Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos

Cell. 2016 May 5;165(4):1012-26. doi: 10.1016/j.cell.2016.03.023. Epub 2016 Apr 7.


Mouse studies have been instrumental in forming our current understanding of early cell-lineage decisions; however, similar insights into the early human development are severely limited. Here, we present a comprehensive transcriptional map of human embryo development, including the sequenced transcriptomes of 1,529 individual cells from 88 human preimplantation embryos. These data show that cells undergo an intermediate state of co-expression of lineage-specific genes, followed by a concurrent establishment of the trophectoderm, epiblast, and primitive endoderm lineages, which coincide with blastocyst formation. Female cells of all three lineages achieve dosage compensation of X chromosome RNA levels prior to implantation. However, in contrast to the mouse, XIST is transcribed from both alleles throughout the progression of this expression dampening, and X chromosome genes maintain biallelic expression while dosage compensation proceeds. We envision broad utility of this transcriptional atlas in future studies on human development as well as in stem cell research.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Blastocyst / metabolism*
  • Blastocyst Inner Cell Mass / metabolism
  • Chromosomes, Human, X*
  • Dosage Compensation, Genetic
  • Female
  • Humans
  • Male
  • RNA, Long Noncoding / genetics
  • Sequence Analysis, RNA
  • Sex Characteristics
  • Single-Cell Analysis*
  • Transcriptome


  • RNA, Long Noncoding
  • XIST non-coding RNA