DNA damage and chromatin rearrangement in promoting neurodegeneration: role of hallmark proteins

Angeline Julius, Suresh Malakondaiah, Raghu Babu Pothireddy

Genome Instability & Disease ›› 2024

Genome Instability & Disease ›› 2024 DOI: 10.1007/s42764-024-00142-8
Review Article

DNA damage and chromatin rearrangement in promoting neurodegeneration: role of hallmark proteins

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Abstract

Numerous genetic and environmental factors contribute to neurodegenerative diseases characterized by damage to the DNA and changes in the chromatin structure. Many studies have shown that DNA damage and chromatin organization are closely linked, but more research is needed to fully understand this connection, especially in neurodegenerative diseases. Important proteins implicated in neurodegenerative disorders have been linked to chromatin reconfiguration and DNA damage, according to recent research. Epigenetic interventions such as HDAC inhibitors approved for cancer therapy, can be repurposed for neurodegenerative diseases. Furthermore, microRNAs, often dysregulated in neurodegenerative conditions, could be targeted to restore normal gene regulation. Exploring these strategies could lead to more effective treatments by addressing the fundamental epigenetic and chromatin-related mechanisms involved in neurodegeneration. This review discusses the relationship between the contributing proteins and various neurodegenerative diseases, with particular attention to key proteins like tau, which is associated with microtubules, superoxide dismutase 1, huntingtin, α-synuclein, β-amyloid precursor protein and TAR DNA/RNA binding protein 43 and their role in DNA protection and damage repair.

Keywords

Neurodegenerative diseases / DNA damage / Chromatin organization / Hallmark proteins / Neurological disorders

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Angeline Julius, Suresh Malakondaiah, Raghu Babu Pothireddy. DNA damage and chromatin rearrangement in promoting neurodegeneration: role of hallmark proteins. Genome Instability & Disease, 2024 https://doi.org/10.1007/s42764-024-00142-8

References

Aricthota S, Rana PP, Haldar D. Histone acetylation dynamics in repair of DNA double-strand breaks. Frontiers in Genetics, 2022, 13
CrossRef Google scholar
Bampton A, Gittings LM, Fratta P, Lashley T, Gatt A. The role of hnRNPs in frontotemporal dementia and amyotrophic lateral sclerosis. Acta Neuropathologica, 2020, 140(5): 599-623
CrossRef Google scholar
Benhelli-Mokrani H, Mansuroglu Z, Chauderlier A, Albaud B, Gentien D, Sommer S, Schirmer C, Laqueuvre L, Josse T, Buée L. Genome-wide identification of genic and intergenic neuronal DNA regions bound by Tau protein under physiological and stress conditions. Nucleic Acids Research, 2018, 46(21): 11405-11422
Boutajangout A, Sigurdsson EM, Krishnamurthy K, P. . Tau as a therapeutic target for Alzheimer’s disease. Current Alzheimer Research, 2011, 8(6): 666-677
CrossRef Google scholar
Chantalat S, Depaux A, Héry P, Barral S, Thuret J-Y, Dimitrov S, Gérard M. Histone H3 trimethylation at lysine 36 is associated with constitutive and facultative heterochromatin. Genome Research, 2011, 21(9): 1426-1437
CrossRef Google scholar
Chen Y, Yu Y. Tau and neuroinflammation in Alzheimer’s disease: Interplay mechanisms and clinical translation. Journal of Neuroinflammation, 2023, 20(1): 165
CrossRef Google scholar
Costa RG, Conceição A, Matos CA, Nóbrega C. The polyglutamine protein ATXN2: From its molecular functions to its involvement in disease. Cell Death and Disease, 2024, 15(6): 415
CrossRef Google scholar
Fujii J, Homma T, Osaki T. Superoxide radicals in the execution of cell death. Antioxidants, 2022, 11(3): 501
CrossRef Google scholar
Gao R, Chakraborty A, Geater C, Pradhan S, Gordon KL, Snowden J, Yuan S, Dickey AS, Choudhary S, Ashizawa T. Mutant huntingtin impairs PNKP and ATXN3, disrupting DNA repair and transcription. eLife, 2019, 8
CrossRef Google scholar
Gimenez J, Spalloni A, Cappelli S, Ciaiola F, Orlando V, Buratti E, Longone P. TDP-43 epigenetic facets and their neurodegenerative implications. International Journal of Molecular Sciences, 2023, 24(18): 13807
CrossRef Google scholar
Gomes TM, Sousa P, Campos C, Perestrelo R, Câmara JS. Secondary bioactive metabolites from foods of plant origin as theravention agents against neurodegenerative disorders. Foods, 2024, 13(14): 2289
CrossRef Google scholar
Gong J, Huang M, Wang F, Ma X, Liu H, Tu Y, Xing L, Zhu X, Zheng H, Fang J. RBM45 competes with HDAC1 for binding to FUS in response to DNA damage. Nucleic Acids Research, 2017, 45(22): 12862-12876
CrossRef Google scholar
Goodnight AV, Kremsky I, Khampang S, Jung YH, Billingsley JM, Bosinger SE, Corces VG, Chan AWS. Chromatin accessibility and transcription dynamics during in vitro astrocyte differentiation of Huntington’s disease monkey pluripotent stem cells. Epigenetics and Chromatin, 2019, 12: 1-25
CrossRef Google scholar
Hitchler MJ, Domann FE. The epigenetic and morphogenetic effects of molecular oxygen and its derived reactive species in development. Free Radical Biology and Medicine, 2021, 170: 70-84
CrossRef Google scholar
Hwang YJ, Hyeon SJ, Kim Y, Lim S, Lee MY, Kim J, Londhe AM, Gotina L, Kim Y, Pae AN. Modulation of SETDB1 activity by APQ ameliorates heterochromatin condensation, motor function, and neuropathology in a Huntington’s disease mouse model. Journal of Enzyme Inhibition and Medicinal Chemistry, 2021, 36(1): 856-868
CrossRef Google scholar
Jagaraj CJ, Shadfar S, Kashani SA, Saravanabavan S, Farzana F, Atkin JD. Molecular hallmarks of ageing in amyotrophic lateral sclerosis. Cellular and Molecular Life Sciences, 2024, 81(1): 111
CrossRef Google scholar
Jo M, Lee S, Jeon Y-M, Kim S, Kwon Y, Kim H-J. The role of TDP-43 propagation in neurodegenerative diseases: Integrating insights from clinical and experimental studies. Experimental and Molecular Medicine, 2020, 52(10): 1652-1662
CrossRef Google scholar
Klaric JA, Wüst S, Panier S. New faces of old friends: Emerging new roles of RNA-binding proteins in the DNA double-strand break response. Frontiers in Molecular Biosciences, 2021, 8
CrossRef Google scholar
Konopka A, Atkin JD. The role of DNA damage in neural plasticity in physiology and neurodegeneration. Frontiers in Cellular Neuroscience, 2022, 16
CrossRef Google scholar
Li JY, Popovic N, Brundin P. The use of the R6 transgenic mouse models of Huntington’s disease in attempts to develop novel therapeutic strategies. NeuroRx, 2005, 2(3): 447-464
CrossRef Google scholar
Liu L, Tong H, Sun Y, Chen X, Yang T, Zhou G, Li X-J, Li S. Huntingtin interacting proteins and pathological implications. International Journal of Molecular Sciences, 2023, 24(17): 13060
CrossRef Google scholar
Liu R, Wu J, Guo H, Yao W, Li S, Lu Y, Jia Y, Liang X, Tang J, Zhang H. Post-translational modifications of histones: Mechanisms, biological functions, and therapeutic targets. MedComm, 2023, 4(3):
CrossRef Google scholar
Mariño-Ramírez L, Kann MG, Shoemaker BA, Landsman D. Histone structure and nucleosome stability. Expert Review of Proteomics, 2005, 2(5): 719-729
CrossRef Google scholar
Mateos-Aparicio P, Rodríguez-Moreno A. The impact of studying brain plasticity. Frontiers in Cellular Neuroscience, 2019, 13: 66
CrossRef Google scholar
McCarthy RL, Kaeding KE, Keller SH, Zhong Y, Xu L, Hsieh A, Hou Y, Donahue G, Becker JS, Alberto O. Diverse heterochromatin-associated proteins repress distinct classes of genes and repetitive elements. Nature Cell Biology, 2021, 23(8): 905-914
CrossRef Google scholar
Nacev BA, Dabas Y, Paul MR, Pacheco C, Mitchener M, Perez Y, Fang Y, Soshnev AA, Barrows D, Carroll T. Cancer-associated histone H3 N-terminal arginine mutations disrupt PRC2 activity and impair differentiation. Nature Communications, 2024, 15(1): 5155
CrossRef Google scholar
Niu Y, Pal A, Szewczyk B, Japtok J, Naumann M, Glaß H, Hermann A. Cell-type-dependent recruitment dynamics of FUS protein at laser-induced DNA damage sites. International Journal of Molecular Sciences, 2024, 25(6): 3526
CrossRef Google scholar
Orobets KS, Karamyshev AL. Amyloid precursor protein and Alzheimer’s disease. International Journal of Molecular Sciences, 2023, 24(19): 14794
CrossRef Google scholar
Otero-Garcia M, Mahajani SU, Wakhloo D, Tang W, Xue Y-Q, Morabito S, Pan J, Oberhauser J, Madira AE, Shakouri T. Molecular signatures underlying neurofibrillary tangle susceptibility in Alzheimer’s disease. Neuron, 2022, 110(18): 2929-2948
CrossRef Google scholar
Provasek VE, Bacolla A, Rangaswamy S, Mitra J, Kodavati M, Yusuf IO, Malojirao VH, Vasquez V, Britz GW, Li G-M (2024) RNA/DNA binding protein TDP43 regulates DNA mismatch repair genes with implications for genome stability. BioRxiv
Rane JS, Kumari A, Panda D. The acetyl mimicking mutation, K274Q in tau, enhances the metal binding affinity of tau and reduces the ability of tau to protect DNA. ACS Chemical Neuroscience, 2019, 11(3): 291-303
CrossRef Google scholar
Roberts A, Swerdlow RH, Wang N. Adaptive and maladaptive DNA breaks in neuronal physiology and Alzheimer’s disease. International Journal of Molecular Sciences, 2024, 25(14): 7774
CrossRef Google scholar
Sharma H. DNA damage and chromatin rearrangement work together to promote neurodegeneration.. Molecular Neurobiology, 2024, 2024: 1-19
Shishido R, Kunii Y, Hino M, Izumi R, Nagaoka A, Hayashi H, Kakita A, Tomita H, Yabe H. Evidence for increased DNA damage repair in the postmortem brain of the high stress-response group of schizophrenia. Frontiers in Psychiatry, 2023, 14: 1183696
CrossRef Google scholar
Shrivastav M, De Haro LP, Nickoloff JA. Regulation of DNA double-strand break repair pathway choice. Cell Research, 2008, 18(1): 134-147
CrossRef Google scholar
Shukla S, Tekwani BL. Histone deacetylases inhibitors in neurodegenerative diseases, neuroprotection and neuronal differentiation. Frontiers in Pharmacology, 2020, 11: 537
CrossRef Google scholar
Shum C, Hedges EC, Allison J, Lee Y, Arias N, Cocks G, Chandran S, Ruepp M-D, Shaw CE, Nishimura AL. Mutations in FUS lead to synaptic dysregulation in ALS-iPSC derived neurons. Stem Cell Reports, 2024, 19(2): 187-195
CrossRef Google scholar
Song H, Shen R, Liu X, Yang X, Xie K, Guo Z, Wang D. Histone post-translational modification and the DNA damage response. Genes and Diseases, 2023, 10(4): 1429-1444
CrossRef Google scholar
Sugeno N, Hasegawa T. Unraveling the complex interplay between alpha-synuclein and epigenetic modification. International Journal of Molecular Sciences, 2023, 24(7): 6645
CrossRef Google scholar
Sun X, Gao C, Xu X, Li M, Zhao X, Wang Y, Wang Y, Zhang S, Yan Z, Liu X. FBL promotes cancer cell resistance to DNA damage and BRCA1 transcription via YBX1. EMBO Reports, 2023, 24(9):
CrossRef Google scholar
Surguchov A. α-Synuclein and mechanisms of epigenetic regulation. Brain Sciences, 2023, 13(1): 150
CrossRef Google scholar
Suzuki N, Nishiyama A, Warita H, Aoki M. Genetics of amyotrophic lateral sclerosis: Seeking therapeutic targets in the era of gene therapy. Journal of Human Genetics, 2023, 68(3): 131-152
CrossRef Google scholar
Tiwari V, Wilson DM. DNA damage and associated DNA repair defects in disease and premature aging. The American Journal of Human Genetics, 2019, 105(2): 237-257
CrossRef Google scholar
Welch G, Tsai L. Mechanisms of DNA damage-mediated neurotoxicity in neurodegenerative disease. EMBO Reports, 2022, 23(6):
CrossRef Google scholar
Wiench M, Miranda TB, Hager GL. Control of nuclear receptor function by local chromatin structure. The FEBS Journal, 2011, 278(13): 2211-2230
CrossRef Google scholar
Xiao W, Zhou Q, Wen X, Wang R, Liu R, Wang T, Shi J, Hu Y, Hou J. Small-molecule inhibitors overcome epigenetic reprogramming for cancer therapy. Frontiers in Pharmacology, 2021, 12
CrossRef Google scholar
Yabata H, Riku Y, Miyahara H, Akagi A, Sone J, Urushitani M, Yoshida M, Iwasaki Y. Nuclear expression of TDP-43 is linked with morphology and ubiquitylation of cytoplasmic aggregates in amyotrophic lateral sclerosis. International Journal of Molecular Sciences, 2023, 24(15): 12176
CrossRef Google scholar
Yazar V, Kühlwein JK, Knehr A, Grozdanov V, Ekici AB, Ludolph AC, Danzer KM. Impaired ATF3 signaling involves SNAP25 in SOD1 mutant ALS patients. Scientific Reports, 2023, 13(1): 12019
CrossRef Google scholar

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