This two year project leverages previous work and uses computational tools, along with published sequence and data on levels of mRNA, to hypothesize specific function for noncoding sequences in higher plants. The project takes advantage of the recent release of two important paleopolyploid genomes, maize and Brassica rapa (Chinese cabbage). Having diverged approximately 12 million years ago, each of these ancient polyploids has close relative genomes that can serve as outgroups - sorghum and the other grasses for maize and Arabidopsis, and several recently sequenced crucifers for the cabbages.
There are four objectives with the goal of developing a better understanding of the function of enhancers and cis-acting modules, those sequences that regulate gene expression in plants: 1) to develop a new application for CoGe that brings motifs and transcription factor binding sites into view when comparing the sequences of chromosomal segments. CoGe is a popular, public toolbox for visualizing and comparing sequences; 2) to discover genes with new regulatory capabilities by finding rare cases of new sequence corresponding to new patterns of expression. Finding genes that switch their patterns of genome dominance should relate to this aim; 3) to find the means by which plant regulatory DNA evolves into non-detectability without losing its function, a process known as "binding site turnover" in mammals; and, 4) to elucidate enhancer evaluation in plants by using the natural process of fractionation mutagenesis to generate specific sequences with specific functions using computational data only. Hypotheses based on the predicted enhancers will be tested using transient and stable expression of engineered reporter genes.
Broader aims of the project include a summer internship program for underserved, local high school students, and continued development of the popular CoGe website (http://genomevolution.org/CoGe/) containing applications that help find meaning when genes and genomes are compared. This project will host one or two students each summer. Additionally, this project involves improvements to the CoGe suite of free, on-the fly applications now powered by iPlant (www.iplantcollaborative.org/) that will provide broad access to the broader scientific community.
