Dysfunctional regulation of transcription and chromatin state can confer selective growth advantages onto cells and are a primary characteristic of cancer progression. This project will develop a kinetic theory for the role of chromatin remodeling during activation of the zygotic genome and test the theory with precise, quantitative measurements. This approach requires an analytically tractable system; we will work with Drosophila embryos. My graduate training in physics, single-molecule microscopy and data analysis gives me the necessary background to tackle this question. The DePace lab has extensive experience with the experimental tools necessary to interrogate this process, and recently developed two kinetic modeling frameworks that will play a critical role in developing theoretical models specific to this problem. Our research strategy will involve perturbing regulatory DNA sequence in MS2 reporter genes and manipulating transcription factor levels to assess the impact on the dynamics of transcription using lightsheet-based fluorescence imaging of live embryos. We will contextualize these experimental results using theory. My goal is to develop the experimental and theoretical tools necessary to interrogate eukaryotic transcription at the level of quantitative rigor that has been successful in bacteria. It is widely recognized that predictive models of transcriptional regulation in eukaryotes will be transformative for personalized medicine and bioengineering. We therefore expect this work to have a broad impact both technically and conceptually.
Chromatin remodeling and associated transcriptional regulation dictates zygotic genome reprogramming during development, cellular differentiation, homeostatic transcription during adulthood and altered gene expression during aging and disease. This proposal will develop a kinetic theory for the role of chromatin remodeling during activation of the zygotic genome and test the theory with precise, quantitative measurements. By helping us gain a predictive understanding of a regulatory mechanism that exists in all eukaryotes, I predict this work will have a broad impact both technically and conceptually.
| Vincent, Ben J; Staller, Max V; Lopez-Rivera, Francheska et al. (2018) Hunchback is counter-repressed to regulate even-skipped stripe 2 expression in Drosophila embryos. PLoS Genet 14:e1007644 |
