The human genome, it turns out, is a very busy and interesting place. Rather than serving as a passive template for gene transcription, the genome is an integral part of cell function, highly sensitive to external environmental cues and capable o responding to those cues by reading and regulating itself. We have hypothesized that many human diseases characterized by chronic, low-grade inflammation, emerge because the capacity of the genome to read and regulate itself is compromised by environmentally-induced epigenetic alterations. While multiple investigations into epigenetic effects on gene transcriptio have focused on protein-coding genes, we now know that both epigenetic alterations and RNA expression occur throughout the genome, not simply within or adjacent to well-annotated genes. Thus, when our group found methylation changes associated with gene expression changes in an in vitro model of inflammation in human choriocarcinoma Jeg-3 cells, we were not surprised to find that that methylation occurred in genomic regions quite distant from the differentially-expressed genes. We are anxious to know what's in those differentially-methylated regions, as they are likely to tell us a great deal about how trophoblasts respond to inflammation on a genome-wide basis. Before we do anything else, however, we need to reproduce these data in a pathologically-relevant cell, i.e., term chorionic trophoblasts from fetal membranes. While we're doing that, we also have the opportunity to geta richer and better understanding of the trophoblast transcriptome. We propose to perform genome-wide methylation analysis and genome-wide transcriptome analysis on term chorionic trophoblasts using state-of-the art sequencing techniques. We will map RNA transcripts to the genome and correlate transcripts and transcript levels with methylation changes that occur as a result of inflammation. After 2 years, we will have an extraordinarily useful data set from which we can organize both patient-oriented and in vitro studies focusing on inflammation and functional genomics in pregnancy.
In this research, we will be studying how the genome of trophoblasts, the cells that form the barrier between mothers and infants, function. The genome of each cell type functions a little differently, and we are interested in how the trophoblast genome responds to infection and inflammation. By doing this, we hope to better understand why inflammation is so harmful to developing infants.