DISSERTATION RESEARCH: Evolution of transcription factor specificity and cooperativity

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This project will combine evolutionary genetics and biochemistry to dissect how a fundamental system of gene regulation in animals has evolved. It will explore how specific control molecules that can turn particular genes on or off have evolved. This will be done by tracing the ancient evolutionary changes in the structure of critical control molecules and their corresponding genes. It will integrate laboratory tests of protein to DNA binding with computer analysis of molecular evolution. Broader impacts include training of a graduate student in the integration of computer and experimental approaches to molecular evolution. Dissemination of techniques in statistical programming through software boot camps and science outreach presentations will also increase the representation of women in inter-disciplinary science.Transcription is the first step in the expression of any gene and hence is thought by many to be the fundamental step in regulation of the genome. Proper regulation of an organism's genes depends on the correct pairing of thousands of different proteins, called transcription factors, with their respective genes. Understanding how new control pairing occurs without loss of original functions is central to regulation in complex genomes. Steroid receptors are biologically important transcription factors. They are also an excellent model system for the study of transcriptional control since they consist of two related but functionally divergent groups that differ in the way they bind to specific genes. One group predominantly binds to a major groove of the DNA molecule; the other group binds to both major and minor grooves of DNA. To understand the evolution of DNA binding and recognition in these two groups this research utilizes ancestral sequence reconstruction, along with functional laboratory assays. Computational analysis of receptor function and evolution will be combined with laboratory protein binding assays to explore the hypothesis that the shape of the DNA minor groove as well as the DNA sequence was important in the evolution of novel specificity. The proposed experiments will delineate the genetic and physical mechanisms by which different modes of DNA recognition diversified in this group of molecules.