Transcription Factor Competition Allows Embryonic Stem Cells to Distinguish Authentic Signals from Noise

Abstract

Stem cells occupy variable environments where they must distinguish stochastic fluctuations from developmental cues. Here, we use optogenetics to investigate how the pluripotency network in embryonic stem (ES) cells achieves a robust response to differentiation cues but not to gene expression fluctuations. We engineered ES cells in which we could quantitatively ontrol the endogenous mechanism of neural differentiation through a light-inducible Brn2 transgene and monitor differentiation status through a genome-integrated Nanog-GFP reporter. By exposing cells to pulses of Brn2, we find that the pluripotency network rejects Brn2 inputs that are below specific magnitude or duration thresholds, but allows rapid differentiation when both thresholds are satisfied. The filtering properties of the network arise through its positive feedback architecture and the intrinsic half-life of Nanog, which determines the duration threshold in the network. Together our results suggest that the dynamic properties of positive-feedback networks might determine how inputs are classified as signal or noise by stem cells.

Modeling heterogeneity in the pluripotent state: A promising strategy for improving the efficiency and fidelity of stem cell differentiation

“…In this model, the authors also found other important genes associated to pluripotency ( Tbx3 , Klf4 , Esrrb , and Sal4 ), which constitute checkpoints in the PGRN, demarcating the transition toward differentiation 4. In another study 22, the authors analyze how PSCs filter out stochastic gene expression fluctuations, arising in the heterogeneous pluripotent state that include expression of lineage‐specific genes alongside pluripotency regulators 3. A detailed quantitative analysis of the response of the regulatory circuit formed between Nanog , Oct4 , and Sox2 to the fluctuations of Brn2 , which determines Nanog expression for triggering neural cell commitment 22, shows that Nanog responds to the fluctuations in Brn2 expression in different subpopulations of ESCs like a two‐state switch.…”

“…In another study 22, the authors analyze how PSCs filter out stochastic gene expression fluctuations, arising in the heterogeneous pluripotent state that include expression of lineage‐specific genes alongside pluripotency regulators 3. A detailed quantitative analysis of the response of the regulatory circuit formed between Nanog , Oct4 , and Sox2 to the fluctuations of Brn2 , which determines Nanog expression for triggering neural cell commitment 22, shows that Nanog responds to the fluctuations in Brn2 expression in different subpopulations of ESCs like a two‐state switch. In pluripotent cells expressing high levels of Nanog , fluctuations below a 100‐fold increase of Brn2 are considered as noise and do not cause a response of the cells.…”

“…In pluripotent cells expressing high levels of Nanog , fluctuations below a 100‐fold increase of Brn2 are considered as noise and do not cause a response of the cells. However, Brn2 induction above this threshold disrupts the Oct4 / Nanog / Sox2 pluripotency complex, which generates a sharp response causing a significant silencing of Nanog , priming cells toward differentiation 22. It was also found that this circuit integrates Brn2 fluctuations based upon both magnitude and duration of the input, and the rapid response is highly dependent on Nanog transcript lifetime 22.…”

“…It has been suggested that different topologies of pluripotent gene regulatory networks maintain the heterogeneous molecular states characteristic of individual PSCs 60. Recently, different studies have addressed this important question by integrating single cell expression and perturbation data for identifying the underlying PGRNs 4, 16, 22, 61, which are involved in the stabilization of the pluripotent state and lineage commitment 62, 63. In most of these studies, topological analyses of PGRNs have identified feed forward loops (FFLs) linked to regulation of the balance between self‐renewal and differentiation.…”

“…The mechanisms underlying gene expression heterogeneity in the pluripotent state are still not well understood, and evidence suggests that gene fluctuations could arise from stochastic noise in gene expression regulatory mechanisms 18, 19, 20, 21. These fluctuations in gene expression are possible due to a permissive chromatin configuration across the genome of PSCs 22, allowing stochastic expression of lineage‐specific and differentiation‐promoting genes even before cell‐fate commitment 3. A central challenge nowadays is to characterize the transcriptional states of different phenotypic stem cell subpopulations, and the mechanisms that control their stability and promote transitions among them 5.…”