1
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Watowich MM, Costa CE, Chiou KL, Goldman EA, Petersen RM, Patterson S, Martínez MI, Sterner KN, Horvath JE, Montague MJ, Platt ML, Brent LJN, Higham JP, Lea AJ, Snyder-Mackler N. Immune gene regulation is associated with age and environmental adversity in a nonhuman primate. Mol Ecol 2024:e17445. [PMID: 39032090 DOI: 10.1111/mec.17445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/27/2024] [Accepted: 06/14/2024] [Indexed: 07/22/2024]
Abstract
Phenotypic aging is ubiquitous across mammalian species, suggesting shared underlying mechanisms of aging. Aging is linked to molecular changes to DNA methylation and gene expression, and environmental factors, such as severe external challenges or adversities, can moderate these age-related changes. Yet, it remains unclear whether environmental adversities affect gene regulation via the same molecular pathways as chronological, or 'primary', aging. Investigating molecular aging in naturalistic animal populations can fill this gap by providing insight into shared molecular mechanisms of aging and the effects of a greater diversity of environmental adversities - particularly those that can be challenging to study in humans or laboratory organisms. Here, we characterised molecular aging - specifically, CpG methylation - in a sample of free-ranging rhesus macaques living off the coast of Puerto Rico (n samples = 571, n individuals = 499), which endured a major hurricane during our study. Age was associated with methylation at 78,661 sites (31% of all sites tested). Age-associated hypermethylation occurred more frequently in areas of active gene regulation, while hypomethylation was enriched in regions that show less activity in immune cells, suggesting these regions may become de-repressed in older individuals. Age-associated hypomethylation also co-occurred with increased chromatin accessibility while hypermethylation showed the opposite trend, hinting at a coordinated, multi-level loss of epigenetic stability during aging. We detected 32,048 CpG sites significantly associated with exposure to a hurricane, and these sites overlapped age-associated sites, most strongly in regulatory regions and most weakly in quiescent regions. Together, our results suggest that environmental adversity may contribute to aging-related molecular phenotypes in regions of active gene transcription, but that primary aging has specific signatures in non-regulatory regions.
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Affiliation(s)
- Marina M Watowich
- Department of Biology, University of Washington, Seattle, Washington, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Christina E Costa
- Department of Anthropology, New York University, New York, New York, USA
- New York Consortium in Evolutionary Primatology, New York, New York, USA
| | - Kenneth L Chiou
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Elisabeth A Goldman
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Rachel M Petersen
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Sam Patterson
- Department of Anthropology, New York University, New York, New York, USA
| | - Melween I Martínez
- Caribbean Primate Research Center, Unit of Comparative Medicine, University of Puerto Rico, San Juan, Puerto Rico, USA
| | - Kirstin N Sterner
- Department of Anthropology, University of Oregon, Eugene, Oregon, USA
| | - Julie E Horvath
- Research and Collections Section, North Carolina Museum of Natural Sciences, Raleigh, North Carolina, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Michael J Montague
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael L Platt
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Psychology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Marketing Department, Wharton School of Business, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lauren J N Brent
- Centre for Research in Animal Behaviour, University of Exeter, Exeter, UK
| | - James P Higham
- Department of Anthropology, New York University, New York, New York, USA
- New York Consortium in Evolutionary Primatology, New York, New York, USA
| | - Amanda J Lea
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Noah Snyder-Mackler
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
- Neurodegenerative Disease Research Center, Arizona State University, Tempe, Arizona, USA
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2
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Matveeva K, Vasilieva M, Minskaia E, Rybtsov S, Shevyrev D. T-cell immunity against senescence: potential role and perspectives. Front Immunol 2024; 15:1360109. [PMID: 38504990 PMCID: PMC10948549 DOI: 10.3389/fimmu.2024.1360109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/19/2024] [Indexed: 03/21/2024] Open
Abstract
The development of age-associated diseases is related to the accumulation of senescent cells in the body. These are old non-functional cells with impaired metabolism, which are unable to divide. Such cells are also resistant to programmed cell death and prone to spontaneous production of some inflammatory factors. The accumulation of senescent cells is related to the age-associated dysfunction of organs and tissues as well as chronic inflammation that enhances with age. In the young organism, senescent cells are removed with the innate immunity system. However, the efficiency of this process decreases with age. Nowadays, more and more evidences are accumulating to support the involvement of specific immunity and T-lymphocytes in the fight against senescent cells. It has great physiological importance since the efficient elimination of senescent cells requires a high diversity of antigen-recognizing receptors to cover the entire spectrum of senescent-associated antigens with high precision and specificity. Developing the approaches of T-cell immunity stimulation to generate or amplify a physiological immune response against senescent cells can provide new perspectives to extend active longevity. In this mini-review, the authors summarize the current understanding of the role of T-cell immunity in the fight against senescent cells and discuss the prospects of stimulating adaptive immunity for combating the accumulation of senescent cells that occurs with age.
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Singh AK, Mohanty A, Kumar SL, Kumari A, Beniwal R, Kumar Etikuppam A, Birajdar P, Mohd A, Prasada Rao HBD. Diminished NAD+ levels and activation of retrotransposons promote postovulatory aged oocyte (POAO) death. Cell Death Discov 2024; 10:104. [PMID: 38418811 PMCID: PMC10902361 DOI: 10.1038/s41420-024-01876-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/06/2024] [Accepted: 02/19/2024] [Indexed: 03/02/2024] Open
Abstract
Death is the fate of postovulatory aged or unfertilized oocytes (POAO) in many animals. However, precise molecular mechanisms are yet to be discovered. Here, we demonstrate that increased amounts of reactive oxygen species (ROS), calcium ion (Ca+2) channels, and retrotransposon activity induce apoptosis, which in turn causes POAO death. Notably, suppression of ROS, Ca+2 channels, and retrotransposons delayed POAO death. Further, we found that the histone H4K12 and K16 acetylation increased via downregulation of NAD+ and NAD+ -dependent histone deacetylase SIRT3. Furthermore, adding NMN, sodium pyruvate, or CD38 inhibition delayed the death of postovulatory aged oocytes. Finally, we demonstrate the conservation of retrotransposon-induced DNA damage-dependent POAO death in higher-order vertebrates. Our findings suggest that POAO mortality is caused by cyclic cascade metabolic interactions in which low NAD+ levels increase histone acetylation by inhibiting histone deacetylases, resulting in an increase in retrotransposons, ROS, and Ca+2 channel activity and thus contributing to DNA damage-induced apoptosis.
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Affiliation(s)
- Ajay K Singh
- National Institute of Animal Biotechnology, Hyderabad, Telangana, 500032, India
- Department of Ophthalmology, University of Rochester, Rochester, NY, 14620, USA
| | - Aradhana Mohanty
- National Institute of Animal Biotechnology, Hyderabad, Telangana, 500032, India
- Graduate studies, Regional Centre for Biotechnology, Faridabad, 121 001, India
| | - S Lava Kumar
- National Institute of Animal Biotechnology, Hyderabad, Telangana, 500032, India
- Graduate studies, Regional Centre for Biotechnology, Faridabad, 121 001, India
| | - Anjali Kumari
- National Institute of Animal Biotechnology, Hyderabad, Telangana, 500032, India
- Graduate studies, Regional Centre for Biotechnology, Faridabad, 121 001, India
| | - Rohit Beniwal
- National Institute of Animal Biotechnology, Hyderabad, Telangana, 500032, India
- Graduate studies, Regional Centre for Biotechnology, Faridabad, 121 001, India
| | - Ajith Kumar Etikuppam
- National Institute of Animal Biotechnology, Hyderabad, Telangana, 500032, India
- Graduate studies, Regional Centre for Biotechnology, Faridabad, 121 001, India
| | - Pravin Birajdar
- National Institute of Animal Biotechnology, Hyderabad, Telangana, 500032, India
- Graduate studies, Regional Centre for Biotechnology, Faridabad, 121 001, India
| | - Athar Mohd
- National Institute of Animal Biotechnology, Hyderabad, Telangana, 500032, India
- Graduate studies, Regional Centre for Biotechnology, Faridabad, 121 001, India
| | - H B D Prasada Rao
- National Institute of Animal Biotechnology, Hyderabad, Telangana, 500032, India.
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4
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Farahmandnejad M, Mosaddeghi P, Dorvash M, Sakhteman A, Negahdaripour M, Faridi P. Correlation of Myeloid-Derived Suppressor Cell Expansion with Upregulated Transposable Elements in Severe COVID-19 Unveiled in Single-Cell RNA Sequencing Reanalysis. Biomedicines 2024; 12:315. [PMID: 38397917 PMCID: PMC10887269 DOI: 10.3390/biomedicines12020315] [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: 12/07/2023] [Revised: 01/14/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Some studies have investigated the potential role of transposable elements (TEs) in COVID-19 pathogenesis and complications. However, to the best of our knowledge, there is no study to examine the possible association of TE expression in cell functions and its potential role in COVID-19 immune response at the single-cell level. In this study, we reanalyzed single-cell RNA seq data of bronchoalveolar lavage (BAL) samples obtained from six severe COVID-19 patients and three healthy donors to assess the probable correlation of TE expression with the immune responses induced by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in COVID-19 patients. Our findings indicate that the expansion of myeloid-derived suppressor cells (MDSCs) may be a characteristic feature of COVID-19. Additionally, a significant increase in TE expression in MDSCs was observed. This upregulation of TEs in COVID-19 may be linked to the adaptability of these cells in response to their microenvironments. Furthermore, it appears that the identification of overexpressed TEs by pattern recognition receptors (PRRs) in MDSCs may enhance the suppressive capacity of these cells. Thus, this study emphasizes the crucial role of TEs in the functionality of MDSCs during COVID-19.
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Affiliation(s)
- Mitra Farahmandnejad
- Quality Control of Drug Products Department, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz 71348-14336, Iran;
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz 71348-14336, Iran
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz 71348-14336, Iran
| | - Pouria Mosaddeghi
- Medicinal Plants Processing Research Center, School of Pharmacy, Shiraz University of Medical Science, Shiraz 71348-14336, Iran;
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz 71348-14336, Iran
| | - Mohammadreza Dorvash
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia;
| | - Amirhossein Sakhteman
- Proteomics and Bioanalytics, Department of Molecular Life Sciences, School of Life Sciences, Technical University of Munich, 80333 Munich, Germany;
| | - Manica Negahdaripour
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz 71348-14336, Iran
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz 71348-14336, Iran
| | - Pouya Faridi
- Monash Proteomics and Metabolomics Platform, Department of Medicine, School of Clinical Sciences, Monash University, Clayton, VIC 3800, Australia
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
- Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
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5
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Alonso ADC, El Idrissi A, Candia R, Morozova V, Kleiman FE. Tau: More than a microtubule-binding protein in neurons. Cytoskeleton (Hoboken) 2024; 81:71-77. [PMID: 37819542 DOI: 10.1002/cm.21795] [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: 07/29/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023]
Abstract
Tau protein was discovered as a microtubule-associated protein nearly 50 years ago, and our understanding of tau has revolved around that role. Even with tau's rise to stardom as a central player in neurodegenerative disease, therapeutic efforts have largely been targeted toward cytoskeletal changes. While some studies hinted toward non-cytoskeletal roles for tau, it is only fairly recently that these ideas have begun to receive considerable attention. Many new binding partners for tau have been identified, including DNA, RNA, RNA-binding proteins, some receptors, and other tau molecules. The diversity of tau binding partners coupled with the discovery of tau other than axonal compartments such as nucleus, dendrites, and synapses have led to the proposal of novel functions for tau in roles such as nuclear stability, cell signaling, transcriptional processing, and protein synthesis. Tau self-assembly in particular has made an impact, leading to the hypothesis that a prion-like function of hyperphosphorylated tau is central to tauopathies. With tau emerging as a multifaceted protein that operates in many parts of the cell and with many molecular partners, the field of tau biology is primed for discoveries that can provide new perspectives on both the unique biochemistry of tau and the nature of devastating neurological diseases.
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Affiliation(s)
- Alejandra Del Carmen Alonso
- Biology Department and Center for Developmental Neuroscience, College of Staten Island, Staten Island, New York, USA
- Biology Program, The Graduate Center, The City University of New York, New York, New York, USA
| | - Abdeslem El Idrissi
- Biology Department and Center for Developmental Neuroscience, College of Staten Island, Staten Island, New York, USA
- Biology Program, The Graduate Center, The City University of New York, New York, New York, USA
| | - Robert Candia
- Biology Department and Center for Developmental Neuroscience, College of Staten Island, Staten Island, New York, USA
- Biology Program, The Graduate Center, The City University of New York, New York, New York, USA
| | - Viktoriya Morozova
- Biology Department and Center for Developmental Neuroscience, College of Staten Island, Staten Island, New York, USA
- Biology Program, The Graduate Center, The City University of New York, New York, New York, USA
- Helene Fuld College of Nursing, New York, New York, USA
| | - Frida Esther Kleiman
- Biology Program, The Graduate Center, The City University of New York, New York, New York, USA
- Chemistry Department, Hunter College, The City University of New York, New York, New York, USA
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6
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Duhamel M, Hood ME, Rodríguez de la Vega RC, Giraud T. Dynamics of transposable element accumulation in the non-recombining regions of mating-type chromosomes in anther-smut fungi. Nat Commun 2023; 14:5692. [PMID: 37709766 PMCID: PMC10502011 DOI: 10.1038/s41467-023-41413-4] [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: 12/23/2022] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
In the absence of recombination, the number of transposable elements (TEs) increases due to less efficient selection, but the dynamics of such TE accumulations are not well characterized. Leveraging a dataset of 21 independent events of recombination cessation of different ages in mating-type chromosomes of Microbotryum fungi, we show that TEs rapidly accumulated in regions lacking recombination, but that TE content reached a plateau at ca. 50% of occupied base pairs by 1.5 million years following recombination suppression. The same TE superfamilies have expanded in independently evolved non-recombining regions, in particular rolling-circle replication elements (Helitrons). Long-terminal repeat (LTR) retrotransposons of the Copia and Ty3 superfamilies also expanded, through transposition bursts (distinguished from gene conversion based on LTR divergence), with both non-recombining regions and autosomes affected, suggesting that non-recombining regions constitute TE reservoirs. This study improves our knowledge of genome evolution by showing that TEs can accumulate through bursts, following non-linear decelerating dynamics.
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Affiliation(s)
- Marine Duhamel
- Ecologie Systématique Evolution, IDEEV, CNRS, Université Paris-Saclay, AgroParisTech, Bâtiment 680, 12 route RD128, 91190, Gif-sur-Yvette, France.
- Evolution der Pflanzen und Pilze, Ruhr-Universität Bochum, Universitätsstraße 150, 44780, Bochum, Germany.
| | - Michael E Hood
- Department of Biology, Amherst College, 01002-5000, Amherst, MA, USA
| | - Ricardo C Rodríguez de la Vega
- Ecologie Systématique Evolution, IDEEV, CNRS, Université Paris-Saclay, AgroParisTech, Bâtiment 680, 12 route RD128, 91190, Gif-sur-Yvette, France
| | - Tatiana Giraud
- Ecologie Systématique Evolution, IDEEV, CNRS, Université Paris-Saclay, AgroParisTech, Bâtiment 680, 12 route RD128, 91190, Gif-sur-Yvette, France
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7
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Baechle JJ, Chen N, Makhijani P, Winer S, Furman D, Winer DA. Chronic inflammation and the hallmarks of aging. Mol Metab 2023; 74:101755. [PMID: 37329949 PMCID: PMC10359950 DOI: 10.1016/j.molmet.2023.101755] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/30/2023] [Accepted: 06/13/2023] [Indexed: 06/19/2023] Open
Abstract
BACKGROUND Recently, the hallmarks of aging were updated to include dysbiosis, disabled macroautophagy, and chronic inflammation. In particular, the low-grade chronic inflammation during aging, without overt infection, is defined as "inflammaging," which is associated with increased morbidity and mortality in the aging population. Emerging evidence suggests a bidirectional and cyclical relationship between chronic inflammation and the development of age-related conditions, such as cardiovascular diseases, neurodegeneration, cancer, and frailty. How the crosstalk between chronic inflammation and other hallmarks of aging underlies biological mechanisms of aging and age-related disease is thus of particular interest to the current geroscience research. SCOPE OF REVIEW This review integrates the cellular and molecular mechanisms of age-associated chronic inflammation with the other eleven hallmarks of aging. Extra discussion is dedicated to the hallmark of "altered nutrient sensing," given the scope of Molecular Metabolism. The deregulation of hallmark processes during aging disrupts the delicate balance between pro-inflammatory and anti-inflammatory signaling, leading to a persistent inflammatory state. The resultant chronic inflammation, in turn, further aggravates the dysfunction of each hallmark, thereby driving the progression of aging and age-related diseases. MAIN CONCLUSIONS The crosstalk between chronic inflammation and other hallmarks of aging results in a vicious cycle that exacerbates the decline in cellular functions and promotes aging. Understanding this complex interplay will provide new insights into the mechanisms of aging and the development of potential anti-aging interventions. Given their interconnectedness and ability to accentuate the primary elements of aging, drivers of chronic inflammation may be an ideal target with high translational potential to address the pathological conditions associated with aging.
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Affiliation(s)
- Jordan J Baechle
- Buck Artificial Intelligence Platform, the Buck Institute for Research on Aging, Novato, CA, USA
| | - Nan Chen
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Division of Cellular & Molecular Biology, Diabetes Research Group, Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON, Canada
| | - Priya Makhijani
- Buck Artificial Intelligence Platform, the Buck Institute for Research on Aging, Novato, CA, USA; Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Shawn Winer
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - David Furman
- Buck Artificial Intelligence Platform, the Buck Institute for Research on Aging, Novato, CA, USA; Stanford 1000 Immunomes Project, Stanford University School of Medicine, Stanford, CA, USA; Instituto de Investigaciones en Medicina Traslacional (IIMT), Universidad Austral, CONICET, Pilar, Argentina.
| | - Daniel A Winer
- Buck Artificial Intelligence Platform, the Buck Institute for Research on Aging, Novato, CA, USA; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Division of Cellular & Molecular Biology, Diabetes Research Group, Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON, Canada; Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.
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8
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Escobedo SE, McGovern SE, Jauregui-Lozano JP, Stanhope SC, Anik P, Singhal K, DeBernardis R, Weake VM. Targeted RNAi screen identifies transcriptional mechanisms that prevent premature degeneration of adult photoreceptors. FRONTIERS IN EPIGENETICS AND EPIGENOMICS 2023; 1:1187980. [PMID: 37901602 PMCID: PMC10603763 DOI: 10.3389/freae.2023.1187980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
Aging is associated with a decline in visual function and increased prevalence of ocular disease, correlating with changes in the transcriptome and epigenome of cells in the eye. Here, we sought to identify the transcriptional mechanisms that are necessary to maintain photoreceptor viability and function during aging. To do this, we performed a targeted photoreceptor-specific RNAi screen in Drosophila to identify transcriptional regulators whose knockdown results in premature, age-dependent retinal degeneration. From an initial set of 155 RNAi lines each targeting a unique gene and spanning a diverse set of transcription factors, chromatin remodelers, and histone modifiers, we identified 18 high-confidence target genes whose decreased expression in adult photoreceptors leads to premature and progressive retinal degeneration. These 18 target genes were enriched for factors involved in the regulation of transcription initiation, pausing, and elongation, suggesting that these processes are essential for maintaining the health of aging photoreceptors. To identify the genes regulated by these factors, we profiled the photoreceptor transcriptome in a subset of lines. Strikingly, two of the 18 target genes, Spt5 and domino, show similar changes in gene expression to those observed in photoreceptors with advanced age. Together, our data suggest that dysregulation of factors involved in transcription initiation and elongation plays a key role in shaping the transcriptome of aging photoreceptors. Further, our findings indicate that the age-dependent changes in gene expression not only correlate but might also contribute to an increased risk of retinal degeneration.
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Affiliation(s)
- Spencer E. Escobedo
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Sarah E. McGovern
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | | | - Sarah C. Stanhope
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Paul Anik
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Kratika Singhal
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Ryan DeBernardis
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Vikki M. Weake
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, United States
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Wahl D, Smith ME, McEntee CM, Cavalier AN, Osburn SC, Burke SD, Grant RA, Nerguizian D, Lark DS, Link CD, LaRocca TJ. The reverse transcriptase inhibitor 3TC protects against age-related cognitive dysfunction. Aging Cell 2023; 22:e13798. [PMID: 36949552 PMCID: PMC10186603 DOI: 10.1111/acel.13798] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 03/24/2023] Open
Abstract
Aging is the primary risk factor for most neurodegenerative diseases, including Alzheimer's disease. Major hallmarks of brain aging include neuroinflammation/immune activation and reduced neuronal health/function. These processes contribute to cognitive dysfunction (a key risk factor for Alzheimer's disease), but their upstream causes are incompletely understood. Age-related increases in transposable element (TE) transcripts might contribute to reduced cognitive function with brain aging, as the reverse transcriptase inhibitor 3TC reduces inflammation in peripheral tissues and TE transcripts have been linked with tau pathology in Alzheimer's disease. However, the effects of 3TC on cognitive function with aging have not been investigated. Here, in support of a role for TE transcripts in brain aging/cognitive decline, we show that 3TC: (a) improves cognitive function and reduces neuroinflammation in old wild-type mice; (b) preserves neuronal health with aging in mice and Caenorhabditis elegans; and (c) enhances cognitive function in a mouse model of tauopathy. We also provide insight on potential underlying mechanisms, as well as evidence of translational relevance for these observations by showing that TE transcripts accumulate with brain aging in humans, and that these age-related increases intersect with those observed in Alzheimer's disease. Collectively, our results suggest that TE transcript accumulation during aging may contribute to cognitive decline and neurodegeneration, and that targeting these events with reverse transcriptase inhibitors like 3TC could be a viable therapeutic strategy.
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Affiliation(s)
- Devin Wahl
- Department of Health and Exercise ScienceColorado State UniversityFort CollinsColoradoUSA
- Center for Healthy AgingColorado State UniversityFort CollinsColoradoUSA
| | - Meghan E. Smith
- Department of Health and Exercise ScienceColorado State UniversityFort CollinsColoradoUSA
- Center for Healthy AgingColorado State UniversityFort CollinsColoradoUSA
| | - Cali M. McEntee
- Department of Health and Exercise ScienceColorado State UniversityFort CollinsColoradoUSA
- Center for Healthy AgingColorado State UniversityFort CollinsColoradoUSA
| | - Alyssa N. Cavalier
- Department of Health and Exercise ScienceColorado State UniversityFort CollinsColoradoUSA
- Center for Healthy AgingColorado State UniversityFort CollinsColoradoUSA
| | - Shelby C. Osburn
- Department of Health and Exercise ScienceColorado State UniversityFort CollinsColoradoUSA
- Center for Healthy AgingColorado State UniversityFort CollinsColoradoUSA
| | - Samuel D. Burke
- Department of Health and Exercise ScienceColorado State UniversityFort CollinsColoradoUSA
- Center for Healthy AgingColorado State UniversityFort CollinsColoradoUSA
| | - Randy A. Grant
- Department of Health and Exercise ScienceColorado State UniversityFort CollinsColoradoUSA
- Center for Healthy AgingColorado State UniversityFort CollinsColoradoUSA
| | - David Nerguizian
- Department of Biochemistry and Molecular GeneticsUniversity of Colorado School of MedicineAuroraColoradoUSA
| | - Daniel S. Lark
- Department of Health and Exercise ScienceColorado State UniversityFort CollinsColoradoUSA
| | - Christopher D. Link
- Department of Integrative PhysiologyUniversity of Colorado BoulderBoulderColoradoUSA
| | - Thomas J. LaRocca
- Department of Health and Exercise ScienceColorado State UniversityFort CollinsColoradoUSA
- Center for Healthy AgingColorado State UniversityFort CollinsColoradoUSA
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10
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Yushkova E, Moskalev A. Transposable elements and their role in aging. Ageing Res Rev 2023; 86:101881. [PMID: 36773759 DOI: 10.1016/j.arr.2023.101881] [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: 11/17/2022] [Revised: 01/16/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023]
Abstract
Transposable elements (TEs) are an important part of eukaryotic genomes. The role of somatic transposition in aging, carcinogenesis, and other age-related diseases has been determined. This review discusses the fundamental properties of TEs and their complex interactions with cellular processes, which are crucial for understanding the diverse effects of their activity on the genetics and epigenetics of the organism. The interactions of TEs with recombination, replication, repair, and chromosomal regulation; the ability of TEs to maintain a balance between their own activity and repression, the involvement of TEs in the creation of new or alternative genes, the expression of coding/non-coding RNA, and the role in DNA damage and modification of regulatory networks are reviewed. The contribution of the derepressed TEs to age-dependent effects in individual cells/tissues in different organisms was assessed. Conflicting information about TE activity under stress as well as theories of aging mechanisms related to TEs is discussed. On the one hand, transposition activity in response to stressors can lead to organisms acquiring adaptive innovations of great importance for evolution at the population level. On the other hand, the TE expression can cause decreased longevity and stress tolerance at the individual level. The specific features of TE effects on aging processes in germline and soma and the ways of their regulation in cells are highlighted. Recent results considering somatic mutations in normal human and animal tissues are indicated, with the emphasis on their possible functional consequences. In the context of aging, the correlation between somatic TE activation and age-related changes in the number of proteins required for heterochromatin maintenance and longevity regulation was analyzed. One of the original features of this review is a discussion of not only effects based on the TEs insertions and the associated consequences for the germline cell dynamics and somatic genome, but also the differences between transposon- and retrotransposon-mediated structural genome changes and possible phenotypic characteristics associated with aging and various age-related pathologies. Based on the analysis of published data, a hypothesis about the influence of the species-specific features of number, composition, and distribution of TEs on aging dynamics of different animal genomes was formulated.
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Affiliation(s)
- Elena Yushkova
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Center, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya st., 167982 Syktyvkar, Russian Federation
| | - Alexey Moskalev
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Center, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya st., 167982 Syktyvkar, Russian Federation; Laboratory of Genetics and Epigenetics of Aging, Russian Clinical Research Center for Gerontology, Pirogov Russian National Research Medical University, Moscow 129226, Russian Federation; Longaevus Technologies, London, UK.
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11
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Balaji AK, Saha S, Deshpande S, Poola D, Sengupta K. Nuclear envelope, chromatin organizers, histones, and DNA: The many achilles heels exploited across cancers. Front Cell Dev Biol 2022; 10:1068347. [PMID: 36589746 PMCID: PMC9800887 DOI: 10.3389/fcell.2022.1068347] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
In eukaryotic cells, the genome is organized in the form of chromatin composed of DNA and histones that organize and regulate gene expression. The dysregulation of chromatin remodeling, including the aberrant incorporation of histone variants and their consequent post-translational modifications, is prevalent across cancers. Additionally, nuclear envelope proteins are often deregulated in cancers, which impacts the 3D organization of the genome. Altered nuclear morphology, genome organization, and gene expression are defining features of cancers. With advances in single-cell sequencing, imaging technologies, and high-end data mining approaches, we are now at the forefront of designing appropriate small molecules to selectively inhibit the growth and proliferation of cancer cells in a genome- and epigenome-specific manner. Here, we review recent advances and the emerging significance of aberrations in nuclear envelope proteins, histone variants, and oncohistones in deregulating chromatin organization and gene expression in oncogenesis.
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12
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Aminzadeh-Gohari S, Kofler B, Herzog C. Dietary restriction in senolysis and prevention and treatment of disease. Crit Rev Food Sci Nutr 2022; 64:5242-5268. [PMID: 36484738 PMCID: PMC7616065 DOI: 10.1080/10408398.2022.2153355] [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] [Indexed: 12/13/2022]
Abstract
Aging represents a key risk factor for a plethora of diseases. Targeting detrimental processes which occur during aging, especially before onset of age-related disease, could provide drastic improvements in healthspan. There is increasing evidence that dietary restriction (DR), including caloric restriction, fasting, or fasting-mimicking diets, extend both lifespan and healthspan. This has sparked interest in the use of dietary regimens as a non-pharmacological means to slow aging and prevent disease. Here, we review the current evidence on the molecular mechanisms underlying DR-induced health improvements, including removal of senescent cells, metabolic reprogramming, and epigenetic rejuvenation.
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Affiliation(s)
- Sepideh Aminzadeh-Gohari
- Research Program for Receptor Biochemistry and Tumor Metabollism, Department of Pediatrics, University Hospital of the Paracelsus Medical University, Salzburg, Austria
- European Translational Oncology Prevention and Screening Institute, Universität Innsbruck, Innsbruck, Austria
- Research Institute for Biomedical Ageing, Universität Innsbruck, Innsbruck, Austria
| | - Barbara Kofler
- Research Program for Receptor Biochemistry and Tumor Metabollism, Department of Pediatrics, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | - Chiara Herzog
- European Translational Oncology Prevention and Screening Institute, Universität Innsbruck, Innsbruck, Austria
- Research Institute for Biomedical Ageing, Universität Innsbruck, Innsbruck, Austria
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13
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Ramini D, Latini S, Giuliani A, Matacchione G, Sabbatinelli J, Mensà E, Bacalini MG, Garagnani P, Rippo MR, Bronte G, Bonafè M, Cardelli M, Olivieri F. Replicative Senescence-Associated LINE1 Methylation and LINE1-Alu Expression Levels in Human Endothelial Cells. Cells 2022; 11:cells11233799. [PMID: 36497059 PMCID: PMC9739197 DOI: 10.3390/cells11233799] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/22/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022] Open
Abstract
One of the main challenges of current research on aging is to identify the complex epigenetic mechanisms involved in the acquisition of the cellular senescent phenotype. Despite some evidence suggested that epigenetic changes of DNA repetitive elements, including transposable elements (TE) sequences, are associated with replicative senescence of fibroblasts, data on different types of cells are scarce. We previously analysed genome-wide DNA methylation of young and replicative senescent human endothelial cells (HUVECs), highlighting increased levels of demethylated sequences in senescent cells. Here, we aligned the most significantly demethylated single CpG sites to the reference genome and annotated their localization inside TE sequences and found a significant hypomethylation of sequences belonging to the Long-Interspersed Element-1 (LINE-1 or L1) subfamilies L1M, L1P, and L1HS. To verify the hypothesis that L1 demethylation could be associated with increased transcription/activation of L1s and/or Alu elements (non-autonomous retroelements that usually depend on L1 sequences for reverse transcription and retrotransposition), we quantified the RNA expression levels of both L1 (generic L1 elements or site-specific L1PA2 on chromosome 14) and Alu elements in young and senescent HUVECs and human dermal fibroblasts (NHDFs). The RNA expression of Alu and L1 sequences was significantly increased in both senescent HUVECs and NHDFs, whereas the RNA transcript of L1PA2 on chromosome 14 was not significantly modulated in senescent cells. Moreover, we found an increased amount of TE DNA copies in the cytoplasm of senescent HUVECs and NHDFs. Our results support the hypothesis that TE, which are significantly increased in senescent cells, could be retrotranscribed to DNA sequences.
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Affiliation(s)
- Deborah Ramini
- Clinic of Laboratory and Precision Medicine, IRCCS INRCA, 60121 Ancona, Italy
| | - Silvia Latini
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
| | - Angelica Giuliani
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
- Correspondence: ; Tel.: +39-071-220-6243
| | - Giulia Matacchione
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
| | - Jacopo Sabbatinelli
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
- Laboratory Medicine Unit, Azienda Ospedaliero Universitaria delle Marche, 60126 Ancona, Italy
| | - Emanuela Mensà
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
| | | | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126 Bologna, Italy
- Applied Biomedical Research Center (CRBA), S. Orsola-Malpighi Polyclinic, 40126 Bologna, Italy
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”-Unit of Bologna, 40126 Bologna, Italy
- Department of Laboratory Medicine, Clinical Chemistry, Karolinska Institutet, Karolinska University Hospital, 141 86 Huddinge, Sweden
| | - Maria Rita Rippo
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
| | - Giuseppe Bronte
- Clinic of Laboratory and Precision Medicine, IRCCS INRCA, 60121 Ancona, Italy
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
| | - Massimiliano Bonafè
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126 Bologna, Italy
| | - Maurizio Cardelli
- Advanced Technology Center for Aging Research, IRCCS INRCA, 60121 Ancona, Italy
| | - Fabiola Olivieri
- Clinic of Laboratory and Precision Medicine, IRCCS INRCA, 60121 Ancona, Italy
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
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14
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Zhang X, Jiang Q, Li J, Zhang S, Cao Y, Xia X, Cai D, Tan J, Chen J, Han JDJ. KCNQ1OT1 promotes genome-wide transposon repression by guiding RNA-DNA triplexes and HP1 binding. Nat Cell Biol 2022; 24:1617-1629. [PMID: 36266489 DOI: 10.1038/s41556-022-01008-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 09/07/2022] [Indexed: 01/18/2023]
Abstract
Transposon (de)repression and heterochromatin reorganization are dynamically regulated during cell fate determination and are hallmarks of cellular senescence. However, whether they are sequence specifically regulated remains unknown. Here we uncover that the KCNQ1OT1 lncRNA, by sequence-specific Hoogsteen base pairing with double-stranded genomic DNA via its repeat-rich region and binding to the heterochromatin protein HP1α, guides, induces and maintains epigenetic silencing at specific repetitive DNA elements. Repressing KCNQ1OT1 or deleting its repeat-rich region reduces DNA methylation and H3K9me3 on KCNQ1OT1-targeted transposons. Engineering a fusion KCNQ1OT1 with an ectopically targeting guiding triplex sequence induces de novo DNA methylation at the target site. Phenotypically, repressing KCNQ1OT1 induces senescence-associated heterochromatin foci, transposon activation and retrotransposition as well as cellular senescence, demonstrating an essential role of KCNQ1OT1 to safeguard against genome instability and senescence.
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Affiliation(s)
- Xiaoli Zhang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
| | - Quanlong Jiang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiyang Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Shiqiang Zhang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yaqiang Cao
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xian Xia
- Department of Pharmacology, Nanjing University of Chinese Medicine, Nanjing, China
| | - Donghong Cai
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiaqi Tan
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
| | - Jiekai Chen
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China.
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15
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Savytska N, Heutink P, Bansal V. Transcription start site signal profiling improves transposable element RNA expression analysis at locus-level. Front Genet 2022; 13:1026847. [PMID: 36338986 PMCID: PMC9633680 DOI: 10.3389/fgene.2022.1026847] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/11/2022] [Indexed: 08/31/2023] Open
Abstract
The transcriptional activity of Transposable Elements (TEs) has been involved in numerous pathological processes, including neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal lobar degeneration. The TE expression analysis from short-read sequencing technologies is, however, challenging due to the multitude of similar sequences derived from singular TEs subfamilies and the exaptation of TEs within longer coding or non-coding RNAs. Specialised tools have been developed to quantify the expression of TEs that either relies on probabilistic re-distribution of multimapper count fractions or allow for discarding multimappers altogether. Until now, the benchmarking across those tools was largely limited to aggregated expression estimates over whole TEs subfamilies. Here, we compared the performance of recently published tools (SQuIRE, TElocal, SalmonTE) with simplistic quantification strategies (featureCounts in unique, fraction and random modes) at the individual loci level. Using simulated datasets, we examined the false discovery rate and the primary driver of those false positive hits in the optimal quantification strategy. Our findings suggest a high false discovery number that exceeds the total number of correctly recovered active loci for all the quantification strategies, including the best performing tool TElocal. As a remedy, filtering based on the minimum number of read counts or baseMean expression improves the F1 score and decreases the number of false positives. Finally, we demonstrate that additional profiling of Transcription Start Site mapping statistics (using a k-means clustering approach) significantly improves the performance of TElocal while reporting a reliable set of detected and differentially expressed TEs in human simulated RNA-seq data.
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Affiliation(s)
| | | | - Vikas Bansal
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
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16
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Mustafin RN. Interrelation of MicroRNAs and Transposons in Aging and Carcinogenesis. ADVANCES IN GERONTOLOGY 2022. [DOI: 10.1134/s2079057022030092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Della Valle F, Reddy P, Yamamoto M, Liu P, Saera-Vila A, Bensaddek D, Zhang H, Prieto Martinez J, Abassi L, Celii M, Ocampo A, Nuñez Delicado E, Mangiavacchi A, Aiese Cigliano R, Rodriguez Esteban C, Horvath S, Izpisua Belmonte JC, Orlando V. LINE-1 RNA causes heterochromatin erosion and is a target for amelioration of senescent phenotypes in progeroid syndromes. Sci Transl Med 2022; 14:eabl6057. [PMID: 35947677 DOI: 10.1126/scitranslmed.abl6057] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Constitutive heterochromatin is responsible for genome repression of DNA enriched in repetitive sequences, telomeres, and centromeres. During physiological and pathological premature aging, heterochromatin homeostasis is profoundly compromised. Here, we showed that LINE-1 (Long Interspersed Nuclear Element-1; L1) RNA accumulation was an early event in both typical and atypical human progeroid syndromes. L1 RNA negatively regulated the enzymatic activity of the histone-lysine N-methyltransferase SUV39H1 (suppression of variegation 3-9 homolog 1), resulting in heterochromatin loss and onset of senescent phenotypes in vitro. Depletion of L1 RNA in dermal fibroblast cells from patients with different progeroid syndromes using specific antisense oligonucleotides (ASOs) restored heterochromatin histone 3 lysine 9 and histone 3 lysine 27 trimethylation marks, reversed DNA methylation age, and counteracted the expression of senescence-associated secretory phenotype genes such as p16, p21, activating transcription factor 3 (ATF3), matrix metallopeptidase 13 (MMP13), interleukin 1a (IL1a), BTG anti-proliferation factor 2 (BTG2), and growth arrest and DNA damage inducible beta (GADD45b). Moreover, systemic delivery of ASOs rescued the histophysiology of tissues and increased the life span of a Hutchinson-Gilford progeria syndrome mouse model. Transcriptional profiling of human and mouse samples after L1 RNA depletion demonstrated that pathways associated with nuclear chromatin organization, cell proliferation, and transcription regulation were enriched. Similarly, pathways associated with aging, inflammatory response, innate immune response, and DNA damage were down-regulated. Our results highlight the role of L1 RNA in heterochromatin homeostasis in progeroid syndromes and identify a possible therapeutic approach to treat premature aging and related syndromes.
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Affiliation(s)
- Francesco Della Valle
- King Abdullah University of Science and Technology (KAUST), Biological Environmental Sciences and Engineering Division BESE, KAUST Environmental Epigenetics Program, Thuwal, Saudi Arabia
| | - Pradeep Reddy
- Salk Institute for Biological Studies, La Jolla, CA, USA.,Altos Labs, San Diego, CA, USA
| | - Mako Yamamoto
- Salk Institute for Biological Studies, La Jolla, CA, USA.,Altos Labs, San Diego, CA, USA
| | - Peng Liu
- King Abdullah University of Science and Technology (KAUST), Biological Environmental Sciences and Engineering Division BESE, KAUST Environmental Epigenetics Program, Thuwal, Saudi Arabia
| | | | - Dalila Bensaddek
- King Abdullah University of Science and Technology (KAUST), Bioscience Core Lab
| | - Huoming Zhang
- King Abdullah University of Science and Technology (KAUST), Bioscience Core Lab
| | | | - Leila Abassi
- King Abdullah University of Science and Technology (KAUST), Biological Environmental Sciences and Engineering Division BESE, KAUST Environmental Epigenetics Program, Thuwal, Saudi Arabia
| | - Mirko Celii
- King Abdullah University of Science and Technology (KAUST), Biological Environmental Sciences and Engineering Division BESE, KAUST Environmental Epigenetics Program, Thuwal, Saudi Arabia
| | | | | | - Arianna Mangiavacchi
- King Abdullah University of Science and Technology (KAUST), Biological Environmental Sciences and Engineering Division BESE, KAUST Environmental Epigenetics Program, Thuwal, Saudi Arabia
| | | | | | | | | | - Valerio Orlando
- King Abdullah University of Science and Technology (KAUST), Biological Environmental Sciences and Engineering Division BESE, KAUST Environmental Epigenetics Program, Thuwal, Saudi Arabia
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18
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Antón-Fernández A, Vallés-Saiz L, Avila J, Hernández F. Neuronal nuclear tau and neurodegeneration. Neuroscience 2022; 518:178-184. [PMID: 35872252 DOI: 10.1016/j.neuroscience.2022.07.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/23/2022] [Accepted: 07/13/2022] [Indexed: 02/08/2023]
Abstract
Tau is a well-known microtubule-associated protein related to its cytoplasmic localization in a neuronal cell. However, tau has been located at the cell nucleus where it could be a nucleic acid-associated protein by its preferential binding to DNA sequences present in the nucleolus and pericentromeric heterochromatin. This less well-known localization of tau could not be trivial, since during aging, an increase in the amount of nuclear tau takes place and it may be related to the described role of tau in the activation of transposons and further aging acceleration.
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Affiliation(s)
- Alejandro Antón-Fernández
- Centro de Biología Molecular "Severo Ochoa", CSIC/UAM, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Laura Vallés-Saiz
- Centro de Biología Molecular "Severo Ochoa", CSIC/UAM, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Jesús Avila
- Centro de Biología Molecular "Severo Ochoa", CSIC/UAM, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain.
| | - Félix Hernández
- Centro de Biología Molecular "Severo Ochoa", CSIC/UAM, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain.
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Colonna Romano N, Fanti L. Transposable Elements: Major Players in Shaping Genomic and Evolutionary Patterns. Cells 2022; 11:cells11061048. [PMID: 35326499 PMCID: PMC8947103 DOI: 10.3390/cells11061048] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/04/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
Transposable elements (TEs) are ubiquitous genetic elements, able to jump from one location of the genome to another, in all organisms. For this reason, on the one hand, TEs can induce deleterious mutations, causing dysfunction, disease and even lethality in individuals. On the other hand, TEs can increase genetic variability, making populations better equipped to respond adaptively to environmental change. To counteract the deleterious effects of TEs, organisms have evolved strategies to avoid their activation. However, their mobilization does occur. Usually, TEs are maintained silent through several mechanisms, but they can be reactivated during certain developmental windows. Moreover, TEs can become de-repressed because of drastic changes in the external environment. Here, we describe the ‘double life’ of TEs, being both ‘parasites’ and ‘symbionts’ of the genome. We also argue that the transposition of TEs contributes to two important evolutionary processes: the temporal dynamic of evolution and the induction of genetic variability. Finally, we discuss how the interplay between two TE-dependent phenomena, insertional mutagenesis and epigenetic plasticity, plays a role in the process of evolution.
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Mustafin RN, Khusnutdinova EK. The relationship of lamins with epigenetic factors during aging. Vavilovskii Zhurnal Genet Selektsii 2022; 26:40-49. [PMID: 35342861 PMCID: PMC8892175 DOI: 10.18699/vjgb-22-06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 05/23/2021] [Accepted: 09/28/2021] [Indexed: 11/26/2022] Open
Abstract
The key factor of genome instability during aging is transposon dysregulation. This may be due to senile changes in the expression of lamins, which epigenetically modulate transposons. Lamins directly physically interact with transposons. Epigenetic regulators such as SIRT7, BAF, and microRNA can also serve as intermediaries for their interactions. There is also an inverse regulation, since transposons are sources of miRNAs that affect lamins. We suggest that lamins can be attributed to epigenetic factors, since they are part of the NURD, interact with histone deacetylases and regulate gene expression without changing the nucleotide sequences. The role of lamins in the etiopathogenesis of premature aging syndromes may be associated with interactions with transposons. In various human cells, LINE1 is present in the heterochromatin domains of the genome associated with lamins, while SIRT7 facilitates the interaction of this retroelement with lamins. Both retroelements and the nuclear lamina play an important role in the antiviral response of organisms. This may be due to the role of lamins in protection from both viruses and transposons, since viruses and transposons are evolutionarily related. Transposable elements and lamins are secondary messengers of environmental stressors that can serve as triggers for aging and carcinogenesis. Transposons play a role in the development of cancer, while the microRNAs derived from them, participating in the etiopathogenesis of tumors, are important in human aging. Lamins have similar properties, since lamins are dysregulated in cancer, and microRNAs affecting them are involved in carcinogenesis. Changes in the expression of specif ic microRNAs were also revealed
in laminopathies. Identif ication of the epigenetic mechanisms of interaction of lamins with transposons during
aging
can become the basis for the development of methods of life extension and targeted therapy of age-associated
cancer
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Affiliation(s)
| | - E. K. Khusnutdinova
- Institute of Biochemistry and Genetics – Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences
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21
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Bakhtogarimov IR, Kudryavtseva AV, Krasnov GS, Gladysh NS, Volodin VV, Kudryavtsev AA, Bulavkina EV, Goncharova MA, Ledyaeva VS, Pastukhov IS, Vershinina YS, Starkova AM, Snezhkina AV, Shuvalova AI, Pavlov VS, Nikiforov-Nikishin DL, Moskalev AA, Guvatova ZG. The Effect of Meclofenoxate on the Transcriptome of Aging Brain of Nothobranchius guentheri Annual Killifish. Int J Mol Sci 2022; 23:ijms23052491. [PMID: 35269638 PMCID: PMC8910246 DOI: 10.3390/ijms23052491] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 02/04/2023] Open
Abstract
Annual fish of the genus Nothobranchius are promising models for aging research. Nothobranchius reproduces typical aspects of vertebrate aging, including hallmarks of brain aging. Meclofenoxate (MF) is a well-known compound that can enhance cognitive performance. The drug is prescribed for asthenic conditions, trauma, and vascular diseases of the brain. It is believed that MF is able to delay age-dependent changes in the human brain. However, until now, there has been no study of the MF effect on the brain transcriptome. In the present work, we performed an RNA-Seq study of brain tissues from aged Nothobranchius guentheri, which were almost lifetime administered with MF, as well as young and aged control fish. As expected, in response to MF, we revealed significant overexpression of neuron-specific genes including genes involved in synaptic activity and plasticity, neurotransmitter secretion, and neuron projection. The effect was more pronounced in female fish. In this aspect, MF alleviated age-dependent decreased expression of genes involved in neuronal activity. In both treated and untreated animals, we observed strong aging-associated overexpression of immune and inflammatory response genes. MF treatment did not prevent this effect, and moreover, some of these genes tended to be slightly upregulated under MF treatment. Additionally, we noticed upregulation of some genes associated with aging and cellular senescence, including isoforms of putative vascular cell adhesion molecule 1 (VCAM1), protein O-GlcNAcase (OGA), protein kinase C alpha type (KPCA), prolow-density lipoprotein receptor-related protein 1 (LRP1). Noteworthy, MF treatment was also associated with the elevated transcription of transposons, which are highly abundant in the N. guentheri genome. In conclusion, MF compensates for the age-dependent downregulation of neuronal activity genes, but its effect on aging brain transcriptome still cannot be considered unambiguously positive.
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Affiliation(s)
- Ildar R. Bakhtogarimov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (I.R.B.); (G.S.K.); (N.S.G.); (V.V.V.); (A.A.M.)
| | - Anna V. Kudryavtseva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (I.R.B.); (G.S.K.); (N.S.G.); (V.V.V.); (A.A.M.)
- Correspondence: (A.V.K.); (Z.G.G.); Tel.: +7-(499)-135-23-91 (A.V.K. & Z.G.G.)
| | - George S. Krasnov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (I.R.B.); (G.S.K.); (N.S.G.); (V.V.V.); (A.A.M.)
| | - Natalya S. Gladysh
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (I.R.B.); (G.S.K.); (N.S.G.); (V.V.V.); (A.A.M.)
| | - Vsevolod V. Volodin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (I.R.B.); (G.S.K.); (N.S.G.); (V.V.V.); (A.A.M.)
| | - Alexander A. Kudryavtsev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.A.K.); (E.V.B.); (M.A.G.); (V.S.L.); (Y.S.V.); (A.M.S.); (A.V.S.); (A.I.S.); (V.S.P.)
| | - Elizaveta V. Bulavkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.A.K.); (E.V.B.); (M.A.G.); (V.S.L.); (Y.S.V.); (A.M.S.); (A.V.S.); (A.I.S.); (V.S.P.)
| | - Margarita A. Goncharova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.A.K.); (E.V.B.); (M.A.G.); (V.S.L.); (Y.S.V.); (A.M.S.); (A.V.S.); (A.I.S.); (V.S.P.)
| | - Veronika S. Ledyaeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.A.K.); (E.V.B.); (M.A.G.); (V.S.L.); (Y.S.V.); (A.M.S.); (A.V.S.); (A.I.S.); (V.S.P.)
| | - Ivan S. Pastukhov
- Institute of Biotechnology and Fisheries, K.G. Razumovsky Moscow State University of Technologies and Management (the First Cossack University), 109004 Moscow, Russia; (I.S.P.); (D.L.N.-N.)
| | - Yulia S. Vershinina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.A.K.); (E.V.B.); (M.A.G.); (V.S.L.); (Y.S.V.); (A.M.S.); (A.V.S.); (A.I.S.); (V.S.P.)
| | - Anna M. Starkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.A.K.); (E.V.B.); (M.A.G.); (V.S.L.); (Y.S.V.); (A.M.S.); (A.V.S.); (A.I.S.); (V.S.P.)
| | - Anastasiya V. Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.A.K.); (E.V.B.); (M.A.G.); (V.S.L.); (Y.S.V.); (A.M.S.); (A.V.S.); (A.I.S.); (V.S.P.)
| | - Anastasija I. Shuvalova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.A.K.); (E.V.B.); (M.A.G.); (V.S.L.); (Y.S.V.); (A.M.S.); (A.V.S.); (A.I.S.); (V.S.P.)
| | - Vladislav S. Pavlov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.A.K.); (E.V.B.); (M.A.G.); (V.S.L.); (Y.S.V.); (A.M.S.); (A.V.S.); (A.I.S.); (V.S.P.)
| | - Dmitry L. Nikiforov-Nikishin
- Institute of Biotechnology and Fisheries, K.G. Razumovsky Moscow State University of Technologies and Management (the First Cossack University), 109004 Moscow, Russia; (I.S.P.); (D.L.N.-N.)
| | - Alexey A. Moskalev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (I.R.B.); (G.S.K.); (N.S.G.); (V.V.V.); (A.A.M.)
| | - Zulfiya G. Guvatova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (I.R.B.); (G.S.K.); (N.S.G.); (V.V.V.); (A.A.M.)
- Correspondence: (A.V.K.); (Z.G.G.); Tel.: +7-(499)-135-23-91 (A.V.K. & Z.G.G.)
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22
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Constitutive Heterochromatin in Eukaryotic Genomes: A Mine of Transposable Elements. Cells 2022; 11:cells11050761. [PMID: 35269383 PMCID: PMC8909793 DOI: 10.3390/cells11050761] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/10/2022] [Accepted: 02/18/2022] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) are abundant components of constitutive heterochromatin of the most diverse evolutionarily distant organisms. TEs enrichment in constitutive heterochromatin was originally described in the model organism Drosophila melanogaster, but it is now considered as a general feature of this peculiar portion of the genomes. The phenomenon of TE enrichment in constitutive heterochromatin has been proposed to be the consequence of a progressive accumulation of transposable elements caused by both reduced recombination and lack of functional genes in constitutive heterochromatin. However, this view does not take into account classical genetics studies and most recent evidence derived by genomic analyses of heterochromatin in Drosophila and other species. In particular, the lack of functional genes does not seem to be any more a general feature of heterochromatin. Sequencing and annotation of Drosophila melanogaster constitutive heterochromatin have shown that this peculiar genomic compartment contains hundreds of transcriptionally active genes, generally larger in size than that of euchromatic ones. Together, these genes occupy a significant fraction of the genomic territory of heterochromatin. Moreover, transposable elements have been suggested to drive the formation of heterochromatin by recruiting HP1 and repressive chromatin marks. In addition, there are several pieces of evidence that transposable elements accumulation in the heterochromatin might be important for centromere and telomere structure. Thus, there may be more complexity to the relationship between transposable elements and constitutive heterochromatin, in that different forces could drive the dynamic of this phenomenon. Among those forces, preferential transposition may be an important factor. In this article, we present an overview of experimental findings showing cases of transposon enrichment into the heterochromatin and their positive evolutionary interactions with an impact to host genomes.
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23
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Niss F, Bergqvist C, Ström AL, Hallberg E. Monitoring of Chromatin Organization at the Nuclear Pore Complex, Inner Nuclear Membrane, and Nuclear Interior in Live Cells by Fluorescence Ratiometric Imaging of Chromatin (FRIC). Methods Mol Biol 2022; 2502:151-160. [PMID: 35412237 DOI: 10.1007/978-1-0716-2337-4_10] [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] [Indexed: 06/14/2023]
Abstract
The image analysis tool FRIC (Fluorescence Ratiometric Imaging of Chromatin) quantitatively monitors dynamic spatiotemporal distribution of euchromatin and total chromatin in live cells. A vector (pTandemH) assures stoichiometrically constant expression of the histone variants Histone 3.3 and Histone 2B, fused to EGFP and mCherry, respectively. Quantitative ratiometric (H3.3/H2B) imaging displayed a concentrated distribution of heterochromatin in the periphery of U2OS cell nuclei. As a proof of concept, peripheral heterochromatin responded to experimental manipulation of histone acetylation as well as expression of the mutant lamin A protein "progerin," which causes Hutchinson-Gilford Progeria Syndrome. In summary FRIC is versatile, unbiased, robust, requires a minimum of experimental steps and is suitable for screening purposes.
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Affiliation(s)
- Frida Niss
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Cecilia Bergqvist
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Anna-Lena Ström
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Einar Hallberg
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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24
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Retrotransposons Down- and Up-Regulation in Aging Somatic Tissues. Cells 2021; 11:cells11010079. [PMID: 35011640 PMCID: PMC8750722 DOI: 10.3390/cells11010079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/22/2021] [Accepted: 12/26/2021] [Indexed: 01/19/2023] Open
Abstract
The transposon theory of aging hypothesizes the activation of transposable elements (TEs) in somatic tissues with age, leading to a shortening of the lifespan. It is thought that TE activation in aging produces an increase in DNA double-strand breaks, contributing to genome instability and promoting the activation of inflammatory responses. To investigate how TE regulation changes in somatic tissues during aging, we analyzed the expression of some TEs, as well as a source of small RNAs that specifically silence the analyzed TEs; the Drosophila cluster named flamenco. We found significant variations in the expression levels of all the analyzed TEs during aging, with a trend toward reduction in middle-aged adults and reactivation in older individuals that suggests dynamic regulation during the lifespan.
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25
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Guo X, Xuan N, Liu G, Xie H, Lou Q, Arnaud P, Offmann B, Picimbon JF. An Expanded Survey of the Moth PBP/GOBP Clade in Bombyx mori: New Insight into Expression and Functional Roles. Front Physiol 2021; 12:712593. [PMID: 34776998 PMCID: PMC8582636 DOI: 10.3389/fphys.2021.712593] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/13/2021] [Indexed: 02/01/2023] Open
Abstract
We studied the expression profile and ontogeny (from the egg stage through the larval stages and pupal stages, to the elderly adult age) of four OBPs from the silkworm moth Bombyx mori. We first showed that male responsiveness to female sex pheromone in the silkworm moth B. mori does not depend on age variation; whereas the expression of BmorPBP1, BmorPBP2, BmorGOBP1, and BmorGOBP2 varies with age. The expression profile analysis revealed that the studied OBPs are expressed in non-olfactory tissues at different developmental stages. In addition, we tested the effect of insecticide exposure on the expression of the four OBPs studied. Exposure to a toxic macrolide insecticide endectocide molecule (abamectin) led to the modulated expression of all four genes in different tissues. The higher expression of OBPs was detected in metabolic tissues, such as the thorax, gut, and fat body. All these data strongly suggest some alternative functions for these proteins other than olfaction. Finally, we carried out ligand docking studies and reported that PBP1 and GOBP2 have the capacity of binding vitamin K1 and multiple different vitamins.
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Affiliation(s)
- Xia Guo
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Ning Xuan
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Guoxia Liu
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Hongyan Xie
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Qinian Lou
- Shandong Silkworm Institute, Shandong Academy of Agricultural Sciences, Yantai, China
| | - Philippe Arnaud
- Protein Engineering and Functionality Unit, UMR CNRS 6286, University of Nantes, Nantes, France
| | - Bernard Offmann
- Protein Engineering and Functionality Unit, UMR CNRS 6286, University of Nantes, Nantes, France
| | - Jean-François Picimbon
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China.,School of Bioengineering, QILU University of Technology, Jinan, China
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26
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Gil L, Niño SA, Guerrero C, Jiménez-Capdeville ME. Phospho-Tau and Chromatin Landscapes in Early and Late Alzheimer's Disease. Int J Mol Sci 2021; 22:ijms221910283. [PMID: 34638632 PMCID: PMC8509045 DOI: 10.3390/ijms221910283] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 12/25/2022] Open
Abstract
Cellular identity is determined through complex patterns of gene expression. Chromatin, the dynamic structure containing genetic information, is regulated through epigenetic modulators, mainly by the histone code. One of the main challenges for the cell is maintaining functionality and identity, despite the accumulation of DNA damage throughout the aging process. Replicative cells can remain in a senescent state or develop a malign cancer phenotype. In contrast, post-mitotic cells such as pyramidal neurons maintain extraordinary functionality despite advanced age, but they lose their identity. This review focuses on tau, a protein that protects DNA, organizes chromatin, and plays a crucial role in genomic stability. In contrast, tau cytosolic aggregates are considered hallmarks of Alzheimer´s disease (AD) and other neurodegenerative disorders called tauopathies. Here, we explain AD as a phenomenon of chromatin dysregulation directly involving the epigenetic histone code and a progressive destabilization of the tau–chromatin interaction, leading to the consequent dysregulation of gene expression. Although this destabilization could be lethal for post-mitotic neurons, tau protein mediates profound cellular transformations that allow for their temporal survival.
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Affiliation(s)
- Laura Gil
- Departamento de Genética, Escuela de Medicina, Universidad “Alfonso X el Sabio”, 28691 Madrid, Spain;
| | - Sandra A. Niño
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma, de San Luis Potosí 78210, Mexico;
| | - Carmen Guerrero
- Banco de Cerebros (Biobanco), Hospital Universitario Fundación Alcorcón, Alcorcón, 28922 Madrid, Spain;
| | - María E. Jiménez-Capdeville
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma, de San Luis Potosí 78210, Mexico;
- Correspondence: ; Tel.: +52-444-826-2366
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27
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Peona V, Palacios-Gimenez OM, Blommaert J, Liu J, Haryoko T, Jønsson KA, Irestedt M, Zhou Q, Jern P, Suh A. The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200186. [PMID: 34304594 PMCID: PMC8310711 DOI: 10.1098/rstb.2020.0186] [Citation(s) in RCA: 21] [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] [Accepted: 11/20/2020] [Indexed: 12/17/2022] Open
Abstract
It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, probably leading to female-biased mutational load that may influence female physiology similar to the 'toxic-Y' effect in Drosophila males. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Valentina Peona
- Department of Organismal Biology—Systematic Biology, Uppsala University, Uppsala, Sweden
| | | | - Julie Blommaert
- Department of Organismal Biology—Systematic Biology, Uppsala University, Uppsala, Sweden
| | - Jing Liu
- MOE Laboratory of Biosystems Homeostasis and Protection, Life Sciences Institute, Zhejiang University, Hangzhou, People's Republic of China
- Department of Neuroscience and Development, University of Vienna, Vienna, Austria
| | - Tri Haryoko
- Museum Zoologicum Bogoriense, Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Knud A. Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection, Life Sciences Institute, Zhejiang University, Hangzhou, People's Republic of China
- Department of Neuroscience and Development, University of Vienna, Vienna, Austria
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, People's Republic of China
| | - Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Alexander Suh
- Department of Organismal Biology—Systematic Biology, Uppsala University, Uppsala, Sweden
- School of Biological Sciences—Organisms and the Environment, University of East Anglia, Norwich, UK
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28
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Zhang X, Liu X, Du Z, Wei L, Fang H, Dong Q, Niu J, Li Y, Gao J, Zhang MQ, Xie W, Wang X. The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence. Genome Res 2021; 31:1121-1135. [PMID: 34140314 PMCID: PMC8256869 DOI: 10.1101/gr.275235.121] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 04/27/2021] [Indexed: 01/10/2023]
Abstract
Heterochromatin remodeling is critical for various cell processes. In particular, the "loss of heterochromatin" phenotype in cellular senescence is associated with the process of aging and age-related disorders. Although biological processes of senescent cells, including senescence-associated heterochromatin foci (SAHF) formation, chromosome compaction, and redistribution of key proteins, have been closely associated with high-order chromatin structure, the relationship between the high-order chromatin reorganization and the loss of heterochromatin phenotype during senescence has not been fully understood. By using senescent and deep senescent fibroblasts induced by DNA damage harboring the "loss of heterochromatin" phenotype, we observed progressive 3D reorganization of heterochromatin during senescence. Facultative and constitutive heterochromatin marked by H3K27me3 and H3K9me3, respectively, show different alterations. Facultative heterochromatin tends to switch from the repressive B-compartment to the active A-compartment, whereas constitutive heterochromatin shows no significant changes at the compartment level but enhanced interactions between themselves. Both types of heterochromatin show increased chromatin accessibility and gene expression leakage during senescence. Furthermore, increased chromatin accessibility in potential CTCF binding sites accompanies the establishment of novel loops in constitutive heterochromatin. Finally, we also observed aberrant expression of repetitive elements, including LTR (long terminal repeat) and satellite classes. Overall, facultative and constitutive heterochromatin show both similar and distinct multiscale alterations in the 3D map, chromatin accessibility, and gene expression leakage. This study provides an epigenomic map of heterochromatin reorganization during senescence.
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Affiliation(s)
- Xianglin Zhang
- MOE Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Department of Automation, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Beijing 100084, China
| | - Xuehui Liu
- MOE Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Department of Automation, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Beijing 100084, China
- State Key Laboratory of Medical Molecular Biology, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Zhenhai Du
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- THU-PKU Center for Life Sciences, Beijing 100084, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lei Wei
- MOE Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Department of Automation, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Beijing 100084, China
| | - Huan Fang
- MOE Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Department of Automation, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Beijing 100084, China
| | - Qiongye Dong
- MOE Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Department of Automation, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Beijing 100084, China
| | - Jing Niu
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yanda Li
- MOE Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Department of Automation, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Beijing 100084, China
| | - Juntao Gao
- MOE Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Department of Automation, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Beijing 100084, China
| | - Michael Q Zhang
- Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas, Richardson, Texas 75080-3021, USA
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- THU-PKU Center for Life Sciences, Beijing 100084, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaowo Wang
- MOE Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Department of Automation, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Beijing 100084, China
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29
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Cayuela H, Dorant Y, Forester BR, Jeffries DL, Mccaffery RM, Eby LA, Hossack BR, Gippet JMW, Pilliod DS, Chris Funk W. Genomic signatures of thermal adaptation are associated with clinal shifts of life history in a broadly distributed frog. J Anim Ecol 2021; 91:1222-1238. [PMID: 34048026 PMCID: PMC9292533 DOI: 10.1111/1365-2656.13545] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/17/2021] [Indexed: 12/14/2022]
Abstract
Temperature is a critical driver of ectotherm life‐history strategies, whereby a warmer environment is associated with increased growth, reduced longevity and accelerated senescence. Increasing evidence indicates that thermal adaptation may underlie such life‐history shifts in wild populations. Single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) can help uncover the molecular mechanisms of temperature‐driven variation in growth, longevity and senescence. However, our understanding of these mechanisms is still limited, which reduces our ability to predict the response of non‐model ectotherms to global temperature change. In this study, we examined the potential role of thermal adaptation in clinal shifts of life‐history traits (i.e. life span, senescence rate and recruitment) in the Columbia spotted frog Rana luteiventris along a broad temperature gradient in the western United States. We took advantage of extensive capture–recapture datasets of 20,033 marked individuals from eight populations surveyed annually for 14–18 years to examine how mean annual temperature and precipitation influenced demographic parameters (i.e. adult survival, life span, senescence rate, recruitment and population growth). After showing that temperature was the main climatic predictor influencing demography, we used RAD‐seq data (50,829 SNPs and 6,599 putative CNVs) generated for 352 individuals from 31 breeding sites to identify the genomic signatures of thermal adaptation. Our results showed that temperature was negatively associated with annual adult survival and reproductive life span and positively associated with senescence rate. By contrast, recruitment increased with temperature, promoting the long‐term viability of most populations. These temperature‐dependent demographic changes were associated with strong genomic signatures of thermal adaptation. We identified 148 SNP candidates associated with temperature including three SNPs located within protein‐coding genes regulating resistance to cold and hypoxia, immunity and reproduction in ranids. We also identified 39 CNV candidates (including within 38 transposable elements) for which normalized read depth was associated with temperature. Our study indicates that both SNPs and structural variants are associated with temperature and could eventually be found to play a functional role in clinal shifts in senescence rate and life‐history strategies in R. luteiventris. These results highlight the potential role of different sources of molecular variation in the response of ectotherms to environmental temperature variation in the context of global warming.
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Affiliation(s)
- Hugo Cayuela
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Yann Dorant
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Brenna R Forester
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
| | - Dan L Jeffries
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Rebecca M Mccaffery
- US Geological Survey, Forest and Rangeland Ecosystem Science Center, Port Angeles, WA, USA
| | - Lisa A Eby
- Wildlife Biology Program, W. A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT, USA
| | - Blake R Hossack
- US Geological Survey, Northern Rocky Mountain Science Center, Missoula, MT, USA
| | - Jérôme M W Gippet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - David S Pilliod
- US Geological Survey, Forest and Rangeland Ecosystem Science Center, Boise, ID, USA
| | - W Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
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30
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Bitman-Lotan E, Orian A. Nuclear organization and regulation of the differentiated state. Cell Mol Life Sci 2021; 78:3141-3158. [PMID: 33507327 PMCID: PMC8038961 DOI: 10.1007/s00018-020-03731-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 12/22/2022]
Abstract
Regulation of the differentiated identity requires active and continued supervision. Inability to maintain the differentiated state is a hallmark of aging and aging-related disease. To maintain cellular identity, a network of nuclear regulators is devoted to silencing previous and non-relevant gene programs. This network involves transcription factors, epigenetic regulators, and the localization of silent genes to heterochromatin. Together, identity supervisors mold and maintain the unique nuclear environment of the differentiated cell. This review describes recent discoveries regarding mechanisms and regulators that supervise the differentiated identity and protect from de-differentiation, tumorigenesis, and attenuate forced somatic cell reprograming. The review focuses on mechanisms involved in H3K9me3-decorated heterochromatin and the importance of nuclear lamins in cell identity. We outline how the biophysical properties of these factors are involved in self-compartmentalization of heterochromatin and cell identity. Finally, we discuss the relevance of these regulators to aging and age-related disease.
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Affiliation(s)
- Eliya Bitman-Lotan
- Rappaport Research Institute and Faculty of Medicine, The Rappaport Faculty of Medicine Technion-IIT, Technion Integrative Cancer Center (TICC), Technion-Israel Institute of Technology, Bat-Galim, 3109610, Haifa, Israel
| | - Amir Orian
- Rappaport Research Institute and Faculty of Medicine, The Rappaport Faculty of Medicine Technion-IIT, Technion Integrative Cancer Center (TICC), Technion-Israel Institute of Technology, Bat-Galim, 3109610, Haifa, Israel.
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Proshkina EN, Solovev IA, Shaposhnikov MV, Moskalev AA. Key Molecular Mechanisms of Aging, Biomarkers, and Potential Interventions. Mol Biol 2021. [DOI: 10.1134/s0026893320060096] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Transcriptome wide SSR discovery cross-taxa transferability and development of marker database for studying genetic diversity population structure of Lilium species. Sci Rep 2020; 10:18621. [PMID: 33122761 PMCID: PMC7596044 DOI: 10.1038/s41598-020-75553-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 10/05/2020] [Indexed: 01/06/2023] Open
Abstract
Lily belongs to family liliaceae, which mainly propagates vegetatively. Therefore, sufficient number of polymorphic, informative, and functional molecular markers are essential for studying a wide range of genetic parameters in Lilium species. We attempted to develop, characterize and design SSR (simple sequence repeat) markers using online genetic resources for analyzing genetic diversity and population structure of Lilium species. We found di-nucleotide repeat motif were more frequent (4684) within 0.14 gb (giga bases) transcriptome than other repeats, of which was two times higher than tetra-repeat motifs. Frequency of di-(AG/CT), tri-(AGG/CTT), tetra-(AAAT), penta-(AGAGG), and hexa-(AGAGGG) repeats was 34.9%, 7.0%, 0.4%, 0.3%, and 0.2%, respectively. A total of 3607 non-redundant SSR primer pairs was designed based on the sequences of CDS, 5'-UTR and 3'-UTR region covering 34%, 14%, 23%, respectively. Among them, a sub set of primers (245 SSR) was validated using polymerase chain reaction (PCR) amplification, of which 167 primers gave expected PCR amplicon and 101 primers showed polymorphism. Each locus contained 2 to 12 alleles on average 0.82 PIC (polymorphic information content) value. A total of 87 lily accessions was subjected to genetic diversity analysis using polymorphic SSRs and found to separate into seven groups with 0.73 to 0.79 heterozygosity. Our data on large scale SSR based genetic diversity and population structure analysis may help to accelerate the breeding programs of lily through utilizing different genomes, understanding genetics and characterizing germplasm with efficient manner.
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Petrozziello T, Mills AN, Vaine CA, Penney EB, Fernandez-Cerado C, Legarda GPA, Velasco-Andrada MS, Acuña PJ, Ang MA, Muñoz EL, Diesta CCE, Macalintal-Canlas R, Acuña-Sunshine G, Ozelius LJ, Sharma N, Bragg DC, Sadri-Vakili G. Neuroinflammation and histone H3 citrullination are increased in X-linked Dystonia Parkinsonism post-mortem prefrontal cortex. Neurobiol Dis 2020; 144:105032. [PMID: 32739252 DOI: 10.1016/j.nbd.2020.105032] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/17/2020] [Accepted: 07/26/2020] [Indexed: 12/16/2022] Open
Abstract
Neuroinflammation plays a pathogenic role in neurodegenerative diseases and recent findings suggest that it may also be involved in X-linked Dystonia-Parkinsonism (XDP) pathogenesis. Previously, fibroblasts and neuronal stem cells derived from XDP patients demonstrated hypersensitivity to TNF-α, dysregulation in NFκB signaling, and an increase in several pro-inflammatory markers. However, the role of inflammatory processes in XDP patient brain remains unknown. Here we demonstrate that there is a significant increase in astrogliosis and microgliosis in human post-mortem XDP prefrontal cortex (PFC) compared to control. Furthermore, there is a significant increase in histone H3 citrullination (H3R2R8R17cit3) with a concomitant increase in peptidylarginine deaminase 2 (PAD2) and 4 (PAD4), the enzymes catalyzing citrullination, in XDP post-mortem PFC. While there is a significant increase in myeloperoxidase (MPO) levels in XDP PFC, neutrophil elastase (NE) levels are not altered, suggesting that MPO may be released by activated microglia or reactive astrocytes in the brain. Similarly, there was an increase in H3R2R8R17cit3, PAD2 and PAD4 levels in XDP-derived fibroblasts. Importantly, treatment of fibroblasts with Cl-amidine, a pan inhibitor of PAD enzymes, reduced histone H3 citrullination and pro-inflammatory chemokine expression, without affecting cell survival. Taken together, our results demonstrate that inflammation is increased in XDP post-mortem brain and fibroblasts and unveil a new epigenetic potential therapeutic target.
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Affiliation(s)
- Tiziana Petrozziello
- NeuroEpigenetics Laboratory, Healey Center for ALS at Mass General, Massachusetts General Hospital, Boston, MA 02129, United States of America
| | - Alexandra N Mills
- NeuroEpigenetics Laboratory, Healey Center for ALS at Mass General, Massachusetts General Hospital, Boston, MA 02129, United States of America
| | - Christine A Vaine
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, United States of America
| | - Ellen B Penney
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, United States of America
| | | | | | | | - Patrick J Acuña
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, United States of America; Sunshine Care Foundation, Roxas City, 5800, Capiz, Philippines
| | - Mark A Ang
- Department of Pathology, College of Medicine, University of the Philippines, Manila, Philippines
| | - Edwin L Muñoz
- Department of Pathology, College of Medicine, University of the Philippines, Manila, Philippines
| | | | | | - Geraldine Acuña-Sunshine
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, United States of America; Sunshine Care Foundation, Roxas City, 5800, Capiz, Philippines
| | - Laurie J Ozelius
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, United States of America
| | - Nutan Sharma
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, United States of America
| | - D Cristopher Bragg
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, United States of America
| | - Ghazaleh Sadri-Vakili
- NeuroEpigenetics Laboratory, Healey Center for ALS at Mass General, Massachusetts General Hospital, Boston, MA 02129, United States of America.
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Proshkina E, Shaposhnikov M, Moskalev A. Genome-Protecting Compounds as Potential Geroprotectors. Int J Mol Sci 2020; 21:E4484. [PMID: 32599754 PMCID: PMC7350017 DOI: 10.3390/ijms21124484] [Citation(s) in RCA: 12] [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: 05/31/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 02/06/2023] Open
Abstract
Throughout life, organisms are exposed to various exogenous and endogenous factors that cause DNA damages and somatic mutations provoking genomic instability. At a young age, compensatory mechanisms of genome protection are activated to prevent phenotypic and functional changes. However, the increasing stress and age-related deterioration in the functioning of these mechanisms result in damage accumulation, overcoming the functional threshold. This leads to aging and the development of age-related diseases. There are several ways to counteract these changes: 1) prevention of DNA damage through stimulation of antioxidant and detoxification systems, as well as transition metal chelation; 2) regulation of DNA methylation, chromatin structure, non-coding RNA activity and prevention of nuclear architecture alterations; 3) improving DNA damage response and repair; 4) selective removal of damaged non-functional and senescent cells. In the article, we have reviewed data about the effects of various trace elements, vitamins, polyphenols, terpenes, and other phytochemicals, as well as a number of synthetic pharmacological substances in these ways. Most of the compounds demonstrate the geroprotective potential and increase the lifespan in model organisms. However, their genome-protecting effects are non-selective and often are conditioned by hormesis. Consequently, the development of selective drugs targeting genome protection is an advanced direction.
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Affiliation(s)
- Ekaterina Proshkina
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya st., 167982 Syktyvkar, Russia; (E.P.); (M.S.)
| | - Mikhail Shaposhnikov
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya st., 167982 Syktyvkar, Russia; (E.P.); (M.S.)
| | - Alexey Moskalev
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya st., 167982 Syktyvkar, Russia; (E.P.); (M.S.)
- Pitirim Sorokin Syktyvkar State University, 55 Oktyabrsky prosp., 167001 Syktyvkar, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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Cavaliere V, Lattanzi G, Andrenacci D. Silencing of Euchromatic Transposable Elements as a Consequence of Nuclear Lamina Dysfunction. Cells 2020; 9:cells9030625. [PMID: 32151001 PMCID: PMC7140440 DOI: 10.3390/cells9030625] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/28/2020] [Accepted: 03/02/2020] [Indexed: 02/07/2023] Open
Abstract
Transposable elements (TEs) are mobile genomic sequences that are normally repressed to avoid proliferation and genome instability. Gene silencing mechanisms repress TEs by RNA degradation or heterochromatin formation. Heterochromatin maintenance is therefore important to keep TEs silent. Loss of heterochromatic domains has been linked to lamin mutations, which have also been associated with derepression of TEs. In fact, lamins are structural components of the nuclear lamina (NL), which is considered a pivotal structure in the maintenance of heterochromatin domains at the nuclear periphery in a silent state. Here, we show that a lethal phenotype associated with Lamin loss-of-function mutations is influenced by Drosophila gypsy retrotransposons located in euchromatic regions, suggesting that NL dysfunction has also effects on active TEs located in euchromatic loci. In fact, expression analysis of different long terminal repeat (LTR) retrotransposons and of one non-LTR retrotransposon located near active genes shows that Lamin inactivation determines the silencing of euchromatic TEs. Furthermore, we show that the silencing effect on euchromatic TEs spreads to the neighboring genomic regions, with a repressive effect on nearby genes. We propose that NL dysfunction may have opposed regulatory effects on TEs that depend on their localization in active or repressed regions of the genome.
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Affiliation(s)
- Valeria Cavaliere
- Dipartimento di Farmacia e Biotecnologie, Alma Mater Studiorum Università di Bologna, 40126 Bologna, Italy;
| | - Giovanna Lattanzi
- CNR Institute of Molecular Genetics “Luigi-Luca Cavalli-Sforza”, Unit of Bologna, 40136 Bologna, Italy;
- IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Davide Andrenacci
- CNR Institute of Molecular Genetics “Luigi-Luca Cavalli-Sforza”, Unit of Bologna, 40136 Bologna, Italy;
- IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
- Correspondence:
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