Figure 1: Ribo-Seq in parallel with RNA-Seq reveals extensive translational regulation of key signalling components.

(a) Double-fluorescent T-Cre reporter system allows marking of mesodermal lineage. T-Cre mediates the excision of the ubiquitously expressed mTomato cassette which results in expression of mGFP. Cross section shows distribution of GFP⁺ mesodermal cells in the E11.5 embryo. Arrows and labels indicate NT (neural tube), Som (somites), and FL (forelimbs). (b) The distribution of log₂TE (translational efficiency) over mRNA abundance (log₂ normalized reads) in the mesodermal lineage at E11.5, with the densities of data points indicated as colours. 1,186 and 185 genes comprising 9.8 and 1.5% of the total analysed genes are defined as TE-low and TE-high respectively, whose TE is significantly lower or higher than the median (false-discovery rate (FDR)<0.05) and the difference at least threefolds. (c) The network of enriched GO categories (biological process) among TE-low genes clusters into several functional groups represented by circles of different colours. Each node represents one enriched GO category colour-coded by its adjusted P-value (FDR) of enrichment, with the size of the node proportional to the number of associated TE-low genes. Edges indicate similarity (Kappa score >0.4) between the two connected GO categories. Edges with an arrowhead indicate a regulation relationship between nodes. The number of TE-low genes is shown in the parenthesis underneath the name of each GO term. The most significantly enriched GO category from each group is designated as the leading group term and highlighted in italic. Signal transduction and cell communication categories are highlighted with a yellow outline.