Gene Order Polymorphisms in Yeast (2008)

Undergraduates: Frederick Mann, Dina Faddah

Faculty Advisor: Jason Lieb
Department: Biology

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DNA polymorphisms across populations are well-documented, as are the molecular events of point mutations and changes in gene copy number. However, the transposition of genes from one chromosomal location to another is poorly understood. Additionally, it is known that genetic location can influence gene expression, through both chromatin states and regulatory element distribution. One of the major implications of transpositions is their role in deleterious recombination. Such events play roles in color blindness, neurodegenerative disorders, and infertility. The scope of this project is to design a method for mapping all of the transpositions across an entire genome. We combined two microarray-based techniques to develop a high-throughput method of identifying and locating transpositions in Saccharomyces cerevisiae. Southern Blotting and PCR techniques were used to confirm the validity of our method. The following experiments were performed on genomic DNA resulting from a cross between two strains of yeast: one very similar to the sequenced strain, the other known to have many transpositions in its genome. Under our most stringent criteria we found six transpositions ranging from 1.5 kilobases to 13.5 kilobases each. Our focused analysis with PCR and Southern Blotting targeted the largest of these six transpositions. The data obtained confirm the success of our array-based methods. Interestingly, the PCR analysis allowed us to detect a several kilobase inversion within this largest transposed segment. Data from several reactions indicate that this inversion occurred prior to transposition.