1
|
Suganuma T, Workman JL. Chromatin balances cell redox and energy homeostasis. Epigenetics Chromatin 2023; 16:46. [PMID: 38017471 PMCID: PMC10683155 DOI: 10.1186/s13072-023-00520-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/30/2023] [Indexed: 11/30/2023] Open
Abstract
Chromatin plays a central role in the conversion of energy in cells: alteration of chromatin structure to make DNA accessible consumes energy, and compaction of chromatin preserves energy. Alteration of chromatin structure uses energy sources derived from carbon metabolism such as ATP and acetyl-CoA; conversely, chromatin compaction and epigenetic modification feedback to metabolism and energy homeostasis by controlling gene expression and storing metabolites. Coordination of these dual chromatin events must be flexibly modulated in response to environmental changes such as during development and exposure to stress. Aging also alters chromatin structure and the coordination of metabolism, chromatin dynamics, and other cell processes. Noncoding RNAs and other RNA species that associate directly with chromatin or with chromatin modifiers contribute to spatiotemporal control of transcription and energy conversion. The time required for generating the large amounts of RNAs and chromatin modifiers observed in super-enhancers may be critical for regulation of transcription and may be impacted by aging. Here, taking into account these factors, we review alterations of chromatin that are fundamental to cell responses to metabolic changes due to stress and aging to maintain redox and energy homeostasis. We discuss the relationship between spatiotemporal control of energy and chromatin function, as this emerging concept must be considered to understand how cell homeostasis is maintained.
Collapse
Affiliation(s)
- Tamaki Suganuma
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA.
| | - Jerry L Workman
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
| |
Collapse
|
2
|
Sun Y, Zhang H, Qiu T, Liao L, Su X. Epigenetic regulation of mesenchymal stem cell aging through histone modifications. Genes Dis 2023; 10:2443-2456. [PMID: 37554203 PMCID: PMC10404871 DOI: 10.1016/j.gendis.2022.10.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/18/2022] [Accepted: 10/23/2022] [Indexed: 12/12/2022] Open
Abstract
Stem cell senescence and exhaustion, a hallmark of aging, lead to declines in tissue repair and regeneration in aged individuals. Emerging evidence has revealed that epigenetic regulation plays critical roles in the self-renew, lineage-commitment, survival, and function of stem cells. Moreover, epigenetic alterations are considered important drivers of stem cell dysfunction during aging. In this review, we focused on current knowledge of the histone modifications in the aging of mesenchymal stem cells (MSCs). The aberrant epigenetic modifications on histones, including methylation and acetylation, have been found in aging MSCs. By disturbing the expression of specific genes, these epigenetic modifications affect the self-renew, survival, and differentiation of MSCs. A set of epigenetic enzymes that write or erase these modifications are critical in regulating the aging of MSCs. Furthermore, we discussed the rejuvenation strategies based on epigenetics to prevent stem cell aging and/or rejuvenate senescent MSCs.
Collapse
Affiliation(s)
| | | | - Tao Qiu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Pediatrics & Engineering Research Center of Oral Translational Medicine, Ministry of Education, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| | - Li Liao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Pediatrics & Engineering Research Center of Oral Translational Medicine, Ministry of Education, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xiaoxia Su
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Pediatrics & Engineering Research Center of Oral Translational Medicine, Ministry of Education, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| |
Collapse
|
3
|
Li YM, Mei YC, Liu AH, Wang RX, Chen R, Du HN. Gcn5- and Bre1-mediated Set2 degradation promotes chronological aging of Saccharomyces cerevisiae. Cell Rep 2023; 42:113186. [PMID: 37796660 DOI: 10.1016/j.celrep.2023.113186] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 07/19/2023] [Accepted: 09/13/2023] [Indexed: 10/07/2023] Open
Abstract
Loss of transcription-coupled histone H3 lysine 36 trimethylation (H3K36me3) contributes to shorter lifespans in eukaryotes. However, the molecular mechanism of the decline of H3K36me3 during aging remains poorly understood. Here, we report that the degradation of the methyltransferase Set2 is the cause of decreased H3K36me3 levels during chronological aging in budding yeast. We show that Set2 protein degradation during cellular senescence and chronological aging is mainly mediated by the ubiquitin-conjugating E2 enzyme Ubc3 and the E3 ligase Bre1. Lack of Bre1 or abolishment of the ubiquitination stabilizes Set2 protein, sustains H3K36me3 levels at the aging-related gene loci, and upregulates their gene expression, thus leading to extended chronological lifespan. We further illustrate that Gcn5-mediated Set2 acetylation is a prerequisite for Bre1-catalyzed Set2 polyubiquitination and proteolysis during aging. We propose that two sequential post-translational modifications regulate Set2 homeostasis, suggesting a potential strategy to target the Gcn5-Bre1-Set2 axis for intervention of longevity.
Collapse
Affiliation(s)
- Yu-Min Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, RNA Institute, Wuhan University, Wuhan 430072, China
| | - Yu-Chao Mei
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, RNA Institute, Wuhan University, Wuhan 430072, China
| | - Ao-Hui Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, RNA Institute, Wuhan University, Wuhan 430072, China
| | - Ru-Xin Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, RNA Institute, Wuhan University, Wuhan 430072, China
| | - Runfa Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, RNA Institute, Wuhan University, Wuhan 430072, China
| | - Hai-Ning Du
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, RNA Institute, Wuhan University, Wuhan 430072, China.
| |
Collapse
|
4
|
Church MC, Price A, Li H, Workman JL. The Swi-Snf chromatin remodeling complex mediates gene repression through metabolic control. Nucleic Acids Res 2023; 51:10278-10291. [PMID: 37650639 PMCID: PMC10602859 DOI: 10.1093/nar/gkad711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 08/02/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023] Open
Abstract
In eukaryotes, ATP-dependent chromatin remodelers regulate gene expression in response to nutritional and metabolic stimuli. However, altered transcription of metabolic genes may have significant indirect consequences which are currently poorly understood. In this study, we use genetic and molecular approaches to uncover a role for the remodeler Swi-Snf as a critical regulator of metabolism. We find that snfΔ mutants display a cysteine-deficient phenotype, despite growth in nutrient-rich media. This correlates with widespread perturbations in sulfur metabolic gene transcription, including global redistribution of the sulfur-sensing transcription factor Met4. Our findings show how a chromatin remodeler can have a significant impact on a whole metabolic pathway by directly regulating an important gene subset and demonstrate an emerging role for chromatin remodeling complexes as decisive factors in metabolic control.
Collapse
Affiliation(s)
- Michael C Church
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Andrew Price
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Hua Li
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jerry L Workman
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| |
Collapse
|
5
|
López-Gil L, Pascual-Ahuir A, Proft M. Genomic Instability and Epigenetic Changes during Aging. Int J Mol Sci 2023; 24:14279. [PMID: 37762580 PMCID: PMC10531692 DOI: 10.3390/ijms241814279] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Aging is considered the deterioration of physiological functions along with an increased mortality rate. This scientific review focuses on the central importance of genomic instability during the aging process, encompassing a range of cellular and molecular changes that occur with advancing age. In particular, this revision addresses the genetic and epigenetic alterations that contribute to genomic instability, such as telomere shortening, DNA damage accumulation, and decreased DNA repair capacity. Furthermore, the review explores the epigenetic changes that occur with aging, including modifications to histones, DNA methylation patterns, and the role of non-coding RNAs. Finally, the review discusses the organization of chromatin and its contribution to genomic instability, including heterochromatin loss, chromatin remodeling, and changes in nucleosome and histone abundance. In conclusion, this review highlights the fundamental role that genomic instability plays in the aging process and underscores the need for continued research into these complex biological mechanisms.
Collapse
Affiliation(s)
- Lucía López-Gil
- Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain;
- Department of Molecular and Cellular Pathology and Therapy, Instituto de Biomedicina de Valencia IBV-CSIC, Consejo Superior de Investigaciones Científicas CSIC, Jaime Roig 11, 46010 Valencia, Spain
| | - Amparo Pascual-Ahuir
- Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain;
| | - Markus Proft
- Department of Molecular and Cellular Pathology and Therapy, Instituto de Biomedicina de Valencia IBV-CSIC, Consejo Superior de Investigaciones Científicas CSIC, Jaime Roig 11, 46010 Valencia, Spain
| |
Collapse
|
6
|
Caligaris M, Sampaio-Marques B, Hatakeyama R, Pillet B, Ludovico P, De Virgilio C, Winderickx J, Nicastro R. The Yeast Protein Kinase Sch9 Functions as a Central Nutrient-Responsive Hub That Calibrates Metabolic and Stress-Related Responses. J Fungi (Basel) 2023; 9:787. [PMID: 37623558 PMCID: PMC10455444 DOI: 10.3390/jof9080787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Yeast cells are equipped with different nutrient signaling pathways that enable them to sense the availability of various nutrients and adjust metabolism and growth accordingly. These pathways are part of an intricate network since most of them are cross-regulated and subject to feedback regulation at different levels. In yeast, a central role is played by Sch9, a protein kinase that functions as a proximal effector of the conserved growth-regulatory TORC1 complex to mediate information on the availability of free amino acids. However, recent studies established that Sch9 is more than a TORC1-effector as its activity is tuned by several other kinases. This allows Sch9 to function as an integrator that aligns different input signals to achieve accuracy in metabolic responses and stress-related molecular adaptations. In this review, we highlight the latest findings on the structure and regulation of Sch9, as well as its role as a nutrient-responsive hub that impacts on growth and longevity of yeast cells. Given that most key players impinging on Sch9 are well-conserved, we also discuss how studies on Sch9 can be instrumental to further elucidate mechanisms underpinning healthy aging in mammalians.
Collapse
Affiliation(s)
- Marco Caligaris
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; (M.C.); (B.P.); (C.D.V.)
| | - Belém Sampaio-Marques
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; (B.S.-M.); (P.L.)
- ICVS/3B’s-PT Government Associate Laboratory, 4806-909 Guimarães, Portugal
| | - Riko Hatakeyama
- Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK;
| | - Benjamin Pillet
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; (M.C.); (B.P.); (C.D.V.)
| | - Paula Ludovico
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; (B.S.-M.); (P.L.)
- ICVS/3B’s-PT Government Associate Laboratory, 4806-909 Guimarães, Portugal
| | - Claudio De Virgilio
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; (M.C.); (B.P.); (C.D.V.)
| | - Joris Winderickx
- Department of Biology, Functional Biology, KU Leuven, B-3001 Heverlee, Belgium;
| | - Raffaele Nicastro
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; (M.C.); (B.P.); (C.D.V.)
| |
Collapse
|
7
|
Müller H, Lesur A, Dittmar G, Gentzel M, Kettner K. Proteomic consequences of TDA1 deficiency in Saccharomyces cerevisiae: Protein kinase Tda1 is essential for Hxk1 and Hxk2 serine 15 phosphorylation. Sci Rep 2022; 12:18084. [PMID: 36302925 PMCID: PMC9613766 DOI: 10.1038/s41598-022-21414-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 09/27/2022] [Indexed: 02/05/2023] Open
Abstract
Hexokinase 2 (Hxk2) of Saccharomyces cerevisiae is a dual function hexokinase, acting as a glycolytic enzyme and being involved in the transcriptional regulation of glucose-repressible genes. Relief from glucose repression is accompanied by phosphorylation of Hxk2 at serine 15, which has been attributed to the protein kinase Tda1. To explore the role of Tda1 beyond Hxk2 phosphorylation, the proteomic consequences of TDA1 deficiency were investigated by difference gel electrophoresis (2D-DIGE) comparing a wild type and a Δtda1 deletion mutant. To additionally address possible consequences of glucose repression/derepression, both were grown at 2% and 0.1% (w/v) glucose. A total of eight protein spots exhibiting a minimum twofold enhanced or reduced fluorescence upon TDA1 deficiency was detected and identified by mass spectrometry. Among the spot identities are-besides the expected Hxk2-two proteoforms of hexokinase 1 (Hxk1). Targeted proteomics analyses in conjunction with 2D-DIGE demonstrated that TDA1 is indispensable for Hxk2 and Hxk1 phosphorylation at serine 15. Thirty-six glucose-concentration-dependent protein spots were identified. A simple method to improve spot quantification, approximating spots as rotationally symmetric solids, is presented along with new data on the quantities of Hxk1 and Hxk2 and their serine 15 phosphorylated forms at high and low glucose growth conditions. The Δtda1 deletion mutant exhibited no altered growth under high or low glucose conditions or on alternative carbon sources. Also, invertase activity, serving as a reporter for glucose derepression, was not significantly altered. Instead, an involvement of Tda1 in oxidative stress response is suggested.
Collapse
Affiliation(s)
- Henry Müller
- grid.4488.00000 0001 2111 7257Institute of Physiological Chemistry, Technische Universität Dresden, Medizinische Fakultät Carl Gustav Carus, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Antoine Lesur
- grid.451012.30000 0004 0621 531XLuxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Gunnar Dittmar
- grid.451012.30000 0004 0621 531XLuxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg ,grid.16008.3f0000 0001 2295 9843Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue de Swing, 4367 Belvaux, Luxembourg
| | - Marc Gentzel
- grid.4488.00000 0001 2111 7257Center for Molecular and Cellular Bioengineering (CMCB), TP Molecular Analysis / Mass Spectrometry, Technische Universität Dresden, Tatzberg 46/47, 01307 Dresden, Germany
| | - Karina Kettner
- grid.4488.00000 0001 2111 7257Institute of Physiological Chemistry, Technische Universität Dresden, Medizinische Fakultät Carl Gustav Carus, Fetscherstrasse 74, 01307 Dresden, Germany
| |
Collapse
|
8
|
Romero AM, Maciaszczyk-Dziubinska E, Mombeinipour M, Lorentzon E, Aspholm E, Wysocki R, Tamás MJ. OUP accepted manuscript. FEMS Yeast Res 2022; 22:6551893. [PMID: 35323907 PMCID: PMC9041338 DOI: 10.1093/femsyr/foac018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/08/2022] [Accepted: 03/16/2022] [Indexed: 11/23/2022] Open
Abstract
In a high-throughput yeast two-hybrid screen of predicted coiled-coil motif interactions in the Saccharomyces cerevisiae proteome, the protein Etp1 was found to interact with the yeast AP-1-like transcription factors Yap8, Yap1 and Yap6. Yap8 plays a crucial role during arsenic stress since it regulates expression of the resistance genes ACR2 and ACR3. The function of Etp1 is not well understood but the protein has been implicated in transcription and protein turnover during ethanol stress, and the etp1∆ mutant is sensitive to ethanol. In this current study, we investigated whether Etp1 is implicated in Yap8-dependent functions. We show that Etp1 is required for optimal growth in the presence of trivalent arsenite and for optimal expression of the arsenite export protein encoded by ACR3. Since Yap8 is the only known transcription factor that regulates ACR3 expression, we investigated whether Etp1 regulates Yap8. Yap8 ubiquitination, stability, nuclear localization and ACR3 promoter association were unaffected in etp1∆ cells, indicating that Etp1 affects ACR3 expression independently of Yap8. Thus, Etp1 impacts gene expression under arsenic and other stress conditions but the mechanistic details remain to be elucidated.
Collapse
Affiliation(s)
| | | | - Mandana Mombeinipour
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-405 30 Göteborg, Sweden
| | - Emma Lorentzon
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-405 30 Göteborg, Sweden
| | - Emelie Aspholm
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-405 30 Göteborg, Sweden
| | - Robert Wysocki
- Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Markus J Tamás
- Corresponding author: Department of Chemistry and Molecular Biology, University of Gothenburg, PO Box 462, S-405 30 Göteborg, Sweden. Tel: +46-31-786-2548; E-mail:
| |
Collapse
|
9
|
Mawer JSP, Massen J, Reichert C, Grabenhorst N, Mylonas C, Tessarz P. Nhp2 is a reader of H2AQ105me and part of a network integrating metabolism with rRNA synthesis. EMBO Rep 2021; 22:e52435. [PMID: 34409714 PMCID: PMC8490984 DOI: 10.15252/embr.202152435] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 01/16/2023] Open
Abstract
Ribosome biogenesis is an essential cellular process that requires integration of extracellular cues, such as metabolic state, with intracellular signalling, transcriptional regulation and chromatin accessibility at the ribosomal DNA. Here, we demonstrate that the recently identified histone modification, methylation of H2AQ105 (H2AQ105me), is an integral part of a dynamic chromatin network at the rDNA locus. Its deposition depends on a functional mTor signalling pathway and acetylation of histone H3 at position K56, thus integrating metabolic and proliferative signals. Furthermore, we identify a first epigenetic reader of this modification, the ribonucleoprotein Nhp2, which specifically recognizes H2AQ105me. Based on functional and proteomic data, we suggest that Nhp2 functions as an adapter to bridge rDNA chromatin with components of the small subunit processome to efficiently coordinate transcription of rRNA with its post‐transcriptional processing. We support this by showing that an H2AQ105A mutant has a mild defect in early processing of rRNA.
Collapse
Affiliation(s)
- Julia S P Mawer
- Max Planck Research Group "Chromatin and Ageing", Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Jennifer Massen
- Max Planck Research Group "Chromatin and Ageing", Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Christina Reichert
- Max Planck Research Group "Chromatin and Ageing", Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Niklas Grabenhorst
- Max Planck Research Group "Chromatin and Ageing", Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Constantine Mylonas
- Max Planck Research Group "Chromatin and Ageing", Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Peter Tessarz
- Max Planck Research Group "Chromatin and Ageing", Max Planck Institute for Biology of Ageing, Cologne, Germany.,Cologne Excellence Cluster on Stress Responses in ageing-associated Diseases (CECAD), Cologne, Germany
| |
Collapse
|
10
|
Abstract
Aging represents the multifactorial decline in physiological function of every living organism. Over the past decades, several hallmarks of aging have been defined, including epigenetic deregulation. Indeed, multiple epigenetic events were found altered across different species during aging. Epigenetic changes directly contributing to aging and aging-related diseases include the accumulation of histone variants, changes in chromatin accessibility, loss of histones and heterochromatin, aberrant histone modifications, and deregulated expression/activity of miRNAs. As a consequence, cellular processes are affected, which results in the development or progression of several human pathologies, including cancer, diabetes, osteoporosis, and neurodegenerative disorders. In this review, we focus on epigenetic mechanisms underlying aging-related processes in various species and describe how these deregulations contribute to human diseases.
Collapse
Affiliation(s)
- Dominik Saul
- Kogod Center on Aging and Division of Endocrinology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA;
- Department of Trauma, Orthopedics and Reconstructive Surgery, Georg-August-University of Goettingen, 37075 Goettingen, Germany
| | - Robyn Laura Kosinsky
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA
- Correspondence: ; Tel.: +1-507-293-2386
| |
Collapse
|
11
|
Abstract
The mechanisms of epigenetic gene regulation-histone modifications, chromatin remodeling, DNA methylation, and noncoding RNA-use metabolites as enzymatic cofactors and substrates in reactions that allow chromatin formation, nucleotide biogenesis, transcription, RNA processing, and translation. Gene expression responds to demands from cellular processes that use specific metabolites and alters or maintains cellular metabolic status. However, the roles of metabolites-particularly nucleotides-as regulatory molecules in epigenetic regulation and biological processes remain largely unknown. Here we review the crosstalk between gene expression, nucleotide metabolism, and cellular processes, and explore the role of metabolism in epigenetics as a critical regulator of biological events.
Collapse
|
12
|
Oh S, Lee J, Swanson SK, Florens L, Washburn MP, Workman JL. Yeast Nuak1 phosphorylates histone H3 threonine 11 in low glucose stress by the cooperation of AMPK and CK2 signaling. eLife 2020; 9:64588. [PMID: 33372657 PMCID: PMC7781599 DOI: 10.7554/elife.64588] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/26/2020] [Indexed: 12/26/2022] Open
Abstract
Changes in available nutrients are inevitable events for most living organisms. Upon nutritional stress, several signaling pathways cooperate to change the transcription program through chromatin regulation to rewire cellular metabolism. In budding yeast, histone H3 threonine 11 phosphorylation (H3pT11) acts as a marker of low glucose stress and regulates the transcription of nutritional stress-responsive genes. Understanding how this histone modification ‘senses’ external glucose changes remains elusive. Here, we show that Tda1, the yeast ortholog of human Nuak1, is a direct kinase for H3pT11 upon low glucose stress. Yeast AMP-activated protein kinase (AMPK) directly phosphorylates Tda1 to govern Tda1 activity, while CK2 regulates Tda1 nuclear localization. Collectively, AMPK and CK2 signaling converge on histone kinase Tda1 to link external low glucose stress to chromatin regulation.
Collapse
Affiliation(s)
- Seunghee Oh
- Stowers Institute for Medical Research, Kansas City, United States
| | - Jaehyoun Lee
- Stowers Institute for Medical Research, Kansas City, United States
| | - Selene K Swanson
- Stowers Institute for Medical Research, Kansas City, United States
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, United States
| | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, United States.,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, United States
| | - Jerry L Workman
- Stowers Institute for Medical Research, Kansas City, United States
| |
Collapse
|
13
|
|
14
|
Abstract
Aging is the progressive decline or loss of function at the cellular, tissue, and organismal levels that ultimately leads to death. A number of external and internal factors, including diet, exercise, metabolic dysfunction, genome instability, and epigenetic imbalance, affect the lifespan of an organism. These aging factors regulate transcriptome changes related to the aging process through chromatin remodeling. Many epigenetic regulators, such as histone modification, histone variants, and ATP-dependent chromatin remodeling factors, play roles in chromatin reorganization. The key to understanding the role of gene regulatory networks in aging lies in characterizing the epigenetic regulators responsible for reorganizing and potentiating particular chromatin structures. This review covers epigenetic studies on aging, discusses the impact of epigenetic modifications on gene expression, and provides future directions in this area.
Collapse
|
15
|
Lee J, Oh S, Abmayr SM, Workman JL. When histones are under glucose starvation. J Biosci 2020; 45:17. [PMID: 31965995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Under nutritional stress, cells undergo metabolic rewiring that results in changes of various cellular processes that include gene transcription. This transcriptional regulation requires dynamic chromatin remodeling that involves histone post-translational modifications. There are several histone marks that may act as switches upon starvation for stress-response pathways.
Collapse
Affiliation(s)
- Jaehyoun Lee
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | | | | |
Collapse
|
16
|
Yong-Quan Ng G, Fann DYW, Jo DG, Sobey CG, Arumugam TV. Epigenetic Regulation by Dietary Restriction: Part II. Cond Med 2019; 2:300-310. [PMID: 32039346 PMCID: PMC7007178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In the first part of our review, we extensively discuss the different variants of dietary restriction (DR) regimens, as well as its corresponding mechanism(s) and subsequent effects. We also provide a detailed analysis of the different epigenetic mechanisms based on current knowledge. We postulate that DR may represent an environmental intervention that can modulate the epigenomic profile of an individual. It is highly plausible that epigenetic regulation by DR may help explain the asymmetric manifestation of DR effects in different individuals. Additionally, epigenetic modifications via DR may lead to epigenetic programming, providing protection against age-associated diseases, which in turn could lead to reduced morbidity and increased lifespan. In the second part of the review, we summarize recent findings that highlight the epigenomic axis of DR, which provides a better understanding of the mechanisms by which its numerous health benefits are achieved.
Collapse
Affiliation(s)
- Gavin Yong-Quan Ng
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - David Yang-Wei Fann
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Dong-Gyu Jo
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Christopher G. Sobey
- Department of Physiology, Anatomy & Microbiology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Thiruma V. Arumugam
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
- Department of Physiology, Anatomy & Microbiology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| |
Collapse
|
17
|
Romero-Bueno R, de la Cruz Ruiz P, Artal-Sanz M, Askjaer P, Dobrzynska A. Nuclear Organization in Stress and Aging. Cells 2019; 8:cells8070664. [PMID: 31266244 PMCID: PMC6678840 DOI: 10.3390/cells8070664] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/23/2019] [Accepted: 06/25/2019] [Indexed: 12/18/2022] Open
Abstract
The eukaryotic nucleus controls most cellular processes. It is isolated from the cytoplasm by the nuclear envelope, which plays a prominent role in the structural organization of the cell, including nucleocytoplasmic communication, chromatin positioning, and gene expression. Alterations in nuclear composition and function are eminently pronounced upon stress and during premature and physiological aging. These alterations are often accompanied by epigenetic changes in histone modifications. We review, here, the role of nuclear envelope proteins and histone modifiers in the 3-dimensional organization of the genome and the implications for gene expression. In particular, we focus on the nuclear lamins and the chromatin-associated protein BAF, which are linked to Hutchinson–Gilford and Nestor–Guillermo progeria syndromes, respectively. We also discuss alterations in nuclear organization and the epigenetic landscapes during normal aging and various stress conditions, ranging from yeast to humans.
Collapse
Affiliation(s)
- Raquel Romero-Bueno
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Patricia de la Cruz Ruiz
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Marta Artal-Sanz
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Peter Askjaer
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain.
| | - Agnieszka Dobrzynska
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain.
| |
Collapse
|
18
|
Abstract
Histone modifications are key epigenetic regulators that control chromatin structure and gene transcription, thereby impacting on various important cellular phenotypes. Over the past decade, a growing number of studies have indicated that changes in various histone modifications have a significant influence on the aging process. Furthermore, it has been revealed that the abundance and localization of histone modifications are responsive to various environmental stimuli, such as diet, which can also affect gene expression and lifespan. This supports the notion that histone modifications can serve as a main cellular platform for signal integration. Hence, in this review we focus on the role of histone modifications during aging, report the data indicating that diet affects histone modification levels and explore the idea that histone modifications may function as an intersection through which diet regulates lifespan. A greater understanding of the epigenetic mechanisms that link environmental signals to longevity may provide new strategies for therapeutic intervention in age-related diseases and for promoting healthy aging.
Collapse
Affiliation(s)
- Diego Molina-Serrano
- UMR 6290, Centre National de la Recherche Scientifique, Rennes, France.,Institute of Genetics and Development of Rennes (IGDR), Université de Rennes 1, Rennes, France
| | - Dimitris Kyriakou
- Efevre Tech Ltd., Larnaca, Cyprus.,Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Antonis Kirmizis
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| |
Collapse
|
19
|
Campos SE, DeLuna A. Functional genomics of dietary restriction and longevity in yeast. Mech Ageing Dev 2019; 179:36-43. [PMID: 30790575 DOI: 10.1016/j.mad.2019.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 02/11/2019] [Accepted: 02/18/2019] [Indexed: 11/22/2022]
Abstract
Dietary restriction-limitation of calories or other specific nutrients in the diet-is the sole non-genetic intervention known to extend the lifespan of a wide range of model organisms from yeast to mammals. Cell biology studies on the responses to dietary restriction have provided important clues about the mechanisms of longevity; however, a comprehensive genome-wide description of lifespan by dietary restriction has been mostly absent. Large-scale genetic analysis in the budding yeast Saccharomyces cerevisiae offers a great opportunity to uncover the conserved systems-level mechanisms that give way to longevity in response to diet. Here, we review recent advances in high-throughput phenotyping of the replicative and chronological life spans of yeast cells, which have contributed to our understanding of longevity by dietary restriction and the cellular crosstalks of nutrient-sensing regulation.
Collapse
|