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Fig. 5 | Genome Biology

Fig. 5

From: Translational contributions to tissue specificity in rhythmic and constitutive gene expression

Fig. 5

Tissue specificity in core clock gene expression at the level of RNA abundance and translation. a Scatterplot of transcript abundance (RNA-seq) vs. footprint abundance (RPF-seq) for liver (grey) and kidney (sepia) (n = 10,289), where core clock components are highlighted (kidney, dots with dashed circles). Coloured dashed lines join the relative locations of each core clock gene between organs. b Bar graph of the average RPKM ratio between kidney and liver for the main circadian core clock genes, at the level of mRNA abundance (dark shades) and ribosome footprints (light shades) suggested that translational compensation led to higher similarity at the level of protein biosynthesis (RPF) for several core clock genes. c Hierarchical clustering of the organs’ RNA and RPF profiles based on the similarities of the core clock genes expression patterns (n = 12, genes shown in B). The height of the branches represents weighted average distances over the considered genes (see ‘Methods’). Note that RPF rhythms in two organs were more similar than RNA and RPF rhythms within an organ. d Hierarchical clustering as in (c) based on the genes detected as rhythmic throughout (n = 178, see Fig. 3c). When compared to the clustering based on core clock gene expression patterns in (c), this rhythmic gene set showed an organ-based clustering. e Scatterplot of kidney/liver ratios of uORF vs. CDS translation efficiencies for genes containing AUG-initiated translated uORFs in both organs (n = 1199). uORF-containing core clock genes are highlighted. As also shown in Additional file 1: Figure S8E, differential uORF usage could not globally explain differences in CDS TE across organs (note the lack of negative correlation between the two variables, R2 = 0.005, p = 0.008). As an exception, the lower uORF TE of Nr1d2 might have a role in setting relatively higher CDS TE in kidney. f RPF (blue) and RNA (orange) reads mapping along the Nr1d2 transcript in kidney (top) and liver (bottom) for the timepoint of maximal CDS translation (ZT10). 5′ UTR and CDS are shown in full, but for better visualization only a portion of the 3′ UTR (the same length as the 5′ UTR) is shown. Red boxes indicate the predicted AUG-initiated translated uORFs. Right panels show that, similar to the CDS, the uORFs showed clear frame preference, indicative of active translation

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