Embryonic stem cells (ESCs), derived from the inner cell mass of the blastocyst, can self-renew indefinitely and can differentiate into all derivatives of the three germ layers, making them an attractive model for regenerative medicine and disease modeling. Successful development of ESC-based therapies, however, largely depends on our understanding of the genes and pathways that constitute the genetic network governing ESC self-renewal and differentiation. ESCs maintain a plastic yet stable program of self-renewal while allowing rapid induction of alternate gene expression programs to initiate differentiation. The mechanisms that maintain this intricate homeostatic balance remain unclear and have been the subject of intense investigation. Despite the elucidation of many genes and pathways critical for the maintenance of the pluripotent state, the mechanisms that coordinate the activities of master regulators, key signaling pathways, and epigenetic features remain poorly understood, owing largely to incomplete characterization of the genetic network underlying ESCs. RNAi-based screens of nearly all genes in mouse and human ESCs have collectively revealed over 400 genes with roles in ESC maintenance. Despite the success of RNAi screens, false discovery and sensitivity remain a significant challenge, with surprisingly small overlap among screen hits from independent but related screens. The lack of concordance and the presence of unique hits in each screen suggest that the screens have not reached saturation, and that additional genes essential for ESC self-renewal and pluripotency remain to be discovered. Motivated by the need for an alternative approach for identification of key cell identity genes, we developed a computational approach that leverages relative gene expression across various cell types/states from independent perturbation experiments (genetic, exposure, differentiation, etc) to rank-order genes based on how likely they are to have a role in the maintenance of the cell identity of interest; ESCs in our case. Integrating evidence from multiple datasets using the proposed framework proved to be extremely effective in identifying several genes with previously unknown roles in ESC Biology. To understand the roles of these potential ESC regulators, we have been studying a select few to gain insights into their mechanistic roles in the maintenance of ESCs. Thus far, we have been successful in characterizing the roles of Nucleolin, and the NF-Y complex. We found that Nucleolin maintains ESC homeostasis by shielding against differentiation-inducing redox imbalance-induced oxidative stress, and the NF-Y complex facilitates chromatin accessibility for master ESC transcription factors. Collectively, these studies will provide a foundation for defining the mechanism and scope of Nucleolin and NF-Y activity within developmentally- and environmentally- responsive gene networks.
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