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Lee JH. Oxidative stress and the multifaceted roles of ATM in maintaining cellular redox homeostasis. Redox Biol 2024; 75:103269. [PMID: 39018798 PMCID: PMC11301354 DOI: 10.1016/j.redox.2024.103269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 07/19/2024] Open
Abstract
The ataxia telangiectasia mutated (ATM) protein kinase is best known as a master regulator of the DNA damage response. However, accumulating evidence has unveiled an equally vital function for ATM in sensing oxidative stress and orchestrating cellular antioxidant defenses to maintain redox homeostasis. ATM can be activated through a non-canonical pathway involving intermolecular disulfide crosslinking of the kinase dimers, distinct from its canonical activation by DNA double-strand breaks. Structural studies have elucidated the conformational changes that allow ATM to switch into an active redox-sensing state upon oxidation. Notably, loss of ATM function results in elevated reactive oxygen species (ROS) levels, altered antioxidant profiles, and mitochondrial dysfunction across multiple cell types and tissues. This oxidative stress arising from ATM deficiency has been implicated as a central driver of the neurodegenerative phenotypes in ataxia-telangiectasia (A-T) patients, potentially through mechanisms involving oxidative DNA damage, PARP hyperactivation, and widespread protein aggregation. Moreover, defective ATM oxidation sensing disrupts transcriptional programs and RNA metabolism, with detrimental impacts on neuronal homeostasis. Significantly, antioxidant therapy can ameliorate cellular and organismal abnormalities in various ATM-deficient models. This review synthesizes recent advances illuminating the multifaceted roles of ATM in preserving redox balance and mitigating oxidative insults, providing a unifying paradigm for understanding the complex pathogenesis of A-T disease.
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Affiliation(s)
- Ji-Hoon Lee
- Department of Biological Sciences, Research Center of Ecomimetics, Chonnam National University, Gwangju, 61186, Republic of Korea.
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2
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Rinaldi F, Girotto S. Structure-based approaches in synthetic lethality strategies. Curr Opin Struct Biol 2024; 88:102895. [PMID: 39137490 DOI: 10.1016/j.sbi.2024.102895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/15/2024] [Accepted: 07/17/2024] [Indexed: 08/15/2024]
Abstract
Evolution has fostered robust DNA damage response (DDR) mechanisms to combat DNA lesions. However, disruptions in this intricate machinery can render cells overly reliant on the remaining functional but often less accurate DNA repair pathways. This increased dependence on error-prone pathways may result in improper repair and the accumulation of mutations, fostering genomic instability and facilitating the uncontrolled cell proliferation characteristic of cancer initiation and progression. Strategies based on the concept of synthetic lethality (SL) leverage the inherent genomic instability of cancer cells by targeting alternative pathways, thereby inducing selective death of cancer cells. This review emphasizes recent advancements in structural investigations of pivotal SL targets. The significant contribution of structure-based methodologies to SL research underscores their potential impact in characterizing the growing number of SL targets, largely due to advances in next-generation sequencing. Harnessing these approaches is essential for advancing the development of precise and personalized SL therapeutic strategies.
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Affiliation(s)
- Francesco Rinaldi
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - Stefania Girotto
- Structural Biophysics Facility, Istituto Italiano di Tecnologia, 16163 Genoa, Italy.
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3
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Jenni R, Klaa H, Khamessi O, Chikhaoui A, Najjar D, Ghedira K, Kraoua I, Turki I, Yacoub-Youssef H. Clinical and genetic spectrum of Ataxia Telangiectasia Tunisian patients: Bioinformatic analysis unveil mechanisms of ATM variants pathogenicity. Int J Biol Macromol 2024; 278:134444. [PMID: 39098699 DOI: 10.1016/j.ijbiomac.2024.134444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/28/2024] [Accepted: 08/01/2024] [Indexed: 08/06/2024]
Abstract
Ataxia Telangiectasia (AT) is a rare multisystemic neurodegenerative disease caused by biallelic mutations in the ATM gene. Few clinical studies on AT disease have been conducted in Tunisia, however, the mutational landscape is still undefined. Our aim is to determine the clinical and genetic spectrum of AT Tunisian patients and to explore the potential underlying mechanism of variant pathogenicity. Sanger sequencing was performed for nine AT patients. A comprehensive computational analysis was conducted to evaluate the possible pathogenic effect of ATM identified variants. Genetic screening of ATM gene has identified nine different variants from which six have not been previously reported. In silico analysis has predicted a pathogenic effect of identified mutations. This was corroborated by a structural bioinformatics study based on molecular modeling and docking for novel missense mutations. Our findings suggest a profound impact of identified mutations not only on the ATM protein stability, but also on the ATM-ligand interactions. Our study characterizes the mutational landscape of AT Tunisian patients which will allow to set up genetic counseling and prenatal diagnosis for families at risk and expand the spectrum of ATM variants worldwide. Furthermore, understanding the mechanism that underpin variant pathogenicity could provide further insights into disease pathogenesis.
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Affiliation(s)
- Rim Jenni
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, University Tunis El Manar, Tunis 1002, Tunisia.
| | - Hedia Klaa
- LR18SP04 and Department of Child and Adolescent Neurology, National Institute Mongi Ben Hmida of Neurology, 1007 Tunis, Tunisia.
| | - Oussema Khamessi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Institut Pasteur de Tunis (IPT), University of Tunis El Manar, Tunis, Tunisia; Institut de Biotechnologie de Sidi Thabet, Université de la Manouba, Ariana BP-66, Manouba 2010, Tunisia.
| | - Asma Chikhaoui
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, University Tunis El Manar, Tunis 1002, Tunisia.
| | - Dorra Najjar
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, University Tunis El Manar, Tunis 1002, Tunisia.
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Institut Pasteur de Tunis (IPT), University of Tunis El Manar, Tunis, Tunisia.
| | - Ichraf Kraoua
- LR18SP04 and Department of Child and Adolescent Neurology, National Institute Mongi Ben Hmida of Neurology, 1007 Tunis, Tunisia.
| | - Ilhem Turki
- LR18SP04 and Department of Child and Adolescent Neurology, National Institute Mongi Ben Hmida of Neurology, 1007 Tunis, Tunisia.
| | - Houda Yacoub-Youssef
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, University Tunis El Manar, Tunis 1002, Tunisia.
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4
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Comstock W, Sanford E, Navarro M, Smolka MB. Profiling Tel1 Signaling Reveals a Non-Canonical Motif Targeting DNA Repair and Telomere Control Machineries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.03.601872. [PMID: 39005478 PMCID: PMC11244986 DOI: 10.1101/2024.07.03.601872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The stability of the genome relies on Phosphatidyl Inositol 3-Kinase-related Kinases (PIKKs) that sense DNA damage and trigger elaborate downstream signaling responses. In S. cerevisiae, the Tel1 kinase (ortholog of human ATM) is activated at DNA double strand breaks (DSBs) and short telomeres. Despite the well-established roles of Tel1 in the control of telomere maintenance, suppression of chromosomal rearrangements, activation of cell cycle checkpoints, and repair of DSBs, the substrates through which Tel1 controls these processes remain incompletely understood. Here we performed an in depth phosphoproteomic screen for Tel1-dependent phosphorylation events. To achieve maximal coverage of the phosphoproteome, we developed a scaled-up approach that accommodates large amounts of protein extracts and chromatographic fractions. Compared to previous reports, we expanded the number of detected Tel1-dependent phosphorylation events by over 10-fold. Surprisingly, in addition to the identification of phosphorylation sites featuring the canonical motif for Tel1 phosphorylation (S/T-Q), the results revealed a novel motif (D/E-S/T) highly prevalent and enriched in the set of Tel1-dependent events. This motif is unique to Tel1 signaling and not shared with the Mec1 kinase, providing clues to how Tel1 plays specialized roles in DNA repair and telomere length control. Overall, these findings define a Tel1-signaling network targeting numerous proteins involved in DNA repair, chromatin regulation, and telomere maintenance that represents a framework for dissecting the molecular mechanisms of Tel1 action.
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Affiliation(s)
- Will Comstock
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Ethan Sanford
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Marcos Navarro
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Marcus B Smolka
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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5
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Marshall S, Navarro MVAS, Ascenҫão CFR, Dibitetto D, Smolka MB. In-depth mapping of DNA-PKcs signaling uncovers noncanonical features of its kinase specificity. J Biol Chem 2024; 300:107513. [PMID: 38945450 PMCID: PMC11327452 DOI: 10.1016/j.jbc.2024.107513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 06/11/2024] [Accepted: 06/25/2024] [Indexed: 07/02/2024] Open
Abstract
DNA-PKcs is a DNA damage sensor kinase with established roles in DNA double-strand break repair via nonhomologous end joining. Recent studies have revealed additional roles of DNA-PKcs in the regulation of transcription, translation, and DNA replication. However, the substrates through which DNA-PKcs regulates these processes remain largely undefined. Here, we utilized quantitative phosphoproteomics to generate a high coverage map of DNA-PKcs signaling in response to ionizing radiation and mapped its interplay with the ATM kinase. Beyond the detection of the canonical S/T-Q phosphorylation motif, we uncovered a noncanonical mode of DNA-PKcs signaling targeting S/T-ψ-D/E motifs. Sequence and structural analyses of the DNA-PKcs substrate recognition pocket revealed unique features compared to closely related phosphatidylinositol 3-kinase-related kinases that may explain its broader substrate preference. These findings expand the repertoire of DNA-PKcs and ATM substrates while establishing a novel preferential phosphorylation motif for DNA-PKcs.
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Affiliation(s)
- Shannon Marshall
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Marcos V A S Navarro
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA; IFSC Institute of Physics of São Carlos, University of São Paulo, São Carlos, São Paulo, Brazil.
| | - Carolline F R Ascenҫão
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Diego Dibitetto
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA; Department of Experimental Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Marcus B Smolka
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA.
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6
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Stuart A, de Lange T. Replicative senescence is ATM driven, reversible, and accelerated by hyperactivation of ATM at normoxia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600514. [PMID: 38979390 PMCID: PMC11230194 DOI: 10.1101/2024.06.24.600514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Programmed telomere shortening limits tumorigenesis through the induction of replicative senescence. Here we address three long-standing questions concerning senescence. First, we show that the ATM kinase is solely responsible for the induction of replicative senescence. Senescence was delayed by ATM inhibition (ATMi) or overexpression of TRF2, the shelterin subunit dedicated to ATM repression. In contrast, there was no evidence for ATR signaling contributing to replicative senescence even when ATMi was combined with ATR inhibition. Second, we show ATMi can induce apparently normal cell divisions in a subset of senescent cells, indicating that senescence can be reversed. Third, we show that the extended replicative life span at low (physiological) oxygen is due to diminished ATM activity. At low oxygen, cells show a decreased ATM response to dysfunctional telomeres and genome-wide DSBs compared to 20% oxygen. As this effect could be reversed by NAC, the attenuated response of ATM to critically short telomeres and the resulting extended life span at low oxygen is likely due to ROS-induced formation of cysteine disulfide-bridges that crosslink ATM dimers into a form that is not activated by DSBs. These findings show how primary human cells detect shortened telomeres and reveal the molecular mechanism underlying the telomere tumor suppressor pathway.
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Affiliation(s)
- Alexander Stuart
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, USA
| | - Titia de Lange
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, USA
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7
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Gathings A, Zaman V, Banik NL, Haque A. Insights into Calpain Activation and Rho-ROCK Signaling in Parkinson's Disease and Aging. Biomedicines 2024; 12:1074. [PMID: 38791036 PMCID: PMC11117523 DOI: 10.3390/biomedicines12051074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/26/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024] Open
Abstract
Parkinson's disease (PD), a progressive neurodegenerative disease, has no cure, and current therapies are not effective at halting disease progression. The disease affects mid-brain dopaminergic neurons and, subsequently, the spinal cord, contributing to many debilitating symptoms associated with PD. The GTP-binding protein, Rho, plays a significant role in the cellular pathology of PD. The downstream effector of Rho, Rho-associated kinase (ROCK), plays multiple functions, including microglial activation and induction of inflammatory responses. Activated microglia have been implicated in the pathology of many neurodegenerative diseases, including PD, that initiate inflammatory responses, leading to neuron death. Calpain expression and activity is increased following glial activation, which triggers the Rho-ROCK pathway and induces inflammatory T cell activation and migration as well as mediates toxic α-synuclein (α-syn) aggregation and neuron death, indicating a pivotal role for calpain in the inflammatory and degenerative processes in PD. Increased calpain activity and Rho-ROCK activation may represent a new mechanism for increased oxidative damage in aging. This review will summarize calpain activation and the role of the Rho-ROCK pathway in oxidative stress and α-syn aggregation, their influence on the neurodegenerative process in PD and aging, and possible strategies and research directions for therapeutic intervention.
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Affiliation(s)
- Amy Gathings
- Department of Microbiology and Immunology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC 29425, USA; (A.G.); (N.L.B.)
- Department of Neurosurgery, Medical University of South Carolina, 96 Jonathan Lucas Street, Charleston, SC 29425, USA;
| | - Vandana Zaman
- Department of Neurosurgery, Medical University of South Carolina, 96 Jonathan Lucas Street, Charleston, SC 29425, USA;
- Ralph H. Johnson Veterans Administration Medical Center, 109 Bee Street, Charleston, SC 29401, USA
| | - Narendra L. Banik
- Department of Microbiology and Immunology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC 29425, USA; (A.G.); (N.L.B.)
- Department of Neurosurgery, Medical University of South Carolina, 96 Jonathan Lucas Street, Charleston, SC 29425, USA;
- Ralph H. Johnson Veterans Administration Medical Center, 109 Bee Street, Charleston, SC 29401, USA
| | - Azizul Haque
- Department of Microbiology and Immunology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC 29425, USA; (A.G.); (N.L.B.)
- Department of Neurosurgery, Medical University of South Carolina, 96 Jonathan Lucas Street, Charleston, SC 29425, USA;
- Ralph H. Johnson Veterans Administration Medical Center, 109 Bee Street, Charleston, SC 29401, USA
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8
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Alanazi AFR, Parkinson GN, Haider S. Structural Motifs at the Telomeres and Their Role in Regulatory Pathways. Biochemistry 2024; 63:827-842. [PMID: 38481135 PMCID: PMC10993422 DOI: 10.1021/acs.biochem.4c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Telomeres are specialized structures, found at the ends of linear chromosomes in eukaryotic cells, that play a crucial role in maintaining the stability and integrity of genomes. They are composed of repetitive DNA sequences, ssDNA overhangs, and several associated proteins. The length of telomeres is linked to cellular aging in humans, and deficiencies in their maintenance are associated with various diseases. Key structural motifs at the telomeres serve to protect vulnerable chromosomal ends. Telomeric DNA also has the ability to form diverse complex DNA higher-order structures, including T-loops, D-loops, R-loops, G-loops, G-quadruplexes, and i-motifs, in the complementary C-rich strand. While many essential proteins at telomeres have been identified, the intricacies of their interactions and structural details are still not fully understood. This Perspective highlights recent advancements in comprehending the structures associated with human telomeres. It emphasizes the significance of telomeres, explores various telomeric structural motifs, and delves into the structural biology surrounding telomeres and telomerase. Furthermore, telomeric loops, their topologies, and the associated proteins that contribute to the safeguarding of telomeres are discussed.
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Affiliation(s)
- Abeer F R Alanazi
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Gary N Parkinson
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Shozeb Haider
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
- UCL Centre for Advanced Research Computing, University College London, London WC1H 9RN, United Kingdom
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Woolley PR, Wen X, Conway OM, Ender NA, Lee JH, Paull TT. Regulation of transcription patterns, poly(ADP-ribose), and RNA-DNA hybrids by the ATM protein kinase. Cell Rep 2024; 43:113896. [PMID: 38442018 PMCID: PMC11022685 DOI: 10.1016/j.celrep.2024.113896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 01/11/2024] [Accepted: 02/15/2024] [Indexed: 03/07/2024] Open
Abstract
The ataxia telangiectasia mutated (ATM) protein kinase is a master regulator of the DNA damage response and also an important sensor of oxidative stress. Analysis of gene expression in ataxia-telangiectasia (A-T) patient brain tissue shows that large-scale transcriptional changes occur in patient cerebellum that correlate with the expression level and guanine-cytosine (GC) content of transcribed genes. In human neuron-like cells in culture, we map locations of poly(ADP-ribose) and RNA-DNA hybrid accumulation genome-wide with ATM inhibition and find that these marks also coincide with high transcription levels, active transcription histone marks, and high GC content. Antioxidant treatment reverses the accumulation of R-loops in transcribed regions, consistent with the central role of reactive oxygen species in promoting these lesions. Based on these results, we postulate that transcription-associated lesions accumulate in ATM-deficient cells and that the single-strand breaks and PARylation at these sites ultimately generate changes in transcription that compromise cerebellum function and lead to neurodegeneration over time in A-T patients.
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Affiliation(s)
- Phillip R Woolley
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Xuemei Wen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Olivia M Conway
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Nicolette A Ender
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ji-Hoon Lee
- Department of Biological Sciences, Research Center of Ecomimetics, Chonnam National University, Gwangju 61186, Republic of Korea.
| | - Tanya T Paull
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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10
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Paull TT, Woolley PR. A-T neurodegeneration and DNA damage-induced transcriptional stress. DNA Repair (Amst) 2024; 135:103647. [PMID: 38377644 DOI: 10.1016/j.dnarep.2024.103647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/08/2024] [Indexed: 02/22/2024]
Abstract
Loss of the ATM protein kinase in humans results in Ataxia-telangiectasia, a disorder characterized by childhood-onset neurodegeneration of the cerebellum as well as cancer predisposition and immunodeficiency. Although many aspects of ATM function are well-understood, the mechanistic basis of the progressive cerebellar ataxia that occurs in patients is not. Here we review recent progress related to the role of ATM in neurons and the cerebellum that comes from many sources: animal models, post-mortem brain tissue samples, and human neurons in culture. These observations have revealed new insights into the consequences of ATM loss on DNA damage, gene expression, and immune signaling in the brain. Many results point to the importance of reactive oxygen species as well as single-strand DNA breaks in the progression of molecular events leading to neuronal dysfunction. In addition, innate immunity signaling pathways appear to play a critical role in ATM functions in microglia, responding to various forms of nucleic acid sensors and regulating survival of neurons and other cell types. Overall, the results lead to an updated view of transcriptional stress and DNA damage resulting from ATM loss that results in changes in gene expression as well as neuroinflammation that contribute to the cerebellar neurodegeneration observed in patients.
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Affiliation(s)
- Tanya T Paull
- The University of Texas at Austin, Department of Molecular Biosciences, Austin, TX 78712, USA.
| | - Phillip R Woolley
- The University of Texas at Austin, Department of Molecular Biosciences, Austin, TX 78712, USA
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11
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Woolley PR, Wen X, Conway OM, Ender NA, Lee JH, Paull TT. Regulation of transcription patterns, poly-ADP-ribose, and RNA-DNA hybrids by the ATM protein kinase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.570417. [PMID: 38106035 PMCID: PMC10723464 DOI: 10.1101/2023.12.06.570417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The ATM protein kinase is a master regulator of the DNA damage response and also an important sensor of oxidative stress. Analysis of gene expression in Ataxia-telangiectasia patient brain tissue shows that large-scale transcriptional changes occur in patient cerebellum that correlate with expression level and GC content of transcribed genes. In human neuron-like cells in culture we map locations of poly-ADP-ribose and RNA-DNA hybrid accumulation genome-wide with ATM inhibition and find that these marks also coincide with high transcription levels, active transcription histone marks, and high GC content. Antioxidant treatment reverses the accumulation of R-loops in transcribed regions, consistent with the central role of ROS in promoting these lesions. Based on these results we postulate that transcription-associated lesions accumulate in ATM-deficient cells and that the single-strand breaks and PARylation at these sites ultimately generate changes in transcription that compromise cerebellum function and lead to neurodegeneration over time in A-T patients.
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Affiliation(s)
- Phillip R. Woolley
- The University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, 78712
| | - Xuemei Wen
- The University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, 78712
| | - Olivia M. Conway
- The University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, 78712
| | - Nicolette A. Ender
- The University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, 78712
| | - Ji-Hoon Lee
- Department of Biological Sciences, Research Center of Ecomimetics, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Tanya T. Paull
- The University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, 78712
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