Proper regulation of gene expression is essential in ensuring an organism's function, fitness and thus survival. Cells possess many regulatory mechanisms for the control of gene expression. Variation at any level of this regulation can contribute to variation in gene expression that can ultimately result in differences in morphology, physiology and behavior that are the root cause of many human diseases including heart disease, neurodegenerative disease and cancer. This proposal is focused on the regulation of transcription, the first step in gene expression and arguably the most tractable experimental system. The rate of transcription is determined by the interaction of transcription factor (TF) proteins that bind to regulatory DNA sequences of each gene and act as activators or repressors to modulate gene expression level. Each gene is tightly controlled by networks of regulatory interactions that contain all the genes in the genome and are inherently complex and difficult to enumerate and quantify. Additionally, the structure, connections and regulatory relationships of genes are highly context dependent, capable of dramatic change in response to intrinsic or extrinsic environmental cues. One of the best-studied regulatory networks is that of the baker's yeast Saccharomyces cerevisiae, yet despite numerous studies designed to identify the TF-target gene connections in this network, very little is known about the quantitative relationship between TF expression level and the resultant changes in the expression levels of target genes. This relationship, termed the gene regulation function (GRF), has only been quantified in detail in a small number of studies that focused on individual pairs of TF and how they regulate a single target gene. Because we have so few examples of the GRF, fundamental questions remain about this relationship and almost nothing is known about how the GRF changes in response to environmental differences. This proposal will fill this knowledge gap by titrating the expression level of a well-studied TF (RAP1) that has diverse roles in the the cell and regulates hundreds of genes, to determine how the location of DNA binding changes and therefore the specific regulatory connections it makes in response to altered TF abundance and the ultimate effect TF abundance has on target gene expression levels. By determining the GRF for hundreds of TF-target relationships we will dramatically improve our understanding of this critically important aspect of how gene expression works and gain unprecedented insight into the dynamic nature of the GRF in response to environmental change, which should have impacts on many areas of biological science and especially human disease. Furthermore, this project will provide dozens of undergraduate students the opportunity of engaging in a course-based research project where they will participate in scientific discovery that yields skills in bioinformatics programming, training in scientific thinking, writing experience, and ultimately result in authorship on generated manuscripts. Through this student research experience, we aim to increase the retention of underrepresented groups in STEM, provide transferrable scientific skills and begin building human network connections for the next generation of scientists.
Gene expression, defined in its simplest form as the process by which DNA genotype is converted into functional molecular machines that give rise to organismal traits or phenotypes, is fundamental to all aspects of biology and alterations in gene expression lead to changes in morphology, physiology and behavior that are frequently the root cause of disease states in humans. Despite its universal importance in biology, fundamental questions remain about some of the most basic rules governing how transcription of a gene is controlled, including how changes in the abundance of regulatory factors are quantitatively manifested in the expression levels of their direct target genes. In this proposal I will fill this knowledge gap by titrating the expression level of the yeast transcription factor RAP1, determine the resulting effects on where it binds in the genome, how this influences the expression level of its target genes and how both are dynamic in response to environmental change.
