1
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Li Y, Tian X, Luo J, Bao T, Wang S, Wu X. Molecular mechanisms of aging and anti-aging strategies. Cell Commun Signal 2024; 22:285. [PMID: 38790068 PMCID: PMC11118732 DOI: 10.1186/s12964-024-01663-1] [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: 02/03/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Aging is a complex and multifaceted process involving a variety of interrelated molecular mechanisms and cellular systems. Phenotypically, the biological aging process is accompanied by a gradual loss of cellular function and the systemic deterioration of multiple tissues, resulting in susceptibility to aging-related diseases. Emerging evidence suggests that aging is closely associated with telomere attrition, DNA damage, mitochondrial dysfunction, loss of nicotinamide adenine dinucleotide levels, impaired macro-autophagy, stem cell exhaustion, inflammation, loss of protein balance, deregulated nutrient sensing, altered intercellular communication, and dysbiosis. These age-related changes may be alleviated by intervention strategies, such as calorie restriction, improved sleep quality, enhanced physical activity, and targeted longevity genes. In this review, we summarise the key historical progress in the exploration of important causes of aging and anti-aging strategies in recent decades, which provides a basis for further understanding of the reversibility of aging phenotypes, the application prospect of synthetic biotechnology in anti-aging therapy is also prospected.
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Affiliation(s)
- Yumeng Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences; National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Xutong Tian
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences; National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Juyue Luo
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences; National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Tongtong Bao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences; National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Shujin Wang
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Xin Wu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences; National Center of Technology Innovation for Synthetic Biology, Tianjin, China.
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2
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Dubey SK, Dubey R, Kleinman ME. Unraveling Histone Loss in Aging and Senescence. Cells 2024; 13:320. [PMID: 38391933 PMCID: PMC10886805 DOI: 10.3390/cells13040320] [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: 12/31/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
As the global population experiences a notable surge in aging demographics, the need to understand the intricate molecular pathways exacerbated by age-related stresses, including epigenetic dysregulation, becomes a priority. Epigenetic mechanisms play a critical role in driving age-related diseases through altered gene expression, genomic instability, and irregular chromatin remodeling. In this review, we focus on histones, a central component of the epigenome, and consolidate the key findings of histone loss and genome-wide redistribution as fundamental processes contributing to aging and senescence. The review provides insights into novel histone expression profiles, nucleosome occupancy, disruptions in higher-order chromatin architecture, and the emergence of noncanonical histone variants in the aging cellular landscape. Furthermore, we explore the current state of our understanding of the molecular mechanisms of histone deficiency in aging cells. Specific emphasis is placed on highlighting histone degradation pathways in the cell and studies that have explored potential strategies to mitigate histone loss or restore histone levels in aging cells. Finally, in addressing future perspectives, the insights gained from this review hold profound implications for advancing strategies that actively intervene in modulating histone expression profiles in the context of cellular aging and identifying potential therapeutic targets for alleviating a multitude of age-related diseases.
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Affiliation(s)
| | | | - Mark Ellsworth Kleinman
- Department of Surgery, East Tennessee State University, Johnson City, TN 37614, USA; (S.K.D.); (R.D.)
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3
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Khamwachirapithak P, Guillaume-Schoepfer D, Chansongkrow P, Teichmann SA, Wigge PA, Charoensawan V. Characterizing Different Modes of Interplay Between Rap1 and H3 Using Inducible H3-depletion Yeast. J Mol Biol 2023; 435:168355. [PMID: 37935256 DOI: 10.1016/j.jmb.2023.168355] [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: 08/02/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/09/2023]
Abstract
Histones and transcription factors (TFs) are two important DNA-binding proteins that interact, compete, and together regulate transcriptional processes in response to diverse internal and external stimuli. Condition-specific depletion of histones in Saccharomyces cerevisiae using a galactose-inducible H3 promoter provides a suitable framework for examining transcriptional alteration resulting from reduced nucleosome content. However, the effect on DNA binding activities of TFs is yet to be fully explored. In this work, we combine ChIP-seq of H3 with RNA-seq to elucidate the genome-scale relationships between H3 occupancy patterns and transcriptional dynamics before and after global H3 depletion. ChIP-seq of Rap1 is also conducted in the H3-depletion and control treatments, to investigate the interplay between this master regulator TF and nucleosomal H3, and to explore the impact on diverse transcriptional responses of different groups of target genes and functions. Ultimately, we propose a working model and testable hypotheses regarding the impact of global and local H3 depletion on transcriptional changes. We also demonstrate different potential modes of interaction between Rap1 and H3, which sheds light on the potential multifunctional regulatory capabilities of Rap1 and potentially other pioneer factors.
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Affiliation(s)
- Peerapat Khamwachirapithak
- Doctor of Philosophy Program in Biochemistry (International Program), Faculty of Science, Mahidol University, Bangkok, Thailand; Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Pakkanan Chansongkrow
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK; Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK.
| | - Philip A Wigge
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom; University Potsdam, Institute for Biochemistry and Biology, Molecular Biology, Karl-Liebknecht-Str, Potsdam-Golm, Germany; Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany.
| | - Varodom Charoensawan
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand; Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom; Systems Biology of Diseases Research Unit, Faculty of Science, Mahidol University, Bangkok, Thailand; Integrative Computational BioScience (ICBS) center, Mahidol University, Nakhon Pathom, Thailand; School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand.
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4
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Abstract
Keratinocyte senescence contributes to skin ageing and epidermal dysfunction. According to the existing knowledge, the transcription factor ΔNp63α plays pivotal roles in differentiation and proliferation of keratinocytes. It is traditionally accepted that ΔNp63α exerts its functions via binding to promoter regions to activate or repress gene transcription. However, accumulating evidence demonstrates that ΔNp63α can bind to elements away from promoter regions of its target genes, mediating epigenetic regulation. On the other hand, several epigenetic alterations, including DNA methylation, histone modification and variation, chromatin remodelling, as well as enhancer-promoter looping, are found to be related to cell senescence. To systematically elucidate how ΔNp63α affects keratinocyte senescence via epigenetic regulation, we comprehensively compiled the literatures on the roles of ΔNp63α in keratinocyte senescence, epigenetics in cellular senescence, and the relation between ΔNp63α-mediated epigenetic regulation and keratinocyte senescence. Based on the published data, we conclude that ΔNp63α mediates epigenetic regulation via multiple mechanisms: recruiting epigenetic enzymes to modify DNA or histones, coordinating chromatin remodelling complexes (CRCs) or regulating their expression, and mediating enhancer-promoter looping. Consequently, the expression of genes related to cell cycle is modulated, and proliferation of keratinocytes and renewal of stem cells are maintained, by ΔNp63α. During skin inflammaging, the decline of ΔNp63α may lead to epigenetic dysregulation, resultantly deteriorating keratinocyte senescence.
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Affiliation(s)
- Linghan Kuang
- Department of Laboratory Medicine, West China Second University Hospital, Sichuan University, Chengdu 610041, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu 610041, China
| | - Chenghua Li
- Center of Growth, Metabolism and Aging, Key Laboratory of Biological Resources and Ecological Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
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5
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Touray AO, Rajesh R, Isebe T, Sternlieb T, Loock M, Kutova O, Cestari I. PI(3,4,5)P3 allosteric regulation of repressor activator protein 1 controls antigenic variation in trypanosomes. eLife 2023; 12:RP89331. [PMID: 38019264 PMCID: PMC10686619 DOI: 10.7554/elife.89331] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023] Open
Abstract
African trypanosomes evade host immune clearance by antigenic variation, causing persistent infections in humans and animals. These parasites express a homogeneous surface coat of variant surface glycoproteins (VSGs). They transcribe one out of hundreds of VSG genes at a time from telomeric expression sites (ESs) and periodically change the VSG expressed by transcriptional switching or recombination. The mechanisms underlying the control of VSG switching and its developmental silencing remain elusive. We report that telomeric ES activation and silencing entail an on/off genetic switch controlled by a nuclear phosphoinositide signaling system. This system includes a nuclear phosphatidylinositol 5-phosphatase (PIP5Pase), its substrate PI(3,4,5)P3, and the repressor-activator protein 1 (RAP1). RAP1 binds to ES sequences flanking VSG genes via its DNA binding domains and represses VSG transcription. In contrast, PI(3,4,5)P3 binds to the N-terminus of RAP1 and controls its DNA binding activity. Transient inactivation of PIP5Pase results in the accumulation of nuclear PI(3,4,5)P3, which binds RAP1 and displaces it from ESs, activating transcription of silent ESs and VSG switching. The system is also required for the developmental silencing of VSG genes. The data provides a mechanism controlling reversible telomere silencing essential for the periodic switching in VSG expression and its developmental regulation.
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Affiliation(s)
- Abdoulie O Touray
- Institute of Parasitology, McGill University, Sainte-Anne-de-BellevueMontrealCanada
- Division of Experimental Medicine, Department of Medicine, McGill UniversityMontrealCanada
| | - Rishi Rajesh
- Institute of Parasitology, McGill University, Sainte-Anne-de-BellevueMontrealCanada
| | - Tony Isebe
- Institute of Parasitology, McGill University, Sainte-Anne-de-BellevueMontrealCanada
| | - Tamara Sternlieb
- Institute of Parasitology, McGill University, Sainte-Anne-de-BellevueMontrealCanada
| | - Mira Loock
- Institute of Parasitology, McGill University, Sainte-Anne-de-BellevueMontrealCanada
| | - Oksana Kutova
- Institute of Parasitology, McGill University, Sainte-Anne-de-BellevueMontrealCanada
| | - Igor Cestari
- Institute of Parasitology, McGill University, Sainte-Anne-de-BellevueMontrealCanada
- Division of Experimental Medicine, Department of Medicine, McGill UniversityMontrealCanada
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6
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Kalmykova A. Telomere Checkpoint in Development and Aging. Int J Mol Sci 2023; 24:15979. [PMID: 37958962 PMCID: PMC10647821 DOI: 10.3390/ijms242115979] [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: 09/01/2023] [Revised: 10/19/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023] Open
Abstract
The maintenance of genome integrity through generations is largely determined by the stability of telomeres. Increasing evidence suggests that telomere dysfunction may trigger changes in cell fate, independently of telomere length. Telomeric multiple tandem repeats are potentially highly recombinogenic. Heterochromatin formation, transcriptional repression, the suppression of homologous recombination and chromosome end protection are all required for telomere stability. Genetic and epigenetic defects affecting telomere homeostasis may cause length-independent internal telomeric DNA damage. Growing evidence, including that based on Drosophila research, points to a telomere checkpoint mechanism that coordinates cell fate with telomere state. According to this scenario, telomeres, irrespective of their length, serve as a primary sensor of genome instability that is capable of triggering cell death or developmental arrest. Telomeric factors released from shortened or dysfunctional telomeres are thought to mediate these processes. Here, we discuss a novel signaling role for telomeric RNAs in cell fate and early development. Telomere checkpoint ensures genome stability in multicellular organisms but aggravates the aging process, promoting the accumulation of damaged and senescent cells.
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Affiliation(s)
- Alla Kalmykova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
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7
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Banerjee P, Rosales JE, Chau K, Nguyen MTH, Kotla S, Lin SH, Deswal A, Dantzer R, Olmsted-Davis EA, Nguyen H, Wang G, Cooke JP, Abe JI, Le NT. Possible molecular mechanisms underlying the development of atherosclerosis in cancer survivors. Front Cardiovasc Med 2023; 10:1186679. [PMID: 37332576 PMCID: PMC10272458 DOI: 10.3389/fcvm.2023.1186679] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/17/2023] [Indexed: 06/20/2023] Open
Abstract
Cancer survivors undergone treatment face an increased risk of developing atherosclerotic cardiovascular disease (CVD), yet the underlying mechanisms remain elusive. Recent studies have revealed that chemotherapy can drive senescent cancer cells to acquire a proliferative phenotype known as senescence-associated stemness (SAS). These SAS cells exhibit enhanced growth and resistance to cancer treatment, thereby contributing to disease progression. Endothelial cell (EC) senescence has been implicated in atherosclerosis and cancer, including among cancer survivors. Treatment modalities for cancer can induce EC senescence, leading to the development of SAS phenotype and subsequent atherosclerosis in cancer survivors. Consequently, targeting senescent ECs displaying the SAS phenotype hold promise as a therapeutic approach for managing atherosclerotic CVD in this population. This review aims to provide a mechanistic understanding of SAS induction in ECs and its contribution to atherosclerosis among cancer survivors. We delve into the mechanisms underlying EC senescence in response to disturbed flow and ionizing radiation, which play pivotal role in atherosclerosis and cancer. Key pathways, including p90RSK/TERF2IP, TGFβR1/SMAD, and BH4 signaling are explored as potential targets for cancer treatment. By comprehending the similarities and distinctions between different types of senescence and the associated pathways, we can pave the way for targeted interventions aim at enhancing the cardiovascular health of this vulnerable population. The insights gained from this review may facilitate the development of novel therapeutic strategies for managing atherosclerotic CVD in cancer survivors.
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Affiliation(s)
- Priyanka Banerjee
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, United States
| | - Julia Enterría Rosales
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- School of Medicine, Instituto Tecnológico de Monterrey, Guadalajara, Mexico
| | - Khanh Chau
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, United States
| | - Minh T. H. Nguyen
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, United States
- Department of Life Science, University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Sivareddy Kotla
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Steven H. Lin
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Anita Deswal
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Robert Dantzer
- Department of Symptom Research, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Elizabeth A. Olmsted-Davis
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, United States
| | - Hung Nguyen
- Cancer Division, Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Guangyu Wang
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, United States
| | - John P. Cooke
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, United States
| | - Jun-ichi Abe
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Nhat-Tu Le
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, United States
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8
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Rey-Millet M, Pousse M, Soithong C, Ye J, Mendez-Bermudez A, Gilson E. Senescence-associated transcriptional derepression in subtelomeres is determined in a chromosome-end-specific manner. Aging Cell 2023; 22:e13804. [PMID: 36924026 DOI: 10.1111/acel.13804] [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: 09/28/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 03/18/2023] Open
Abstract
Aging is a continuous process leading to physiological deterioration with age. One of the factors contributing to aging is telomere shortening, causing alterations in the protein protective complex named shelterin and replicative senescence. Here, we address the question of the link between this telomere shortening and the transcriptional changes occurring in senescent cells. We found that in replicative senescent cells, the genes whose expression escaped repression are enriched in subtelomeres. The shelterin protein TRF2 and the nuclear lamina factor Lamin B1, both downregulated in senescent cells, are involved in the regulation of some but not all of these subtelomeric genes, suggesting complex mechanisms of transcriptional regulation. Indeed, the subtelomeres containing these derepressed genes are enriched in factors of polycomb repression (EZH2 and H3K27me3), insulation (CTCF and MAZ), and cohesion (RAD21 and SMC3) while being associated with the open A-type chromatin compartment. These findings unveil that the subtelomere transcriptome associated with senescence is determined in a chromosome-end-specific manner according to the type of higher-order chromatin structure.
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Affiliation(s)
- Martin Rey-Millet
- CNRS, INSERM, IRCAN, Faculty of Medicine Nice, Université Côte d'Azur, Nice, France
| | - Mélanie Pousse
- CNRS, INSERM, IRCAN, Faculty of Medicine Nice, Université Côte d'Azur, Nice, France
| | - Chan Soithong
- CNRS, INSERM, IRCAN, Faculty of Medicine Nice, Université Côte d'Azur, Nice, France
| | - Jing Ye
- Department of Geriatrics, Medical center on Aging of Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,International Laboratory in Hematology, Cancer and Aging, Pôle Sino-Français de Recherches en Sciences du Vivant et Génomique, RuiJin Hospital, Shanghai Jiao Tong University School of Medicine/CNRS/INSERM/University Côte d'Azur, Shanghai, China
| | - Aaron Mendez-Bermudez
- CNRS, INSERM, IRCAN, Faculty of Medicine Nice, Université Côte d'Azur, Nice, France.,Department of Geriatrics, Medical center on Aging of Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,International Laboratory in Hematology, Cancer and Aging, Pôle Sino-Français de Recherches en Sciences du Vivant et Génomique, RuiJin Hospital, Shanghai Jiao Tong University School of Medicine/CNRS/INSERM/University Côte d'Azur, Shanghai, China
| | - Eric Gilson
- CNRS, INSERM, IRCAN, Faculty of Medicine Nice, Université Côte d'Azur, Nice, France.,Department of Geriatrics, Medical center on Aging of Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,International Laboratory in Hematology, Cancer and Aging, Pôle Sino-Français de Recherches en Sciences du Vivant et Génomique, RuiJin Hospital, Shanghai Jiao Tong University School of Medicine/CNRS/INSERM/University Côte d'Azur, Shanghai, China.,Department of medical genetics, CHU, Nice, France
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9
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D’Angiolo M, Yue JX, De Chiara M, Barré BP, Giraud Panis MJ, Gilson E, Liti G. Telomeres are shorter in wild Saccharomyces cerevisiae isolates than in domesticated ones. Genetics 2023; 223:iyac186. [PMID: 36563016 PMCID: PMC9991508 DOI: 10.1093/genetics/iyac186] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/02/2022] [Accepted: 12/03/2022] [Indexed: 12/24/2022] Open
Abstract
Telomeres are ribonucleoproteins that cap chromosome-ends and their DNA length is controlled by counteracting elongation and shortening processes. The budding yeast Saccharomyces cerevisiae has been a leading model to study telomere DNA length control and dynamics. Its telomeric DNA is maintained at a length that slightly varies between laboratory strains, but little is known about its variation at the species level. The recent publication of the genomes of over 1,000 S. cerevisiae strains enabled us to explore telomere DNA length variation at an unprecedented scale. Here, we developed a bioinformatic pipeline (YeaISTY) to estimate telomere DNA length from whole-genome sequences and applied it to the sequenced S. cerevisiae collection. Our results revealed broad natural telomere DNA length variation among the isolates. Notably, telomere DNA length is shorter in those derived from wild rather than domesticated environments. Moreover, telomere DNA length variation is associated with mitochondrial metabolism, and this association is driven by wild strains. Overall, these findings reveal broad variation in budding yeast's telomere DNA length regulation, which might be shaped by its different ecological life-styles.
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Affiliation(s)
- Melania D’Angiolo
- Institute for Research on Cancer and Aging (IRCAN), Université Côte d’Azur, 28 Avenue de Valombrose, 06107 Nice, France
| | - Jia-Xing Yue
- Institute for Research on Cancer and Aging (IRCAN), Université Côte d’Azur, 28 Avenue de Valombrose, 06107 Nice, France
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center (SYSUCC), 651 Dongfeng Road East, China
| | - Matteo De Chiara
- Institute for Research on Cancer and Aging (IRCAN), Université Côte d’Azur, 28 Avenue de Valombrose, 06107 Nice, France
| | - Benjamin P Barré
- Institute for Research on Cancer and Aging (IRCAN), Université Côte d’Azur, 28 Avenue de Valombrose, 06107 Nice, France
| | - Marie-Josèphe Giraud Panis
- Institute for Research on Cancer and Aging (IRCAN), Université Côte d’Azur, 28 Avenue de Valombrose, 06107 Nice, France
| | - Eric Gilson
- Institute for Research on Cancer and Aging (IRCAN), Université Côte d’Azur, 28 Avenue de Valombrose, 06107 Nice, France
- Department of Genetics, CHU, 06107 Nice, France
| | - Gianni Liti
- Institute for Research on Cancer and Aging (IRCAN), Université Côte d’Azur, 28 Avenue de Valombrose, 06107 Nice, France
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10
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Vinayagamurthy S, Bagri S, Mergny JL, Chowdhury S. Telomeres expand sphere of influence: emerging molecular impact of telomeres in non-telomeric functions. Trends Genet 2023; 39:59-73. [PMID: 36404192 PMCID: PMC7614491 DOI: 10.1016/j.tig.2022.10.002] [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: 06/05/2022] [Revised: 09/12/2022] [Accepted: 10/26/2022] [Indexed: 11/18/2022]
Abstract
Although the impact of telomeres on physiology stands well established, a question remains: how do telomeres impact cellular functions at a molecular level? This is because current understanding limits the influence of telomeres to adjacent subtelomeric regions despite the wide-ranging impact of telomeres. Emerging work in two distinct aspects offers opportunities to bridge this gap. First, telomere-binding factors were found with non-telomeric functions. Second, locally induced DNA secondary structures called G-quadruplexes are notably abundant in telomeres, and gene regulatory regions genome wide. Many telomeric factors bind to G-quadruplexes for non-telomeric functions. Here we discuss a more general model of how telomeres impact the non-telomeric genome - through factors that associate at telomeres and genome wide - and influence cell-intrinsic functions, particularly aging, cancer, and pluripotency.
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Affiliation(s)
- Soujanya Vinayagamurthy
- Integrative and Functional Biology Unit, CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sulochana Bagri
- Integrative and Functional Biology Unit, CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Jean-Louis Mergny
- Institute of Biophysics of the CAS, v.v.i. Královopolská 135, 612 65 Brno, Czech Republic; Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Shantanu Chowdhury
- Integrative and Functional Biology Unit, CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; GNR Knowledge Centre for Genome and Informatics, CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India.
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11
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Stock AJ, McDevitt RA, Puligilla C, Wang Y, Zhang Y, Wang K, Sun C, Becker KG, Lehrmann E, Wood WH, Gong Y, Aqdas M, Sung MH, Hoffmann V, Liu C, Gorospe M, Harrington L, Ferrucci L, Liu Y. Aberrant expression and localization of the RAP1 shelterin protein contribute to age-related phenotypes. PLoS Genet 2022; 18:e1010506. [PMID: 36441670 PMCID: PMC9704629 DOI: 10.1371/journal.pgen.1010506] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 11/02/2022] [Indexed: 11/29/2022] Open
Abstract
Short telomeres induce a DNA damage response (DDR) that evokes apoptosis and senescence in human cells. An extant question is the contribution of telomere dysfunction-induced DDR to the phenotypes observed in aging and telomere biology disorders. One candidate is RAP1, a telomere-associated protein that also controls transcription at extratelomeric regions. To distinguish these roles, we generated a knockin mouse carrying a mutated Rap1, which was incapable of binding telomeres and did not result in eroded telomeres or a DDR. Primary Rap1 knockin embryonic fibroblasts showed decreased RAP1 expression and re-localization away from telomeres, with an increased cytosolic distribution akin to that observed in human fibroblasts undergoing telomere erosion. Rap1 knockin mice were viable, but exhibited transcriptomic alterations, proinflammatory cytokine/chemokine signaling, reduced lifespan, and decreased healthspan with increased body weight/fasting blood glucose levels, spontaneous tumor incidence, and behavioral deficits. Taken together, our data present mechanisms distinct from telomere-induced DDR that underlie age-related phenotypes.
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Affiliation(s)
- Amanda J. Stock
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Ross A. McDevitt
- Comparative Medicine Section, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Chandrakala Puligilla
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Yajun Wang
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Yongqing Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Kun Wang
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Chongkui Sun
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Kevin G. Becker
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Elin Lehrmann
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - William H. Wood
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Yi Gong
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Mohammad Aqdas
- Laboratory of Molecular Biology and Immunology, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Victoria Hoffmann
- Division of Veterinary Resources, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chengyu Liu
- Transgenic Core Facility, National Heart, Lung, and Blood Institute/National Institutes of Health, Bethesda, Maryland, United States of America
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Lea Harrington
- Institute for Research in Immunology & Cancer, Marcelle-Coutu Pavilion, Université de Montréal, Montreal, Quebec, Canada
| | - Luigi Ferrucci
- Translational Gerontology Branch, Biomedical Research Center, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Yie Liu
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
- * E-mail:
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12
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Borges G, Criqui M, Harrington L. Tieing together loose ends: telomere instability in cancer and aging. Mol Oncol 2022; 16:3380-3396. [PMID: 35920280 PMCID: PMC9490142 DOI: 10.1002/1878-0261.13299] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/27/2022] [Accepted: 08/02/2022] [Indexed: 11/29/2022] Open
Abstract
Telomere maintenance is essential for maintaining genome integrity in both normal and cancer cells. Without functional telomeres, chromosomes lose their protective structure and undergo fusion and breakage events that drive further genome instability, including cell arrest or death. One means by which this loss can be overcome in stem cells and cancer cells is via re-addition of G-rich telomeric repeats by the telomerase reverse transcriptase (TERT). During aging of somatic tissues, however, insufficient telomerase expression leads to a proliferative arrest called replicative senescence, which is triggered when telomeres reach a critically short threshold that induces a DNA damage response. Cancer cells express telomerase but do not entirely escape telomere instability as they often possess short telomeres; hence there is often selection for genetic alterations in the TERT promoter that result in increased telomerase expression. In this review, we discuss our current understanding of the consequences of telomere instability in cancer and aging, and outline the opportunities and challenges that lie ahead in exploiting the reliance of cells on telomere maintenance for preserving genome stability.
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Affiliation(s)
- Gustavo Borges
- Molecular Biology Programme, Institute for Research in Immunology and CancerUniversity of MontrealQCCanada
| | - Mélanie Criqui
- Molecular Biology Programme, Institute for Research in Immunology and CancerUniversity of MontrealQCCanada
| | - Lea Harrington
- Molecular Biology Programme, Institute for Research in Immunology and CancerUniversity of MontrealQCCanada
- Departments of Medicine and Biochemistry and Molecular MedicineUniversity of MontrealQCCanada
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13
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Ngubo M, Reid JL, Patterton H. Distinct structural groups of histone H3 and H4 residues have divergent effects on chronological lifespan in Saccharomyces cerevisiae. PLoS One 2022; 17:e0268760. [PMID: 35622816 PMCID: PMC9140238 DOI: 10.1371/journal.pone.0268760] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 05/06/2022] [Indexed: 11/19/2022] Open
Abstract
We have performed a comprehensive analysis of the involvement of histone H3 and H4 residues in the regulation of chronological lifespan in yeast and identify four structural groups in the nucleosome that influence lifespan. We also identify residues where substitution with an epigenetic mimic extends lifespan, providing evidence that a simple epigenetic switch, without possible additional background modifications, causes longevity. Residues where substitution result in the most pronounced lifespan extension are all on the exposed face of the nucleosome, with the exception of H3E50, which is present on the lateral surface, between two DNA gyres. Other residues that have a more modest effect on lifespan extension are concentrated at the extremities of the H3-H4 dimer, suggesting a role in stabilizing the dimer in its nucleosome frame. Residues that reduce lifespan are buried in the histone handshake motif, suggesting that these mutations destabilize the octamer structure. All residues exposed on the nucleosome disk face and that cause lifespan extension are known to interact with Sir3. We find that substitution of H4K16 and H4H18 cause Sir3 to redistribute from telomeres and silent mating loci to secondary positions, often enriched for Rap1, Abf1 or Reb1 binding sites, whereas H3E50 does not. The redistribution of Sir3 in the genome can be reproduced by an equilibrium model based on primary and secondary binding sites with different affinities for Sir3. The redistributed Sir3 cause transcriptional repression at most of the new loci, including of genes where null mutants were previously shown to extend chronological lifespan. The transcriptomic profiles of H4K16 and H4H18 mutant strains are very similar, and compatible with a DNA replication stress response. This is distinct from the transcriptomic profile of H3E50, which matches strong induction of oxidative phosphorylation. We propose that the different groups of residues are involved in binding to heterochromatin proteins, in destabilizing the association of the nucleosome DNA, disrupting binding of the H3-H4 dimer in the nucleosome, or disrupting the structural stability of the octamer, each category impacting on chronological lifespan by a different mechanism.
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Affiliation(s)
- Mzwanele Ngubo
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Jessica Laura Reid
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | - Hugh–George Patterton
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
- * E-mail:
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14
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Barry RM, Sacco O, Mameri A, Stojaspal M, Kartsonis W, Shah P, De Ioannes P, Hofr C, Côté J, Sfeir A. Rap1 regulates TIP60 function during fate transition between two-cell-like and pluripotent states. Genes Dev 2022; 36:313-330. [PMID: 35210222 PMCID: PMC8973845 DOI: 10.1101/gad.349039.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/08/2022] [Indexed: 01/05/2023]
Abstract
In mammals, the conserved telomere binding protein Rap1 serves a diverse set of nontelomeric functions, including activation of the NF-kB signaling pathway, maintenance of metabolic function in vivo, and transcriptional regulation. Here, we uncover the mechanism by which Rap1 modulates gene expression. Using a separation-of-function allele, we show that Rap1 transcriptional regulation is largely independent of TRF2-mediated binding to telomeres and does not involve direct binding to genomic loci. Instead, Rap1 interacts with the TIP60/p400 complex and modulates its histone acetyltransferase activity. Notably, we show that deletion of Rap1 in mouse embryonic stem cells increases the fraction of two-cell-like cells. Specifically, Rap1 enhances the repressive activity of Tip60/p400 across a subset of two-cell-stage genes, including Zscan4 and the endogenous retrovirus MERVL. Preferential up-regulation of genes proximal to MERVL elements in Rap1-deficient settings implicates these endogenous retroviral elements in the derepression of proximal genes. Altogether, our study reveals an unprecedented link between Rap1 and the TIP60/p400 complex in the regulation of pluripotency.
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Affiliation(s)
- Raymond Mario Barry
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, New York 10016, USA
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Olivia Sacco
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Amel Mameri
- St-Patrick Research Group in Basic Oncology; CHU de Québec-Université Laval Research Center-Oncology Division, Laval University Cancer Research Center, Quebec City, Quebec G1R 3S3, Canada
| | - Martin Stojaspal
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, New York 10016, USA
- LifeB, Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - William Kartsonis
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, New York 10016, USA
| | - Pooja Shah
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, New York 10016, USA
| | - Pablo De Ioannes
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
| | - Ctirad Hofr
- LifeB, Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Scientific Incubator, 612 65 Brno, Czech Republic
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology; CHU de Québec-Université Laval Research Center-Oncology Division, Laval University Cancer Research Center, Quebec City, Quebec G1R 3S3, Canada
| | - Agnel Sfeir
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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15
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Stem cells at odds with telomere maintenance and protection. Trends Cell Biol 2022; 32:527-536. [DOI: 10.1016/j.tcb.2021.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 11/23/2022]
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16
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Loss of telomere silencing is accompanied by dysfunction of Polo kinase and centrosomes during Drosophila oogenesis and early development. PLoS One 2021; 16:e0258156. [PMID: 34624021 PMCID: PMC8500440 DOI: 10.1371/journal.pone.0258156] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/18/2021] [Indexed: 12/03/2022] Open
Abstract
Telomeres are nucleoprotein complexes that protect the ends of eukaryotic linear chromosomes from degradation and fusions. Telomere dysfunction leads to cell growth arrest, oncogenesis, and premature aging. Telomeric RNAs have been found in all studied species; however, their functions and biogenesis are not clearly understood. We studied the mechanisms of development disorders observed upon overexpression of telomeric repeats in Drosophila. In somatic cells, overexpression of telomeric retrotransposon HeT-A is cytotoxic and leads to the accumulation of HeT-A Gag near centrosomes. We found that RNA and RNA-binding protein Gag encoded by the telomeric retrotransposon HeT-A interact with Polo and Cdk1 mitotic kinases, which are conserved regulators of centrosome biogenesis and cell cycle. The depletion of proteins Spindle E, Ccr4 or Ars2 resulting in HeT-A overexpression in the germline was accompanied by mislocalization of Polo as well as its abnormal stabilization during oogenesis and severe deregulation of centrosome biogenesis leading to maternal-effect embryonic lethality. These data suggest a mechanistic link between telomeric HeT-A ribonucleoproteins and cell cycle regulators that ensures the cell response to telomere dysfunction.
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17
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Mitra S, Zhong J, Tran TQ, MacAlpine DM, Hartemink AJ. RoboCOP: jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data. Nucleic Acids Res 2021; 49:7925-7938. [PMID: 34255854 PMCID: PMC8373080 DOI: 10.1093/nar/gkab553] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 05/28/2021] [Accepted: 07/08/2021] [Indexed: 01/25/2023] Open
Abstract
Chromatin is a tightly packaged structure of DNA and protein within the nucleus of a cell. The arrangement of different protein complexes along the DNA modulates and is modulated by gene expression. Measuring the binding locations and occupancy levels of different transcription factors (TFs) and nucleosomes is therefore crucial to understanding gene regulation. Antibody-based methods for assaying chromatin occupancy are capable of identifying the binding sites of specific DNA binding factors, but only one factor at a time. In contrast, epigenomic accessibility data like MNase-seq, DNase-seq, and ATAC-seq provide insight into the chromatin landscape of all factors bound along the genome, but with little insight into the identities of those factors. Here, we present RoboCOP, a multivariate state space model that integrates chromatin accessibility data with nucleotide sequence to jointly compute genome-wide probabilistic scores of nucleosome and TF occupancy, for hundreds of different factors. We apply RoboCOP to MNase-seq and ATAC-seq data to elucidate the protein-binding landscape of nucleosomes and 150 TFs across the yeast genome, and show that our model makes better predictions than existing methods. We also compute a chromatin occupancy profile of the yeast genome under cadmium stress, revealing chromatin dynamics associated with transcriptional regulation.
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Affiliation(s)
- Sneha Mitra
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | - Jianling Zhong
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA
| | - Trung Q Tran
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | - David M MacAlpine
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA.,Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA.,Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
| | - Alexander J Hartemink
- Department of Computer Science, Duke University, Durham, NC 27708, USA.,Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
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18
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The Power of Stress: The Telo-Hormesis Hypothesis. Cells 2021; 10:cells10051156. [PMID: 34064566 PMCID: PMC8151059 DOI: 10.3390/cells10051156] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023] Open
Abstract
Adaptative response to stress is a strategy conserved across evolution to promote survival. In this context, the groundbreaking findings of Miroslav Radman on the adaptative value of changing mutation rates opened new avenues in our understanding of stress response. Inspired by this work, we explore here the putative beneficial effects of changing the ends of eukaryotic chromosomes, the telomeres, in response to stress. We first summarize basic principles in telomere biology and then describe how various types of stress can alter telomere structure and functions. Finally, we discuss the hypothesis of stress-induced telomere signaling with hormetic effects.
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19
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Galli M, Frigerio C, Longhese MP, Clerici M. The regulation of the DNA damage response at telomeres: focus on kinases. Biochem Soc Trans 2021; 49:933-943. [PMID: 33769480 DOI: 10.1042/bst20200856] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 11/17/2022]
Abstract
The natural ends of linear chromosomes resemble those of accidental double-strand breaks (DSBs). DSBs induce a multifaceted cellular response that promotes the repair of lesions and slows down cell cycle progression. This response is not elicited at chromosome ends, which are organized in nucleoprotein structures called telomeres. Besides counteracting DSB response through specialized telomere-binding proteins, telomeres also prevent chromosome shortening. Despite of the different fate of telomeres and DSBs, many proteins involved in the DSB response also localize at telomeres and participate in telomere homeostasis. In particular, the DSB master regulators Tel1/ATM and Mec1/ATR contribute to telomere length maintenance and arrest cell cycle progression when chromosome ends shorten, thus promoting a tumor-suppressive process known as replicative senescence. During senescence, the actions of both these apical kinases and telomere-binding proteins allow checkpoint activation while bulk DNA repair activities at telomeres are still inhibited. Checkpoint-mediated cell cycle arrest also prevents further telomere erosion and deprotection that would favor chromosome rearrangements, which are known to increase cancer-associated genome instability. This review summarizes recent insights into functions and regulation of Tel1/ATM and Mec1/ATR at telomeres both in the presence and in the absence of telomerase, focusing mainly on discoveries in budding yeast.
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Affiliation(s)
- Michela Galli
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Chiara Frigerio
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Michela Clerici
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
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20
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Ogrodnik M. Cellular aging beyond cellular senescence: Markers of senescence prior to cell cycle arrest in vitro and in vivo. Aging Cell 2021; 20:e13338. [PMID: 33711211 PMCID: PMC8045927 DOI: 10.1111/acel.13338] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/09/2021] [Accepted: 02/19/2021] [Indexed: 12/14/2022] Open
Abstract
The field of research on cellular senescence experienced a rapid expansion from being primarily focused on in vitro aspects of aging to the vast territories of animal and clinical research. Cellular senescence is defined by a set of markers, many of which are present and accumulate in a gradual manner prior to senescence induction or are found outside of the context of cellular senescence. These markers are now used to measure the impact of cellular senescence on aging and disease as well as outcomes of anti-senescence interventions, many of which are at the stage of clinical trials. It is thus of primary importance to discuss their specificity as well as their role in the establishment of senescence. Here, the presence and role of senescence markers are described in cells prior to cell cycle arrest, especially in the context of replicative aging and in vivo conditions. Specifically, this review article seeks to describe the process of "cellular aging": the progression of internal changes occurring in primary cells leading to the induction of cellular senescence and culminating in cell death. Phenotypic changes associated with aging prior to senescence induction will be characterized, as well as their effect on the induction of cell senescence and the final fate of cells reviewed. Using published datasets on assessments of senescence markers in vivo, it will be described how disparities between quantifications can be explained by the concept of cellular aging. Finally, throughout the article the applicational value of broadening cellular senescence paradigm will be discussed.
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Affiliation(s)
- Mikolaj Ogrodnik
- Ludwig Boltzmann Research Group Senescence and Healing of Wounds Vienna Austria
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology in AUVA Research Center Vienna Austria
- Austrian Cluster for Tissue Regeneration Vienna Austria
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21
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Chromatin modifiers and recombination factors promote a telomere fold-back structure, that is lost during replicative senescence. PLoS Genet 2020; 16:e1008603. [PMID: 33370275 PMCID: PMC7793543 DOI: 10.1371/journal.pgen.1008603] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 01/08/2021] [Accepted: 11/03/2020] [Indexed: 12/27/2022] Open
Abstract
Telomeres have the ability to adopt a lariat conformation and hence, engage in long and short distance intra-chromosome interactions. Budding yeast telomeres were proposed to fold back into subtelomeric regions, but a robust assay to quantitatively characterize this structure has been lacking. Therefore, it is not well understood how the interactions between telomeres and non-telomeric regions are established and regulated. We employ a telomere chromosome conformation capture (Telo-3C) approach to directly analyze telomere folding and its maintenance in S. cerevisiae. We identify the histone modifiers Sir2, Sin3 and Set2 as critical regulators for telomere folding, which suggests that a distinct telomeric chromatin environment is a major requirement for the folding of yeast telomeres. We demonstrate that telomeres are not folded when cells enter replicative senescence, which occurs independently of short telomere length. Indeed, Sir2, Sin3 and Set2 protein levels are decreased during senescence and their absence may thereby prevent telomere folding. Additionally, we show that the homologous recombination machinery, including the Rad51 and Rad52 proteins, as well as the checkpoint component Rad53 are essential for establishing the telomere fold-back structure. This study outlines a method to interrogate telomere-subtelomere interactions at a single unmodified yeast telomere. Using this method, we provide insights into how the spatial arrangement of the chromosome end structure is established and demonstrate that telomere folding is compromised throughout replicative senescence.
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22
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Chen SY, Osimiri LC, Chevalier M, Bugaj LJ, Nguyen TH, Greenstein RA, Ng AH, Stewart-Ornstein J, Neves LT, El-Samad H. Optogenetic Control Reveals Differential Promoter Interpretation of Transcription Factor Nuclear Translocation Dynamics. Cell Syst 2020; 11:336-353.e24. [PMID: 32898473 PMCID: PMC7648432 DOI: 10.1016/j.cels.2020.08.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/08/2020] [Accepted: 08/10/2020] [Indexed: 02/07/2023]
Abstract
Gene expression is thought to be affected not only by the concentration of transcription factors (TFs) but also the dynamics of their nuclear translocation. Testing this hypothesis requires direct control of TF dynamics. Here, we engineer CLASP, an optogenetic tool for rapid and tunable translocation of a TF of interest. Using CLASP fused to Crz1, we observe that, for the same integrated concentration of nuclear TF over time, changing input dynamics changes target gene expression: pulsatile inputs yield higher expression than continuous inputs, or vice versa, depending on the target gene. Computational modeling reveals that a dose-response saturating at low TF input can yield higher gene expression for pulsatile versus continuous input, and that multi-state promoter activation can yield the opposite behavior. Our integrated tool development and modeling approach characterize promoter responses to Crz1 nuclear translocation dynamics, extracting quantitative features that may help explain the differential expression of target genes. CLASP is a modular optogenetic strategy to control the nuclear localization of transcription factors (TFs) and elicit gene expression from their cognate promoters. CLASP control of Crz1 nuclear localization, coupled with computational modeling, revealed how promoters can differentially decode dynamic transcription factor signals. The integrated strategy of CLASP development and modeling presents a generalized approach to causally investigate the transcriptional consequences of dynamic TF nuclear shuttling.
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Affiliation(s)
- Susan Y Chen
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lindsey C Osimiri
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA; The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA 94143, USA
| | - Michael Chevalier
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lukasz J Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Taylor H Nguyen
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - R A Greenstein
- Department of Microbiology and Immunology, George Williams Hooper Foundation, Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Andrew H Ng
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA; The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA 94143, USA; Cell Design Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jacob Stewart-Ornstein
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Lauren T Neves
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hana El-Samad
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Cell Design Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
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23
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Abstract
Several decades elapsed between the first descriptions of G-quadruplex nucleic acid structures (G4s) assembled in vitro and the emergence of experimental findings indicating that such structures can form and function in living systems. A large body of evidence now supports roles for G4s in many aspects of nucleic acid biology, spanning processes from transcription and chromatin structure, mRNA processing, protein translation, DNA replication and genome stability, and telomere and mitochondrial function. Nonetheless, it must be acknowledged that some of this evidence is tentative, which is not surprising given the technical challenges associated with demonstrating G4s in biology. Here I provide an overview of evidence for G4 biology, focusing particularly on the many potential pitfalls that can be encountered in its investigation, and briefly discuss some of broader biological processes that may be impacted by G4s including cancer.
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Affiliation(s)
- F. Brad Johnson
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
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24
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Vinayagamurthy S, Ganguly A, Chowdhury S. Extra-telomeric impact of telomeres: Emerging molecular connections in pluripotency or stemness. J Biol Chem 2020; 295:10245-10254. [PMID: 32444498 PMCID: PMC7383370 DOI: 10.1074/jbc.rev119.009710] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 05/21/2020] [Indexed: 12/26/2022] Open
Abstract
Telomeres comprise specialized nucleic acid-protein complexes that help protect chromosome ends from DNA damage. Moreover, telomeres associate with subtelomeric regions through looping. This results in altered expression of subtelomeric genes. Recent observations further reveal telomere length-dependent gene regulation and epigenetic modifications at sites spread across the genome and distant from telomeres. This regulation is mediated through the telomere-binding protein telomeric repeat-binding factor 2 (TRF2). These observations suggest a role of telomeres in extra-telomeric functions. Most notably, telomeres have a broad impact on pluripotency and differentiation. For example, cardiomyocytes differentiate with higher efficacy from induced pluripotent stem cells having long telomeres, and differentiated cells obtained from human embryonic stem cells with relatively long telomeres have a longer lifespan. Here, we first highlight reports on these two seemingly distinct research areas: the extra-telomeric role of telomere-binding factors and the role of telomeres in pluripotency/stemness. On the basis of the observations reported in these studies, we draw attention to potential molecular connections between extra-telomeric biology and pluripotency. Finally, in the context of the nonlocal influence of telomeres on pluripotency and stemness, we discuss major opportunities for progress in molecular understanding of aging-related disorders and neurodegenerative diseases.
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Affiliation(s)
- Soujanya Vinayagamurthy
- Integrative and Functional Biology Unit, CSIR Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Akansha Ganguly
- Integrative and Functional Biology Unit, CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Shantanu Chowdhury
- Integrative and Functional Biology Unit, CSIR Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR Institute of Genomics and Integrative Biology, New Delhi, India
- G.N.R. Knowledge Centre for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, New Delhi, India
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25
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Mir SM, Samavarchi Tehrani S, Goodarzi G, Jamalpoor Z, Asadi J, Khelghati N, Qujeq D, Maniati M. Shelterin Complex at Telomeres: Implications in Ageing. Clin Interv Aging 2020; 15:827-839. [PMID: 32581523 PMCID: PMC7276337 DOI: 10.2147/cia.s256425] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/18/2020] [Indexed: 12/16/2022] Open
Abstract
Different factors influence the development and control of ageing. It is well known that progressive telomere shorting is one of the molecular mechanisms underlying ageing. The shelterin complex consists of six telomere-specific proteins which are involved in the protection of chromosome ends. More particularly, this vital complex protects the telomeres from degradation, prevents from activation of unwanted repair systems, regulates the activity of telomerase, and has a crucial role in cellular senescent and ageing-related pathologies. This review explores the organization and function of telomeric DNA along with the mechanism of telomeres during ageing, followed by a discussion of the critical role of shelterin components and their changes during ageing.
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Affiliation(s)
- Seyed Mostafa Mir
- Trauma Research Center, AJA University of Medical Sciences, Tehran, Iran.,Student Research Committee, Babol University of Medical Sciences, Babol, Iran.,Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Sadra Samavarchi Tehrani
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Student Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Golnaz Goodarzi
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Student Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Jamalpoor
- Trauma Research Center, AJA University of Medical Sciences, Tehran, Iran
| | - Jahanbakhsh Asadi
- Metabolic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Nafiseh Khelghati
- Department of Clinical Biochemistry, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Durdi Qujeq
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran.,Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Mahmood Maniati
- School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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26
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Mitra S, Zhong J, MacAlpine DM, Hartemink AJ. RoboCOP: Multivariate State Space Model Integrating Epigenomic Accessibility Data to Elucidate Genome-Wide Chromatin Occupancy. RESEARCH IN COMPUTATIONAL MOLECULAR BIOLOGY : ... ANNUAL INTERNATIONAL CONFERENCE, RECOMB ... : PROCEEDINGS. RECOMB (CONFERENCE : 2005- ) 2020; 12074:136-151. [PMID: 34386808 PMCID: PMC8356533 DOI: 10.1007/978-3-030-45257-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Chromatin is the tightly packaged structure of DNA and protein within the nucleus of a cell. The arrangement of different protein complexes along the DNA modulates and is modulated by gene expression. Measuring the binding locations and level of occupancy of different transcription factors (TFs) and nucleosomes is therefore crucial to understanding gene regulation. Antibody-based methods for assaying chromatin occupancy are capable of identifying the binding sites of specific DNA binding factors, but only one factor at a time. On the other hand, epigenomic accessibility data like ATAC-seq, DNase-seq, and MNase-seq provide insight into the chromatin landscape of all factors bound along the genome, but with minimal insight into the identities of those factors. Here, we present RoboCOP, a multivariate state space model that integrates chromatin information from epigenomic accessibility data with nucleotide sequence to compute genome-wide probabilistic scores of nucleosome and TF occupancy, for hundreds of different factors at once. RoboCOP can be applied to any epigenomic dataset that provides quantitative insight into chromatin accessibility in any organism, but here we apply it to MNase-seq data to elucidate the protein-binding landscape of nucleosomes and 150 TFs across the yeast genome. Using available protein-binding datasets from the literature, we show that our model more accurately predicts the binding of these factors genome-wide.
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Affiliation(s)
- Sneha Mitra
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | - Jianling Zhong
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA
| | - David M MacAlpine
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
| | - Alexander J Hartemink
- Department of Computer Science, Duke University, Durham, NC 27708, USA
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
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27
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Criqui M, Qamra A, Chu TW, Sharma M, Tsao J, Henry DA, Barsyte-Lovejoy D, Arrowsmith CH, Winegarden N, Lupien M, Harrington L. Telomere dysfunction cooperates with epigenetic alterations to impair murine embryonic stem cell fate commitment. eLife 2020; 9:47333. [PMID: 32297856 PMCID: PMC7192583 DOI: 10.7554/elife.47333] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 04/06/2020] [Indexed: 12/11/2022] Open
Abstract
The precise relationship between epigenetic alterations and telomere dysfunction is still an extant question. Previously, we showed that eroded telomeres lead to differentiation instability in murine embryonic stem cells (mESCs) via DNA hypomethylation at pluripotency-factor promoters. Here, we uncovered that telomerase reverse transcriptase null (Tert-/-) mESCs exhibit genome-wide alterations in chromatin accessibility and gene expression during differentiation. These changes were accompanied by an increase of H3K27me3 globally, an altered chromatin landscape at the Pou5f1/Oct4 promoter, and a refractory response to differentiation cues. Inhibition of the Polycomb Repressive Complex 2 (PRC2), an H3K27 tri-methyltransferase, exacerbated the impairment in differentiation and pluripotency gene repression in Tert-/-mESCs but not wild-type mESCs, whereas inhibition of H3K27me3 demethylation led to a partial rescue of the Tert-/- phenotype. These data reveal a new interdependent relationship between H3K27me3 and telomere integrity in stem cell lineage commitment that may have implications in aging and cancer.
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Affiliation(s)
- Mélanie Criqui
- Institut de Recherche en Immunologie et Cancérologie (IRIC), Département de biologie moléculaire, Faculté de Médecine, Université de Montréal, Montréal, Canada
| | - Aditi Qamra
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Tsz Wai Chu
- Institut de Recherche en Immunologie et Cancérologie (IRIC), Département de biologie moléculaire, Faculté de Médecine, Université de Montréal, Montréal, Canada
| | - Monika Sharma
- Princess Margaret Genomics Centre, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Julissa Tsao
- Princess Margaret Genomics Centre, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Danielle A Henry
- Institut de Recherche en Immunologie et Cancérologie (IRIC), Département de biologie moléculaire, Faculté de Médecine, Université de Montréal, Montréal, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, Princess Margaret Cancer Centre, University of Toronto, Department of Medical Biophysics, Toronto, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, Princess Margaret Cancer Centre, University of Toronto, Department of Medical Biophysics, Toronto, Canada
| | - Neil Winegarden
- Princess Margaret Genomics Centre, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Lea Harrington
- Institut de Recherche en Immunologie et Cancérologie (IRIC), Département de biologie moléculaire, Faculté de Médecine, Université de Montréal, Montréal, Canada
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28
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Panchy NL, Lloyd JP, Shiu SH. Improved recovery of cell-cycle gene expression in Saccharomyces cerevisiae from regulatory interactions in multiple omics data. BMC Genomics 2020; 21:159. [PMID: 32054475 PMCID: PMC7020519 DOI: 10.1186/s12864-020-6554-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/04/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Gene expression is regulated by DNA-binding transcription factors (TFs). Together with their target genes, these factors and their interactions collectively form a gene regulatory network (GRN), which is responsible for producing patterns of transcription, including cyclical processes such as genome replication and cell division. However, identifying how this network regulates the timing of these patterns, including important interactions and regulatory motifs, remains a challenging task. RESULTS We employed four in vivo and in vitro regulatory data sets to investigate the regulatory basis of expression timing and phase-specific patterns cell-cycle expression in Saccharomyces cerevisiae. Specifically, we considered interactions based on direct binding between TF and target gene, indirect effects of TF deletion on gene expression, and computational inference. We found that the source of regulatory information significantly impacts the accuracy and completeness of recovering known cell-cycle expressed genes. The best approach involved combining TF-target and TF-TF interactions features from multiple datasets in a single model. In addition, TFs important to multiple phases of cell-cycle expression also have the greatest impact on individual phases. Important TFs regulating a cell-cycle phase also tend to form modules in the GRN, including two sub-modules composed entirely of unannotated cell-cycle regulators (STE12-TEC1 and RAP1-HAP1-MSN4). CONCLUSION Our findings illustrate the importance of integrating both multiple omics data and regulatory motifs in order to understand the significance regulatory interactions involved in timing gene expression. This integrated approached allowed us to recover both known cell-cycles interactions and the overall pattern of phase-specific expression across the cell-cycle better than any single data set. Likewise, by looking at regulatory motifs in the form of TF-TF interactions, we identified sets of TFs whose co-regulation of target genes was important for cell-cycle expression, even when regulation by individual TFs was not. Overall, this demonstrates the power of integrating multiple data sets and models of interaction in order to understand the regulatory basis of established biological processes and their associated gene regulatory networks.
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Affiliation(s)
- Nicholas L Panchy
- Genetics Graduate Program, Michigan State University, East Lansing, MI, 48824, USA.,Present address: National Institute for Mathematical and Biological Synthesis, University of Tennessee, 1122 Volunteer Blvd., Suite 106, Knoxville, TN, 37996-3410, USA
| | - John P Lloyd
- Department of Human Genetics and Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Shin-Han Shiu
- Genetics Graduate Program, Michigan State University, East Lansing, MI, 48824, USA. .,Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA. .,Michigan State University, Plant Biology Laboratories, 612 Wilson Road, Room 166, East Lansing, MI, 48824-1312, USA.
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29
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Henninger E, Teixeira MT. Telomere-driven mutational processes in yeast. Curr Opin Genet Dev 2020; 60:99-106. [DOI: 10.1016/j.gde.2020.02.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 12/18/2022]
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30
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Yu R, McCauley B, Dang W. Loss of chromatin structural integrity is a source of stress during aging. Hum Genet 2020; 139:371-380. [PMID: 31900586 DOI: 10.1007/s00439-019-02100-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/09/2019] [Indexed: 12/19/2022]
Abstract
Dysfunction and dysregulation at multiple levels, from organismal to molecular, are associated with the biological process of aging. In a eukaryotic nucleus, multiple lines of evidence have shown that the fundamental structure of chromatin is affected by aging. Not only euchromatic and heterochromatic regions shift locations, global changes, such as reduced levels of histones, have been reported for certain aged cell types and tissues. The physiological effects caused by such broad chromatin changes are complex and the cell's responses to it can be profound and in turn influence the aging process. In this review, we summarize recent findings on the interplay between chromatin architecture and aging with an emphasis on the cellular response to chromatin stress and its antagonistic effects on aging.
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Affiliation(s)
- Ruofan Yu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, 77030, USA.,Huffington Center on Aging, Baylor College of Medicine, Houston, 77030, USA
| | - Brenna McCauley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, 77030, USA.,Huffington Center on Aging, Baylor College of Medicine, Houston, 77030, USA
| | - Weiwei Dang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, 77030, USA. .,Huffington Center on Aging, Baylor College of Medicine, Houston, 77030, USA.
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31
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Song S, Perez JV, Svitko W, Ricketts MD, Dean E, Schultz D, Marmorstein R, Johnson FB. Rap1-mediated nucleosome displacement can regulate gene expression in senescent cells without impacting the pace of senescence. Aging Cell 2020; 19:e13061. [PMID: 31742863 PMCID: PMC6974733 DOI: 10.1111/acel.13061] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 09/19/2019] [Accepted: 10/13/2019] [Indexed: 01/18/2023] Open
Abstract
Cell senescence is accompanied, and in part mediated, by changes in chromatin, including histone losses, but underlying mechanisms are not well understood. We reported previously that during yeast cell senescence driven by telomere shortening, the telomeric protein Rap1 plays a major role in reprogramming gene expression by relocalizing hundreds of new target genes (called NRTS, for new Rap1 targets at senescence) to the promoters. This leads to two types of histone loss: Rap1 lowers histone level globally by repressing histone gene expression, and it also causes local nucleosome displacement at the promoters of upregulated NRTS. Here, we present evidence of direct binding between Rap1 and histone H3/H4 heterotetramers, and map amino acids involved in the interaction within the Rap1 SANT domain to amino acids 392-394 (SHY). Introduction of a point mutation within the native RAP1 locus that converts these residues to alanines (RAP1SHY ), and thus disrupts Rap1-H3/H4 interaction, does not interfere with Rap1 relocalization to NRTS at senescence, but prevents full nucleosome displacement and gene upregulation, indicating direct Rap1-H3/H4 contacts are involved in nucleosome displacement. Consistent with this, the histone H3/H4 chaperone Asf1 is similarly unnecessary for Rap1 localization to NRTS but is required for full Rap1-mediated nucleosome displacement and gene activation. Remarkably, RAP1SHY does not affect the pace of senescence-related cell cycle arrest, indicating that some changes in gene expression at senescence are not coupled to this arrest.
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Affiliation(s)
- Shufei Song
- Department of Biochemistry and Molecular Biophysics University of Pennsylvania Philadelphia PA USA
- Graduate Group in Biochemistry and Molecular Biophysics University of Pennsylvania Philadelphia PA USA
- Department of Pathology and Laboratory Medicine University of Pennsylvania Philadelphia PA USA
| | - Javier V. Perez
- Department of Pathology and Laboratory Medicine University of Pennsylvania Philadelphia PA USA
| | - William Svitko
- Department of Pathology and Laboratory Medicine University of Pennsylvania Philadelphia PA USA
| | - M. Daniel Ricketts
- Department of Biochemistry and Molecular Biophysics University of Pennsylvania Philadelphia PA USA
- Abramson Family Cancer Research Institute University of Pennsylvania Philadelphia PA USA
| | - Elliot Dean
- High‐Throughput Screening Core University of Pennsylvania Philadelphia PA USA
| | - David Schultz
- High‐Throughput Screening Core University of Pennsylvania Philadelphia PA USA
| | - Ronen Marmorstein
- Department of Biochemistry and Molecular Biophysics University of Pennsylvania Philadelphia PA USA
- Abramson Family Cancer Research Institute University of Pennsylvania Philadelphia PA USA
| | - F. Brad Johnson
- Department of Biochemistry and Molecular Biophysics University of Pennsylvania Philadelphia PA USA
- Department of Pathology and Laboratory Medicine University of Pennsylvania Philadelphia PA USA
- Institute on Aging University of Pennsylvania Philadelphia PA USA
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32
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Xu Z, Teixeira MT. The many types of heterogeneity in replicative senescence. Yeast 2019; 36:637-648. [PMID: 31306505 PMCID: PMC6900063 DOI: 10.1002/yea.3433] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/04/2019] [Accepted: 07/07/2019] [Indexed: 11/10/2022] Open
Abstract
Replicative senescence, which is induced by telomere shortening, underlies the loss of regeneration capacity of organs and is ultimately detrimental to the organism. At the same time, it is required to protect organisms from unlimited cell proliferation that may arise from numerous stimuli or deregulations. One important feature of replicative senescence is its high level of heterogeneity and asynchrony, which promote genome instability and senescence escape. Characterizing this heterogeneity and investigating its sources are thus critical to understanding the robustness of replicative senescence. Here we review the different aspects of senescence driven by telomere attrition that are subject to variation in Saccharomyces cerevisiae, the current understanding of the molecular processes at play, and the consequences of heterogeneity in replicative senescence.
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Affiliation(s)
- Zhou Xu
- CNRS, UMR7238, Institut de Biologie Paris‐Seine, Laboratory of Computational and Quantitative BiologySorbonne UniversitéParisFrance
| | - Maria Teresa Teixeira
- CNRS, UMR8226, Institut de Biologie Physico‐Chimique, Laboratory of Molecular and Cell Biology of EukaryotesSorbonne Université, PSL Research UniversityParisFrance
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33
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Barbero Barcenilla B, Shippen DE. Back to the future: The intimate and evolving connection between telomere-related factors and genotoxic stress. J Biol Chem 2019; 294:14803-14813. [PMID: 31434740 DOI: 10.1074/jbc.aw119.008145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The conversion of circular genomes to linear chromosomes during molecular evolution required the invention of telomeres. This entailed the acquisition of factors necessary to fulfill two new requirements: the need to fully replicate terminal DNA sequences and the ability to distinguish chromosome ends from damaged DNA. Here we consider the multifaceted functions of factors recruited to perpetuate and stabilize telomeres. We discuss recent theories for how telomere factors evolved from existing cellular machineries and examine their engagement in nontelomeric functions such as DNA repair, replication, and transcriptional regulation. We highlight the remarkable versatility of protection of telomeres 1 (POT1) proteins that was fueled by gene duplication and divergence events that occurred independently across several eukaryotic lineages. Finally, we consider the relationship between oxidative stress and telomeres and the enigmatic role of telomere-associated proteins in mitochondria. These findings point to an evolving and intimate connection between telomeres and cellular physiology and the strong drive to maintain chromosome integrity.
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Affiliation(s)
- Borja Barbero Barcenilla
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128
| | - Dorothy E Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128
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34
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Calvo O, Grandin N, Jordán-Pla A, Miñambres E, González-Polo N, Pérez-Ortín JE, Charbonneau M. The telomeric Cdc13-Stn1-Ten1 complex regulates RNA polymerase II transcription. Nucleic Acids Res 2019; 47:6250-6268. [PMID: 31006804 PMCID: PMC6614848 DOI: 10.1093/nar/gkz279] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/18/2019] [Accepted: 04/08/2019] [Indexed: 12/11/2022] Open
Abstract
Specialized telomeric proteins have an essential role in maintaining genome stability through chromosome end protection and telomere length regulation. In the yeast Saccharomyces cerevisiae, the evolutionary conserved CST complex, composed of the Cdc13, Stn1 and Ten1 proteins, largely contributes to these functions. Here, we report genetic interactions between TEN1 and several genes coding for transcription regulators. Molecular assays confirmed this novel function of Ten1 and further established that it regulates the occupancies of RNA polymerase II and the Spt5 elongation factor within transcribed genes. Since Ten1, but also Cdc13 and Stn1, were found to physically associate with Spt5, we propose that Spt5 represents the target of CST in transcription regulation. Moreover, CST physically associates with Hmo1, previously shown to mediate the architecture of S-phase transcribed genes. The fact that, genome-wide, the promoters of genes down-regulated in the ten1-31 mutant are prefentially bound by Hmo1, leads us to propose a potential role for CST in synchronizing transcription with replication fork progression following head-on collisions.
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Affiliation(s)
- Olga Calvo
- Instituto de Biología Funcional y Genómica, CSIC-USAL, Salamanca, Spain
| | - Nathalie Grandin
- GReD laboratory, CNRS UMR6293, INSERM U1103, Faculty of Medicine, University Clermont-Auvergne, 28 place Henri Dunant, BP 38, 63001 Clermont-Ferrand Cedex, France
| | - Antonio Jordán-Pla
- ERI Biotecmed, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain
| | | | | | - José E Pérez-Ortín
- ERI Biotecmed, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain
| | - Michel Charbonneau
- GReD laboratory, CNRS UMR6293, INSERM U1103, Faculty of Medicine, University Clermont-Auvergne, 28 place Henri Dunant, BP 38, 63001 Clermont-Ferrand Cedex, France
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35
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Eberhard S, Valuchova S, Ravat J, Fulneček J, Jolivet P, Bujaldon S, Lemaire SD, Wollman FA, Teixeira MT, Riha K, Xu Z. Molecular characterization of Chlamydomonas reinhardtii telomeres and telomerase mutants. Life Sci Alliance 2019; 2:2/3/e201900315. [PMID: 31160377 PMCID: PMC6549138 DOI: 10.26508/lsa.201900315] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 05/27/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022] Open
Abstract
This study characterizes the sequence, end structure, and length distribution of Chlamydomonas reinhardtii telomeres and shows that telomerase mutants are defective in telomere maintenance. Telomeres are repeated sequences found at the end of the linear chromosomes of most eukaryotes and are required for chromosome integrity. Expression of the reverse-transcriptase telomerase allows for extension of telomeric repeats to counteract natural telomere shortening. Although Chlamydomonas reinhardtii, a photosynthetic unicellular green alga, is widely used as a model organism in photosynthesis and flagella research, and for biotechnological applications, the biology of its telomeres has not been investigated in depth. Here, we show that the C. reinhardtii (TTTTAGGG)n telomeric repeats are mostly nondegenerate and that the telomeres form a protective structure, with a subset ending with a 3′ overhang and another subset presenting a blunt end. Although telomere size and length distributions are stable under various standard growth conditions, they vary substantially between 12 genetically close reference strains. Finally, we identify CrTERT, the gene encoding the catalytic subunit of telomerase and show that telomeres shorten progressively in mutants of this gene. Telomerase mutants eventually enter replicative senescence, demonstrating that telomerase is required for long-term maintenance of telomeres in C. reinhardtii.
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Affiliation(s)
- Stephan Eberhard
- Sorbonne Université, CNRS, UMR 7141, Institut de Biologie Physico-Chimique, Biologie du Chloroplaste et Perception de la Lumière chez les Micro-algues, Paris, France
| | - Sona Valuchova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Julie Ravat
- Sorbonne Université, CNRS, UMR 7141, Institut de Biologie Physico-Chimique, Biologie du Chloroplaste et Perception de la Lumière chez les Micro-algues, Paris, France
| | - Jaroslav Fulneček
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Pascale Jolivet
- Sorbonne Université, PSL Research University, CNRS, UMR 8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Paris, France
| | - Sandrine Bujaldon
- Sorbonne Université, CNRS, UMR 7141, Institut de Biologie Physico-Chimique, Biologie du Chloroplaste et Perception de la Lumière chez les Micro-algues, Paris, France
| | - Stéphane D Lemaire
- Sorbonne Université, PSL Research University, CNRS, UMR 8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Paris, France
| | - Francis-André Wollman
- Sorbonne Université, CNRS, UMR 7141, Institut de Biologie Physico-Chimique, Biologie du Chloroplaste et Perception de la Lumière chez les Micro-algues, Paris, France
| | - Maria Teresa Teixeira
- Sorbonne Université, PSL Research University, CNRS, UMR 8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Paris, France
| | - Karel Riha
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Zhou Xu
- Sorbonne Université, PSL Research University, CNRS, UMR 8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Paris, France .,Sorbonne Université, CNRS, UMR 7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France
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36
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Kotla S, Vu HT, Ko KA, Wang Y, Imanishi M, Heo KS, Fujii Y, Thomas TN, Gi YJ, Mazhar H, Paez-Mayorga J, Shin JH, Tao Y, Giancursio CJ, Medina JL, Taunton J, Lusis AJ, Cooke JP, Fujiwara K, Le NT, Abe JI. Endothelial senescence is induced by phosphorylation and nuclear export of telomeric repeat binding factor 2-interacting protein. JCI Insight 2019; 4:124867. [PMID: 31045573 PMCID: PMC6538340 DOI: 10.1172/jci.insight.124867] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/19/2019] [Indexed: 01/03/2023] Open
Abstract
The interplay among signaling events for endothelial cell (EC) senescence, apoptosis, and activation and how these pathological conditions promote atherosclerosis in the area exposed to disturbed flow (d-flow) in concert remain unclear. The aim of this study was to determine whether telomeric repeat-binding factor 2-interacting protein (TERF2IP), a member of the shelterin complex at the telomere, can regulate EC senescence, apoptosis, and activation simultaneously, and if so, by what molecular mechanisms. We found that d-flow induced p90RSK and TERF2IP interaction in a p90RSK kinase activity-dependent manner. An in vitro kinase assay revealed that p90RSK directly phosphorylated TERF2IP at the serine 205 (S205) residue, and d-flow increased TERF2IP S205 phosphorylation as well as EC senescence, apoptosis, and activation by activating p90RSK. TERF2IP phosphorylation was crucial for nuclear export of the TERF2IP-TRF2 complex, which led to EC activation by cytosolic TERF2IP-mediated NF-κB activation and also to senescence and apoptosis of ECs by depleting TRF2 from the nucleus. Lastly, using EC-specific TERF2IP-knockout (TERF2IP-KO) mice, we found that the depletion of TERF2IP inhibited d-flow-induced EC senescence, apoptosis, and activation, as well as atherosclerotic plaque formation. These findings demonstrate that TERF2IP is an important molecular switch that simultaneously accelerates EC senescence, apoptosis, and activation by S205 phosphorylation.
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Affiliation(s)
- Sivareddy Kotla
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hang Thi Vu
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kyung Ae Ko
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yin Wang
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Masaki Imanishi
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kyung-Sun Heo
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yuka Fujii
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Tamlyn N. Thomas
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Young Jin Gi
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hira Mazhar
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jesus Paez-Mayorga
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, Texas, USA
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Nuevo Leon, Mexico
| | - Ji-Hyun Shin
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yunting Tao
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, Texas, USA
| | - Carolyn J. Giancursio
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, Texas, USA
| | - Jan L.M. Medina
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, UCSF, San Francisco, California, USA
| | - Aldos J. Lusis
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - John P. Cooke
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, Texas, USA
| | - Keigi Fujiwara
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Nhat-Tu Le
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, Texas, USA
| | - Jun-ichi Abe
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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37
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Holt S, Miks MH, de Carvalho BT, Foulquié-Moreno MR, Thevelein JM. The molecular biology of fruity and floral aromas in beer and other alcoholic beverages. FEMS Microbiol Rev 2019; 43:193-222. [PMID: 30445501 PMCID: PMC6524682 DOI: 10.1093/femsre/fuy041] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 11/13/2018] [Indexed: 12/03/2022] Open
Abstract
Aroma compounds provide attractiveness and variety to alcoholic beverages. We discuss the molecular biology of a major subset of beer aroma volatiles, fruity and floral compounds, originating from raw materials (malt and hops), or formed by yeast during fermentation. We introduce aroma perception, describe the most aroma-active, fruity and floral compounds in fruits and their presence and origin in beer. They are classified into categories based on their functional groups and biosynthesis pathways: (1) higher alcohols and esters, (2) polyfunctional thiols, (3) lactones and furanones, and (4) terpenoids. Yeast and hops are the main sources of fruity and flowery aroma compounds in beer. For yeast, the focus is on higher alcohols and esters, and particularly the complex regulation of the alcohol acetyl transferase ATF1 gene. We discuss the release of polyfunctional thiols and monoterpenoids from cysteine- and glutathione-S-conjugated compounds and glucosides, respectively, the primary biological functions of the yeast enzymes involved, their mode of action and mechanisms of regulation that control aroma compound production. Furthermore, we discuss biochemistry and genetics of terpenoid production and formation of non-volatile precursors in Humulus lupulus (hops). Insight in these pathways provides a toolbox for creating innovative products with a diversity of pleasant aromas.
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Affiliation(s)
- Sylvester Holt
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Marta H Miks
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark
- Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, 10–726 Olsztyn, Poland
| | - Bruna Trindade de Carvalho
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Maria R Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
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38
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Harrington L, Pucci F. In medio stat virtus: unanticipated consequences of telomere dysequilibrium. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2016.0444. [PMID: 29335368 PMCID: PMC5784064 DOI: 10.1098/rstb.2016.0444] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2017] [Indexed: 12/13/2022] Open
Abstract
The integrity of chromosome ends, or telomeres, depends on myriad processes that must balance the need to compact and protect the telomeric, G-rich DNA from detection as a double-stranded DNA break, and yet still permit access to enzymes that process, replicate and maintain a sufficient reserve of telomeric DNA. When unable to maintain this equilibrium, erosion of telomeres leads to perturbations at or near the telomeres themselves, including loss of binding by the telomere protective complex, shelterin, and alterations in transcription and post-translational modifications of histones. Although the catastrophic consequences of full telomere de-protection are well described, recent evidence points to other, less obvious perturbations that arise when telomere length equilibrium is altered. For example, critically short telomeres also perturb DNA methylation and histone post-translational modifications at distal sites throughout the genome. In murine stem cells for example, this dysregulated chromatin leads to inappropriate suppression of pluripotency regulator factors such as Nanog. This review summarizes these recent findings, with an emphasis on how these genome-wide, telomere-induced perturbations can have profound consequences on cell function and fate. This article is part of the theme issue ‘Understanding diversity in telomere dynamics’.
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Affiliation(s)
- Lea Harrington
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, College of Science and Engineering, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Fabio Pucci
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, College of Science and Engineering, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, UK
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39
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Sorrells TR, Johnson AN, Howard CJ, Britton CS, Fowler KR, Feigerle JT, Weil PA, Johnson AD. Intrinsic cooperativity potentiates parallel cis-regulatory evolution. eLife 2018; 7:37563. [PMID: 30198843 PMCID: PMC6173580 DOI: 10.7554/elife.37563] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 09/09/2018] [Indexed: 12/27/2022] Open
Abstract
Convergent evolutionary events in independent lineages provide an opportunity to understand why evolution favors certain outcomes over others. We studied such a case where a large set of genes-those coding for the ribosomal proteins-gained cis-regulatory sequences for a particular transcription regulator (Mcm1) in independent fungal lineages. We present evidence that these gains occurred because Mcm1 shares a mechanism of transcriptional activation with an ancestral regulator of the ribosomal protein genes, Rap1. Specifically, we show that Mcm1 and Rap1 have the inherent ability to cooperatively activate transcription through contacts with the general transcription factor TFIID. Because the two regulatory proteins share a common interaction partner, the presence of one ancestral cis-regulatory sequence can 'channel' random mutations into functional sites for the second regulator. At a genomic scale, this type of intrinsic cooperativity can account for a pattern of parallel evolution involving the fixation of hundreds of substitutions.
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Affiliation(s)
- Trevor R Sorrells
- Department of Biochemistry and Biophysics, Tetrad Graduate Program, University of California, San Francisco, United States.,Department of Microbiology and Immunology, University of California, San Francisco, United States
| | - Amanda N Johnson
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Conor J Howard
- Department of Biochemistry and Biophysics, Tetrad Graduate Program, University of California, San Francisco, United States.,Department of Microbiology and Immunology, University of California, San Francisco, United States
| | - Candace S Britton
- Department of Biochemistry and Biophysics, Tetrad Graduate Program, University of California, San Francisco, United States.,Department of Microbiology and Immunology, University of California, San Francisco, United States
| | - Kyle R Fowler
- Department of Biochemistry and Biophysics, Tetrad Graduate Program, University of California, San Francisco, United States.,Department of Microbiology and Immunology, University of California, San Francisco, United States
| | - Jordan T Feigerle
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - P Anthony Weil
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Alexander D Johnson
- Department of Biochemistry and Biophysics, Tetrad Graduate Program, University of California, San Francisco, United States.,Department of Microbiology and Immunology, University of California, San Francisco, United States
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40
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Barrientos-Moreno M, Murillo-Pineda M, Muñoz-Cabello AM, Prado F. Histone depletion prevents telomere fusions in pre-senescent cells. PLoS Genet 2018; 14:e1007407. [PMID: 29879139 PMCID: PMC5991667 DOI: 10.1371/journal.pgen.1007407] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 05/09/2018] [Indexed: 12/20/2022] Open
Abstract
Upon telomerase inactivation, telomeres gradually shorten with each cell division until cells enter replicative senescence. In Saccharomyces cerevisiae, the kinases Mec1/ATR and Tel1/ATM protect the genome during pre-senescence by preventing telomere-telomere fusions (T-TFs) and the subsequent genetic instability associated with fusion-bridge-breakage cycles. Here we report that T-TFs in mec1Δ tel1Δ cells can be suppressed by reducing the pool of available histones. This protection associates neither with changes in bulk telomere length nor with major changes in the structure of subtelomeric chromatin. We show that the absence of Mec1 and Tel1 strongly augments double-strand break (DSB) repair by non-homologous end joining (NHEJ), which might contribute to the high frequency of T-TFs in mec1Δ tel1Δ cells. However, histone depletion does not prevent telomere fusions by inhibiting NHEJ, which is actually increased in histone-depleted cells. Rather, histone depletion protects telomeres from fusions by homologous recombination (HR), even though HR is proficient in maintaining the proliferative state of pre-senescent mec1Δ tel1Δ cells. Therefore, HR during pre-senescence not only helps stalled replication forks but also prevents T-TFs by a mechanism that, in contrast to the previous one, is promoted by a reduction in the histone pool and can occur in the absence of Rad51. Our results further suggest that the Mec1-dependent depletion of histones that occurs during pre-senescence in cells without telomerase (tlc1Δ) prevents T-TFs by favoring the processing of unprotected telomeres by Rad51-independent HR. Telomere shortening upon telomerase inactivation leads to an irreversible cell division arrest known as replicative senescence, which is considered as a tumor suppressor mechanism. Since pre-senescence is critical for tissue homeostasis, cells are endowed with recombination mechanisms that facilitate the replication of short telomeres and prevent premature entry into senescence. Consequently, pre-senescent cells divide with critically short telomeres, which have lost most of their shelterin proteins. The tumor suppressor genes ATR and ATM, as well as their yeast homologs Mec1 and Tel1, prevent telomere fusions during pre-senescence by unknown mechanisms. Here we show that the absence of Mec1 and Tel1 strongly augments DSB repair by non-homologous end joining, which might explain the high rate of telomere fusions in mec1Δ tel1Δ cells. Moreover, we show that a reduction in the pool of available histones prevents telomere fusions in mec1Δ tel1Δ cells by stimulating Rad51-independent homologous recombination. Our results suggest that the Mec1-dependent process of histone depletion that accompanies pre-senescence in cells lacking telomerase activity is required to prevent telomere fusions by promoting the processing of unprotected telomeres by recombination instead of non-homologous end joining.
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Affiliation(s)
- Marta Barrientos-Moreno
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine Center (CABIMER), CSIC-University of Seville-University Pablo de Olavide, Seville, Spain
| | - Marina Murillo-Pineda
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine Center (CABIMER), CSIC-University of Seville-University Pablo de Olavide, Seville, Spain
| | - Ana M. Muñoz-Cabello
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine Center (CABIMER), CSIC-University of Seville-University Pablo de Olavide, Seville, Spain
| | - Félix Prado
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine Center (CABIMER), CSIC-University of Seville-University Pablo de Olavide, Seville, Spain
- * E-mail:
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41
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Wanat JJ, Logsdon GA, Driskill JH, Deng Z, Lieberman PM, Johnson FB. TERRA and the histone methyltransferase Dot1 cooperate to regulate senescence in budding yeast. PLoS One 2018; 13:e0195698. [PMID: 29649255 PMCID: PMC5896980 DOI: 10.1371/journal.pone.0195698] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 03/27/2018] [Indexed: 01/27/2023] Open
Abstract
The events underlying senescence induced by critical telomere shortening are not fully understood. Here we provide evidence that TERRA, a non-coding RNA transcribed from subtelomeres, contributes to senescence in yeast lacking telomerase (tlc1Δ). Levels of TERRA expressed from multiple telomere ends appear elevated at senescence, and expression of an artificial RNA complementary to TERRA (anti-TERRA) binds TERRA in vivo and delays senescence. Anti-TERRA acts independently from several other mechanisms known to delay senescence, including those elicited by deletions of EXO1, TEL1, SAS2, and genes encoding RNase H enzymes. Further, it acts independently of the senescence delay provided by RAD52-dependent recombination. However, anti-TERRA delays senescence in a fashion epistatic to inactivation of the conserved histone methyltransferase Dot1. Dot1 associates with TERRA, and anti-TERRA disrupts this interaction in vitro and in vivo. Surprisingly, the anti-TERRA delay is independent of the C-terminal methyltransferase domain of Dot1 and instead requires only its N-terminus, which was previously found to facilitate release of telomeres from the nuclear periphery. Together, these data suggest that TERRA and Dot1 cooperate to drive senescence.
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Affiliation(s)
- Jennifer J. Wanat
- University of Pennsylvania School of Medicine, Pathology and Laboratory Medicine, Philadelphia, Pennsylvania, United States of America
- Washington College, Department of Biology, Chestertown, Maryland, United States of America
| | - Glennis A. Logsdon
- University of Pennsylvania School of Medicine, Pathology and Laboratory Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jordan H. Driskill
- University of Pennsylvania School of Medicine, Pathology and Laboratory Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Zhong Deng
- The Wistar Institute, Gene Expression and Regulation, Philadelphia, Pennsylvania, United States of America
| | - Paul M. Lieberman
- The Wistar Institute, Gene Expression and Regulation, Philadelphia, Pennsylvania, United States of America
| | - F. Brad Johnson
- University of Pennsylvania School of Medicine, Pathology and Laboratory Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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42
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Song S, Johnson FB. Epigenetic Mechanisms Impacting Aging: A Focus on Histone Levels and Telomeres. Genes (Basel) 2018; 9:genes9040201. [PMID: 29642537 PMCID: PMC5924543 DOI: 10.3390/genes9040201] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 03/27/2018] [Accepted: 03/29/2018] [Indexed: 12/13/2022] Open
Abstract
Aging and age-related diseases pose some of the most significant and difficult challenges to modern society as well as to the scientific and medical communities. Biological aging is a complex, and, under normal circumstances, seemingly irreversible collection of processes that involves numerous underlying mechanisms. Among these, chromatin-based processes have emerged as major regulators of cellular and organismal aging. These include DNA methylation, histone modifications, nucleosome positioning, and telomere regulation, including how these are influenced by environmental factors such as diet. Here we focus on two interconnected categories of chromatin-based mechanisms impacting aging: those involving changes in the levels of histones or in the functions of telomeres.
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Affiliation(s)
- Shufei Song
- Biochemistry and Molecular Biophysics Graduate Group, Biomedical Graduate Studies, University of Pennsylvania, Philadelphia, PA 19104, USA.
- Department of Pathology and Laboratory Medicine, and Institute on Aging, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - F Brad Johnson
- Department of Pathology and Laboratory Medicine, and Institute on Aging, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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43
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Kim W, Shay JW. Long-range telomere regulation of gene expression: Telomere looping and telomere position effect over long distances (TPE-OLD). Differentiation 2018; 99:1-9. [PMID: 29197683 PMCID: PMC5826875 DOI: 10.1016/j.diff.2017.11.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/11/2017] [Accepted: 11/21/2017] [Indexed: 01/09/2023]
Abstract
The human cellular reverse transcriptase, telomerase, is very tightly regulated in large long-lived species. Telomerase is expressed during early human fetal development, is turned off in most adult tissues, and then becomes reactivated in almost all human cancers. However, the exact mechanism regulating these switches in expression are not known. We recently described a phenomenon where genes are regulated by telomere length dependent loops (telomere position effects over long distances; TPE-OLD). The hTERT gene is ~ 1.2Mb from the human chromosome 5p end. We observed that when telomeres are long hTERT gene expression is repressed and a probe next to the 5p telomere and the hTERT locus are spatially co-localized. When telomeres are short at least one of the hTERT alleles is spatially separated from the telomere, developing more active histone marks and changes in DNA methylation in the hTERT promoter region. These findings have implications for how cells turn off telomerase when telomeres are long during fetal development and how cancer cells reactivate telomerase in cells that have short telomeres. In addition to TPE-OLD, in proliferating stem cells such as activated T-lymphocytes, telomerase can be reversibly activated and silenced by telomere looping. In telomerase positive cancer cells that are induced to differentiate and downregulate telomerase, telomere looping correlates with silencing of the hTERT gene. These studies and others support a role of telomeres in regulating gene expression via telomere looping that may involve interactions with internal telomeric sequences (ITS). In addition to telomere looping, TPE-OLD may be one mechanism of how cells time changes in physiology without initiating a DNA damage response.
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Affiliation(s)
- Wanil Kim
- Department of Cell Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Jerry W Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.
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44
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Yang CW, Tseng SF, Yu CJ, Chung CY, Chang CY, Pobiega S, Teng SC. Telomere shortening triggers a feedback loop to enhance end protection. Nucleic Acids Res 2017; 45:8314-8328. [PMID: 28575419 PMCID: PMC5737367 DOI: 10.1093/nar/gkx503] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 05/26/2017] [Indexed: 01/20/2023] Open
Abstract
Telomere homeostasis is controlled by both telomerase machinery and end protection. Telomere shortening induces DNA damage sensing kinases ATM/ATR for telomerase recruitment. Yet, whether telomere shortening also governs end protection is poorly understood. Here we discover that yeast ATM/ATR controls end protection. Rap1 is phosphorylated by Tel1 and Mec1 kinases at serine 731, and this regulation is stimulated by DNA damage and telomere shortening. Compromised Rap1 phosphorylation hampers the interaction between Rap1 and its interacting partner Rif1, which thereby disturbs the end protection. As expected, reduction of Rap1–Rif1 association impairs telomere length regulation and increases telomere–telomere recombination. These results indicate that ATM/ATR DNA damage checkpoint signal contributes to telomere protection by strengthening the Rap1–Rif1 interaction at short telomeres, and the checkpoint signal oversees both telomerase recruitment and end capping pathways to maintain telomere homeostasis.
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Affiliation(s)
- Chia-Wei Yang
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Shun-Fu Tseng
- Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, Taipei 100, Taiwan
| | - Chia-Jung Yu
- Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Tao-Yuan 333, Taiwan.,Department of Thoracic Medicine, Chang Gung Memorial Hospital, Linkou, Tao-Yuan 333, Taiwan
| | - Chia-Yu Chung
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Cheng-Yen Chang
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Sabrina Pobiega
- INSERM UMR 967, Institut de Biologie François Jacob, CEA Paris-Saclay, 92265 Fontenay-aux-roses, France
| | - Shu-Chun Teng
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
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45
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Epigenetic regulation in cell senescence. J Mol Med (Berl) 2017; 95:1257-1268. [DOI: 10.1007/s00109-017-1581-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/14/2017] [Accepted: 08/16/2017] [Indexed: 12/26/2022]
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46
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Politano G, Logrand F, Brancaccio M, Di Carlo S. In-silico cardiac aging regulatory model including microRNA post-transcriptional regulation. Methods 2017; 124:57-68. [DOI: 10.1016/j.ymeth.2017.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/26/2017] [Accepted: 06/02/2017] [Indexed: 12/28/2022] Open
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47
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Beletsky AV, Malyavko AN, Sukhanova MV, Mardanova ES, Zvereva MI, Petrova OA, Parfenova YY, Rubtsova MP, Mardanov AV, Lavrik OI, Dontsova OA, Ravin NV. The genome-wide transcription response to telomerase deficiency in the thermotolerant yeast Hansenula polymorpha DL-1. BMC Genomics 2017; 18:492. [PMID: 28659185 PMCID: PMC5490237 DOI: 10.1186/s12864-017-3889-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 06/21/2017] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND In the course of replication of eukaryotic chromosomes, the telomere length is maintained due to activity of telomerase, the ribonucleoprotein reverse transcriptase. Abolishing telomerase function causes progressive shortening of telomeres and, ultimately, cell cycle arrest and replicative senescence. To better understand the cellular response to telomerase deficiency, we performed a transcriptomic study for the thermotolerant methylotrophic yeast Hansenula polymorpha DL-1 lacking telomerase activity. RESULTS Mutant strain of H. polymorpha carrying a disrupted telomerase RNA gene was produced, grown to senescence and analyzed by RNA-seq along with wild type strain. Telomere shortening induced a transcriptional response involving genes relevant to telomere structure and maintenance, DNA damage response, information processing, and some metabolic pathways. Genes involved in DNA replication and repair, response to environmental stresses and intracellular traffic were up-regulated in senescent H. polymorpha cells, while strong down-regulation was observed for genes involved in transcription and translation, as well as core histones. CONCLUSIONS Comparison of the telomerase deletion transcription responses by Saccharomyces cerevisiae and H. polymorpha demonstrates that senescence makes different impact on the main metabolic pathways of these yeast species but induces similar changes in processes related to nucleic acids metabolism and protein synthesis. Up-regulation of a subunit of the TORC1 complex is clearly relevant for both types of yeast.
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Affiliation(s)
- Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld 2, Moscow, 119071, Russia
| | - Alexander N Malyavko
- Faculty of Chemistry, Moscow State University, Leninskie Gory 1, bld. 3, Moscow, 119991, Russia.,Center of Functional Genomics, Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
| | - Maria V Sukhanova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentiev Ave. 8, Novosibirsk, 630090, Russia
| | - Eugenia S Mardanova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld 2, Moscow, 119071, Russia
| | - Maria I Zvereva
- Faculty of Chemistry, Moscow State University, Leninskie Gory 1, bld. 3, Moscow, 119991, Russia
| | - Olga A Petrova
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory 1, bld. 40, Moscow, 119992, Russia
| | - Yulia Yu Parfenova
- Faculty of Chemistry, Moscow State University, Leninskie Gory 1, bld. 3, Moscow, 119991, Russia
| | - Maria P Rubtsova
- Faculty of Chemistry, Moscow State University, Leninskie Gory 1, bld. 3, Moscow, 119991, Russia
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld 2, Moscow, 119071, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentiev Ave. 8, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Olga A Dontsova
- Faculty of Chemistry, Moscow State University, Leninskie Gory 1, bld. 3, Moscow, 119991, Russia.,Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory 1, bld. 40, Moscow, 119992, Russia.,Center of Functional Genomics, Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld 2, Moscow, 119071, Russia.
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48
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Prado F, Maya D. Regulation of Replication Fork Advance and Stability by Nucleosome Assembly. Genes (Basel) 2017; 8:genes8020049. [PMID: 28125036 PMCID: PMC5333038 DOI: 10.3390/genes8020049] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/04/2017] [Accepted: 01/16/2017] [Indexed: 12/13/2022] Open
Abstract
The advance of replication forks to duplicate chromosomes in dividing cells requires the disassembly of nucleosomes ahead of the fork and the rapid assembly of parental and de novo histones at the newly synthesized strands behind the fork. Replication-coupled chromatin assembly provides a unique opportunity to regulate fork advance and stability. Through post-translational histone modifications and tightly regulated physical and genetic interactions between chromatin assembly factors and replisome components, chromatin assembly: (1) controls the rate of DNA synthesis and adjusts it to histone availability; (2) provides a mechanism to protect the integrity of the advancing fork; and (3) regulates the mechanisms of DNA damage tolerance in response to replication-blocking lesions. Uncoupling DNA synthesis from nucleosome assembly has deleterious effects on genome integrity and cell cycle progression and is linked to genetic diseases, cancer, and aging.
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Affiliation(s)
- Felix Prado
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine Center (CABIMER), Spanish National Research Council (CSIC), Seville 41092, Spain.
| | - Douglas Maya
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine Center (CABIMER), Spanish National Research Council (CSIC), Seville 41092, Spain.
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Martínez P, Gómez-López G, Pisano DG, Flores JM, Blasco MA. A genetic interaction between RAP1 and telomerase reveals an unanticipated role for RAP1 in telomere maintenance. Aging Cell 2016; 15:1113-1125. [PMID: 27586969 PMCID: PMC5114719 DOI: 10.1111/acel.12517] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2016] [Indexed: 11/30/2022] Open
Abstract
RAP1 is one of the components of shelterin, the capping complex at chromosome ends or telomeres, although its role in telomere length maintenance and protection has remained elusive. RAP1 also binds subtelomeric repeats and along chromosome arms, where it regulates gene expression and has been shown to function in metabolism control. Telomerase is the enzyme that elongates telomeres, and its deficiency causes a premature aging in humans and mice. We describe an unanticipated genetic interaction between RAP1 and telomerase. While RAP1 deficiency alone does not impact on mouse survival, mice lacking both RAP1 and telomerase show a progressively decreased survival with increasing mouse generations compared to telomerase single mutants. Telomere shortening is more pronounced in Rap1−/−Terc−/− doubly deficient mice than in the single‐mutant Terc−/− counterparts, leading to an earlier onset of telomere‐induced DNA damage and degenerative pathologies. Telomerase deficiency abolishes obesity and liver steatohepatitis provoked by RAP1 deficiency. Using genomewide ChIP sequencing, we find that progressive telomere shortening owing to telomerase deficiency leads to re‐localization of RAP1 from telomeres and subtelomeric regions to extratelomeric sites in a genomewide manner. These findings suggest that although in the presence of sufficient telomere reserve RAP1 is not a key factor for telomere maintenance and protection, it plays a crucial role in the context of telomerase deficiency, thus in agreement with its evolutionary conservation as a telomere component from yeast to humans.
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Affiliation(s)
- Paula Martínez
- Telomeres and Telomerase Group; Molecular Oncology Program; Spanish National Cancer Centre (CNIO); Melchor Fernández Almagro 3 Madrid E-28029 Spain
| | - Gonzalo Gómez-López
- Bioinformatics Core Unit; Structural Biology and Biocomputing Program; Spanish National Cancer Centre (CNIO); Melchor Fernández Almagro 3 Madrid E-28029 Spain
| | - David G. Pisano
- Bioinformatics Core Unit; Structural Biology and Biocomputing Program; Spanish National Cancer Centre (CNIO); Melchor Fernández Almagro 3 Madrid E-28029 Spain
| | - Juana M. Flores
- Animal Surgery and Medicine Department; Faculty of Veterinarian; Complutense University of Madrid; Madrid 28029 Spain
| | - Maria A. Blasco
- Telomeres and Telomerase Group; Molecular Oncology Program; Spanish National Cancer Centre (CNIO); Melchor Fernández Almagro 3 Madrid E-28029 Spain
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50
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Abstract
Aging is an inevitable outcome of life, characterized by progressive decline in tissue and organ function and increased risk of mortality. Accumulating evidence links aging to genetic and epigenetic alterations. Given the reversible nature of epigenetic mechanisms, these pathways provide promising avenues for therapeutics against age-related decline and disease. In this review, we provide a comprehensive overview of epigenetic studies from invertebrate organisms, vertebrate models, tissues, and in vitro systems. We establish links between common operative aging pathways and hallmark chromatin signatures that can be used to identify "druggable" targets to counter human aging and age-related disease.
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Affiliation(s)
- Payel Sen
- Epigenetics Program, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19130, USA
| | - Parisha P Shah
- Epigenetics Program, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19130, USA
| | - Raffaella Nativio
- Epigenetics Program, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19130, USA
| | - Shelley L Berger
- Epigenetics Program, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19130, USA.
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