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

Summary

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.

Graphical Abstract

Highlights

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  Transcriptomes of 1,529 individual cells from 88 human preimplantation embryos

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  Lineage segregation of trophectoderm, primitive endoderm, and pluripotent epiblast

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  X chromosome dosage compensation in the human blastocyst

Abstract

A comprehensive transcriptional map of human preimplantation development reveals a concurrent establishment of trophectoderm, epiblast, and primitive endoderm lineages and unique features of X chromosome dosage compensation in human.