Supplementary Figure 3: Gene validation by RNA-FISH and chromosome-wide representation of parental expression ratio. | Nature Structural & Molecular Biology

Supplementary Figure 3: Gene validation by RNA-FISH and chromosome-wide representation of parental expression ratio.

From: Xist-dependent imprinted X inactivation and the early developmental consequences of its failure

Supplementary Figure 3

(a) Nascent RNA FISH using probes recognizing Xist (signal in green) and Atrx (signal in red) RNAs on a 16C female embryo. DAPI is in blue. Right pictures are enhanced pictures of two individual blastomeres. Percentage of nuclei showing pinpoints of nascent transcripts by RNA FISH from Xp and Xm has been assessed and summarized as the median + s.e.m. under the picture. Normalization of the primary transcript detection frequency obtained for the paternal (Xist RNA-associated) allele in female embryos was achieved thanks to the detection frequency obtained for the maternal allele in male embryos at the same stage. Number of embryos and single cell processed are indicated under each genotype. Scale bars represent 10μm.

(b) Heatmaps are shown representing the mean of allele-specific expression of X-linked genes, from Oocytes to blastocysts in CB and BC crosses. Strictly maternally expressed genes (allelic ratio ≤0.15) are represented in red and strictly paternally expressed genes (allelic ratio ≥0.85) in blue. Color gradients are used in between and genes have been ordered by genomic position. Oocytes and 2C stage data, as well as strain-specific gene expression data, have been included, in addition to the heatmaps for the stages shown in Figure 2.

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