Fig. 1: Decreased density of translating ribosomes on OXPHOS complex-coding mRNAs during beige adipocyte differentiation.

a Assessment of the steady-state levels and changes in mRNAs, translated mRNAs, and proteins of individual genes during the beige adipocyte differentiation to interrogate transcriptional and post-transcriptional controls. Oil Red O staining of differentiating cells was performed to track differentiation. Representative images among biological triplicates are presented. b Distribution of 5’ end of RPFs near the start and stop codons. Genes that have the most abundant RPFs in each dataset are shown. c Volcano plot of ribosome density fold change during differentiation (left) and cumulative distribution of normalised fold change of mRNA, translated mRNA, and protein levels for genes with decreased or increased ribosome density (ribosome density-differentially expressed genes; RD DEGs) (right). d Gene set enrichment analysis (GSEA) with ribosome density. Each circle represents a GO cellular component term. e Protein-protein interaction network and heat maps displaying ribosome density fold change of genes included in leading edge subsets from the three most significantly enriched terms by GSEA. f Ribosome density at each time point for each indicated MitoCarta pathway. g Normalised fold change of mRNA, translated mRNA, and protein levels for each indicated MitoCarta pathway. Statistical tests and tools: edgeR for FDR-adjusted p-values of (c); GSEApy for NES and FDR-adjusted p-values of (d); two-sided paired t-test for p-values of (f); and two-sided Kolmogorov-Smirnov test for p-values of (g). *p < 0.05, **p < 0.01, ***p < 0.001. Box plots of (f, g) include boxes that extend from first to third quartile with median line and whiskers with 1.5 x interquartile range.