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

Abstract

SUMMARYSequences with the capacity to adopt alternative DNA structures have been implicated in cancer etiology; however, the mechanisms are unclear. For example, H-DNA-forming sequences within oncogenes have been shown to stimulate genetic instability in mammals. Here, we report that H-DNA-forming sequences are enriched at translocation breakpoints in human cancer genomes, further implicating them in cancer etiology. H-DNA-induced mutations were suppressed in human cells deficient in the nucleotide excision repair nucleases, ERCC1-XPF and XPG, but were stimulated in cells deficient in FEN1, a replication-related endonuclease. Further, we found that these nucleases cleaved H-DNA conformations, and the interactions of modeled H-DNA with ERCC1-XPF, XPG, and FEN1 proteins were explored at the sub-molecular level. The results suggest mechanisms of genetic instability triggered by H-DNA through distinct structure-specific, cleavage-based replication-independent and replication-dependent pathways, providing critical evidence for a role of the DNA structure itself in the etiology of cancer and other human diseases.

The role of fork stalling and DNA structures in causing chromosome fragility

“…This mechanism can be either replication‐associated or not. For example, XPF‐ERCC1 ( S. cerevisiae Rad1‐Rad10) cleaves both cruciform structures and H‐DNA independently of replication, suggesting that structures are recognized as DNA damage by the cell and subsequent NER results in their cleavage …”

“…45 A naturally occurring H-DNA forming sequence in the c-myc promoter maps to the Bcl-2 major breakpoint region and implicates secondary structures in common c-myc translocations that occur in lymphomas. [94][95][96][97] Though expanded triplet repeats have not been associated with CFSs, the principles governing their fragility may be similar to structure-forming sequences within CFSs.…”

“…For example, XPF-ERCC1 (S. cerevisiae Rad1-Rad10) cleaves both cruciform structures and H-DNA independently of replication, suggesting that structures are recognized as DNA damage by the cell and subsequent NER results in their cleavage. 97,113,161 Work from the Hickson, Rosselli, and Debatisse labs showed that human complexes MUS81-EME1 (S. cerevisiae Mus81-Mms4) and ERCC1 (S. cerevisiae Rad1-Rad10) are required for CFS expression and sister chromatid separation, 162,163 pointing to a role for structurespecific endonucleases (SSEs) at CFSs. These SSEs are known to target both three-way junctions that occur at stalled forks and recombination intermediates.…”

Peptide Nucleic Acids and Gene Editing: Perspectives on Structure and Repair

“…Insights from how cells repair endogenous triplex structures reveal more potential mechanisms of triplex repair and resolution. In work recently published by the Vasquez group (2018) they describe replication-dependent and replication-independent pathways for the repair of DNA triplexes (H-DNA) that form spontaneously between gDNA strands [3]. While replication-independent repair and cleavage rely on NER factors XPG and XPF, flap endonuclease 1 (FEN1) is a key factor that binds and cleaves endogenous H-DNA during replication [3].…”

“…The consequences of these curious structures have been under investigation for decades revealing critical roles in gene regulation, telomere protection, and recombination processes amongst others. However, while unusual structures expand and nuance the genomic toolbox, these sites have been shown to be associated with genomic instability in some contexts [3]. Consequentially, a suite of dedicated helicases, polymerases, and repair networks evolved in tandem to recognize and resolve these transient structures faithfully and maintain genomic integrity [4].…”