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Fig. 1 | Genome Biology

Fig. 1

From: A rare codon-based translational program of cell proliferation

Fig. 1

mRNAs required for cell proliferation are enriched in rare codons and are poorly adapted to tRNA pools. a NIH-3T3 cells with a stably integrated FUCCI system were sorted according to the cell cycle phase, and the corresponding transcriptomes were profiled by mRNA sequencing. The scatter plot shows the expression of AmCyan and mCherry in individual cells. The percentage of cells in each cell cycle phase is depicted. b Boxplots showing relative usage of synonymous glycine-encoding codons across all genes, or in genes expressed preferentially in either G1 or G2/M phases. Shown are the t and P values determined by the unpaired, two-tailed, Welch t test comparing the codon usage of G1 genes to that of G2/M genes. c Heatmap showing the t value (G2M/G1 codon score) for all codons. Codons that are preferentially used in G2/M genes have positive codon scores, whereas codons enriched in G1 genes have negative codon scores. The amino acid encoded by each codon is shown with a single-letter code: F, phenylalanine; L, leucine; S, serine; Y, tyrosine; C, cysteine; P, proline; H, histidine; Q, glutamine; R, arginine; I, isoleucine; T, threonine; N, asparagine; K, lysine; V, valine; A, alanine; D, aspartate; E, glutamate; G, glycine. d Boxplots showing the distribution of the minimum free energy (MFE) for RNA folding of the translation initiation region ([− 40, + 40] nucleotides with respect to the start codon) of G1- and G2/M-enriched mRNAs. Shown is the P value determined by the non-parametric Mann-Whitney U test. e Scatter plot depicting the fraction of G1- and G2/M-enriched mRNAs with G/C at the third nucleotide position in the first 300 codons. f Boxplots showing the distribution of tRNA adaptation index for G1- and G2/M-enriched mRNAs. Shown is the P value determined by the non-parametric Mann-Whitney U test. g, h Boxplots showing the distribution of the transcriptome-wide usage (weighted by transcript expression (g) or relative adaptiveness to tRNA pools (h) of the codons that are preferentially used (|t value|> 3) in genes associated with a specific cell cycle phase (G1, n = 22 codons, G2/M, n = 29 codons). Shown are the P values determined by the non-parametric Mann-Whitney U test. All boxes extend from the 25th to 75th percentiles (inter-quartile range (IQR)), horizontal lines represent the median, and whiskers indicate the lowest and highest datum within 1.5*IQR from the lower and upper quartiles, respectively

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