Extended Data Figure 8: Investigation of mRNA and protein secondary structure effects on mitochondrial ribosome stalling sites.

a, Identification of mitochondrial RNA secondary structure based on analysis of the mitochondrial transcript data from the dimethyl sulfate sequencing dataset published previously³⁴. R values and Gini differences were calculated to detect changes in nucleotide reactivity between the in vivo and denatured condition for the complete mitochondrial transcriptome. Coloured points indicate structured regions given in Supplementary Table 4. b, Determination of ribosome stalling sites in SHMT2-knockout HCT116 cell lines. Data points represent individual codons of all 13 mitochondrial protein-coding transcripts. For each codon, the y axis indicates the ribosome counts normalized to the gene median in RPM. The x axis indicates the ratio of normalized counts in SHMT2-knockout to normalized counts in wild-type HCT116. Two and three s.d. above the mean of all codons in the genome are indicated by the grey and black dotted line, respectively. Highlighted in red are codons with greater than 2 s.d. c, Mapping of AAG and UUG codons from SHMT2 knockout-specific ribosome stalling sites (>3 s.d.) on protein structures. For b and c, analysis is based on ribosome profiling data in Fig. 3, with two technical replicates of two independent samples. A list of identified codons and mapped AAG and UUG sites is provided in Supplementary Table 5.