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

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.

Lineage specification and pluripotency revealed by transcriptome analysis from oocyte to blastocyst in pig

“…Generally, accumulation of H3K27me3 results in XC inactivation in females for dosage compensation. 35,41 Pereira et al supposed the dosage compensation in human is more likely contributed to XC inactivation. In mouse, the paternal XC is inactive in early cleaving embryos, followed by reactivation in the ICM of blastocyst (excluding TE), and then random XC inactivation happens in the epiblast of the female embryo.…”

Epigenetic aberrations in human pluripotent stem cells

“…However, recent analyses of early human embryos indicate that XIST is expressed in human ICM cells along with apparent dosage compensation (Petropoulos et al, 2016). Nevertheless, there is still a debate as to whether in these cells, X-linked genes are expressed mostly monoallelically, representing initiation of XCI, or biallelically, reflecting the dampening of expression by an unknown mechanism (Petropoulos et al, 2016;Moreira de Mello et al, 2017).…”

Dosage compensation in human pre‐implantation embryos: X‐chromosome inactivation or dampening?

“…Recently, De Mello and colleagues used a novel pipeline to investigate the same scRNA-Seq dataset of human pre-implantation embryos reported by Petropoulos et al [6] and provided evidence for initiation of X-inactivation [7] (Fig 1). In their analysis, genes in the pseudo autosomal regions (PAR) of the X-chromosome were excluded as they are known to escape X-inactivation.…”

“…However, X-chromosome dynamics in human pre-implantation embryos remains elusive, largely due to the restricted availability of human embryos and technical difficulties. Two recent studies, by Petropoulos et al [6] and De Mello et al [7], used singlecell RNA-Sequencing (scRNA-Seq) to investigate dosage compensation in human pre-implantation embryos and yielded conflicting models: X-dampening versus X-inactivation. One study showed progressive accumulation of XIST on one of the X-chromosomes along with the inactivation of X-linked genes in pre-implantation female embryos [3].…”

“…In addition, potential influences of different embryo sources and culture conditions may be other underlying causes of these conflicting results. Two recent studies, by Petropoulos et al [6] and De Mello et al [7], used singlecell RNA-Sequencing (scRNA-Seq) to investigate dosage compensation in human pre-implantation embryos and yielded conflicting models: X-dampening versus X-inactivation. In this Opinion, we provide some critical insights into these recent findings and discuss some enduring questions.…”