Figure 5: Snapshots of translational landscapes of developing mammalian embryos reveal dynamic translational control of signalling between tissues.

(a) Schematic illustration of an E11.5 embryo. The neural tube (NT), in dark green, and forelimb (FL), in yellow, were microdissected and assessed for differences in translational efficiency (TE) at a genome-wide level by Ribo-Seq and RNA-Seq. (b) Scatter plot of Δlog₂ in TE over Δlog₂ in mRNA between the NT and FL. NT-TE-higher and FL-TE-higher are genes with significantly higher TE in NT (FDR<0.2 and Δlog₂TE<−1) or higher TE in FL (FDR<0.2 and Δlog₂TE>1), respectively. The vertical dash lines mark the region with no significant change in the mRNA levels in between (−1<Δlog₂ mRNA<1). (c) Pie chart shows the number and percentage of genes having higher TE in the FL (yellow), higher TE in the NT (dark green) and no significant difference in TE (grey). Genes with distinct TEs are further divided according to the changes in the mRNA levels, shown in the column chart. (d) log₂ change in the percentage of mRNAs associated with actively translating polysomes determined by quantifying mRNA in the heavy polysome fractions and normalized by its total. Ptch1-1b represents the predominant isoform of Ptch1 in both in NT and FL (Supplementary Fig. 8), identified by 5′RACE. Error bars represent s.d. (t-test, **P<0.01; *P<0.05, n≥5). (e) Δlog₂TE between NT and FL from Ribo-Seq and RNA-Seq analysis. (f,g) Scatter plot of Δlog₂TE between tissues over the mRNA abundance (log₂mRNA(normalized reads)) in (f) NT and (g) FL. (h) Shown is the distribution of Δlog₂ in RPFs over the Δlog₂ mRNA between NT and FL at E11.5. (i) Comparison of the probability density distribution of Δlog₂ in mRNA (green) and RPFs (blue) reveals a significantly greater change in the RPFs than mRNAs between the tissues. (b–i) Colour key: higher TE in the FL (yellow), higher TE in the NT (dark green) and no significant difference in TE (grey).