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CisRegulation Info
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A genome is composed of thousands of genes, and each gene encodes instructions to make a protein. Together, these proteins do the work of the cell. In order to use genes, the cell transcribes temporary gene copies and then translates the information into a protein. The use of genes in a cell is described by when they are transcribed, how much is transcribed and translated, and where in the cell the protein is localized. For many genes, exactly when, how much, and where the gene is expressed is extremely important, and mistakes can lead to low fitness or disease. For these genes, any variation from these parameters has important selective consequences for the cell. For other genes, when, how much, and where the gene is expressed is not always important: this type of variation is neutral. In order to map out this fundamental architecture behind gene regulation and identify the evolutionary processes that are responsible, my research focus is to investigate the consequences of variation in gene regulation. My lab has three ongoing experimental research projects in the model organism Saccharomyces cerevisiae (budding yeast) that address complementary questions about variation in gene regulation. Our research uses novel approaches that will yield significant insights into these questions.
1. Fitness Landscapes of Gene Expression
In our first project we are measuring the extent that changes in the expression of genes result in changes in the fitness (reproductive capacity) of cells. We alter the expression level of a given gene using a repressible promoter, and measure the resulting fitness by competing the cells with altered expression against cells with normal expression. The result is an expression-fitness function that indicates the precise relationship between expression level and fitness. For example, the shape of the fitness function for a gene can facilitate an interpretation of the amount of variation in expression among individuals in a population, where flatter functions are expected to show more variation. We have completed measurement of the expression-fitness function for a gene, Lcb2, that is essential for the production of lipids in the cell, and are readying a manuscript that describes our results (described below). We are now using next-generation sequencing technology to scale up this analysis for a larger number of genes.
2. Forbidden Protein Interactions
In a cell, a given protein is expressed at a certain time, place and level so that it can perform its function. However, there are thousands of other proteins also present in the cell, and some proteins interfere with each other. The focus of our second experimental project is on understanding the extent that this interference has shaped the expression patterns of genes by looking at pairs of genes that are naturally anti-correlated in their expression patterns. We artificially turn on these genes at the same time and location in the cell to see if there is a high fitness cost for expressing them at the same time, in comparison to the cost of turning them on separately. We also test to see if the proteins physically interact with each other, indicating direct interference. This project will allow us to estimate the extent that avoidance of negative interactions in a cell is important in shaping the evolution of regulatory patterns.
3. Transcriptional Truth vs. Translational Consequence
A cell must be able to respond and adjust to a varying environment, and changing gene expression is the major way that cells respond. In particular, cells have regulatory programs that enable response and protection from stressors such as heat, acidity and infection. Persistent response genes have changed expression for the duration of a stress, while transient response genes respond initially but then reset to their background level. In our third experimental project, we are investigating the contribution of variation in persistent versus transient responses to a cell's fitness. We predict that variation in transient gene transcription responses will be neutral if they are brief enough that protein levels are not affected, but that even very brief transcriptional responses will be meaningful if there is a resulting change in the amount of translated protein. To address this, we are mapping the relationship between gene transcription responses and protein translational responses. Our initial survey of a dozen genes reveals responses in both categories.