Publication Date

April 2018


Joseph Coolon


Molecular Biology&Biochemistry


English (United States)


In the 1990s and the first decade of the 2000s, much of molecular genetic research focused on genome sequencing. Now, in the post-genome era, inquiry has shifted to attempting to understand how these genes are expressed and how they are regulated. In Saccharomyces cerevisiae, the Repressor Activator Protein 1 (Rap1) transcription factor (TF) binds to 5% of the genome (Lieb et al. 2001) and is thought to be a major regulator of gene expression. In an effort to expand our understanding of genetic regulatory networks and the specific roles of the Rap1 protein, we analyzed RNA-seq data generated from assays done in yeast on the Rap1 TF. Other less high-through put experiments have been done to study where Rap1 binds in the genome and the protein?s effects at specific loci, but a genome-wide expression study had yet to be performed. Additionally, because the protein is essential for cell viability, no group has been able to examine what happens to downstream gene expression when Rap1 is knocked out. We devised a way to titrate the expression of the RAP1 gene by using a tet-titratable promoter, allowing us to examine the downstream effects of decreasing expression of RAP1 using genome-wide RNA-seq. The previous research indicates that Rap1 plays a significant regulatory role at telomere-proximal genes, silent mating loci genes, glycolytic genes and ribosomal protein genes. Our objectives were to assess gene expression patterns at these sites and across the genome that emerge as a consequence of altered TF expression levels. Overall, we found that Rap1 plays a significant role in activating the ribosomal protein genes, but it may not be as significant a regulator of glycolytic genes, telomere-proximal genes and silent mating loci genes as previously thought.

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