Transcriptional Dynamics of the Embryonic Stem Cell Switch

Abstract

Recent ChIP experiments of human and mouse embryonic stem cells have elucidated the architecture of the transcriptional regulatory circuitry responsible for cell determination, which involves the transcription factors OCT4, SOX2, and NANOG. In addition to regulating each other through feedback loops, these genes also regulate downstream target genes involved in the maintenance and differentiation of embryonic stem cells. A search for the OCT4–SOX2–NANOG network motif in other species reveals that it is unique to mammals. With a kinetic modeling approach, we ascribe function to the observed OCT4–SOX2–NANOG network by making plausible assumptions about the interactions between the transcription factors at the gene promoter binding sites and RNA polymerase (RNAP), at each of the three genes as well as at the target genes. We identify a bistable switch in the network, which arises due to several positive feedback loops, and is switched on/off by input environmental signals. The switch stabilizes the expression levels of the three genes, and through their regulatory roles on the downstream target genes, leads to a binary decision: when OCT4, SOX2, and NANOG are expressed and the switch is on, the self-renewal genes are on and the differentiation genes are off. The opposite holds when the switch is off. The model is extremely robust to parameter changes. In addition to providing a self-consistent picture of the transcriptional circuit, the model generates several predictions. Increasing the binding strength of NANOG to OCT4 and SOX2, or increasing its basal transcriptional rate, leads to an irreversible bistable switch: the switch remains on even when the activating signal is removed. Hence, the stem cell can be manipulated to be self-renewing without the requirement of input signals. We also suggest tests that could discriminate between a variety of feedforward regulation architectures of the target genes by OCT4, SOX2, and NANOG. One key issue in developmental biology is how embryonic stem cells are regulated at the genetic level. Recent high throughput experiments have elucidated the architecture of the gene regulatory network responsible for embryonic stem cell fate decisions in human and mouse. In this work the authors develop a computational model to describe the mutual regulation of the genes involved in these networks and their subsequent effects on downstream target genes. They find that the core genetic network incorporates the functionality of a bistable switch, which arises due to positive feedback loops in the system. Also, this switch behaviour is very robust with respect to model parameters. The switch and architecture by which the genetic network regulates the downstream genes, is responsible for either maintaining the genes responsible for self-renewal on, and genes involved with differentiation off, or the opposite outcome, depending on whether the switch is on/off, respectively. The model also provides several predictions which can lead to further understanding of the network. The methods employed are fairly standard and transparent which facilitates further uncovering in future experimental investigations of genetic networks.