Maintenance of Genome Integrity: DNA Damage Sensing, Signaling, Repair and Replication in Plants

DNA double-strand breaks (DSBs) are hazardous to genome integrity and can promote mutations and disease if not handled correctly. Cells respond to these dangers by engaging DNA damage response (DDR) pathways that are able to identify DNA breaks within chromatin leading ultimately to their repair. The recognition and repair of DSBs by the DDR is largely dependent on the ability of DNA damage sensing factors to bind to and interact with nucleic acids, nucleosomes and their modified forms to target these activities to the break site. These contacts orientate and localize factors to lesions within chromatin, allowing signaling and faithful repair of the break to occur. Coordinating these events requires the integration of several signaling and binding events. Studies are revealing an enormously complex array of interactions that contribute to DNA lesion recognition and repair including binding events on DNA, as well as RNA, RNA:DNA hybrids, nucleosomes, histone and non-histone protein post-translational modifications and protein-protein interactions. Here we examine several DDR pathways that highlight and provide prime examples of these emerging concepts. A combination of approaches including genetic, cellular, and structural biology have begun to reveal new insights into the molecular interactions that govern the DDR within chromatin. While many questions remain, a clearer picture has started to emerge for how DNA-templated processes including transcription, replication and DSB repair are coordinated. Multivalent interactions with several biomolecules serve as key signals to recruit and orientate proteins at DNA lesions, which is essential to integrate signaling events and coordinate the DDR within the milieu of the nucleus where competing genome functions take place. Genome architecture, chromatin structure and phase separation have emerged as additional vital regulatory mechanisms that also influence genome integrity pathways including DSB repair. Collectively, recent advancements in the field have not only provided a deeper understanding of these fundamental processes that maintain genome integrity and cellular homeostasis but have also started to identify new strategies to target deficiencies in these pathways that are prevalent in human diseases including cancer.

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A Tale of Ice and Fire: The Dual Role for 17β-Estradiol in Balancing DNA Damage and Genome Integrity

Cancers ◽

10.3390/cancers13071583 ◽

2021 ◽

Vol 13 (7) ◽

pp. 1583

Author(s):

Sara Pescatori ◽

Francesco Berardinelli ◽

Jacopo Albanesi ◽

Paolo Ascenzi ◽

Maria Marino ◽

...

Keyword(s):

Dna Damage ◽

Cellular Transformation ◽

Genome Integrity ◽

Physiological Effects ◽

Dna Damages ◽

Cellular Effects ◽

Damage Response ◽

17Β Estradiol ◽

Cellular Pathways ◽

Definition Of

17β-estradiol (E2) regulates human physiology both in females and in males. At the same time, E2 acts as a genotoxic substance as it could induce DNA damages, causing the initiation of cellular transformation. Indeed, increased E2 plasma levels are a risk factor for the development of several types of cancers including breast cancer. This paradoxical identity of E2 undermines the foundations of the physiological definition of “hormone” as E2 works both as a homeostatic regulator of body functions and as a genotoxic compound. Here, (i) the molecular circuitries underlying this double face of E2 are reviewed, and (ii) a possible framework to reconcile the intrinsic discrepancies of the E2 function is reported. Indeed, E2 is a regulator of the DNA damage response, which this hormone exploits to calibrate its genotoxicity with its physiological effects. Accordingly, the genes required to maintain genome integrity belong to the E2-controlled cellular signaling network and are essential for the appearance of the E2-induced cellular effects. This concept requires an “upgrade” to the vision of E2 as a “genotoxic hormone”, which balances physiological and detrimental pathways to guarantee human body homeostasis. Deregulation of this equilibrium between cellular pathways would determine the E2 pathological effects.

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APE2 Is a General Regulator of the ATR-Chk1 DNA Damage Response Pathway to Maintain Genome Integrity in Pancreatic Cancer Cells

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.738502 ◽

2021 ◽

Vol 9 ◽

Author(s):

Md Akram Hossain ◽

Yunfeng Lin ◽

Garrett Driscoll ◽

Jia Li ◽

Anne McMahon ◽

...

Keyword(s):

Oxidative Stress ◽

Pancreatic Cancer ◽

Dna Damage ◽

Cancer Cells ◽

Dna Damage Response ◽

Human Pancreatic Cancer ◽

Genome Integrity ◽

Pancreatic Cancer Cells ◽

Damage Response ◽

Egg Extracts

The maintenance of genome integrity and fidelity is vital for the proper function and survival of all organisms. Recent studies have revealed that APE2 is required to activate an ATR-Chk1 DNA damage response (DDR) pathway in response to oxidative stress and a defined DNA single-strand break (SSB) in Xenopus laevis egg extracts. However, it remains unclear whether APE2 is a general regulator of the DDR pathway in mammalian cells. Here, we provide evidence using human pancreatic cancer cells that APE2 is essential for ATR DDR pathway activation in response to different stressful conditions including oxidative stress, DNA replication stress, and DNA double-strand breaks. Fluorescence microscopy analysis shows that APE2-knockdown (KD) leads to enhanced γH2AX foci and increased micronuclei formation. In addition, we identified a small molecule compound Celastrol as an APE2 inhibitor that specifically compromises the binding of APE2 but not RPA to ssDNA and 3′-5′ exonuclease activity of APE2 but not APE1. The impairment of ATR-Chk1 DDR pathway by Celastrol in Xenopus egg extracts and human pancreatic cancer cells highlights the physiological significance of Celastrol in the regulation of APE2 functionalities in genome integrity. Notably, cell viability assays demonstrate that APE2-KD or Celastrol sensitizes pancreatic cancer cells to chemotherapy drugs. Overall, we propose APE2 as a general regulator for the DDR pathway in genome integrity maintenance.

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Genome Maintenance Mechanisms at the Chromatin Level

International Journal of Molecular Sciences ◽

10.3390/ijms221910384 ◽

2021 ◽

Vol 22 (19) ◽

pp. 10384

Author(s):

Hirotomo Takatsuka ◽

Atsushi Shibata ◽

Masaaki Umeda

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Genome Stability ◽

Genotoxic Stress ◽

Genome Integrity ◽

Easy Access ◽

Order Structure ◽

Chromatin Modifications ◽

Level Control ◽

Regulatory Systems

Genome integrity is constantly threatened by internal and external stressors, in both animals and plants. As plants are sessile, a variety of environment stressors can damage their DNA. In the nucleus, DNA twines around histone proteins to form the higher-order structure “chromatin”. Unraveling how chromatin transforms on sensing genotoxic stress is, thus, key to understanding plant strategies to cope with fluctuating environments. In recent years, accumulating evidence in plant research has suggested that chromatin plays a crucial role in protecting DNA from genotoxic stress in three ways: (1) changes in chromatin modifications around damaged sites enhance DNA repair by providing a scaffold and/or easy access to DNA repair machinery; (2) DNA damage triggers genome-wide alterations in chromatin modifications, globally modulating gene expression required for DNA damage response, such as stem cell death, cell-cycle arrest, and an early onset of endoreplication; and (3) condensed chromatin functions as a physical barrier against genotoxic stressors to protect DNA. In this review, we highlight the chromatin-level control of genome stability and compare the regulatory systems in plants and animals to find out unique mechanisms maintaining genome integrity under genotoxic stress.

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Numerical and Spatial Patterning of Yeast Meiotic DNA Breaks by Tel1

10.1101/059022 ◽

2016 ◽

Cited By ~ 3

Author(s):

Neeman Mohibullah ◽

Scott Keeney

Keyword(s):

Saccharomyces Cerevisiae ◽

Dna Damage ◽

Deep Sequencing ◽

Meiotic Recombination ◽

Double Strand Breaks ◽

Genome Integrity ◽

Spatial Patterning ◽

Dna Breaks ◽

Strand Breaks ◽

Context Dependent

AbstractThe Spo11-generated double-strand breaks (DSBs) that initiate meiotic recombination are dangerous lesions that can disrupt genome integrity, so meiotic cells regulate their number, timing, and distribution. Here, we use Spo11-oligonucleotide complexes, a byproduct of DSB formation, to examine the contribution of the DNA damage-responsive kinase Tel1 (ortholog of mammalian ATM) to this regulation in Saccharomyces cerevisiae. A tel1Δ mutant had globally increased amounts of Spo11-oligonucleotide complexes and altered Spo11-oligonucleotide lengths, consistent with conserved roles for Tel1 in control of DSB number and processing. A kinase-dead tell mutation also increased Spo11-oligonucleotide levels, but mutating known Tel1 phosphotargets on Hop1 and Rec114 did not. Deep sequencing of Spo11 oligonucleotides from tel1Δ mutants demonstrated that Tel1 shapes the nonrandom DSB distribution in ways that are distinct but partially overlapping with previously described contributions of the recombination regulator Zip3. Finally, we uncover a context-dependent role for Tel1 in hotspot competition, in which an artificial DSB hotspot inhibits nearby hotspots. Evidence for Tel1-dependent competition involving strong natural hotspots is also provided.

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Single-Strand Break End Resection in Genome Integrity: Mechanism and Regulation by APE2

International Journal of Molecular Sciences ◽

10.3390/ijms19082389 ◽

2018 ◽

Vol 19 (8) ◽

pp. 2389 ◽

Cited By ~ 16

Author(s):

Md. Hossain ◽

Yunfeng Lin ◽

Shan Yan

Keyword(s):

Dna Damage ◽

Genome Instability ◽

Strand Break ◽

Single Strand ◽

Genome Integrity ◽

Single Strand Break ◽

Strand Breaks ◽

Single Strand Breaks ◽

Damage Response ◽

End Resection

DNA single-strand breaks (SSBs) occur more than 10,000 times per mammalian cell each day, representing the most common type of DNA damage. Unrepaired SSBs compromise DNA replication and transcription programs, leading to genome instability. Unrepaired SSBs are associated with diseases such as cancer and neurodegenerative disorders. Although canonical SSB repair pathway is activated to repair most SSBs, it remains unclear whether and how unrepaired SSBs are sensed and signaled. In this review, we propose a new concept of SSB end resection for genome integrity. We propose a four-step mechanism of SSB end resection: SSB end sensing and processing, as well as initiation, continuation, and termination of SSB end resection. We also compare different mechanisms of SSB end resection and DSB end resection in DNA repair and DNA damage response (DDR) pathways. We further discuss how SSB end resection contributes to SSB signaling and repair. We focus on the mechanism and regulation by APE2 in SSB end resection in genome integrity. Finally, we identify areas of future study that may help us gain further mechanistic insight into the process of SSB end resection. Overall, this review provides the first comprehensive perspective on SSB end resection in genome integrity.

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Bloom syndrome protein restrains innate immune sensing of micronuclei by cGAS

Journal of Experimental Medicine ◽

10.1084/jem.20181329 ◽

2019 ◽

Vol 216 (5) ◽

pp. 1199-1213 ◽

Cited By ~ 19

Author(s):

Matthieu Gratia ◽

Mathieu P. Rodero ◽

Cécile Conrad ◽

Elias Bou Samra ◽

Mathieu Maurin ◽

...

Keyword(s):

Dna Damage ◽

Immune Responses ◽

Genome Instability ◽

Bloom Syndrome ◽

Innate Immune ◽

Genome Integrity ◽

Immune Sensing ◽

Syndrome Protein ◽

Innate Immune Sensing ◽

Exonuclease Trex1

Cellular innate immune sensors of DNA are essential for host defense against invading pathogens. However, the presence of self-DNA inside cells poses a risk of triggering unchecked immune responses. The mechanisms limiting induction of inflammation by self-DNA are poorly understood. BLM RecQ–like helicase is essential for genome integrity and is deficient in Bloom syndrome (BS), a rare genetic disease characterized by genome instability, accumulation of micronuclei, susceptibility to cancer, and immunodeficiency. Here, we show that BLM-deficient fibroblasts show constitutive up-regulation of inflammatory interferon-stimulated gene (ISG) expression, which is mediated by the cGAS–STING–IRF3 cytosolic DNA–sensing pathway. Increased DNA damage or down-regulation of the cytoplasmic exonuclease TREX1 enhances ISG expression in BLM-deficient fibroblasts. cGAS-containing cytoplasmic micronuclei are increased in BS cells. Finally, BS patients demonstrate elevated ISG expression in peripheral blood. These results reveal that BLM limits ISG induction, thus connecting DNA damage to cellular innate immune response, which may contribute to human pathogenesis.

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Interplay between Cellular Metabolism and the DNA Damage Response in Cancer

Cancers ◽

10.3390/cancers12082051 ◽

2020 ◽

Vol 12 (8) ◽

pp. 2051 ◽

Cited By ~ 2

Author(s):

Amandine Moretton ◽

Joanna I. Loizou

Keyword(s):

Dna Damage ◽

Dna Damage Response ◽

Metabolic Regulation ◽

Current Knowledge ◽

Cellular Metabolism ◽

Genome Integrity ◽

Cancer Treatments ◽

Damage Response ◽

Dynamic Interplay ◽

Remarkable Progress

Metabolism is a fundamental cellular process that can become harmful for cells by leading to DNA damage, for instance by an increase in oxidative stress or through the generation of toxic byproducts. To deal with such insults, cells have evolved sophisticated DNA damage response (DDR) pathways that allow for the maintenance of genome integrity. Recent years have seen remarkable progress in our understanding of the diverse DDR mechanisms, and, through such work, it has emerged that cellular metabolic regulation not only generates DNA damage but also impacts on DNA repair. Cancer cells show an alteration of the DDR coupled with modifications in cellular metabolism, further emphasizing links between these two fundamental processes. Taken together, these compelling findings indicate that metabolic enzymes and metabolites represent a key group of factors within the DDR. Here, we will compile the current knowledge on the dynamic interplay between metabolic factors and the DDR, with a specific focus on cancer. We will also discuss how recently developed high-throughput technologies allow for the identification of novel crosstalk between the DDR and metabolism, which is of crucial importance to better design efficient cancer treatments.

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TopBP1 is required at mitosis to reduce transmission of DNA damage to G1 daughter cells

The Journal of Cell Biology ◽

10.1083/jcb.201502107 ◽

2015 ◽

Vol 210 (4) ◽

pp. 565-582 ◽

Cited By ~ 52

Author(s):

Rune Troelsgaard Pedersen ◽

Thomas Kruse ◽

Jakob Nilsson ◽

Vibe H. Oestergaard ◽

Michael Lisby

Keyword(s):

Dna Damage ◽

Dna Synthesis ◽

Chromosome Segregation ◽

Nuclear Bodies ◽

Genome Integrity ◽

Unscheduled Dna Synthesis ◽

Focus Formation ◽

Mitotic Entry ◽

Daughter Cells ◽

Early Mitosis

Genome integrity is critically dependent on timely DNA replication and accurate chromosome segregation. Replication stress delays replication into G2/M, which in turn impairs proper chromosome segregation and inflicts DNA damage on the daughter cells. Here we show that TopBP1 forms foci upon mitotic entry. In early mitosis, TopBP1 marks sites of and promotes unscheduled DNA synthesis. Moreover, TopBP1 is required for focus formation of the structure-selective nuclease and scaffold protein SLX4 in mitosis. Persistent TopBP1 foci transition into 53BP1 nuclear bodies (NBs) in G1 and precise temporal depletion of TopBP1 just before mitotic entry induced formation of 53BP1 NBs in the next cell cycle, showing that TopBP1 acts to reduce transmission of DNA damage to G1 daughter cells. Based on these results, we propose that TopBP1 maintains genome integrity in mitosis by controlling chromatin recruitment of SLX4 and by facilitating unscheduled DNA synthesis.

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