Evidence for multi-copy Mega-NUMTs in the human genome.

Area of Science:

• Human Genetics
• Molecular Biology
• Mitochondrial DNA Research

Background:

• Maternal inheritance of mitochondrial DNA (mtDNA) is a fundamental concept in human genetics.
• Recent claims of biparental mtDNA inheritance in individuals with mitochondrial disorders necessitate further investigation.
• Distinguishing true mtDNA inheritance patterns from artifacts is crucial for accurate genetic research and diagnostics.

Purpose of the Study:

• To investigate the presence of mixed mitotypes in healthy individuals from a family pedigree.
• To determine if observed mixed mitotypes are due to biparental mtDNA inheritance or nuclear DNA insertions (NUMTs).
• To establish a reliable method for excluding NUMTs in mtDNA research and diagnostics.

Main Methods:

• Sequencing of mtDNA using Sanger and Massively Parallel Sequencing in multiple tissues.
• Generation of mtDNA-depleted ρ° cells from skin biopsies.
• Fluorescence in situ hybridization and quantitative PCR to analyze NUMT sequences and copy numbers.

Main Results:

• Mixed mitotypes were observed in eight out of eleven healthy individuals.
• Hair shafts and thrombocytes exclusively showed the maternal haplogroup V mitotype.
• Skin-derived ρ° cells revealed a haplogroup U4c1 mitotype, consistent with nuclear DNA insertions (Mega-NUMTs).
• Evidence for repetitive, full mitogenome Mega-NUMTs matching haplogroup U4c1 was found in multiple tissues.

Conclusions:

• Multi-copy Mega-NUMTs can artifactually mimic biparental mtDNA inheritance, potentially confounding research and diagnostics.
• Hair shaft mtDNA sequencing is a reliable method to differentiate true mtDNA inheritance from NUMT interference.
• This finding has significant implications for the interpretation of mtDNA sequencing data in various research and clinical settings.