ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress

AbstractATRX is a tumor suppressor that has been associated with protection from DNA replication stress, purportedly through resolution of difficult-to-replicate G-quadruplex (G4) DNA structures. While several studies demonstrate that loss of ATRX sensitizes cells to chemical stabilizers of G4 structures, the molecular function of ATRX at G4 regions during replication remains unknown. Here, we demonstrate that ATRX associates with a number of the MCM replication complex subunits and that loss of ATRX leads to G4 structure accumulation at newly synthesized DNA. We show that both the helicase domain of ATRX and its H3.3 chaperone function are required to protect cells from G4-induced replicative stress. Furthermore, these activities are upstream of heterochromatin formation mediated by the histone methyltransferase, ESET, which is the critical molecular event that protects cells from G4-mediated stress. In support, tumors carrying mutations in either ATRX or ESET show increased mutation burden at G4-enriched DNA sequences. Overall, our study provides new insights into mechanisms by which ATRX promotes genome stability with important implications for understanding impacts of its loss on human disease.

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ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress

10.1101/2021.05.07.443199 ◽

2021 ◽

Author(s):

Yu-Ching Teng ◽

Aishwarys Sundaresan ◽

Ryan O'Hara ◽

Vincent U Gant ◽

Minhua Li ◽

...

Keyword(s):

Dna Sequences ◽

Genome Stability ◽

Helicase Domain ◽

Quadruplex Dna ◽

Heterochromatin Formation ◽

Replicative Stress ◽

G4 Dna ◽

Mutation Burden ◽

G Quadruplex ◽

Dna Replication Stress

ATRX is a tumor suppressor that has been associated with protection from DNA replication stress, purportedly through resolution of difficult-to-replicate G-quadruplex (G4) DNA structures. While several studies demonstrate that loss of ATRX sensitizes cells to chemical stabilizers of G4 structures, the molecular function of ATRX at G4 regions during replication remains unknown. Here, we demonstrate that ATRX associates with the MCM replication complex and that loss of ATRX leads to G4 structure accumulation at newly synthesized DNA. We show that both the helicase domain of ATRX and its H3.3 chaperone function are required to protect cells from G4-induced replicative stress. Furthermore, these activities are upstream of heterochromatin formation mediated by the histone methyltransferase, ESET, which is the critical molecular event that protects cells from G4-mediated stress. In support, tumors carrying mutations in either ATRX or ESET show increased mutation burden at G4-enriched DNA sequences. Overall, our study provides new insights into mechanisms by which ATRX promotes genome stability with important implications for understanding impacts of its loss on human disease.

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Human Pif1 helicase is a G-quadruplex DNA-binding protein with G-quadruplex DNA-unwinding activity

Biochemical Journal ◽

10.1042/bj20100612 ◽

2010 ◽

Vol 430 (1) ◽

pp. 119-128 ◽

Cited By ~ 98

Author(s):

Cyril M. Sanders

Keyword(s):

Dna Binding ◽

Dna Sequences ◽

Genome Stability ◽

Dna Helicase ◽

Dna Unwinding ◽

Helicase Domain ◽

Quadruplex Dna ◽

G4 Dna ◽

G Quadruplex ◽

Pif1 Helicase

Pif1 proteins are helicases that in yeast are implicated in the maintenance of genome stability. One activity of Saccharomyces cerevisiae Pif1 is to stabilize DNA sequences that could otherwise form deleterious G4 (G-quadruplex) structures by acting as a G4 resolvase. The present study shows that human Pif1 (hPif1, nuclear form) is a G4 DNA-binding and resolvase protein and that these activities are properties of the conserved helicase domain (amino acids 206–620 of 641, hPifHD). hPif1 preferentially bound synthetic G4 DNA relative to ssDNA (single-stranded DNA), dsDNA (double-stranded DNA) and a partially single-stranded duplex DNA helicase substrate. G4 DNA unwinding, but not binding, required an extended (>10 nucleotide) 5′ ssDNA tail, and in competition assays, G4 DNA was an ineffective suppressor of helicase activity compared with ssDNA. These results suggest a distinction between the determinants of G4 DNA binding and the ssDNA interactions required for helicase action and that hPif1 may act on G4 substrates by binding alone or as a resolvase. Human Pif1 could therefore have a role in processing G4 structures that arise in the single-stranded nucleic acid intermediates formed during DNA replication and gene expression.

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Subtle structural alterations in G-quadruplex DNA regulate site specificity of fluorescence light-up probes

Nucleic Acids Research ◽

10.1093/nar/gkz1205 ◽

2020 ◽

Vol 48 (3) ◽

pp. 1108-1119 ◽

Cited By ~ 5

Author(s):

Rajendra Kumar ◽

Karam Chand ◽

Sudipta Bhowmik ◽

Rabindra Nath Das ◽

Snehasish Bhattacharjee ◽

...

Keyword(s):

Rational Design ◽

Dna Structure ◽

Biological Processes ◽

Chemical Research ◽

Quadruplex Dna ◽

Dna Structures ◽

Future Studies ◽

G4 Dna ◽

G Quadruplex ◽

Fluorescence Light

Abstract G-quadruplex (G4) DNA structures are linked to key biological processes and human diseases. Small molecules that target specific G4 DNA structures and signal their presence would therefore be of great value as chemical research tools with potential to further advance towards diagnostic and therapeutic developments. However, the development of these types of specific compounds remain as a great challenge. In here, we have developed a compound with ability to specifically signal a certain c-MYC G4 DNA structure through a fluorescence light-up mechanism. Despite the compound's two binding sites on the G4 DNA structure, only one of them result in the fluorescence light-up effect. This G-tetrad selectivity proved to originate from a difference in flexibility that affected the binding affinity and tilt the compound out of the planar conformation required for the fluorescence light-up mechanism. The intertwined relation between the presented factors is likely the reason for the lack of examples using rational design to develop compounds with turn-on emission that specifically target certain G4 DNA structures. However, this study shows that it is indeed possible to develop such compounds and present insights into the molecular details of specific G4 DNA recognition and signaling to advance future studies of G4 biology.

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G-quadruplex DNA drives genomic instability and represents a targetable molecular abnormality in ATRX-deficient malignant glioma

10.1101/347542 ◽

2018 ◽

Author(s):

Yuxiang Wang ◽

Jie Yang ◽

Wei Wu ◽

Rachna Shah ◽

Carla Danussi ◽

...

Keyword(s):

Dna Damage ◽

Malignant Glioma ◽

Model Systems ◽

Copy Number Alterations ◽

Molecular Alteration ◽

Quadruplex Dna ◽

G4 Dna ◽

G Quadruplex

AbstractMutational inactivation of ATRX (α-thalassemia mental retardation X-linked) represents a defining molecular alteration in large subsets of malignant glioma. Yet the pathogenic consequences of ATRX deficiency remain unclear, as do tractable mechanisms for its therapeutic targeting. Here we report that ATRX loss in isogenic glioma model systems induces replication stress and DNA damage by way of G-quadruplex (G4) DNA secondary structure. Moreover, these effects are associated with the acquisition of disease-relevant copy number alterations over time. We then demonstrate, both in vitro and in vivo, that ATRX deficiency selectively enhances DNA damage and cell death following chemical G4 stabilization. Finally, we show that G4 stabilization synergizes with other DNA-damaging therapies, including ionizing radiation, in the ATRX-deficient context. Our findings reveal novel pathogenic mechanisms driven by ATRX deficiency in glioma, while also pointing to tangible strategies for drug development.

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G-rich telomeric and ribosomal DNA sequences from the fission yeast genome form stable G-quadruplex DNA structuresin vitroand are unwound by the Pfh1 DNA helicase

Nucleic Acids Research ◽

10.1093/nar/gkw349 ◽

2016 ◽

Vol 44 (13) ◽

pp. 6213-6231 ◽

Cited By ~ 34

Author(s):

Marcus Wallgren ◽

Jani B. Mohammad ◽

Kok-Phen Yan ◽

Parham Pourbozorgi-Langroudi ◽

Mahsa Ebrahimi ◽

...

Keyword(s):

Fission Yeast ◽

Ribosomal Dna ◽

Dna Sequences ◽

Dna Helicase ◽

Yeast Genome ◽

Quadruplex Dna ◽

G Quadruplex

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Mgs1 protein supports genome stability via recognition of G‐quadruplex DNA structures

The FASEB Journal ◽

10.1096/fj.202000886r ◽

2020 ◽

Vol 34 (9) ◽

pp. 12646-12662 ◽

Cited By ~ 1

Author(s):

Theresa Zacheja ◽

Agnes Toth ◽

Gabor M. Harami ◽

Qianlu Yang ◽

Eike Schwindt ◽

...

Keyword(s):

Genome Stability ◽

Quadruplex Dna ◽

Dna Structures ◽

G Quadruplex

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Macrocyclization of bis-indole quinolines for selective stabilization of G-quadruplex DNA structures

Chemical Science ◽

10.1039/d0sc03519j ◽

2020 ◽

Vol 11 (38) ◽

pp. 10529-10537 ◽

Cited By ~ 1

Author(s):

Rabindra Nath Das ◽

Måns Andréasson ◽

Rajendra Kumar ◽

Erik Chorell

Keyword(s):

Quadruplex Dna ◽

Dna Structures ◽

G4 Dna ◽

Selective Stabilization ◽

G Quadruplex

Macrocyclization improves the selectivity, affinity, and ability to stabilize G4 DNA structures.

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Evidences for Piperine inhibiting cancer by targeting human G-quadruplex DNA sequences

Scientific Reports ◽

10.1038/srep39239 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 32

Author(s):

Arpita Tawani ◽

Ayeman Amanullah ◽

Amit Mishra ◽

Amit Kumar

Keyword(s):

Dna Sequences ◽

Quadruplex Dna ◽

G 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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