A common molecular logic determines embryonic stem cell self-renewal and reprogramming.

Sara‐Jane Dunn,Graziano Martello,Austin Smith,Meng Amy Li,Elena Carbognin

doi:10.15252/embj.2018100003

Sara‐Jane Dunn, Graziano Martello + Show 3 more

Open Access

https://doi.org/10.15252/embj.2018100003

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Abstract

During differentiation and reprogramming, new cell identities are generated by reconfiguration of gene regulatory networks. Here, we combined automated formal reasoning with experimentation to expose the logic of network activation during induction of naïve pluripotency. We find that a Boolean network architecture defined for maintenance of naïve state embryonic stem cells (ESC) also explains transcription factor behaviour and potency during resetting from primed pluripotency. Computationally identified gene activation trajectories were experimentally substantiated at single‐cell resolution by RT–qPCR. Contingency of factor availability explains the counterintuitive observation that Klf2, which is dispensable for ESC maintenance, is required during resetting. We tested 124 predictions formulated by the dynamic network, finding a predictive accuracy of 77.4%. Finally, we show that this network explains and predicts experimental observations of somatic cell reprogramming. We conclude that a common deterministic program of gene regulation is sufficient to govern maintenance and induction of naïve pluripotency. The tools exemplified here could be broadly applied to delineate dynamic networks underlying cell fate transitions.

Highlights

Over the last 10 years, a multitude of protocols have been developed that allow the conversion of one cell type into another (Graf &Enver, 2009)
We define a set of experimental results, such as the effect of genetic perturbations, which serve as constraints to identify those models from the Abstract Boolean Network (ABN) that recapitulate expected behaviour
The set of consistent models is defined as a constrained Abstract Boolean Network, which is subsequently used to generate predictions of untested molecular and cellular behaviour

Summary

Introduction

Over the last 10 years, a multitude of protocols have been developed that allow the conversion of one cell type into another (Graf &Enver, 2009). Bona fide iPSCs are, like murine embryonic stem cells (ESCs), competent to form blastocyst chimaeras and are considered to occupy a state of naıve pluripotency similar to that in the pre-implantation embryo (Nichols & Smith, 2009; Boroviak et al, 2015) This unique identity is determined by a self-reinforcing interaction network of TFs. Experimental and computational efforts have led to circuitry mapping of the core TF program that maintains ESC self-renewal under defined conditions (Chen et al, 2008; Niwa et al, 2009; MacArthur et al, 2012; Dunn et al, 2014; Herberg & Roeder, 2015; Rue & Martinez Arias, 2015; Yachie-Kinoshita et al, 2018)

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