Characterization of transcript isoform variations in human and chimpanzee

Transcript expression and pre-mRNA processing are emerging as important mechanisms that increase the complexity of eukaryotic transcriptomes. These processes allow a genomic locus to produce a number of mRNAs and proteins with distinct properties that affect function, stability, and sub-cellular localization by controlling the rate of transcript expression, by varying the initiation or termination of transcription and by modulating the inclusion of exons (alternative splicing) in mature mRNAs. Thus, it is crucial to determine the extent of these types of variations to better understand their importance in creating organism diversity. The studies described in this thesis provide the first genome-wide estimations of how single nucleotide polymorphisms (SNPs) affect the regulation of transcript expression and pre-mRNA processing in a human population as well as between humans and chimpanzees using a microarray-based approach. We first demonstrated that transcript expression changes at the isoform level are common between two unrelated individuals and that these changes are heritable and therefore have an underlying genetic component. We then investigated what proportion was under genetic control in a normal human population by conducting a genome-wide association analysis between single nucleotide polymorphisms and transcript isoform variants. We found that 50-55% of transcript expression variation is isoform based. We also extended our comparison of human transcript isoform variation to chimpanzee. We showed that genetic substitutions in regulatory sequences are responsible for some of the isoform variations observed between these two closely related species. We ascertained that in our study these isoform variations are responsible for certain phenotypic differences mostly related to immune responses. These results constitute an important change in the way genetic variations are viewed in humans and chimpanzees and they highlight the need for broader investigation into these types of variation and how they affect gene expression. In the last two chapters of this thesis we also provide solutions for some of the methodological and analysis issues we encountered because they could be of a great benefit to scientist conducting experiments with the Exon Array.