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bioRxiv · 10.1101/068288

Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells

Stefan Semrau·Johanna Goldmann·Magali Soumillon·Tarjei S. Mikkelsen·Rudolf Jaenisch·Alexander van Oudenaarden
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Abstract

Gene expression heterogeneity in the pluripotent state of mouse embryonic stem cells (mESCs) has been increasingly well-characterized. In contrast, exit from pluripotency and lineage commitment have not been studied systematically at the single-cell level. Here we measured the gene expression dynamics of retinoic acid driven mESC differentiation using an unbiased single-cell transcriptomics approach. We found that the exit from pluripotency marks the start of a lineage bifurcation as well as a transient phase of susceptibility to lineage specifying signals. Our study revealed several transcriptional signatures of this phase, including a sharp increase of gene expression variability. Importantly, we observed a handover between two classes of transcription factors. The early-expressed class has potential roles in lineage biasing, the late-expressed class in lineage commitment. In summary, we provide a comprehensive analysis of lineage commitment at the single cell level, a potential stepping stone to improved lineage control through timing of differentiation cues.

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Stefan Semrau, Johanna Goldmann, Magali Soumillon, Tarjei S. Mikkelsen, Rudolf Jaenisch, Alexander van Oudenaarden. 2016-08-07. Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells. https://doi.org/10.1101/068288

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