Fig. 4: Pan-adipocyte stalling of elongating ribosomes by A-site glutamate codons.

a Cumulative distribution of stalling score at each time point (left) and meta-gene analysis around sites with top 5% stalling score (upper right) or 47.5-52.5% stalling score (lower right). b Heat maps displaying A-site codon distribution of sites with top 5% stalling score, presented with counts (left) and their row z-scores (right). c Swarm plots showing A-site codon count of sites with top 5% stalling score. d Amino acid sequence preference of sites with top 5% stalling score at each time point. e Relative ribosome stalling of each codon site during beige adipocyte differentiation. The red dots in the left scatter plots indicate sites with differentiation-dependent ribosome stalling (odds ratio > 1, adjusted p-value < 0.01). Right pie charts depict the composition of A-site codon-encoded amino acids at differentiation-dependent stalling sites. p-values were calculated by two-sided Fisher’s exact test and adjusted by Benjamini-Hochberg method. f Amino acid sequence preference of sites where ribosome stalling was significantly increased at 8 d relative to 0 d. g Meta-gene analyses around each amino acid-coding codon group exhibit the differential ribosome occupancy at 8 d relative to 0 d in a nearby region of each codon. Small windows show the differential ribosome occupancy at upstream (left) or downstream (right) sites, as indicated by dashed boxes. h Coverage depth plots of RPF tags near exon 3 and 4 regions of Tef. In top and middle plots, the y-axis represents the average coverage depth of replicates at each indicated time point. In the bottom plot, the y-axis represents the average coverage depth normalised by the total depth of the Tef gene for each time point. i Swarm plots showing the count of A-site codon-encoded amino acids at sites with top 5% stalling score at each time point of beige adipocyte differentiation, in differentiated beige, brown, and white adipocytes, and in cold-treated inguinal white adipose tissue.