RUI- Whole Genome Analysis of Hepatic Gene Silencing

Eastern Illinois University, Charleston IL

Investigators

Abstract

Abstract It is generally believed that genes are under the control of positive-acting factors and, therefore, silent genes are those that simply have yet to be activated. However, there is substantial evidence that this lack-of-activation hypothesis is too simplistic to explain gene control. In this project, the phenomenon of gene silencing will be analyzed using whole-genome microarray analysis. Genome-wide gene expression in liver-derived cells will be compared with that observed in cell types that have silenced liver gene expression (cell hybrids and hepatoma variant cells). Validation of data will be carried out by analysis of gene expression of potentially interesting genes using cell-based read-out assays to screen for restoration or repression of liver gene function. The goal is to identify genes involved in gene silencing in cell hybrids and hepatoma variants. Specifically, genes that show at least 5-fold differences in expression and encode proteins that contain signature motifs associated with transcriptional regulatory proteins will be analyzed. These analyses will include placement of genes into classes depending on DNA sequence similarities to genes of known function. Finally, candidate regulatory genes will be tested for either activation or repression of target genes. Broader Impact Undergraduate college students will play an essential role in each aspect of this research. Microarray data sets obtained will be used in two aspects of undergraduate teaching and training. First, this data will be used as a tool in an existing molecular biology lab course (required for Biology majors) to understand the scope of tissue-specific gene expression and ask open-ended, broad questions about the link between gene expression and cellular identity. Using a team approach, students will also be able to identify and classify candidate genes based on homologies to genes of known function through BLAST searches, thus gaining valuable experience in assessing gene function. Secondly, several undergraduate students will carry out research projects in the PI's lab to screen candidate genes and even test candidate genes for functional rescue of phenotypes. Data obtained will be compiled into poster presentations at regional meetings as well as in publications. This will provide valuable experience in modern molecular biology and prepare students for graduate or professional schools.