Fig. 4

High tissue divergence in translationally driven rhythms. a Venn diagram of rhythmic RPF-seq sets in kidney (yellow, n = 92) and liver (green, n = 142) after the Babel analysis indicated strong tissue specificity of translational control. b Daily profiles of RPF-seq RPKM (blue) and RNA-seq RPKM (orange) for the two genes detected as translationally regulated in both tissues in (a). c, d Circular phase histogram for the 92 (c, kidney) and 142 (d, liver) genes showing footprint rhythmicity in the organs. Note that the translational upregulation of transcripts observed at the day-to-night transition in liver was absent in kidney. e, f Heatmaps of RNA (left panels) and RPF (right panels) rhythms for the 92 and 142 genes translationally regulated in kidney (e) and in liver (f), respectively. Genes are sorted by footprint phase and expression levels are standardized by row (gene). These sets of genes showed rhythmicity in footprint abundance but no oscillation in mRNA. g, h Daily profiles of RPF-seq RPKM (blue) and RNA-seq RPKM (orange) for representative examples of translationally generated rhythms specific for liver (g) and kidney (h). For each gene, the upper panel shows the kidney data and the lower panel the liver data. Hoxd3 was not expressed in liver. i Translation efficiency (TE) around-the-clock for ribosomal protein (RP) genes expressed in liver (green, n = 86) and in kidney (yellow, n = 89). For each timepoint (ZT) boxplots represent the interquartile range and whiskers extend to the minimum and maximum TE within 1.5 times the interquantile range. Lines connect the median of each boxplot to ease visualization. Note the global TE upregulation at ZT10 in liver, whereas TEs in kidney remain high over the day