Embryonic stem (ES) cells are endowed with two distinguishing properties, they can regenerate themselves indefinitely (self-renewal) and simultaneously enable development of all cells in the body (pluripotency). Broadly, the long-term objective of my laboratory is to identify and characterize transcription factors and nuclear proteins that regulate self-renewal and pluripotency. In one project, we are investigating the transcriptional and epigenetic regulation of the nuclear factors GDF3, Dppa3 and the transcription factor Nanog. These genes lie in the same genomic region, or locus, and this Nanog locus appears to constitute a functional module that is important for pluripotency. Nanog locus gene expression and chromatin structure are both highly dependent on the expression of another pluripotency transcription factor, Oct4. Recent discoveries have shown that Oct4 and Nanog are amongst a small group of genes that can reset the developmental clock and reprogram adult cells to an embryonic pluripotent state. The study of these induced pluripotent stem (iPS) cells will be essential for shedding insight on the molecular machinery responsible for the maintenance of self-renewal and pluripotency. Using a combinatorial approach, we are investigating the genetic changes that enable reprogramming to a pluripotent state. A better understanding of iPS cells will be essential for their eventual use toward the correction of hematologic and other disorders in human patients.
With less than 5 percent of the mammalian genome responsible for encoding genes, we know that many of the proteins vital for pluripotency bind DNA at cis- regulatory elements far away from known promoter regions. Another topic of study in the laboratory is determining how pluripotency factor bound enhancers bridge long distance interactions within the Nanog locus, and how this regulates gene expression. Using methods to analyze chromatin structure in pluripotent cell populations, we are studying whether genes that occupy collinear positions within the genome may also exhibit transcriptional co-regulation. To study these questions and achieve our goals, we are employing the tools of molecular biology, genetics, biochemistry and proteomics. Additionally, we are using conditional gene targeting approaches and RNA interference (RNAi) to engineer new ES cell lines and mouse models.