Genome-Wide Association Studies have found genetic variation from across the genome to be associated with various diseases and other traits. In many cases, the exact mechanism by which a genetic variant increases or decreases the risk of a particular condition is poorly understood. Many efforts are now underway to combine data on disease-associated genetic variation with other genome-wide data to understand the way in which genetic variation can alter genomic regulation and affect disease risk. In this project we examine whether disease-associated genetic variation, in the form of single nucleotide polymorphisms, can be found in binding sites for the transcription factors T-bet in Th1 cells and GATA3 in Th1 or Th2 cells. We hypothesise that, in some cases, variation within binding sites for these transcription factors could alter transcription factor binding affinity and subsequent gene regulation. As ’master regulators’ of T helper cell lineage commitment, T-bet and GATA3 play a central role in the fate of a naïve T helper cell and the development of an immune response. We find several single nucleotide polymorphisms in our transcription factor binding sites, some of which are near other genomic features such as potential enhancer elements. Furthermore, we find an enrichment of immune related SNPs in T-bet and GATA3 binding sites compared to the total catalogue of Genome-Wide Association Study hits. We then develop a medium throughput assay which combines oligonucleotide pulldown and flow cytometry to test whether such SNPs alter transcription factor binding in vitro. We find three SNPs, rs1465321, rs11135484 and rs1006353 which alter binding of T-bet in vitro. Of these, rs1465321 is associated with Crohn’s disease, coeliac disease and ulcerative colitis and is in an intron for IL18R1. Therefore, we examine the role of T-bet in IL18R1 expression, IL-18 signalling and two mouse models of disease.
| Identifer | oai:union.ndltd.org:bl.uk/oai:ethos.bl.uk:634128 |
| Date | January 2013 |
| Creators | Soderquest, Katrina |
| Publisher | King's College London (University of London) |
| Source Sets | Ethos UK |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
| Source | https://kclpure.kcl.ac.uk/portal/en/theses/the-role-of-diseaselinked-genetic-variation-in-the-regulation-of-gene-transcription(38853c53-ecf7-4c0f-b7e1-567889400c37).html |
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