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

• Sara‐Jane Dunn ^[3] ; Meng Amy Li ^[1] ; Elena Carbognin ^[2] ; Austin Smith ^[1] ; Graziano Martello ^[2]
  1. [1] University of Cambridge

     University of Cambridge

     Cambridge District, Reino Unido

     
  2. [2] University of Padua

     University of Padua

     Padova, Italia

     
  3. [3] 1 Microsoft Research Cambridge UK; 2 Wellcome‐MRC Cambridge Stem Cell Institute University of Cambridge Cambridge UK

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• Localización: EMBO journal: European Molecular Biology Organization, ISSN 0261-4189, Vol. 38, Nº. 1, 2019, pág. 5
• Idioma: inglés
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• Resumen

  • 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.