Grant: Doctoral Award - Frederick Banting and Charles Best Canada Graduate Scholarships

Transcription factors (TF) are proteins that bind specific regions of our DNA and thereby turn genes on/off. Many diseases, including cancers, are caused by misregulation of gene expression, so fully understanding how a TF functions is key to understanding disease progression. The three-dimensional structures (conformations) of many TFs are known, allowing for limited predictions regarding how these proteins recognize the DNA sequences of the genes that they regulate. However, some of the most important genes controlled by a TF have sequences that do not fit these consensus predictions. One possible explanation for this apparent anomaly is that proteins are very flexible and can easily adopt alternative shapes that are capable of binding variant DNA sequences. The goal of my research is to test this hypothesized explanation by studying how the ensemble of conformations that an individual TF can adopt affects its ability to bind DNA. Starting with a model TF called ETV6, I will use the tools of protein engineering to create mutants that are more flexible than the normal form found in our cells. A more flexible protein can rapidly interconvert between many different shapes, whereas an inflexible protein persists in fewer conformations. I predict that the additional conformations adoptable by the ETV6 mutants will assist in binding non-consensus DNA sequences. To test this prediction, I will use high-throughput methods to compare the DNA-binding preferences of the mutant versus parental forms of ETV6, and to quantitatively measure the strengths of their binding interactions. Through these investigations, I will be able to show how the flexibility of a TF influences the set of genes that it controls. This will help us diagnosis how aberrant TFs can lead to diseases and may lead to new therapies to manipulate their conformations and thereby dictate how they regulate gene expression.