Evidence Suggesting Absence of Mitochondrial DNA Methylation

Methylation of nuclear genes encoding mitochondrial proteins participates in the regulation of mitochondria function. The existence of cytosine methylation in the mitochondrial genome is debated. To investigate whether mitochondrial DNA (mtDNA) is methylated, we used both targeted- and whole mitochondrial genome bisulfite sequencing in cell lines and muscle tissue from mouse and human origin. While unconverted cytosines were detected in some portion of the mitochondrial genome, their abundance was inversely associated to the sequencing depth, indicating that sequencing analysis can bias the estimation of mtDNA methylation levels. In intact mtDNA, few cytosines remained 100% unconverted. However, removal of supercoiled structures of mtDNA with the restriction enzyme BamHI prior to bisulfite sequencing decreased cytosine unconversion rate to <1.5% at all the investigated regions: D-loop, tRNA-F+12S, 16S, ND5 and CYTB, suggesting that mtDNA supercoiled structure blocks the access to bisulfite conversion. Here, we identified an artifact of mtDNA bisulfite sequencing that can lead to an overestimation of mtDNA methylation levels. Our study supports that cytosine methylation is virtually absent in mtDNA

Additional file 4: Figure S5. of Endurance training remodels sperm-borne small RNA expression and methylation at neurological gene hotspots

Observed abundance of all sRNA subtypes at the three different time points, columns represent different participants. (TIFF 218 kb

Additional file 4: Figure S5. of Endurance training remodels sperm-borne small RNA expression and methylation at neurological gene hotspots

Observed abundance of all sRNA subtypes at the three different time points, columns represent different participants. (TIFF 218 kb

Cols bleus : hebdomadaire de la Marine française

05 mai 19901990/05/05 (N2078)-1990/05/05

Additional file 5: Figure S6. of Endurance training remodels sperm-borne small RNA expression and methylation at neurological gene hotspots

Boxplot of the expression levels of selected subsets of sRNA (miRNA, green; tRNA, red; piRNA, purple) are presented at the three different time points for each individual. Data are presented as log-transformed sequence reads per million (1 = Untrained, 2 = Trained, 3 = Detrained). (TIFF 973 kb

Additional file 9: Tables S7 and S8. of Endurance training remodels sperm-borne small RNA expression and methylation at neurological gene hotspots

Gene ontology analysis of gene located at proximity of the Trained (S6) or the Detrained (S7) DMRs. GO: Gene ontology term. FDR: False Discovery Rate. (ZIP 61 kb

Additional file 6: Tables S1 – S4. of Endurance training remodels sperm-borne small RNA expression and methylation at neurological gene hotspots

Differences in sRNA expression profiles in the spermatozoa between the Untrained, Trained and Detrained state. miRNAs, piRNAs, Repetitive Elements, tRNAs and mRNA fragments differentially expressed between Untrained and Trained, Trained and Detrained, Untrained and Detrained. logFC: Log2 Fold Change; logCPM: Log2 counts per million; LR: Likelihood ratio; feature: sRNA name; FDR: False Discovery Rate. (ZIP 1010 kb