RET Supplement to NSF Award MCB-1243849

This request is for an RET Supplement to NSF Award MCB-­?1243849 to support the involvement in this project of Mr. Patrick Thomas, a teacher at Franklin-­?Simpson High School in Franklin, KY. Mr. Thomas will contribute to the computational and bioinformatics aspects of the project, with an emphasis on the development of computational tools to identify differentially-­?utilized poly(A) sites using high throughput DNA sequencing data. By the beginning of the period during which Mr. Thomas will join the lab, a dataset consisting of high throughput cDNA sequences that query the mRNA-­?poly(A) junction will have been completed; this dataset will include samples prepared from total Arabidopsis mRNA as well as from RNA associated with purified polysomes. Mr. Thomas will assist in the analysis of this data with the goal of identifying genes whose poly(A) site usage differs in polysomal mRNAs compared with total mRNAs. These genes and sites will represent sequences associated with differential translation, and thus sites whose differential usages reflect an added layer of gene regulation. Mr. Thomas will also design and execute wet-­?bench studies (primarily 3'-­?RACE and quantitative RT-­?PCR) to confirm several examples. This activity will help in setting up analogous research exercises and projects at Franklin-­?Simpson High School.