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

Abstract

BackgroundMitochondrial 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.ResultsHere, 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-677) contains supplementary material, which is available to authorized users.

A Role for Non-B DNA Forming Sequences in Mediating Microlesions Causing Human Inherited Disease

“…Alternatively, or in addition, base substitution at guanines within G‐quartets may involve preferential oxidation during transcription, as a result of increased exposure to cellular oxidants while in their noncanonical duplex configuration [Clark et al., ; Zhou et al., ]. This latter model appears to be supported by the observation that, in mitochondrial DNA which is likely to come into contact with mitochondrial‐generated oxidants, deletion breakpoints are observed at high frequencies near G‐quartets [Bharti et al., ; Dong et al., ]. The occurrence of a mutation may either follow or precede unwinding of these G4 structures by DNA helicases, such as FANCJ [Wu et al., ], CHL1 [Wu et al., ], PIF1 [Sanders, ], or the recently characterized ATP‐dependent DEAH‐box helicase DHX36 [Chen et al., ].…”

TEFM regulates both transcription elongation and RNA processing in mitochondria

“…We also report that some regions of mtDNA, such as those with clusters of mt-tRNA genes, seem to be particularly difficult sequences to bypass in the absence of TEFM, likely because of strong secondary structures. Recent computational analyses of the human mtDNA sequence suggest that there are $ 200 putative G-quadruplex forming sequences [59,60], whose presence has been confirmed in live cells [61]. The existence of G-quadruplexes in the non-transcribed DNA strand constitutes a very strong transcription barrier for a progressing RNA polymerase [62], and a G-quadruplex in nascent RNA strongly stimulates transcription termination at CSBII [22,23].…”

Evidence That G-quadruplex DNA Accumulates in the Cytoplasm and Participates in Stress Granule Assembly in Response to Oxidative Stress

“…Human mtDNA contains 270 potential G4-forming sequences (52), many of which correlate with DNA breakpoints associated with diseases (52,78,79). It is of note that hypersensitive DNA cleavage sites have been described adjacent to G4DNA sequences in mitochondria (52,78,79) and proto-oncogenes (80,81).…”