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. 2016 Sep 19;5:e19127. doi: 10.7554/eLife.19127

Figure 6. Dynamics of X-linked gene expression in preimplantation embryos.

(A) X/A expression profile in males. Male data were collected from males of RlimKO/WT and XistKO datasets. For each embryo, the total FPKM expression of X-linked genes was divided by the total FPKM expression of autosomal genes. Shown is the average X/A values for each developmental stage. The increase of 1.58-fold in X/A values from the 4-cell stage to E4.5 is highly significant (P<10–11; Student’s t-test). (B) Comparison of gene expression profiles from chromosomes 1 to 19 and X during male pre/peri-implantation development. Data were collected from male embryos of both datasets. At each developmental stage the total FPKM expressed from each chromosome was divided by the total FPKM expression of all autosomal genes. Values obtained for each chromosome at the 4-cell stage are set to 1. (C) Dynamics of the relative gene expression expressed from single chromosomes in male embryos. The total FPKM/total number of annotated genes of each chromosome was divided by the total FPKM of all autosomal genes/total number of autosomal genes. Male data were collected from all males of both datasets. Note that expression from the X is markedly lower at early stages (around x0.5), increasing to x0.77 to that of the average autosome (1.0; dotted line) by E4.5. (D) Female and male X/A expression profiles normalized to annotated genes. The total FPKM/total number of annotated genes on the X was divided by the total FPKM of all autosomal genes/total number of annotated autosomal genes. Female genotypes are indicated. (E) The E4.5/4-cell stage ratios of X/A values are shown for WT/WT, XistWT/Δ and RlimΔ/Δ females as well as males. P values (Student’s t-test) are indicated; n.s. = not significant. (F) Comparison of X/A values according to gender: F/M ratios of X/A values at the 4-cell and E4.5 stages are shown for WT/WT, XistWT/Δ and RlimΔ/Δ. Error bars indicate SEM.

DOI: http://dx.doi.org/10.7554/eLife.19127.012

Figure 6.

Figure 6—figure supplement 1. X/A profile in male mouse embryos comparing data obtained by single embryo RNA-seq (see Figure 6A) with data obtained by single-cell RNA-seq (Deng et al., 2014).

Figure 6—figure supplement 1.

Total FPKM of X-linked genes were divided by total autosomal FPKM. For the Deng et al. dataset, to ensure male gender only cells with high total Y-linked gene expression >5 FPKM (late 2-cell and 4-cell stages) and >50 (8-cell to E4.5) were considered. Early, mid and late blastocyst stages (Deng et al., 2014) were incorporated at E3.25, E3.75 and E4.25, respectively. Note the similar upregulation of X-linked genes in both datasets.
DOI: http://dx.doi.org/10.7554/eLife.19127.013