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Secondary structure of the human mitochondrial genome affects formation of deletions.

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Peer-reviewed

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Abstract

BACKGROUND: Aging in postmitotic tissues is associated with clonal expansion of somatic mitochondrial deletions, the origin of which is not well understood. Such deletions are often flanked by direct nucleotide repeats, but this alone does not fully explain their distribution. Here, we hypothesized that the close proximity of direct repeats on single-stranded mitochondrial DNA (mtDNA) might play a role in the formation of deletions. RESULTS: By analyzing human mtDNA deletions in the major arc of mtDNA, which is single-stranded during replication and is characterized by a high number of deletions, we found a non-uniform distribution with a "hot spot" where one deletion breakpoint occurred within the region of 6-9 kb and another within 13-16 kb of the mtDNA. This distribution was not explained by the presence of direct repeats, suggesting that other factors, such as the spatial proximity of these two regions, can be the cause. In silico analyses revealed that the single-stranded major arc may be organized as a large-scale hairpin-like loop with a center close to 11 kb and contacting regions between 6-9 kb and 13-16 kb, which would explain the high deletion activity in this contact zone. The direct repeats located within the contact zone, such as the well-known common repeat with a first arm at 8470-8482 bp (base pair) and a second arm at 13,447-13,459 bp, are three times more likely to cause deletions compared to direct repeats located outside of the contact zone. A comparison of age- and disease-associated deletions demonstrated that the contact zone plays a crucial role in explaining the age-associated deletions, emphasizing its importance in the rate of healthy aging. CONCLUSIONS: Overall, we provide topological insights into the mechanism of age-associated deletion formation in human mtDNA, which could be used to predict somatic deletion burden and maximum lifespan in different human haplogroups and mammalian species.

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Acknowledgements: We acknowledge Filipe Pereira and Joana Damas for discussion of the MitoBreak database, Maria Falkenberg for the discussion of the potential structure of mtDNA, and Nariman Battulin for the discussion of mtDNA Hi-C data. We acknowledge Scott Lujan and Bill Copeland for providing the metadata of the principal component analysis from their paper, Maxim Ri for editing and improving the manuscript.


Funder: EPFL Lausanne

Keywords

Aging, Contact zone, Deletions, Direct repeats, Global secondary structure, Inverted repeats, Mitochondrial DNA, Single-stranded DNA, mtDNA replication, Animals, Humans, Genome, Mitochondrial, Mitochondria, DNA, Mitochondrial, Genome, Human, Protein Structure, Secondary, DNA, Single-Stranded, Mammals

Journal Title

BMC Biol

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Journal ISSN

1741-7007
1741-7007

Volume Title

21

Publisher

Springer Science and Business Media LLC