Extended Data Fig. 9: Translation efficiency of genes with allelic-biased RNA expression.

For all plots, boxes correspond to interquartile range and the horizontal lines indicate the median. The whiskers extend from the hinge to at most 1.5 times the interquartile range. P-values are calculated using the two-sided Wilcoxon rank sum test. Translation efficiency is defined by average ribosome occupancy (MII n = 5, 1-cell n = 5, 4-cell n = 3, 8-cell n = 4) divided by average RNA expression (MII n = 4, 1-cell n = 4, 4-cell n = 2, 8-cell n = 4) a, Translation efficiency is plotted for two bi-allelic genes (Anapc7 and Plpp5), two maternally biased genes (Tesc and Tubg2) and two paternally biased genes (Prkcz and Shc3). Vertical bars indicate 95% confidence intervals of bootstrap sample based variability in translation efficiency. Horizontal lines depict the median translation efficiency of all bi-allelic genes. b, Translation efficiency of unbiased (bi-allelic), paternally and maternally biased genes are plotted. c, We define a high-confidence set of allelic-biased transcripts that are supported by more than one SNP (Methods). The scatter plot, on the left, shows the paternal ratios of the genes in 4-cell (x-axis) and 8-cell (y-axis) stages. Genes are colored by their allelic bias and unbiased genes are colored in gray. d, A nearest neighbor matching method was used to select a subset of bi-allelic genes with matched distribution of RNA expression and CDS length compared to the allele-specific genes (Methods). e,f, The genes with allele-biased expression at the 4-cell and 8-cell stages were compared to other genes with respect to their translation efficiency at the 1-cell and MII stages. The bi-allelic genes were matched to allele-specific ones with respect to RNA expression levels and CDS lengths. g,h For each transcript, the x-axis represents the mean RPKM in RNA-seq and the y-axis is the corresponding mean translation efficiency. Genes with allelic expression bias are colored.