High-throughput Mapping of Protein Energy Landscapes Using Novel Microfluidic Tools
Dr. Polly Fordyce
Department of Biochemistry and Biophysics, UCSF
February 27, 2014
Foege N130A, Wallace H. Coulter Seminar Room
Precise regulation of gene expression drives virtually all cellular processes. To achieve this regulation, transcription factor proteins bind to genomic DNA regulatory elements, where they either recruit (or block) additional proteins to activate (or repress) transcription. Although new technologies are cataloguing DNA regulatory elements at an unprecedented rate, much less is known about how transcription factors recognize and bind DNA elements or contact additional proteins. To address this, we developed a microfluidic platform that enables quantitative measurement of binding affinities between a single transcription factor and up to 4,000 DNA sequences in parallel, facilitating both transcription factor target site discovery and detailed characterization of binding preferences. Using this platform, we have studied a variety of transcription factors from multiple species, including humans, Saccharomyces cerevisiae, and Candida albicans. These studies have revealed surprising evidence that even structurally simple transcription factors can recognize multiple distinct target sites via conformational rearrangements, and have additionally led to the discovery of an entirely new family of transcription factors thought to have evolved de novo. In recent work, we have also developed a new microfluidic platform for producing potentially very large libraries of spectrally encoded beads, laying the foundation for high-throughput studies of protein-protein interactions. With these tools, we are now poised to reverse engineer the rules that specify gene expression, with far-reaching impacts for understanding how mutations in regulatory elements cause disease, reconstructing genetic networks, and designing new circuits for synthetic biology.
Dr. Fordyce received undergraduate degrees in both physics and biology from the University of Colorado, graduating summa cum laude. As a graduate student, she received her Ph.D. in physics from Stanford University for work done in Steve Block’s laboratory developing new single-molecule techniques and assays and applying them to study kinesin family motor proteins. As a postdoctoral fellow, Dr. Fordyce has worked in Joe DeRisi’s laboratory at the University of California, San Francisco developing new microfluidic tools that allow quantitative measurement of protein binding interactions.