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UBC Theses and Dissertations

The genomic organisation and transcriptional regulation of natural killer receptor genes Wilhelm, Brian Thomas

Abstract

The objective of my thesis was to better characterise the transcriptional regulation of genes within the natural killer gene cluster (NKC). As a first step in analysing why different NKC genes are expressed at different frequencies, we attempted to sequence the promoter region of many Ly49 genes. The resulting sequence comparison showed that the promoter region of all of the genes were too similar to draw any conclusions about what regions might be important, although the inclusion of the expressed human Ly49 gene showed that some of the sequence conservation might be significant. In addition, 5' RACE was performed on 4 genes to map their transcriptional start point (TSP). This work revealed that the promoter region of these genes had highly heterogeneous transcriptional start points. We next utilised mouse genomic sequence available in public databases in order to assemble a sequence contig for the Ly49 gene cluster which could be used to study the gene arrangement and genomic features. This work resulted in a detailed analysis of the Ly49 gene content in B6 mice as well as a hypothetical model for the evolution of the gene cluster. In addition, a large stretch of unique repetitive elements was identified at one end of the cluster which is hypothesised to play a role in the atypical expression pattern of Ly49e. Finally, we examined the transcriptional regulation of the murine CD94 gene in more detail. These experiments showed that this gene has two promoter regions and that lymphoid cell types use them differentially. This work also demonstrated that preferential usage of a particular promoter by a cell type was established during fetal development, but that the use of the distal promoter by freshly isolated NK cells could be drastically reduced by culturing them in media containing IL- 2. The conclusion of this research was that the CD94 gene has a complex promoter structure, and that several features are shared with the human CD94 gene.

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