Fig. 4
From: Multiple links between 5-methylcytosine content of mRNA and translation
Sequence context and structural characteristics of candidate m5C sites. a Base-pairing propensity meta-profile of regions surrounding candidate sites within transcripts derived from protein-coding genes. Regions around randomly selected Cs from transcribed genome regions were used as control (top). The base pairing percentage (white-to-red colour scale) of regions ± 20 nt around candidate sites are displayed within a cloverleaf structure, aligning candidate sites with the C49 structural position of tRNA (bottom). b Sequence context of candidate sites in transcripts derived from protein-coding genes (top) in comparison to all cytosines in the same transcripts (bottom). Sequence logos for sites separated by different transcript regions are shown in Fig. S7C. c Metagene density plot showing distribution of candidate sites within mature mRNAs. Each mRNA region was scaled to its median length, indicated underneath. Candidate site distribution is shown in blue, and background cytosine distribution is shown in grey. d Pie chart showing distribution of candidate sites across 5′UTR, CDS, 3′UTR and introns of transcripts from protein-coding genes. e–f Spatial enrichment analyses of candidate sites within mRNAs. Sites are placed into chosen bins as indicated on the x-axis. Site distribution across bins is compared to matching randomised cytosine sampling (Null) and the log10 Odds-ratio (OR) is plotted as a red line with the 95% confidence interval (CI) shaded. Significance of enrichment is plotted as the log10 p value by blue bars (legend given in panel e). e Distribution of candidate sites across the 5′UTR, CDS and 3′UTR of mRNA. f, g Distribution of candidate sites across the start (f) and stop (g) codon regions (from − 400 nt to + 1000 nt relative to the first position of respective codon) using a bin width of 100 nt. Note that small discrepancies in expected site numbers between panels are due to inclusion of eight sites from the ‘NMD’ RNA biotype in a, and use of different GENCODE annotation versions, i.e. v28 in (a–d) and v20 in (e–g)