Never cared for what they do. High structural stability of Guanine-quadruplexes in presence of strand-break damages

AbstractDNA integrity is an important factor to assure genome stability and, more generally, cells and organisms’ viability. In presence of DNA damage, the normal cell cycle is perturbed while cells activate their repair processes. Although efficient, the repair system is not always able to ensure the complete restoration of gene integrity. In these cases, not only mutations may occur, but the accumulation of lesions can either lead to carcinogenesis or reach a threshold which induces apoptosis and the programmed cell death. Among the different types of DNA lesions, strand breaks produced by ionizing radiations are the most toxic, due to their inherently difficult repair, which may lead to genomic instability. In this article we show, by using classical molecular simulations techniques, that differently from the canonical double-helical B-DNA, guanine-quadruplex (G4) arrangements show a remarkable structural stability, even in presence of two strand breaks. Since G4-DNA are recognized for their regulatory roles in cell senescence and gene expression, also involving oncogene, their stability can be related to an evolutionary cellular response aimed at minimizing the effects of ionizing radiation.

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i-BLESS is an ultra-sensitive method for detection of DNA double-strand breaks

Communications Biology ◽

10.1038/s42003-018-0165-9 ◽

2018 ◽

Vol 1 (1) ◽

Cited By ~ 22

Author(s):

Anna Biernacka ◽

Yingjie Zhu ◽

Magdalena Skrzypczak ◽

Romain Forey ◽

Benjamin Pardo ◽

...

Keyword(s):

Cell Fate ◽

Genome Stability ◽

Strand Break ◽

Double Strand Breaks ◽

Universal Method ◽

Dna Double Strand Breaks ◽

Strand Breaks ◽

Agarose Beads ◽

Genome Wide ◽

Dna Double Strand Break

AbstractMaintenance of genome stability is a key issue for cell fate that could be compromised by chromosome deletions and translocations caused by DNA double-strand breaks (DSBs). Thus development of precise and sensitive tools for DSBs labeling is of great importance for understanding mechanisms of DSB formation, their sensing and repair. Until now there has been no high resolution and specific DSB detection technique that would be applicable to any cells regardless of their size. Here, we present i-BLESS, a universal method for direct genome-wide DNA double-strand break labeling in cells immobilized in agarose beads. i-BLESS has three key advantages: it is the only unbiased method applicable to yeast, achieves a sensitivity of one break at a given position in 100,000 cells, and eliminates background noise while still allowing for fixation of samples. The method allows detection of ultra-rare breaks such as those forming spontaneously at G-quadruplexes.

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Akt: A Double-Edged Sword in Cell Proliferation and Genome Stability

Journal of Oncology ◽

10.1155/2012/951724 ◽

2012 ◽

Vol 2012 ◽

pp. 1-15 ◽

Cited By ~ 110

Author(s):

Naihan Xu ◽

Yuanzhi Lao ◽

Yaou Zhang ◽

David A. Gillespie

Keyword(s):

Genome Stability ◽

Strand Break ◽

Nonhomologous End Joining ◽

Dependent Manner ◽

Dna Double Strand Breaks ◽

End Joining ◽

Cell Behaviour ◽

Cell Cycles ◽

Strand Breaks ◽

Recombination Repair

The Akt family of serine/threonine protein kinases are key regulators of multiple aspects of cell behaviour, including proliferation, survival, metabolism, and tumorigenesis. Growth-factor-activated Akt signalling promotes progression through normal, unperturbed cell cycles by acting on diverse downstream factors involved in controlling the G1/S and G2/M transitions. Remarkably, several recent studies have also implicated Akt in modulating DNA damage responses and genome stability. High Akt activity can suppress ATR/Chk1 signalling and homologous recombination repair (HRR) via direct phosphorylation of Chk1 or TopBP1 or, indirectly, by inhibiting recruitment of double-strand break (DSB) resection factors, such as RPA, Brca1, and Rad51, to sites of damage. Loss of checkpoint and/or HRR proficiency is therefore a potential cause of genomic instability in tumor cells with high Akt. Conversely, Akt is activated by DNA double-strand breaks (DSBs) in a DNA-PK- or ATM/ATR-dependent manner and in some circumstances can contribute to radioresistance by stimulating DNA repair by nonhomologous end joining (NHEJ). Akt therefore modifies both the response to and repair of genotoxic damage in complex ways that are likely to have important consequences for the therapy of tumors with deregulation of the PI3K-Akt-PTEN pathway.

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The Dark Side of UV-Induced DNA Lesion Repair

Genes ◽

10.3390/genes11121450 ◽

2020 ◽

Vol 11 (12) ◽

pp. 1450

Author(s):

Wojciech Strzałka ◽

Piotr Zgłobicki ◽

Ewa Kowalska ◽

Aneta Bażant ◽

Dariusz Dziga ◽

...

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Uv Light ◽

Genetic Material ◽

Dna Lesions ◽

Dark Side ◽

Repair System ◽

Strand Breaks ◽

Dna Lesion ◽

Pyrimidine Dimers

In their life cycle, plants are exposed to various unfavorable environmental factors including ultraviolet (UV) radiation emitted by the Sun. UV-A and UV-B, which are partially absorbed by the ozone layer, reach the surface of the Earth causing harmful effects among the others on plant genetic material. The energy of UV light is sufficient to induce mutations in DNA. Some examples of DNA damage induced by UV are pyrimidine dimers, oxidized nucleotides as well as single and double-strand breaks. When exposed to light, plants can repair major UV-induced DNA lesions, i.e., pyrimidine dimers using photoreactivation. However, this highly efficient light-dependent DNA repair system is ineffective in dim light or at night. Moreover, it is helpless when it comes to the repair of DNA lesions other than pyrimidine dimers. In this review, we have focused on how plants cope with deleterious DNA damage that cannot be repaired by photoreactivation. The current understanding of light-independent mechanisms, classified as dark DNA repair, indispensable for the maintenance of plant genetic material integrity has been presented.

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Regulation of Error-Prone DNA Double-Strand Break Repair and Its Impact on Genome Evolution

Cells ◽

10.3390/cells9071657 ◽

2020 ◽

Vol 9 (7) ◽

pp. 1657 ◽

Cited By ~ 2

Author(s):

Terrence Hanscom ◽

Mitch McVey

Keyword(s):

Strand Break ◽

Double Strand Break ◽

Dna Lesions ◽

Double Strand Break Repair ◽

End Joining ◽

Genetic Changes ◽

Strand Breaks ◽

Dna Double Strand Break ◽

Alternative End Joining ◽

Break Repair

Double-strand breaks are one of the most deleterious DNA lesions. Their repair via error-prone mechanisms can promote mutagenesis, loss of genetic information, and deregulation of the genome. These detrimental outcomes are significant drivers of human diseases, including many cancers. Mutagenic double-strand break repair also facilitates heritable genetic changes that drive organismal adaptation and evolution. In this review, we discuss the mechanisms of various error-prone DNA double-strand break repair processes and the cellular conditions that regulate them, with a focus on alternative end joining. We provide examples that illustrate how mutagenic double-strand break repair drives genome diversity and evolution. Finally, we discuss how error-prone break repair can be crucial to the induction and progression of diseases such as cancer.

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The role of Sp1 in the detection and elimination of cells with persistent DNA strand breaks

NAR Cancer ◽

10.1093/narcan/zcaa004 ◽

2020 ◽

Vol 2 (2) ◽

Author(s):

Polina S Loshchenova ◽

Svetlana V Sergeeva ◽

Sally C Fletcher ◽

Grigory L Dianov

Keyword(s):

Dna Damage ◽

Cancer Therapy ◽

Genome Stability ◽

Dna Strand Breaks ◽

Dna Lesions ◽

Exogenous Dna ◽

Strand Breaks ◽

Specificity Factor ◽

Dna Strand

Abstract Maintenance of genome stability suppresses cancer and other human diseases and is critical for organism survival. Inevitably, during a life span, multiple DNA lesions can arise due to the inherent instability of DNA molecules or due to endogenous or exogenous DNA damaging factors. To avoid malignant transformation of cells with damaged DNA, multiple mechanisms have evolved to repair DNA or to detect and eradicate cells accumulating unrepaired DNA damage. In this review, we discuss recent findings on the role of Sp1 (specificity factor 1) in the detection and elimination of cells accumulating persistent DNA strand breaks. We also discuss how this mechanism may contribute to the maintenance of physiological populations of healthy cells in an organism, thus preventing cancer formation, and the possible application of these findings in cancer therapy.

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Control of genome stability by Slx protein complexes

Biochemical Society Transactions ◽

10.1042/bst0370495 ◽

2009 ◽

Vol 37 (3) ◽

pp. 495-510 ◽

Cited By ~ 26

Author(s):

John Rouse

Keyword(s):

Dna Damage ◽

Dna Replication ◽

Protein Interactions ◽

Cellular Response ◽

Genome Stability ◽

Molecular Mechanisms ◽

Excision Repair ◽

Protein Complexes ◽

Alkylating Agents ◽

Strand Break

The six Saccharomyces cerevisiae SLX genes were identified in a screen for factors required for the viability of cells lacking Sgs1, a member of the RecQ helicase family involved in processing stalled replisomes and in the maintenance of genome stability. The six SLX gene products form three distinct heterodimeric complexes, and all three have catalytic activity. Slx3–Slx2 (also known as Mus81–Mms4) and Slx1–Slx4 are both heterodimeric endonucleases with a marked specificity for branched replication fork-like DNA species, whereas Slx5–Slx8 is a SUMO (small ubiquitin-related modifier)-targeted E3 ubiquitin ligase. All three complexes play important, but distinct, roles in different aspects of the cellular response to DNA damage and perturbed DNA replication. Slx4 interacts physically not only with Slx1, but also with Rad1–Rad10 [XPF (xeroderma pigmentosum complementation group F)–ERCC1 (excision repair cross-complementing 1) in humans], another structure-specific endonuclease that participates in the repair of UV-induced DNA damage and in a subpathway of recombinational DNA DSB (double-strand break) repair. Curiously, Slx4 is essential for repair of DSBs by Rad1–Rad10, but is not required for repair of UV damage. Slx4 also promotes cellular resistance to DNA-alkylating agents that block the progression of replisomes during DNA replication, by facilitating the error-free mode of lesion bypass. This does not require Slx1 or Rad1–Rad10, and so Slx4 has several distinct roles in protecting genome stability. In the present article, I provide an overview of our current understanding of the cellular roles of the Slx proteins, paying particular attention to the advances that have been made in understanding the cellular roles of Slx4. In particular, protein–protein interactions and underlying molecular mechanisms are discussed and I draw attention to the many questions that have yet to be answered.

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New Faces of old Friends: Emerging new Roles of RNA-Binding Proteins in the DNA Double-Strand Break Response

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2021.668821 ◽

2021 ◽

Vol 8 ◽

Author(s):

Julie A. Klaric ◽

Stas Wüst ◽

Stephanie Panier

Keyword(s):

Cellular Response ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Genome Instability ◽

Strand Break ◽

Dna Lesions ◽

Cell Cycle Checkpoints ◽

Dna Double Strand Breaks ◽

Dna Strand

DNA double-strand breaks (DSBs) are highly cytotoxic DNA lesions. To protect genomic stability and ensure cell homeostasis, cells mount a complex signaling-based response that not only coordinates the repair of the broken DNA strand but also activates cell cycle checkpoints and, if necessary, induces cell death. The last decade has seen a flurry of studies that have identified RNA-binding proteins (RBPs) as novel regulators of the DSB response. While many of these RBPs have well-characterized roles in gene expression, it is becoming increasingly clear that they also have non-canonical functions in the DSB response that go well beyond transcription, splicing and mRNA processing. Here, we review the current understanding of how RBPs are integrated into the cellular response to DSBs and describe how these proteins directly participate in signal transduction, amplification and repair at damaged chromatin. In addition, we discuss the implications of an RBP-mediated DSB response for genome instability and age-associated diseases such as cancer and neurodegeneration.

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Beyond reversal: ubiquitin and ubiquitin-like proteases and the orchestration of the DNA double strand break repair response

Biochemical Society Transactions ◽

10.1042/bst20190534 ◽

2019 ◽

Vol 47 (6) ◽

pp. 1881-1893

Author(s):

Alexander J. Garvin

Keyword(s):

Protein Interactions ◽

Cellular Response ◽

Strand Break ◽

Central Component ◽

Protein Protein Interactions ◽

Dna Double Strand Breaks ◽

Dsb Repair ◽

Post Translational Modifications ◽

Strand Breaks ◽

Dna Double Strand Break

The cellular response to genotoxic DNA double strand breaks (DSBs) uses a multitude of post-translational modifications to localise, modulate and ultimately clear DNA repair factors in a timely and accurate manner. Ubiquitination is well established as vital to the DSB response, with a carefully co-ordinated pathway of histone ubiquitination events being a central component of DSB signalling. Other ubiquitin-like modifiers (Ubl) including SUMO and NEDD8 have since been identified as playing important roles in DSB repair. In the last five years ∼20 additional Ub/Ubl proteases have been implicated in the DSB response. The number of proteases identified highlights the complexity of the Ub/Ubl signal present at DSBs. Ub/Ubl proteases regulate turnover, activity and protein–protein interactions of DSB repair factors both catalytically and non-catalytically. This not only ensures efficient repair of breaks but has a role in channelling repair into the correct DSB repair sub-pathways. Ultimately Ub/Ubl proteases have essential roles in maintaining genomic stability. Given that deficiencies in many Ub/Ubl proteases promotes sensitivity to DNA damaging chemotherapies, they could be attractive targets for cancer treatment.

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HP1β Chromo Shadow Domain facilitates H2A ubiquitination for BRCA1 recruitment at DNA double-strand breaks

10.1101/2022.01.11.475809 ◽

2022 ◽

Author(s):

Tej Pandita ◽

Vijay Kumari Charaka ◽

Sharmistha Chakraborty ◽

Chi-Lin Tsai ◽

Xiaoyan Wang ◽

...

Keyword(s):

Dna Damage ◽

Genome Stability ◽

Strand Break ◽

Dna Double Strand Breaks ◽

Dsb Repair ◽

Strand Breaks ◽

Damage Repair ◽

Dna Double Strand Break ◽

Assembly Factor ◽

Chromo Shadow Domain

Efficient DNA double strand break (DSB) repair by homologous recombination (HR), as orchestrated by histone and non-histone proteins, is critical to genome stability, replication, transcription, and cancer avoidance. Here we report that Heterochromatin Protein1 beta (HP1β) acts as a key component of the HR DNA resection step by regulating BRCA1 enrichment at DNA damage sites, a function largely dependent on the HP1β chromo shadow domain (CSD). HP1β itself is enriched at DSBs within gene-rich regions through a CSD interaction with Chromatin Assembly Factor 1 (CAF1) and HP1β depletion impairs subsequent BRCA1 enrichment. An added interaction of the HP1β CSD with the Polycomb Repressor Complex 1 ubiquitinase component RING1A facilitates BRCA1 recruitment by increasing H2A lysine 118-119 ubiquitination, a marker for BRCA1 recruitment. Our findings reveal that HP1β interactions, mediated through its CSD with RING1A, promote H2A ubiquitination and facilitate BRCA1 recruitment at DNA damage sites, a critical step in DSB repair by the HR pathway. These collective results unveil how HP1β is recruited to DSBs in gene-rich regions and how HP1β subsequently promotes BRCA1 recruitment to further HR DNA damage repair by stimulating CtIP-dependent resection.

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SETD2 is required for DNA double-strand break repair and activation of the p53-mediated checkpoint

eLife ◽

10.7554/elife.02482 ◽

2014 ◽

Vol 3 ◽

Cited By ~ 121

Author(s):

Sílvia Carvalho ◽

Alexandra C Vítor ◽

Sreerama C Sridhara ◽

Filipa B Martins ◽

Ana C Raposo ◽

...

Keyword(s):

Dna Damage ◽

Strand Break ◽

Dna Lesions ◽

Alternative Mechanism ◽

Dna Double Strand Breaks ◽

Cell Renal Cell Carcinoma ◽

Strand Breaks ◽

Dna Damage Signaling ◽

Dna Double Strand Break ◽

Recombination Repair

Histone modifications establish the chromatin states that coordinate the DNA damage response. In this study, we show that SETD2, the enzyme that trimethylates histone H3 lysine 36 (H3K36me3), is required for ATM activation upon DNA double-strand breaks (DSBs). Moreover, we find that SETD2 is necessary for homologous recombination repair of DSBs by promoting the formation of RAD51 presynaptic filaments. In agreement, SETD2-mutant clear cell renal cell carcinoma (ccRCC) cells displayed impaired DNA damage signaling. However, despite the persistence of DNA lesions, SETD2-deficient cells failed to activate p53, a master guardian of the genome rarely mutated in ccRCC and showed decreased cell survival after DNA damage. We propose that this novel SETD2-dependent role provides a chromatin bookmarking instrument that facilitates signaling and repair of DSBs. In ccRCC, loss of SETD2 may afford an alternative mechanism for the inactivation of the p53-mediated checkpoint without the need for additional genetic mutations in TP53.

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