA from nucleus accumbens of both B6 and D2 mice was used for multiple bioinformatics analyses (differential expression, gene ontology, semantic similarity, differential exon utilization, splice site location, and alternative splicing) with both B6 aligned D2 counts and D2 aligned D2 counts. End results of each analysis were then compared for significant differences in outcomes. The results of this analysis show that when aligning D2 samples to the D2 genome a majority of differentially expressed genes and differentially utilized exons are retained from the B6 aligned analysis while many new genes and exons are identified that are unique to the D2 aligned analysis.
Rights
© The Author
Is Part Of
VCU University Archives
Is Part Of
VCU Theses and Dissertations
Date of Submission
8-15-2023