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dc.contributor.advisorHorsfield, Julia
dc.contributor.advisorMerriman, Tony
dc.contributor.authorDowdle, Amy Evaline
dc.date.available2015-11-11T04:39:39Z
dc.date.copyright2015
dc.identifier.citationDowdle, A. E. (2015). Searching for a Functional Variant in a Non-Coding Genomic Region Associated with Serum Urate (Thesis, Bachelor of Biomedical Sciences with Honours). University of Otago. Retrieved from http://hdl.handle.net/10523/6062en
dc.identifier.urihttp://hdl.handle.net/10523/6062
dc.description.abstractGout was historically known as the king of diseases and disease of kings, reserved for those of wealthy, extravagant lifestyles. Far from being resigned to history books, gout is on the rise worldwide and in New Zealand – where we have the highest rate of gout in the world – Maori and Polynesian populations have a greatly elevated risk of experiencing the debilitating disease. Gout arises as a direct result of increased urate in the blood, and as such many studies worldwide have investigated gout, using serum urate levels as a proxy measure. Recently, two important genome-wide association studies were published – these compare the genomes of those with elevated serum urate to the genomes of control subjects and identify differences. Single nucleotide polymorphisms (SNPs) were identified upstream of MAF, a gene that had not before been associated with serum urate levels. These SNPs were in what is known as a non-protein-coding region, which often play an important role in gene regulation. MAF is a transcription factor that is expressed in the lens of the eye and immune cells, and many studies into MAF have focused on these aspects. However, MAF has also been shown to be expressed in the developing kidney (in zebrafish and mice), which is of great relevance in a study of gout. Therefore, it was hypothesised that one or more of the SNPs upstream of MAF alter regulation of the MAF gene in the kidney, resulting in a change in serum urate levels. An in silico analysis was carried out, using publicly available datasets to produce candidate causal variants upstream of the MAF gene. When multiple datasets were combined and meta-analysed, no specific candidates were produced – however, some SNPs approached significance. This is noteworthy in such a small sample set (n = 18,503, versus 71,149 and >140,000 in the GWAS analyses), and the analysis needs to be repeated on a larger scale. Based on ENCODE annotations, candidate SNPs were selected in areas that looked to be involved in regulation of gene expression. To investigate the putative cis-regulatory role of SNPs, reporter constructs were used in human cell lines. This enhancer assay indicated that one element acts to enhance gene expression, and that the SNPs within this element increased this effect. Finally, a chromosome conformation capture (3C) experiment aimed to determine the interactions occurring between the MAF promoter and these upstream regions, but unfortunately the results were inconclusive. This study contributes to a growing field of research investigating the effects of non-coding DNA on gene expression, in the context of an important disease affecting the lives of New Zealanders everyday. Future findings may provide a novel mechanism by which non-coding variants affect serum urate levels in a system that has not previously been characterised.
dc.format.mimetypeapplication/pdf
dc.language.isoen
dc.publisherUniversity of Otago
dc.rightsAll items in OUR Archive are provided for private study and research purposes and are protected by copyright with all rights reserved unless otherwise indicated.
dc.subjectgout
dc.subjectserum urate
dc.subjectGWAS
dc.subjectbioinformatics
dc.subjectluciferase
dc.subjectgene regulation
dc.subjectchromosome conformation capture
dc.subject3C
dc.subjectchromatin
dc.titleSearching for a Functional Variant in a Non-Coding Genomic Region Associated with Serum Urate
dc.typeThesis
dc.date.updated2015-11-11T01:47:41Z
dc.language.rfc3066en
thesis.degree.disciplinePathology
thesis.degree.nameBachelor of Biomedical Sciences with Honours
thesis.degree.grantorUniversity of Otago
thesis.degree.levelHonours
otago.openaccessOpen
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