Postdoctoral Fellowship: PRFB: Designing and Evaluating Plant Cell Type Specific Promoters

About This Grant

This action funds an NSF Plant Genome Postdoctoral Research Fellowship in Biology for FY 2025. The fellowship supports a research and training plan in a host laboratory for the Fellow who also presents a plan to broaden participation in biology. The title of the research and training plan for this fellowship to Alexander Borowsky is "Designing and Evaluating Plant Cell Type Specific Promoters". The host institution for the fellowship is Stanford University and the sponsoring scientist is Dr Jennifer Brophy. There are many different types of cells in plant organs like leaves, flowers, roots, and stems that either perform specialized roles in the function and development of these organs or help plants in responding to diseases and stresses like drought. Despite these differences, all cells have the same set of DNA and genes. So how come they develop and function differently? The researchers found that not all genes are active in all cell types. They switch on or off depending on which cell type needs to develop or perform a function. For example, some cells in leaves are designed to carry out photosynthesis whereas the cells in a root are needed to absorb nutrition and take water from soil. Another type of root cell in plants like potatoes function to form a tuber to store food. How these genes get turned on and off is still a mystery, but it is known to depend on stretches of DNA sequences found next to genes in the genome. This project will attempt to use artificial intelligence (AI)-based methods to help define patterns of the genetic regulatory code and predict if they play a role in the function and development of a specific cell type. The researchers will also use experiments to test these naturally occurring and combinations of new sequences predicted by AI to confirm their function in plants. This work may help improve plant varieties with better tolerance to diseases, improved yield, and bearing more nutritious fruits. In addition to doing exciting science experiments and making new discoveries, the fellowship will help the scientist develop their skills in biology, teaching, machine learning, and training students in the laboratory skills. This research will define the cis-regulatory rules governing the strength and cell type specificity of gene expression using machine learning models training on existing single-cell multi-omic (RNA and accessible chromatin) data, as well as develop new methods to validate cell type-specific promoter activity in vivo at orders of magnitude higher than existing methods: including combination reporter systems that allow for quick measurement of both promoter specificity and strength and technology to measure the cell type-specific expression strength of promoter libraries through massively parallel reporter assays. This project will advance knowledge in plant genomics and synthetic biology and is expected to provide breakthroughs in our understanding of plant genome function. Identification of novel cis-regulatory regions and engineering them to generate quantitative trait variation by driving the expression of genes to varied strengths in specific cells will provide new opportunities and tools for pathway engineering and trait improvement in crops. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.