Annoroad Appears at Nature Series Again Together with the Institut Curie, Revealing Mechanism of Chromosome Reactivation

Nature Communocations

At the time of the 150th anniversary of Marie Curie’s birthday, Annoroad made exploration of reactivation mechanism of X chromosomes together with science researchers from Curie Institute in France, and they discovered that different genes would have reactivation at different stages, and the genes of rapid reactivation were under regulation and control of transcription factors, while the genes of slow reactivation would always have H3K27me3 enrichment. The research achievement was published on the international top journal Nature Communications on November 3, 2017. 

During forming process of embryo of female mammals, one of the two X chromosomes comes into inactivation, and completes the dosage compensation effect. For the mice, X chromosome inactivation (XCI) mainly consists of two stages: the first stage is inactivation of imprinting promoting of paternal X chromosome (Xp), and this inactivation status is sustained in trophectoderm (TE) and primitive entoderm (PrE), but in ectoderm cells of inner cell mass (ICM), Xp will have reactivation again, and then enter the progress of the second stage of XCI. Previously, Annoroad has made many explorations on the mechanism of X chromosome inactivation together with science researchers from Curie Institute in France (reference link address: Annoroad’s masterpiece of this year: scRNA-seq publishing in NAT STRUCT MOL BIOL ;Nature’s blockbuster | focus on Annoroad’s Hi-C: Reveal secrete of structural characteristics of mouse inactivated X chromosome), but as for how the Xp in the inner cell mass revokes the inactivation status and has reactivation, the mechanism is still unknown. In the newly-published article this time, in-depth exploration of molecular mechanism of X chromosome reactivation has been made in the method of scRNA-seq. 

Sample selection: 34 embryo samples of male mice

Library type: scRNA-seq library constructed based on Smart-seq2 amplification method

Sequencing platform: Illumina HiSeq platform

Research thought


Summary of highlights

By RNA-FISH and immunofluorescence method, it is discovered that in blastocyst development stages from E3.5 to E4.0, there is a cell subset with decreasing Xist RNA expression and H3K27me3 enrichment degree in the inner cell mass, and it is speculated to be ectoderm precursor cell. 


Early and late blastocysts inner cell mass Xist RNA expression and H3K27me3 model analysis

Through conducting scRNA-seq toward the E3.5 and E4.0 inner cell mass, and making principal component analysis (PCA) of the acquired data combining with the published trophectoderm (TE) and primitive entoderm (PrE) transcriptome data, it is discovered that there is obvious heterogeneity between E3.5 and E4.0 cells, and there are two cell subsets available in either the early cells and the late cells. However, based on expression of multi-potential differentiation factors, E4.0 inner cell mass consists of two big obvious categories: endoderm cell and ectoderm cell. And the cluster analysis based on differentially expressed genes has also drawn the consistent result.



Cluster analysis based on single cell transcriptome data

According to the single cell transcriptome data of E3.5 and E4.0 inner cell mass, the detected X chromosome genes are divided into early reactivation gene, late and very-late reactivation gene and inactivation escape gene.


X chromosome gene reactivation model analysis

In E4.0 stage, the inner cell mass consists of two big categories: primitive endoderm cells and ectoderm cells, and only the ectoderm cells would have X chromosome reactivation phenomenon based on decrease in Xist expression and H3K27me3 enrichment degree.


X chromosome reactivation model

Article summary

In this article, researches are conducted toward inner cell mass of male mouse embryos by scRNA-seq, RNA-FISH, immunofluorescence method and other method, and it is discovered that different genes would have reactivation at different stages, and the early reactivated genes are under regulation and control of transcription factors, and are mainly contained in binding domain of transcription factors, and have lots of H3K4me3 modification forms, while the late reactivated genes would always have H3K27me3 enrichment, thus it has been expounded the molecular mechanism of X chromosome reactivation.

As the leader for integrated solution of domestic single cell sequencing technology, Annoroad Genomics has enriched its single-cell multi-omics research solutions to three big omics (genomics, transcriptomics and epigenomics), which cover single-cell genome sequencing, single-cell exon sequencing, scRNA-seq, single-cell whole transcriptome sequencing, single-cell whole genome methylation sequencing, and G&T-Seq. These technologies could serve different research fields and research strategies in a targeted and accurate way, and enable the science researchers to understand the heterogeneity between the cells in a deeper way. 


  1. Borensztein M, Okamoto I, Syx L, et al. Contribution of epigenetic landscapes and transcription factors to X-chromosome reactivation in the inner cell mass[J]. Nature Communications, 2017, 8(1): 1297.


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