We analyze new and existing expression and transcription factorbinding data to characterize gene regulatory relations in mouse ES cells (ESC). In addition to confirming the key roles of Oct4, Sox2, and Nanog, our analysis identifies several genes, such as Esrrb, Stat3, Tcf7, Sall4, and LRH-1, as statistically significant coregulators. The regulatory interactions among 15 core regulators are used to construct a gene regulatory network in ESC. The network encapsulates extensive cross-regulations among the core regulators, highlights how they may control epigenetic processes, and reveals the surprising roles of nuclear receptors. Our analysis also provides information on the regulation of a large number of putative target genes of the network.cis-regulatory module ͉ transcriptional regulation R ecent research has established the fundamental roles of several transcription factors (TF), namely Oct4, Sox2, and Nanog, in the self-renewal and pluripotency of mouse ES cells (ESC) (reviewed in ref. 1). In addition to these three ''master regulators,'' a large number of additional TF have been implicated to play a role in ESC biology, including Stat3, Esrrb, Tbx3, Foxd3, LRH-1, Klf4, Myc, P53, and Sall4 (2-8). The emerging picture is that these TF regulate each other and interact with epigenetic control factors to form a large gene regulatory network in ESC. However, the regulatory interactions within this network have not been worked out. Here, we analyze new and published gene expression and location (ChIP-chip/ChIP-PET) data sets to reconstruct a part of this network computationally. We identify collaborating TF that may work with the master regulators to activate gene expression in ESC, as well as collaborating factors that may play a repressive role. Our analyses also predict the cis-regulatory sequences (down to the location of binding sites) that mediate the combinatorial control of these TF on their target genes.
Results
Genes Correlated or Affected by Oct4Expression. Several lines of evidence point to Oct4 as one of the most important regulators in ESC. Null mutants of Oct4 are not viable and fail to form a functional inner cell mass (9). A twofold increase or decrease of Oct4 levels leads to differentiation into primitive endoderm/ mesoderm or trophectoderm, respectively (10). ESC show a very dramatic change in gene expression when subject to RNAi knockdown of Oct4, as compared with RNAi knockdowns of other essential regulators (3). Moreover, Oct4 is one of the four regulators that together can reprogram fibroblast cells to pluripotent cells with ESC-like morphology (6). No other ESC regulator shares these properties. Because a transcriptional target is likely to have expression correlated with its regulator, the first step in our analysis was to identify genes whose expression strongly correlates with that of Oct4. To do this, we used an ES line harboring a GFP reporter driven by the Oct4 distal enhancer (11). FACS based on this reporter allowed the purification of subpopulations of cells according to their Oct4...