Understanding how genes are switched on and off is a problem of central importance in biology. Within genes, dedicated regions called enhancers, consist of a patchwork of short sequences that bind to regulators of gene activity, called transcription factors. It is this binding that determines when, where, and how strongly a gene will express its function. The organization of enhancers is dauntingly complex. Despite four decades of extensive study, many general properties of enhancers remain obscure. For example, it is still nearly impossible to predict enhancer function from the DNA sequence or to construct an artificial DNA enhancer that would turn the gene on in the right kind of a cell in response to a right kind of a signal. This project will specifically address this problem. It will study in detail the composition and organization of an enhancer of a gene in a model organism, roundworm Caenorhabditis elegans. Its ultimate goal is to engineer an artificial enhancer that could direct gene expression in specific cells in C. elegans. Not only would this serve as a powerful demonstration of the understanding of basic rules of enhancer organization and function, but also be an important step toward designing biological systems with specific performance characteristics. The work on this project will be also used to provide research experience for Chicago-area school teachers, including those that work in schools located at the communities that are underrepresented in science.
The goal of this project is to investigate in detail the organization and function of an enhancer of a C. elegans gene. General lack of fine-resolution data (at the level of individual binding sites) for any C. elegans gene, hampers the use of this powerful model organism for understanding enhancer structure/function and computational modeling approaches. The project will start with an experimental dissection of a short enhancer expressed in a small number of neurons. These empirical data will be evaluated against comparative sequence data of orthologous and co-regulated enhancers to infer particularly conserved features of sequence composition and structural organization. Finally, a series of artificial enhancer elements will be generated. They will test specific hypotheses by replacing native enhancer sequences with different synthetic ones that retain basic features inferred to be important from the prior experimental and computational analyses. The aim is to construct a family of enhancers that retain little of the original sequences and yet produce a largely correct expression pattern. This work will advance understanding of enhancer function/organization, inform comparative genomic analyses of regulatory regions, and contribute to design of synthetic genetic circuits in multicellular eukaryotes. In a continuing collaboration with the outreach office of the Institute for Genomics and Systems Biology at the University of Systems Biology at the University of Chicago, the project will interact with the area high school teachers, giving them an opportunity for summer research experience and helping to develop teaching modalities that cover modern genetics.
