Pioneer Factor Interactions at Tissue-Specific Enhancers in Pluripotent Cells
Embryonic stem cells (ESC) hold great promise for the treatment of debilitating diseases and for use as research tools to elucidate the molecular mechanisms underlying many diseases. Current knowledge is already quite advanced and has allowed researchers to begin making use of stem cells for clinical applications. However, the full clinical potential of ESC cannot be realized without a better understanding of their fundamental properties. Increased fundamental knowledge is necessary to help overcome technical limitations in our ability to differentiate ESC into clinically useful cell types and to enhance the efficiency and consistency with which differentiated cells obtained from patients in need of stem cell-based therapies can be reprogrammed to an ESC-like state. ESC lines are of great value because of their unique ability to continually divide on laboratory tissue-culture dishes while maintaining pluripotency, which is defined as a capacity to differentiate into almost any cell type. Pluripotency is known to be dependent on the expression of key genes whose protein products function by turning on many other genes that are needed to achieve the pluripotent state. Considerable attention has also been focused on genes encoding proteins that regulate the differentiation of ESC into specific cell lineages. These genes possess intriguing properties that keep them silent in ESC, but poised for activation when the ESC receive appropriate differentiation signals. The research proposed in this application focuses on a third class of genes that have received relatively little attention from researchers studying pluripotency: genes expressed only in differentiated cell types, which generally remain silent until long after the ESC have differentiated into a specific cell lineage. Although prior models suggested that the cascade of events leading to the activation of these typical tissue-specific genes does not begin until the ESC have differentiated, recent evidence from our laboratory and others supports a hypothesis in which the competence of these genes for expression in differentiated cells is dependent on specific marks established at their DNA regulatory regions in the pluripotent state. The proposed examination of this hypothesis will reveal whether the proper marking of tissue-specific genes in ESC is essential for their differentiation into clinical useful cell types and tissues and for the proper functioning of mature ESC-derived tissues.
The research proposed in this application will increase our knowledge of the fundamental properties of embryonic stem cells (ESC) that are important for their pluripotency, defined as their capacity to differentiate into almost all human cell types and tissues. ESC hold great promise for treating or leading to a better understanding of human diseases, which would greatly benefit the State of California and its citizens. However, despite this potential and the rapid progress that has been made toward its fulfillment, our incomplete knowledge of the properties of ESC critical for their pluripotency has limited their utility. Previous studies of the key determinants of pluripotency have focused on genes that are actively expressed in ESC or that play a role in the initial decision to differentiate into specific cell lineages. The research proposed in this application focuses on an emerging hypothesis that pluripotency also requires the active marking of typical tissue-specific genes, which generally remain silent until long after the ESC have begun to differentiate. The proper marking of these genes in ESC may be essential for their competence for activation in differentiated tissues. A rigorous evaluation of this hypothesis will contribute to efforts to identify the sources of variability in the differentiation potential of ESC lines and to develop improved methods for the reprogramming of differentiated cells to a pluripotent state.