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Abstract H-DNA is an intramolecular DNA triplex formed by homopurine-homopyrimidine mirror repeats. Since its discovery, the field has advanced from characterizing the structure in vitro to discovering its existence and role in vivo. H-DNA interacts with cellular machinery in unique ways, stalling DNA and RNA polymerases and causing genome. The foundational S1 nuclease and chemical probing technologies originally used to show H-DNA formation have been updated and combined with genome-wide sequencing methods for large-scale mapping of secondary structures. There is evidence for triplex H-DNA’s role in polycystic kidney disease, cancer, and numerous repeat expansion diseases. In polycystic kidney disease (PKD), an H-DNA forming repeat region within the PKD1 gene stalls DNA replication and induces fragility. H-DNA- forming repeats in various genes have a role in cancer; the most well-studied examples involve H-DNA-mediated fragility causing translocations in multiple lymphomas. Lastly, H-DNA-forming repeats have been implicated in four repeat expansion diseases: Friedreich's ataxia (FRDA), GAA-FGF14-related ataxia, X-linked Dystonia Parkinsonism (XDP), and cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS). In this review, we summarize H-DNA’s discovery and characterization, evidence for its existence and function in vivo, and the field's current knowledge on its role in physiology and pathology. 

Abstract CANVAS is a recently characterized repeat expansion disease, most commonly caused by homozygous expansions of an intronic (A2G3)n repeat in the RFC1 gene. There are a multitude of repeat motifs found in the human population at this locus, some of which are pathogenic and others benign. In this study, we conducted structure-functional analyses of the pathogenic (A2G3)n and nonpathogenic (A4G)n repeats. We found that the pathogenic, but not the nonpathogenic, repeat presents a potent, orientation-dependent impediment to DNA polymerization in vitro. The pattern of the polymerization blockage is consistent with triplex or quadruplex formation in the presence of magnesium or potassium ions, respectively. Chemical probing of both repeats in vitro reveals triplex H-DNA formation by only the pathogenic repeat. Consistently, bioinformatic analysis of S1-END-seq data from human cell lines shows preferential H-DNA formation genome-wide by (A2G3)n motifs over (A4G)n motifs. Finally, the pathogenic, but not the nonpathogenic, repeat stalls replication fork progression in yeast and human cells. We hypothesize that the CANVAS-causing (A2G3)n repeat represents a challenge to genome stability by folding into alternative DNA structures that stall DNA replication. 

Abstract Myotonic dystrophy type 2 (DM2) is a genetic disease caused by expanded CCTG DNA repeats in the first intron of CNBP. The number of CCTG repeats in DM2 patients ranges from 75 to 11,000, yet little is known about the molecular mechanisms responsible for repeat expansions or contractions. We developed an experimental system in Saccharomyces cerevisiae that enables the selection of large-scale contractions of (CCTG)100 within the intron of a reporter gene and subsequent genetic analysis. Contractions exceeded 80 repeat units, causing the final repetitive tract to be well below the threshold for disease. We found that Rad51 and Rad52 are involved in these massive contractions, indicating a mechanism that uses homologous recombination. Srs2 helicase was shown previously to stabilize CTG, CAG, and CGG repeats. Loss of Srs2 did not significantly affect CCTG contraction rates in unperturbed conditions. In contrast, loss of the RecQ helicase Sgs1 resulted in a 6-fold decrease in contraction rate with specific evidence that helicase activity is required for large-scale contractions. Using a genetic assay to evaluate chromosome arm loss, we determined that CCTG and reverse complementary CAGG repeats elevate the rate of chromosomal fragility compared to a short-track control. Overall, our results demonstrate that the genetic control of CCTG repeat contractions is notably distinct among disease-causing microsatellite repeat sequences.