The molecular characterisation of mitochondrial DNA deficient oocytes using a pig mode

STUDY QUESTION: What are the molecular differences between mitochondrial DNA (mtDNA)-deficient and mtDNA-normal oocytes and how does mitochondrial supplementation alter these? SUMMARY ANSWER: Changes to DNA methylation in a 5' cytosine-phosphate-guanine 3' (CpG) island in the mtDNA-specific replication factor (DNA polymerase gamma (POLG)) of mtDNA-deficient oocytes mediates an increase in mtDNA copy number by the 2-cell stage that positively modulates the expression of nuclear genes, which affect cellular and metabolic processes, following autologous mitochondrial supplementation. WHAT IS KNOWN ALREADY: Too few copies of mtDNA in mature oocytes can lead to fertilisation failure or preimplantation embryo arrest mtDNA-deficient oocytes that progress to blastocyst express genes associated with poor cellular and metabolic processes, transcriptional activation and mitochondrial biogenesis. STUDY DESIGN, SIZE, DURATION: Using a pig oocyte model, we assessed mtDNA-deficient and mtDNA-normal oocytes during in vitro maturation for mtDNA variants and levels of DNA methylation in POLG. We supplemented mtDNA-deficient oocytes with autologous populations of mitochondria to determine if there were changes to DNA methylation in POLG that coincided with increases in mtDNA copy number. We assessed metaphase II mtDNA-deficient and mtDNA-normal oocytes by RNA sequencing to identify differentially expressed genes and compared their profiles to blastocysts derived from mtDNA-normal, mtDNA-deficient and supplemented mtDNA-deficient oocytes. PARTICIPANTS/MATERIALS, SETTING, METHODS: mtDNA variant analysis (n = 24), mtDNA copy number (n = 60), POLG gene expression (n = 24), and RNA sequencing (n = 32 single; and 12 pooled cohorts of n = 5) were performed on oocytes and embryos. DNA methylation of a CpG island in POLG was determined quantitatively by pyrosequencing on oocytes to 2-cell embryos (n = 408). Bioinformatics tools were used to assess differences between mtDNA-normal and mtDNA-deficient oocytes and between mtDNA-normal and mtDNA-deficient oocytes and supplemented oocytes and their blastocyst stage equivalents. MAIN RESULTS AND THE ROLE OF CHANCE: Whilst mtDNA-deficient oocytes regulated variants less stringently during maturation (P < 0.05), there were no differences in the ratio of variants in mature-stage oocytes. However, mtDNA-normal mature oocytes had significantly more molecules affected due to their higher copy number (P < 0.0001). Normal mature oocytes differently DNA methylated a CpG island in POLG compared with mtDNA-deficient oocytes (P < 0.01). Supplementation of mtDNA-deficient oocytes modulated DNA methylation at this CpG island leading to a mtDNA replication event prior to embryonic genome activation inducing significant increases in mtDNA copy number. RNA-Seq identified 57 differentially expressed genes (false discovery rate (FDR) < 0.05) between the two cohorts of oocytes with blastocyst stage gene expression altered by supplementation of mtDNA-deficient oocytes (P < 0.05) including genes associated with metabolic disorders. One key factor was branched chain amino acid transaminase 2 (BCAT2), a regulator of amino acid metabolism and associated with diabetes. LARGE SCALE DATA: Sequence data are available on the NCBI Sequence Read Archive under the project number PRJNA422295. RNA sequencing data were deposited into NCBI Gene Expression Omnibus, under the accession number GSE108900. LIMITATIONS, REASONS FOR CAUTION: Whilst this work was conducted in a species that is highly relevant to human reproduction, the outcomes need to be tested in human oocytes and blastocysts prior to clinical application. WIDER IMPLICATIONS OF THE FINDINGS: The outcomes demonstrate a mechanism of action following mtDNA supplementation of mtDNA-deficient oocytes that results in improved gene expression at the blastocyst stage of development.