Extended Data Figure 8: The influence of miRNAs on ribosomes, mRNA abundance and tails in the early zebrafish embryo.

a, The relationship between changes in tail length at 4 hpf (as determined by PAL-seq) and changes in mRNA abundance at 6 hpf (as determined by RNA-seq), after injecting miR-155 (left) or miR-132 (right). Changes observed between miRNA- and mock-injected embryos are plotted for predicted miRNA target genes (red, genes with ≥ 1 cognate miRNA site in their 3′ UTR) and control genes (grey, genes that have no cognate miRNA site yet resemble the targets with respect to 3′-UTR length). Lines indicate mean changes for the respective gene sets; statistically significant differences between the gene sets for each of the two parameters are indicated (*P ≤ 0.05; **P < 10⁻⁴, one-tailed Kolmogorov–Smirnov test). Because injected miRNAs partially inhibited miR-430–mediated repression, genes with a site complementary to nucleotides 2–7 of miR-430 were not considered. All data were normalized to the median changes observed for the controls. b, The relationship between changes in ribosome-protected fragments (RPFs) and changes in mRNA levels (top), and between changes in RPFs and changes in tail lengths (bottom) after injecting miR-132. At 2, 4 and 6 hpf, embryos were analysed using ribosome profiling, RNA-seq and PAL-seq. Plots are as in Fig. 5a.