Alternative DNA structure formation in the mutagenic human c-MYC promoter

Abstract

Mutation ‘hotspot’ regions in the genome are susceptible to genetic instability, implicating them in diseases. These hotspots are not random and often co-localize with DNA sequences potentially capable of adopting alternative DNA structures (non-B DNA, e.g. H-DNA and G4-DNA), which have been identified as endogenous sources of genomic instability. There are regions that contain overlapping sequences that may form more than one non-B DNA structure. The extent to which one structure impacts the formation/stability of another, within the sequence, is not fully understood. To address this issue, we investigated the folding preferences of oligonucleotides from a chromosomal breakpoint hotspot in the human c-MYC oncogene containing both potential G4-forming and H-DNA-forming elements. We characterized the structures formed in the presence of G4-DNA-stabilizing K+ ions or H-DNA-stabilizing Mg2+ ions using multiple techniques. We found that under conditions favorable for H-DNA formation, a stable intramolecular triplex DNA structure predominated; whereas, under K+-rich, G4-DNA-forming conditions, a plurality of unfolded and folded species were present. Thus, within a limited region containing sequences with the potential to adopt multiple structures, only one structure predominates under a given condition. The predominance of H-DNA implicates this structure in the instability associated with the human c-MYC oncogene.

Duplex DNA from Sites of Helicase-Polymerase Uncoupling Links Non-B DNA Structure Formation to Replicative Stress

“…The complete analysis of the hyperdiploid stemline showed that it contained recurrent structural rearrangements involving chromosomes 1, 2, 3, 4, 5, 6, 8, 10, 11, 12, 15, 16, 17, 18, and 19. Numerical gains of chromosomes X, 1,2,3,4,7,11,14,16,17,18,19,20, and 21 were present. Of note, the only chromosome homologues that did not have structural rearrangements were chromosomes 7, 9, 13, 14, 20, 21, 22, (19)t (5;19;5),+20,+20,+21,+21 [5].…”

Distinct Mechanisms of Nuclease-Directed DNA-Structure-Induced Genetic Instability in Cancer Genomes

“…Notably, the 23-bp TFR in the c-MYC gene near a translocation breakage hotspot in lymphoma, as discussed above, was found in three translocation events in the human cancer translocation dataset (data not shown). Although this G-rich repeat also has the potential to form a G-quadruplex structure, we recently demonstrated that this particular sequence preferentially forms a stable H-DNA structure ( Del Mundo et al, 2017 ). Moreover, we previously found that a variant of this sequence that forms H-DNA only, but not the sequence that supports G-quadruplex formation only, stalls transcription similar to the native sequence ( Belotserkovskii et al, 2007 ).…”

Noncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis

“…These alternative structures include triple-helices, hairpins, cruciforms, and slipped structures, and they are more likely to form at particular repetitive sequences such as mirror repeats, inverted repeats, direct repeats, and short tandem repeats (Wells 2007). Noncanonical secondary structures are associated with increased mutability according to in vitro studies of prokaryotic (Todd and Glickman 1982;Hoede et al 2006) and eukaryotic cells (Wang and Vasquez 2004;Wang et al 2006Wang et al , 2008Voineagu et al 2008;Lipps and Rhodes 2009;Biffi et al 2013;Lu et al 2015;Bacolla et al 2016;Kaushik Tiwari et al 2016;Del Mundo et al 2017;Kouzine et al 2017).…”