Single-Cell RNA-Seq Reveals Dynamic Early Embryonic-like Programs during Chemical Reprogramming

Cell Stem Cell. 2018 Jul 5;23(1):31-45.e7. doi: 10.1016/j.stem.2018.05.025. Epub 2018 Jun 21.


Chemical reprogramming provides a powerful platform for exploring the molecular dynamics that lead to pluripotency. Although previous studies have uncovered an intermediate extraembryonic endoderm (XEN)-like state during this process, the molecular underpinnings of pluripotency acquisition remain largely undefined. Here, we profile 36,199 single-cell transcriptomes at multiple time points throughout a highly efficient chemical reprogramming system using RNA-sequencing and reconstruct their progression trajectories. Through identifying sequential molecular events, we reveal that the dynamic early embryonic-like programs are key aspects of successful reprogramming from XEN-like state to pluripotency, including the concomitant transcriptomic signatures of two-cell (2C) embryonic-like and early pluripotency programs and the epigenetic signature of notable genome-wide DNA demethylation. Moreover, via enhancing the 2C-like program by fine-tuning chemical treatment, the reprogramming process is remarkably accelerated. Collectively, our findings offer a high-resolution dissection of cell fate dynamics during chemical reprogramming and shed light on mechanistic insights into the nature of induced pluripotency.

Keywords: 2C-like program; CiPSC; XEN-like cell; Zscan4; chemical reprogramming; early embryonic-like programs; genome-wide hypomethylation; pluripotency; reprogramming trajectory; single-cell RNA-seq.

MeSH terms

  • Animals
  • Cells, Cultured
  • Cellular Reprogramming / drug effects*
  • Embryonic Development / drug effects
  • Embryonic Development / genetics*
  • High-Throughput Screening Assays
  • Mice
  • Mice, Inbred C57BL
  • Mice, Transgenic
  • Pluripotent Stem Cells / cytology*
  • Pluripotent Stem Cells / drug effects*
  • Sequence Analysis, RNA*
  • Single-Cell Analysis*
  • Transcriptome