Topoisomerase IB of Deinococcus radiodurans resolves guanine quadruplex DNA structures in vitro

Guanine quadruplex (G4) structures are among the most stable secondary DNA structures that can form in vitro, and evidence for their existence in vivo has been steadily accumulating. Originally described mainly for their deleterious effects on genome stability, more recent research has focused on (potential) functions of G4 structures in telomere maintenance, gene expression, and other cellular processes. The combined research on G4 structures has revealed that properly regulating G4 DNA structures in cells is important to prevent genome instability and disruption of normal cell function. In this short review we provide some background and historical context of our work resulting in the identification of FANCJ, RTEL1 and BLM as helicases that act on G4 structures in vivo. Taken together these studies highlight important roles of different G4 DNA structures and specific G4 helicases at selected genomic locations and telomeres in regulating gene expression and maintaining genome stability.

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VEZF1–guanine quadruplex DNA interaction regulates alternative polyadenylation and detyrosinase activity of VASH1

Nucleic Acids Research ◽

10.1093/nar/gkaa1092 ◽

2020 ◽

Vol 48 (21) ◽

pp. 11994-12003

Author(s):

Lin Li ◽

Preston Williams ◽

Zi Gao ◽

Yinsheng Wang

Keyword(s):

Binding Protein ◽

Umbilical Vein ◽

Alternative Polyadenylation ◽

Dna Interaction ◽

Vascular Endothelial ◽

Quadruplex Dna ◽

Guanine Quadruplex ◽

Umbilical Vein Endothelial Cells ◽

In Cells

Abstract Vascular endothelial zinc finger 1 (VEZF1) plays important roles in endothelial lineage definition and angiogenesis. Vasohibins 1 and 2 (VASH1 and VASH2) can form heterodimers with small vasohibin-binding protein (SVBP) and were recently shown to regulate angiogenesis by acting as tubulin detyrosinases. Here, we showed that VEZF1 binds directly with DNA guanine quadruplex (G quadruplex, G4) structures in vitro and in cells, which modulates the levels of the two isoforms of VASH1 mRNA. Disruption of this interaction, through genetic depletion of VEZF1 or treatment of cells with G4-stabilizing small molecules, led to increased production of the long over short isoform of VASH1 (i.e. VASH1A and VASH1B, respectively) mRNA and elevated tubulin detyrosinase activity in cells. Moreover, disruption of VEZF1-G4 interactions in human umbilical vein endothelial cells resulted in diminished angiogenesis. These results suggest that the interaction between VEZF1 and G4 structures assumes a crucial role in angiogenesis, which occurs through regulating the relative levels of the two isoforms of VASH1 mRNA and the detyrosinase activity of the VASH1-SVBP complex. Together, our work revealed VEZF1 as a G4-binding protein, identified a novel regulatory mechanism for tubulin detyrosinase, and illustrated that the VEZF1- and VASH1-mediated angiogenesis pathways are functionally connected.

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In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.141229498 ◽

2001 ◽

Vol 98 (15) ◽

pp. 8572-8577 ◽

Cited By ~ 399

Author(s):

C. Schaffitzel ◽

I. Berger ◽

J. Postberg ◽

J. Hanes ◽

H. J. Lipps ◽

...

Keyword(s):

Quadruplex Dna ◽

Guanine Quadruplex

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Human Rev1 polymerase disrupts G-quadruplex DNA

Nucleic Acids Research ◽

10.1093/nar/gkt1314 ◽

2013 ◽

Vol 42 (5) ◽

pp. 3272-3285 ◽

Cited By ~ 37

Author(s):

Sarah Eddy ◽

Amit Ketkar ◽

Maroof K. Zafar ◽

Leena Maddukuri ◽

Jeong-Yun Choi ◽

...

Keyword(s):

Genome Maintenance ◽

Quadruplex Dna ◽

Dna Structures ◽

G4 Dna ◽

G Quadruplex ◽

Steady State Rate ◽

Dna Substrates ◽

Successful Replication ◽

Y Family

Abstract The Y-family DNA polymerase Rev1 is required for successful replication of G-quadruplex DNA (G4 DNA) in higher eukaryotes. Here we show that human Rev1 (hRev1) disrupts G4 DNA structures and prevents refolding in vitro. Nucleotidyl transfer by hRev1 is not necessary for mechanical unfolding to occur. hRev1 binds G4 DNA substrates with Kd,DNA values that are 4–15-fold lower than those of non-G4 DNA substrates. The pre-steady-state rate constant of deoxycytidine monophosphate (dCMP) insertion opposite the first tetrad-guanine by hRev1 is ∼56% as fast as that observed for non-G4 DNA substrates. Thus, hRev1 can promote fork progression by either dislodging tetrad guanines to unfold the G4 DNA, which could assist in extension by other DNA polymerases, or hRev1 can prevent refolding of G4 DNA structures. The hRev1 mechanism of action against G-quadruplexes helps explain why replication progress is impeded at G4 DNA sites in Rev1-deficient cells and illustrates another unique feature of this enzyme with important implications for genome maintenance.

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Sites of instability in the human TCF3 (E2A) gene adopt G-quadruplex DNA structures in vitro

Frontiers in Genetics ◽

10.3389/fgene.2015.00177 ◽

2015 ◽

Vol 6 ◽

Cited By ~ 12

Author(s):

Jonathan D. Williams ◽

Sara Fleetwood ◽

Alexandra Berroyer ◽

Nayun Kim ◽

Erik D. Larson

Keyword(s):

Quadruplex Dna ◽

Dna Structures ◽

G Quadruplex

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Probing Telomeric G-Quadruplex DNA Structures in Cells with In Vitro Generated Single-Chain Antibody Fragments

Methods in Molecular Biology - G-Quadruplex DNA ◽

10.1007/978-1-59745-363-9_11 ◽

2009 ◽

pp. 159-181 ◽

Cited By ~ 21

Author(s):

Christiane Schaffitzel ◽

Jan Postberg ◽

Katrin Paeschke ◽

Hans J. Lipps

Keyword(s):

Antibody Fragments ◽

Single Chain ◽

Single Chain Antibody ◽

Quadruplex Dna ◽

Dna Structures ◽

G Quadruplex ◽

In Cells

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Neil3 and NEIL1 DNA Glycosylases Remove Oxidative Damages from Quadruplex DNA and Exhibit Preferences for Lesions in the Telomeric Sequence Context

Journal of Biological Chemistry ◽

10.1074/jbc.m113.479055 ◽

2013 ◽

Vol 288 (38) ◽

pp. 27263-27272 ◽

Cited By ~ 59

Author(s):

Jia Zhou ◽

Minmin Liu ◽

Aaron M. Fleming ◽

Cynthia J. Burrows ◽

Susan S. Wallace

Keyword(s):

Excision Repair ◽

Telomeric Sequence ◽

Dna Glycosylases ◽

Telomeric Dna ◽

Sequence Context ◽

Quadruplex Dna ◽

Dna Structures ◽

Base Excision

The telomeric DNA of vertebrates consists of d(TTAGGG)n tandem repeats, which can form quadruplex DNA structures in vitro and likely in vivo. Despite the fact that the G-rich telomeric DNA is susceptible to oxidation, few biochemical studies of base excision repair in telomeric DNA and quadruplex structures have been done. Here, we show that telomeric DNA containing thymine glycol (Tg), 8-oxo-7,8-dihydroguanine (8-oxoG), guanidinohydantoin (Gh), or spiroiminodihydantoin (Sp) can form quadruplex DNA structures in vitro. We have tested the base excision activities of five mammalian DNA glycosylases (NEIL1, NEIL2, mNeil3, NTH1, and OGG1) on these lesion-containing quadruplex substrates and found that only mNeil3 had excision activity on Tg in quadruplex DNA and that the glycosylase exhibited a strong preference for Tg in the telomeric sequence context. Although Sp and Gh in quadruplex DNA were good substrates for mNeil3 and NEIL1, none of the glycosylases had activity on quadruplex DNA containing 8-oxoG. In addition, NEIL1 but not mNeil3 showed enhanced glycosylase activity on Gh in the telomeric sequence context. These data suggest that one role for Neil3 and NEIL1 is to repair DNA base damages in telomeres in vivo and that Neil3 and Neil1 may function in quadruplex-mediated cellular events, such as gene regulation via removal of damaged bases from quadruplex DNA.

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Stabilization of G-quadruplex DNA structures in Schizosaccharomyces pombe causes single-strand DNA lesions and impedes DNA replication

Nucleic Acids Research ◽

10.1093/nar/gkaa820 ◽

2020 ◽

Vol 48 (19) ◽

pp. 10998-11015 ◽

Cited By ~ 1

Author(s):

Ikenna Obi ◽

Matilda Rentoft ◽

Vandana Singh ◽

Jan Jamroskovic ◽

Karam Chand ◽

...

Keyword(s):

Breast Cancer ◽

Dna Replication ◽

Schizosaccharomyces Pombe ◽

Dna Lesions ◽

Single Strand ◽

Quadruplex Dna ◽

Dna Structures ◽

Replication Fork Progression ◽

G Quadruplex

Abstract G-quadruplex (G4) structures are stable non-canonical DNA structures that are implicated in the regulation of many cellular pathways. We show here that the G4-stabilizing compound PhenDC3 causes growth defects in Schizosaccharomyces pombe cells, especially during S-phase in synchronized cultures. By visualizing individual DNA molecules, we observed shorter DNA fragments of newly replicated DNA in the PhenDC3-treated cells, suggesting that PhenDC3 impedes replication fork progression. Furthermore, a novel single DNA molecule damage assay revealed increased single-strand DNA lesions in the PhenDC3-treated cells. Moreover, chromatin immunoprecipitation showed enrichment of the leading-strand DNA polymerase at sites of predicted G4 structures, suggesting that these structures impede DNA replication. We tested a subset of these sites and showed that they form G4 structures, that they stall DNA synthesis in vitro and that they can be resolved by the breast cancer-associated Pif1 family helicases. Our results thus suggest that G4 structures occur in S. pombe and that stabilized/unresolved G4 structures are obstacles for the replication machinery. The increased levels of DNA damage might further highlight the association of the human Pif1 helicase with familial breast cancer and the onset of other human diseases connected to unresolved G4 structures.

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