Early X chromosome inactivation during human preimplantation development revealed by single-cell RNA-sequencing

Sci Rep. 2017 Sep 7;7(1):10794. doi: 10.1038/s41598-017-11044-z.

Abstract

In female mammals, one X chromosome is transcriptionally inactivated (XCI), leading to dosage compensation between sexes, fundamental for embryo viability. A previous study using single-cell RNA-sequencing (scRNA-seq) data proposed that female human preimplantation embryos achieve dosage compensation by downregulating both Xs, a phenomenon named dampening of X expression. Using a novel pipeline on those data, we identified a decrease in the proportion of biallelically expressed X-linked genes during development, consistent with XCI. Moreover, we show that while the expression sum of biallelically expressed X-linked genes decreases with embryonic development, their median expression remains constant, rejecting the hypothesis of X dampening. In addition, analyses of a different dataset of scRNA-seq suggest the appearance of X-linked monoallelic expression by the late blastocyst stage in females, another hallmark of initiation of XCI. Finally, we addressed the issue of dosage compensation between the single active X and autosomes in males and females for the first time during human preimplantation development, showing emergence of X to autosome dosage compensation by the upregulation of the active X chromosome in both male and female embryonic stem cells. Our results show compelling evidence of an early process of X chromosome inactivation during human preimplantation development.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Blastocyst / metabolism
  • Computational Biology / methods
  • Databases, Genetic
  • Embryo, Mammalian
  • Embryonic Development / genetics*
  • Female
  • Gene Expression
  • Gene Expression Profiling
  • Genes, X-Linked
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • Male
  • Molecular Sequence Annotation
  • Polymorphism, Single Nucleotide
  • Sex Factors
  • Single-Cell Analysis*
  • X Chromosome Inactivation*