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

Stefan Semrau,Alexander Van Oudenaarden,Rudolf Jaenisch,Johanna E Goldmann,Magali Soumillon,Tarjei S Mikkelsen

doi:10.1038/s41467-017-01076-4

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 measure the gene expression dynamics of retinoic acid driven mESC differentiation from pluripotency to lineage commitment, using an unbiased single-cell transcriptomics approach. We find that the exit from pluripotency marks the start of a lineage transition as well as a transient phase of increased susceptibility to lineage specifying signals. Our study reveals several transcriptional signatures of this phase, including a sharp increase of gene expression variability and sequential expression of two classes of transcriptional regulators. In summary, we provide a comprehensive analysis of the exit from pluripotency and lineage commitment at the single cell level, a potential stepping stone to improved lineage manipulation through timing of differentiation cues.

Highlights

Gene expression heterogeneity in the pluripotent state of mouse embryonic stem cells has been increasingly well-characterized
In summary, we leveraged a recently developed high-throughput single-cell transcriptomics method to dissect the exit from pluripotency and dynamics of lineage commitment in retinoic acid (RA) driven differentiation of mouse embryonic stem cells (mESCs) with high temporal resolution
In agreement with previous results[22] we found mESCs cultured in 2i medium11 plus LIF (2i/L) to be transcriptionally most similar to E4.5 epiblast in vivo (Fig. 4a–c)

Summary

Introduction

Gene expression heterogeneity in the pluripotent state of mouse embryonic stem cells (mESCs) has been increasingly well-characterized. Exit from pluripotency and lineage commitment have not been studied systematically at the single-cell level. We measure the gene expression dynamics of retinoic acid driven mESC differentiation from pluripotency to lineage commitment, using an unbiased single-cell transcriptomics approach. We find that the exit from pluripotency marks the start of a lineage transition as well as a transient phase of increased susceptibility to lineage specifying signals. We provide a comprehensive analysis of the exit from pluripotency and lineage commitment at the single cell level, a potential stepping stone to improved lineage manipulation through timing of differentiation cues. We set out to characterize the single-cell gene expression dynamics of differentiation, from exit from pluripotency to lineage commitment. We identify two classes of transcription factors which have likely distinct roles in the lineage decisionmaking process

Methods

Results

Conclusion