Open Access Research article

Association of G-quadruplex forming sequences with human mtDNA deletion breakpoints

Dawei W Dong12, Filipe Pereira34, Steven P Barrett5, Jill E Kolesar1, Kajia Cao6, Joana Damas3, Liliya A Yatsunyk5, F Brad Johnson7 and Brett A Kaufman1*

Author Affiliations

1 Department of Animal Biology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA

2 Penn Genome Frontiers Institute, University of Pennsylvania, Philadelphia, PA, USA

3 Institute of Molecular Pathology and Immunology, University of Porto, Porto, PORTUGAL

4 Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, PORTUGAL

5 Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA, USA

6 Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA

7 Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA

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BMC Genomics 2014, 15:677  doi:10.1186/1471-2164-15-677

Published: 13 August 2014

Abstract

Background

Mitochondrial DNA (mtDNA) deletions cause disease and accumulate during aging, yet our understanding of the molecular mechanisms underlying their formation remains rudimentary. Guanine-quadruplex (GQ) DNA structures are associated with nuclear DNA instability in cancer; recent evidence indicates they can also form in mitochondrial nucleic acids, suggesting that these non-B DNA structures could be associated with mtDNA deletions. Currently, the multiple types of GQ sequences and their association with human mtDNA stability are unknown.

Results

Here, we show an association between human mtDNA deletion breakpoint locations (sites where DNA ends rejoin after deletion of a section) and sequences with G-quadruplex forming potential (QFP), and establish the ability of selected sequences to form GQ in vitro. QFP contain four runs of either two or three consecutive guanines (2G and 3G, respectively), and we identified four types of QFP for subsequent analysis: intrastrand 2G, intrastrand 3G, duplex derived interstrand (ddi) 2G, and ddi 3G QFP sequences. We analyzed the position of each motif set relative to either 5' or 3' unique mtDNA deletion breakpoints, and found that intrastrand QFP sequences, but not ddi QFP sequences, showed significant association with mtDNA deletion breakpoint locations. Moreover, a large proportion of these QFP sequences occur at smaller distances to breakpoints relative to distribution-matched controls. The positive association of 2G QFP sequences persisted when breakpoints were divided into clinical subgroups. We tested in vitro GQ formation of representative mtDNA sequences containing these 2G QFP sequences and detected robust GQ structures by UV–VIS and CD spectroscopy. Notably, the most frequent deletion breakpoints, including those of the "common deletion", are bounded by 2G QFP sequence motifs.

Conclusions

The potential for GQ to influence mitochondrial genome stability supports a high-priority investigation of these structures and their regulation in normal and pathological mitochondrial biology. These findings emphasize the potential importance of helicases that subsequently resolve GQ to maintain the stability of the mitochondrial genome.

Keywords:
G-quadruplex; mtDNA deletions; Mitochondrial disease; Mitochondrial genome instability; Non-B DNA; Nucleic acid structures