1
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Gigliotti G, Joshi R, Khalid A, Widmer D, Boccellino M, Viggiano D. Epigenetics, Microbiome and Personalized Medicine: Focus on Kidney Disease. Int J Mol Sci 2024; 25:8592. [PMID: 39201279 PMCID: PMC11354516 DOI: 10.3390/ijms25168592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 07/25/2024] [Accepted: 07/31/2024] [Indexed: 09/02/2024] Open
Abstract
Personalized medicine, which involves modifying treatment strategies/drug dosages based on massive laboratory/imaging data, faces large statistical and study design problems. The authors believe that the use of continuous multidimensional data, such as those regarding gut microbiota, or binary multidimensional systems properly transformed into a continuous variable, such as the epigenetic clock, offer an advantageous scenario for the design of trials of personalized medicine. We will discuss examples focusing on kidney diseases, specifically on IgA nephropathy. While gut dysbiosis can provide a treatment strategy to restore the standard gut microbiota using probiotics, transforming epigenetic omics data into epigenetic clocks offers a promising tool for personalized acute and chronic kidney disease care. Epigenetic clocks involve a complex transformation of DNA methylome data into estimated biological age. These clocks can identify people at high risk of developing kidney problems even before symptoms appear. Some of the effects of both the epigenetic clock and microbiota on kidney diseases seem to be mediated by endothelial dysfunction. These "big data" (epigenetic clocks and microbiota) can help tailor treatment plans by pinpointing patients likely to experience rapid declines or those who might not need overly aggressive therapies.
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Affiliation(s)
| | - Rashmi Joshi
- Department Translational Medical Sciences, University of Campania, 81100 Naples, Italy; (R.J.); (A.K.); (D.V.)
| | - Anam Khalid
- Department Translational Medical Sciences, University of Campania, 81100 Naples, Italy; (R.J.); (A.K.); (D.V.)
| | | | - Mariarosaria Boccellino
- Department Experimental Medicine, University of Campania, 81100 Naples, Italy
- Department Life Sciences, Health and Health Professions, Link University, 00165 Rome, Italy
| | - Davide Viggiano
- Department Translational Medical Sciences, University of Campania, 81100 Naples, Italy; (R.J.); (A.K.); (D.V.)
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2
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Le Breton A, Bettencourt MP, Gendrel AV. Navigating the brain and aging: exploring the impact of transposable elements from health to disease. Front Cell Dev Biol 2024; 12:1357576. [PMID: 38476259 PMCID: PMC10927736 DOI: 10.3389/fcell.2024.1357576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/08/2024] [Indexed: 03/14/2024] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that constitute on average 45% of mammalian genomes. Their presence and activity in genomes represent a major source of genetic variability. While this is an important driver of genome evolution, TEs can also have deleterious effects on their hosts. A growing number of studies have focused on the role of TEs in the brain, both in physiological and pathological contexts. In the brain, their activity is believed to be important for neuronal plasticity. In neurological and age-related disorders, aberrant activity of TEs may contribute to disease etiology, although this remains unclear. After providing a comprehensive overview of transposable elements and their interactions with the host, this review summarizes the current understanding of TE activity within the brain, during the aging process, and in the context of neurological and age-related conditions.
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Affiliation(s)
| | | | - Anne-Valerie Gendrel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
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3
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Kho J, Delgado ML, McCracken GR, Munden J, Ruzzante DE. Epigenetic patterns in Atlantic herring (Clupea harengus): Temperature and photoperiod as environmental stressors during larval development. Mol Ecol 2024; 33:e17187. [PMID: 37909655 DOI: 10.1111/mec.17187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023]
Abstract
Understanding the molecular mechanisms underlying individual responses to environmental changes is crucial for species conservation and management. Pelagic fishes including Atlantic herring (Clupea harengus) are of particular interest because of their key ecological and economic roles and their susceptibility to a changing ocean from global warming. Temperature and photoperiod have been linked with spawning time and location in adult herring, but no study has thus far investigated the role of environmental factors on gene regulation during the vulnerable early developmental stages. Here, we examine DNA methylation patterns of larval herring bred under two temperatures (11°C and 13°C) and photoperiod (6 and 12 h) regimes in a 2 × 2 factorial design. We found consistently high levels of global methylation across all individuals and a decline in global methylation with increased developmental stage that was more pronounced at 13°C (p ≤ 0.007) than at 11°C (p ≥ 0.21). Most of the differentially methylated sites were in exon and promoter regions for genes linked to metabolism and development, some of which were hypermethylated at higher temperature. These results demonstrate the important role of DNA methylation during larval development and suggest that this molecular mechanism might be key in regulating early-stage responses to environmental stressors in Atlantic herring.
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Affiliation(s)
- J Kho
- Department of Biology, Dalhousie University, Halifax, Canada
| | - M L Delgado
- Department of Biology, Dalhousie University, Halifax, Canada
| | - G R McCracken
- Department of Biology, Dalhousie University, Halifax, Canada
| | - J Munden
- Herring Science Council, Halifax, Canada
| | - D E Ruzzante
- Department of Biology, Dalhousie University, Halifax, Canada
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4
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Arenas-Báez P, Torres-Hernández G, Castillo-Hernández G, Hernández-Rodríguez M, Sánchez-Gutiérrez RA, Vargas-López S, González-Maldonado J, Domínguez-Martínez PA, Granados-Rivera LD, Maldonado-Jáquez JA. Coat Color in Local Goats: Influence on Environmental Adaptation and Productivity, and Use as a Selection Criterion. BIOLOGY 2023; 12:929. [PMID: 37508360 PMCID: PMC10376610 DOI: 10.3390/biology12070929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/16/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023]
Abstract
This paper aims to review, systematically synthesize, and analyze fragmented information about the importance of coat color in local goats and its relationship with productivity and other important traits. Topics on current research on color expression are addressed, the relationship that has as a mechanism of environmental adaptation, its relationship with the production of meat, milk, and derivates, and the economic value of this characteristic. The use of this attribute as a tool to establish selection criteria in breeding programs based on results reported in the scientific literature is significant, particularly for low-income production systems, where the implementation of classic genetic improvement schemes is limited due to the lack of productive information, which is distinctive of extensive marginal or low scaled production systems around the world.
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Affiliation(s)
- Pablo Arenas-Báez
- Unidad Regional Universitaria de Zonas Áridas, Universidad Autónoma Chapingo, Bermejillo, Durango 35230, Mexico
| | | | - Gabriela Castillo-Hernández
- Colegio de Postgraduados, Campus Montecillo, Montecillo, Texcoco 56264, Mexico
- Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli 54714, Mexico
| | | | - Ricardo Alonso Sánchez-Gutiérrez
- Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Campo Experimental Zacatecas, Calera, Zacatecas 98500, Mexico
| | | | - Juan González-Maldonado
- Instituto de Ciencias Agrícolas, Universidad Autónoma de Baja California, Mexicali 21750, Mexico
| | - Pablo Alfredo Domínguez-Martínez
- Colegio de Postgraduados, Campus Montecillo, Montecillo, Texcoco 56264, Mexico
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Campo Experimental Valle del Guadiana, Durango 34170, Mexico
| | - Lorenzo Danilo Granados-Rivera
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Campo Experimental Genera Terán, General Terán 67400, Mexico
| | - Jorge Alonso Maldonado-Jáquez
- Colegio de Postgraduados, Campus Montecillo, Montecillo, Texcoco 56264, Mexico
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Campo Experimental La Laguna, Matamoros 27440, Mexico
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5
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Faulk C. Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates. Genome Res 2023; 33:948-956. [PMID: 37442577 PMCID: PMC10519409 DOI: 10.1101/gr.277743.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 06/07/2023] [Indexed: 07/15/2023]
Abstract
Genome skimming is defined as low-pass sequencing below 0.05× coverage and is typically used for mitochondrial genome recovery and species identification. Long-read nanopore sequencers enable simultaneous reading of both DNA sequence and methylation and can multiplex samples for low-cost genome skimming. Here I present nanopore sequencing as a highly precise platform for global DNA methylation and transposon assessment. At coverage of just 0.001×, or 30 Mb of reads, accuracy is sub-1%. Biological and technical replicates validate high precision. Skimming 40 vertebrate species reveals conserved patterns of global methylation consistent with whole-genome bisulfite sequencing and an average mapping rate >97%. Genome size directly correlates to global DNA methylation, explaining 39% of its variance. Accurate SINE and LINE transposon methylation in both the mouse and primates can be obtained with just 0.0001× coverage, or 3 Mb of reads. Sample multiplexing, field portability, and the low price of this instrument combine to make genome skimming for DNA methylation an accessible method for epigenetic assessment from ecology to epidemiology and for low-resource groups.
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Affiliation(s)
- Christopher Faulk
- Department of Animal Science, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota, Minneapolis, Minnesota 55455, USA
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6
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Faulk C. Genome Skimming with Nanopore Sequencing Precisely Determines Global and Transposon DNA Methylation in Vertebrates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525540. [PMID: 36747817 PMCID: PMC9900854 DOI: 10.1101/2023.01.25.525540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Genome skimming is defined as low-pass sequencing below 0.05X coverage and is typically used for mitochondrial genome recovery and species identification. Long read nanopore sequencers enable simultaneous reading of both DNA sequence and methylation and can multiplex samples for low-cost genome skimming. Here I present nanopore sequencing as a highly precise platform for global DNA methylation and transposon assessment. At coverage of just 0.001X, or 30 Mb of reads, accuracy is sub-1%. Biological and technical replicates validate high precision. Skimming 40 vertebrate species reveals conserved patterns of global methylation consistent with whole genome bisulfite sequencing and an average mapping rate above 97%. Genome size directly correlates to global DNA methylation, explaining 44% of its variance. Accurate SINE and LINE transposon methylation in both mouse and primates can be obtained with just 0.0001X coverage, or 3 Mb of reads. Sample multiplexing, field portability, and the low price of this instrument combine to make genome skimming for DNA methylation an accessible method for epigenetic assessment from ecology to epidemiology, and by low resource groups.
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Affiliation(s)
- Christopher Faulk
- Department of Animal Science, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota
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7
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Liu X, Liu Z, Wu Z, Ren J, Fan Y, Sun L, Cao G, Niu Y, Zhang B, Ji Q, Jiang X, Wang C, Wang Q, Ji Z, Li L, Esteban CR, Yan K, Li W, Cai Y, Wang S, Zheng A, Zhang YE, Tan S, Cai Y, Song M, Lu F, Tang F, Ji W, Zhou Q, Belmonte JCI, Zhang W, Qu J, Liu GH. Resurrection of endogenous retroviruses during aging reinforces senescence. Cell 2023; 186:287-304.e26. [PMID: 36610399 DOI: 10.1016/j.cell.2022.12.017] [Citation(s) in RCA: 108] [Impact Index Per Article: 108.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 10/13/2022] [Accepted: 12/08/2022] [Indexed: 01/09/2023]
Abstract
Whether and how certain transposable elements with viral origins, such as endogenous retroviruses (ERVs) dormant in our genomes, can become awakened and contribute to the aging process is largely unknown. In human senescent cells, we found that HERVK (HML-2), the most recently integrated human ERVs, are unlocked to transcribe viral genes and produce retrovirus-like particles (RVLPs). These HERVK RVLPs constitute a transmissible message to elicit senescence phenotypes in young cells, which can be blocked by neutralizing antibodies. The activation of ERVs was also observed in organs of aged primates and mice as well as in human tissues and serum from the elderly. Their repression alleviates cellular senescence and tissue degeneration and, to some extent, organismal aging. These findings indicate that the resurrection of ERVs is a hallmark and driving force of cellular senescence and tissue aging.
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Affiliation(s)
- Xiaoqian Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zunpeng Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zeming Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Ren
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanling Fan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liang Sun
- NHC Beijing Institute of Geriatrics, NHC Key Laboratory of Geriatrics, Institute of Geriatric Medicine of Chinese Academy of Medical Sciences, National Center of Gerontology/Beijing Hospital, Beijing 100730, China
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuyu Niu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China; Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Baohu Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianzhao Ji
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyu Jiang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cui Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiaoran Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhejun Ji
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lanzhu Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Kaowen Yan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Li
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
| | - Yusheng Cai
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing Municipal Geriatric Medical Research Center, Beijing 100053, China; The Fifth People's Hospital of Chongqing, Chongqing 400062, China
| | - Aihua Zheng
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong E Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shengjun Tan
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingao Cai
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Moshi Song
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Falong Lu
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Fuchou Tang
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Weizhi Ji
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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8
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Zhang Q, Pan J, Cong Y, Mao J. Transcriptional Regulation of Endogenous Retroviruses and Their Misregulation in Human Diseases. Int J Mol Sci 2022; 23:ijms231710112. [PMID: 36077510 PMCID: PMC9456331 DOI: 10.3390/ijms231710112] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/28/2022] [Accepted: 09/01/2022] [Indexed: 11/22/2022] Open
Abstract
Endogenous retroviruses (ERVs), deriving from exogenous retroviral infections of germ line cells occurred millions of years ago, represent ~8% of human genome. Most ERVs are highly inactivated because of the accumulation of mutations, insertions, deletions, and/or truncations. However, it is becoming increasingly apparent that ERVs influence host biology through genetic and epigenetic mechanisms under particular physiological and pathological conditions, which provide both beneficial and deleterious effects for the host. For instance, certain ERVs expression is essential for human embryonic development. Whereas abnormal activation of ERVs was found to be involved in numbers of human diseases, such as cancer and neurodegenerative diseases. Therefore, understanding the mechanisms of regulation of ERVs would provide insights into the role of ERVs in health and diseases. Here, we provide an overview of mechanisms of transcriptional regulation of ERVs and their dysregulation in human diseases.
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9
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Azuma A, Kobayashi S. Demethylation of the 3' LTR region of retrotransposon in VvMYBA1 BEN allele enhances anthocyanin biosynthesis in berry skin and flesh in 'Brazil' grape. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 322:111341. [PMID: 35667250 DOI: 10.1016/j.plantsci.2022.111341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 05/10/2023]
Abstract
Black-skinned and red-fleshed grape 'Brazil' is a bud sport of rosy-skinned 'Benitaka'. 'Brazil' has a much higher anthocyanin content in the skin than that of 'Benitaka' and is characterized by the accumulation of anthocyanins in the flesh. Our genomic analysis of the VvMYBA loci, which regulate anthocyanin biosynthesis, suggested that the difference in skin and flesh color between 'Brazil' and 'Benitaka' cannot be explained by genomic alteration at the loci. Expression levels of VvMYBA1 and anthocyanin biosynthesis-related genes in skin and flesh were significantly higher in 'Brazil' than in 'Benitaka' throughout berry development. DNA methylation levels in the 3' long terminal repeat (LTR) of a retrotransposon in the upstream region of VvMYBA1BEN allele were clearly higher in the skin and flesh of 'Benitaka' than in those of 'Brazil' throughout berry development. These findings suggest that a dramatic decrease in DNA methylation level in the 3' LTR of the retrotransposon in the VvMYBA1BEN allele in 'Brazil' increases the expression levels of VvMYBA1 and anthocyanin accumulation in skin and flesh. Our findings also suggest that skin and flesh colors are inherited together and vary depending on the presence or absence of the VvMYBA1BEN allele.
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Affiliation(s)
- Akifumi Azuma
- Division of Grape and Persimmon Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Higashihiroshima, Hiroshima 739-2494, Japan.
| | - Shozo Kobayashi
- Division of Grape and Persimmon Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Higashihiroshima, Hiroshima 739-2494, Japan
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10
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Mao J, Zhang Q, Cong YS. Human endogenous retroviruses in development and disease. Comput Struct Biotechnol J 2021; 19:5978-5986. [PMID: 34849202 PMCID: PMC8604659 DOI: 10.1016/j.csbj.2021.10.037] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 12/16/2022] Open
Abstract
Human endogenous retroviruses (HERVs) represent ∼8% of human genome, deriving from exogenous retroviral infections of germ line cells occurred millions of years ago and being inherited by the offspring in a Mendelian fashion. Most of HERVs are nonprotein-coding because of the accumulation of mutations, insertions, deletions, and/or truncations. It has been long thought that HERVs were "junk DNA". However, it is now known that HERVs are involved in various biological processes through encoding proteins, acting as promoters/enhancers, or lncRNAs to affect human health and disease. In this review, we summarized recent findings about HERVs, with implications in embryonic development, pluripotency, cancer, aging, and neurodegenerative diseases.
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Affiliation(s)
- Jian Mao
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Hangzhou Normal University School of Basic Medical Sciences, Hangzhou, China
| | - Qian Zhang
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Hangzhou Normal University School of Basic Medical Sciences, Hangzhou, China
| | - Yu-Sheng Cong
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Hangzhou Normal University School of Basic Medical Sciences, Hangzhou, China
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11
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Saxena S, Choudhury S, Maroju PA, Anne A, Kumar L, Mohan KN. Dysregulation of schizophrenia-associated genes and genome-wide hypomethylation in neurons overexpressing DNMT1. Epigenomics 2021; 13:1539-1555. [PMID: 34647491 DOI: 10.2217/epi-2021-0133] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To study the effects of DNMT1 overexpression on transcript levels of genes dysregulated in schizophrenia and on genome-wide methylation patterns. Materials & methods: Transcriptome and DNA methylome comparisons were made between R1 (wild-type) and Dnmt1tet/tet mouse embryonic stem cells and neurons overexpressing DNMT1. Genes dysregulated in both Dnmt1tet/tet cells and schizophrenia patients were studied further. Results & conclusions: About 50% of dysregulated genes in patients also showed altered transcript levels in Tet/Tet neurons in a DNA methylation-independent manner. These neurons unexpectedly showed genome-wide hypomethylation, increased transcript levels of Tet1 and Apobec 1-3 genes and increased activity and copy number of LINE-1 elements. The observed similarities between Tet/Tet neurons and schizophrenia brain samples reinforce DNMT1 overexpression as a risk factor.
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Affiliation(s)
- Sonal Saxena
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India
| | - Sumana Choudhury
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India.,Centre for Human Disease Research, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India
| | - Pranay Amruth Maroju
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India
| | - Anuhya Anne
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India.,Centre for Human Disease Research, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India
| | - Lov Kumar
- Computer Science & Information Systems, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India
| | - Kommu Naga Mohan
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India.,Centre for Human Disease Research, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India
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12
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Garcia-Venzor A, Toiber D. SIRT6 Through the Brain Evolution, Development, and Aging. Front Aging Neurosci 2021; 13:747989. [PMID: 34720996 PMCID: PMC8548377 DOI: 10.3389/fnagi.2021.747989] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/16/2021] [Indexed: 12/19/2022] Open
Abstract
During an organism's lifespan, two main phenomena are critical for the organism's survival. These are (1) a proper embryonic development, which permits the new organism to function with high fitness, grow and reproduce, and (2) the aging process, which will progressively undermine its competence and fitness for survival, leading to its death. Interestingly these processes present various similarities at the molecular level. Notably, as organisms became more complex, regulation of these processes became coordinated by the brain, and failure in brain activity is detrimental in both development and aging. One of the critical processes regulating brain health is the capacity to keep its genomic integrity and epigenetic regulation-deficiency in DNA repair results in neurodevelopmental and neurodegenerative diseases. As the brain becomes more complex, this effect becomes more evident. In this perspective, we will analyze how the brain evolved and became critical for human survival and the role Sirt6 plays in brain health. Sirt6 belongs to the Sirtuin family of histone deacetylases that control several cellular processes; among them, Sirt6 has been associated with the proper embryonic development and is associated with the aging process. In humans, Sirt6 has a pivotal role during brain aging, and its loss of function is correlated with the appearance of neurodegenerative diseases such as Alzheimer's disease. However, Sirt6 roles during brain development and aging, especially the last one, are not observed in all species. It appears that during the brain organ evolution, Sirt6 has gained more relevance as the brain becomes bigger and more complex, observing the most detrimental effect in the brains of Homo sapiens. In this perspective, we part from the evolution of the brain in metazoans, the biological similarities between brain development and aging, and the relevant functions of Sirt6 in these similar phenomena to conclude with the evidence suggesting a more relevant role of Sirt6 gained in the brain evolution.
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Affiliation(s)
- Alfredo Garcia-Venzor
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Debra Toiber
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva, Israel
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13
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Griñán-Ferré C, Bellver-Sanchis A, Izquierdo V, Corpas R, Roig-Soriano J, Chillón M, Andres-Lacueva C, Somogyvári M, Sőti C, Sanfeliu C, Pallàs M. The pleiotropic neuroprotective effects of resveratrol in cognitive decline and Alzheimer's disease pathology: From antioxidant to epigenetic therapy. Ageing Res Rev 2021; 67:101271. [PMID: 33571701 DOI: 10.1016/j.arr.2021.101271] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 02/03/2021] [Accepted: 02/03/2021] [Indexed: 12/12/2022]
Abstract
While the elderly segment of the population continues growing in importance, neurodegenerative diseases increase exponentially. Lifestyle factors such as nutrition, exercise, and education, among others, influence ageing progression, throughout life. Notably, the Central Nervous System (CNS) can benefit from nutritional strategies and dietary interventions that prevent signs of senescence, such as cognitive decline or neurodegenerative diseases such as Alzheimer's disease and Parkinson's Disease. The dietary polyphenol Resveratrol (RV) possesses antioxidant and cytoprotective effects, producing neuroprotection in several organisms. The oxidative stress (OS) occurs because of Reactive oxygen species (ROS) accumulation that has been proposed to explain the cause of the ageing. One of the most harmful effects of ROS in the cell is DNA damage. Nevertheless, there is also evidence demonstrating that OS can produce other molecular changes such as mitochondrial dysfunction, inflammation, apoptosis, and epigenetic modifications, among others. Interestingly, the dietary polyphenol RV is a potent antioxidant and possesses pleiotropic actions, exerting its activity through various molecular pathways. In addition, recent evidence has shown that RV mediates epigenetic changes involved in ageing and the function of the CNS that persists across generations. Furthermore, it has been demonstrated that RV interacts with gut microbiota, showing modifications in bacterial composition associated with beneficial effects. In this review, we give a comprehensive overview of the main mechanisms of action of RV in different experimental models, including clinical trials and discuss how the interconnection of these molecular events could explain the neuroprotective effects induced by RV.
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Affiliation(s)
- Christian Griñán-Ferré
- Pharmacology Section, Department of Pharmacology, Toxicology, and Therapeutic Chemistry, Faculty of Pharmacy and Food Sciences, Institute of Neuroscience, University of Barcelona (NeuroUB), Av Joan XXIII 27-31, 08028, Barcelona, Spain.
| | - Aina Bellver-Sanchis
- Pharmacology Section, Department of Pharmacology, Toxicology, and Therapeutic Chemistry, Faculty of Pharmacy and Food Sciences, Institute of Neuroscience, University of Barcelona (NeuroUB), Av Joan XXIII 27-31, 08028, Barcelona, Spain
| | - Vanessa Izquierdo
- Pharmacology Section, Department of Pharmacology, Toxicology, and Therapeutic Chemistry, Faculty of Pharmacy and Food Sciences, Institute of Neuroscience, University of Barcelona (NeuroUB), Av Joan XXIII 27-31, 08028, Barcelona, Spain
| | - Rubén Corpas
- Institut d'Investigacions Biomèdiques de Barcelona (IIBB), CSIC, IDIBAPS and CIBERESP, Barcelona, Spain
| | - Joan Roig-Soriano
- Department of Biochemistry and Molecular Biology, Universitat Autònoma Barcelona, Institut de Neurociènces (INc), Universitat Autònoma Barcelona, Bellaterra, Spain
| | - Miguel Chillón
- Department of Biochemistry and Molecular Biology, Universitat Autònoma Barcelona, Institut de Neurociènces (INc), Universitat Autònoma Barcelona, Bellaterra, Spain; Vall d'Hebron Institut de Recerca (VHIR), Research Group on Gene Therapy at Nervous System, Passeig de la Vall d'Hebron, Barcelona, Spain; Unitat producció de Vectors (UPV), Universitat Autònoma Barcelona, Bellaterra, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Cristina Andres-Lacueva
- Biomarkers and Nutrimetabolomics Laboratory, Department of Nutrition, Food Sciences and Gastronomy, Xarta, INSA, Faculty of Pharmacy and Food Sciences, Campus Torribera, University of Barcelona, Spain; CIBER de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salut Carlos III, Barcelona, Spain
| | - Milán Somogyvári
- Department of Medical Chemistry, Semmelweis University, Budapest, Hungary
| | - Csaba Sőti
- Department of Medical Chemistry, Semmelweis University, Budapest, Hungary
| | - Coral Sanfeliu
- Institut d'Investigacions Biomèdiques de Barcelona (IIBB), CSIC, IDIBAPS and CIBERESP, Barcelona, Spain
| | - Mercè Pallàs
- Pharmacology Section, Department of Pharmacology, Toxicology, and Therapeutic Chemistry, Faculty of Pharmacy and Food Sciences, Institute of Neuroscience, University of Barcelona (NeuroUB), Av Joan XXIII 27-31, 08028, Barcelona, Spain
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14
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Geis FK, Goff SP. Silencing and Transcriptional Regulation of Endogenous Retroviruses: An Overview. Viruses 2020; 12:v12080884. [PMID: 32823517 PMCID: PMC7472088 DOI: 10.3390/v12080884] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/03/2020] [Accepted: 08/11/2020] [Indexed: 12/16/2022] Open
Abstract
Almost half of the human genome is made up of transposable elements (TEs), and about 8% consists of endogenous retroviruses (ERVs). ERVs are remnants of ancient exogenous retrovirus infections of the germ line. Most TEs are inactive and not detrimental to the host. They are tightly regulated to ensure genomic stability of the host and avoid deregulation of nearby gene loci. Histone-based posttranslational modifications such as H3K9 trimethylation are one of the main silencing mechanisms. Trim28 is one of the identified master regulators of silencing, which recruits most prominently the H3K9 methyltransferase Setdb1, among other factors. Sumoylation and ATP-dependent chromatin remodeling factors seem to contribute to proper localization of Trim28 to ERV sequences and promote Trim28 interaction with Setdb1. Additionally, DNA methylation as well as RNA-mediated targeting of TEs such as piRNA-based silencing play important roles in ERV regulation. Despite the involvement of ERV overexpression in several cancer types, autoimmune diseases, and viral pathologies, ERVs are now also appreciated for their potential positive role in evolution. ERVs can provide new regulatory gene elements or novel binding sites for transcription factors, and ERV gene products can even be repurposed for the benefit of the host.
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Affiliation(s)
- Franziska K. Geis
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA;
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
- Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY 10032, USA
| | - Stephen P. Goff
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA;
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
- Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY 10032, USA
- Correspondence: ; Tel.: +1-212-305-3794
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15
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Halim MA, Tan FHP, Azlan A, Rasyid II, Rosli N, Shamsuddin S, Azzam G. Ageing, Drosophila melanogaster and Epigenetics. Malays J Med Sci 2020; 27:7-19. [PMID: 32684802 PMCID: PMC7337951 DOI: 10.21315/mjms2020.27.3.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 01/31/2020] [Indexed: 11/03/2022] Open
Abstract
Ageing is a phenomenon where the accumulation of all the stresses that alter the functions of living organisms, halter them from maintaining their physiological balance and eventually lead to death. The emergence of epigenetic tremendously contributed to the knowledge of ageing. Epigenetic changes in cells or tissues like deoxyribonucleic acid (DNA) methylation, modification of histone proteins, transcriptional modification and also the involvement of non-coding DNA has been documented to be associated with ageing. In order to study ageing, scientists have taken advantage of several potential organisms to aid them in their study. Drosophila melanogaster has been an essential model in establishing current understanding of the mechanism of ageing as they possess several advantages over other competitors like having homologues to more than 75% of human disease genes, having 50% of Drosophila genes are homologues to human genes and most importantly they are genetically amenable. Here, we would like to summarise the extant knowledge about ageing and epigenetic process and the role of Drosophila as an ideal model to study epigenetics in association with ageing process.
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Affiliation(s)
- Mardani Abdul Halim
- USM-RIKEN International Centre for Ageing Science (URICAS), Universiti Sains Malaysia, Pulau Pinang, Malaysia.,School of Biological Sciences, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Florence Hui Ping Tan
- USM-RIKEN International Centre for Ageing Science (URICAS), Universiti Sains Malaysia, Pulau Pinang, Malaysia.,School of Biological Sciences, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Azali Azlan
- USM-RIKEN International Centre for Ageing Science (URICAS), Universiti Sains Malaysia, Pulau Pinang, Malaysia.,School of Biological Sciences, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Ian Ilham Rasyid
- School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Nurlina Rosli
- School of Biological Sciences, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Shaharum Shamsuddin
- USM-RIKEN International Centre for Ageing Science (URICAS), Universiti Sains Malaysia, Pulau Pinang, Malaysia.,School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Ghows Azzam
- USM-RIKEN International Centre for Ageing Science (URICAS), Universiti Sains Malaysia, Pulau Pinang, Malaysia.,School of Biological Sciences, Universiti Sains Malaysia, Pulau Pinang, Malaysia
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16
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Chalmers TJ, Wu LE. Transposable Elements Cross Kingdom Boundaries and Contribute to Inflammation and Ageing: Somatic Acquisition of Foreign Transposable Elements as a Catalyst of Genome Instability, Epigenetic Dysregulation, Inflammation, Senescence, and Ageing. Bioessays 2020; 42:e1900197. [PMID: 31994769 DOI: 10.1002/bies.201900197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/23/2019] [Indexed: 01/07/2023]
Abstract
The de-repression of transposable elements (TEs) in mammalian genomes is thought to contribute to genome instability, inflammation, and ageing, yet is viewed as a cell-autonomous event. In contrast to mammalian cells, prokaryotes constantly exchange genetic material through TEs, crossing both cell and species barriers, contributing to rapid microbial evolution and diversity in complex communities such as the mammalian gut. Here, it is proposed that TEs released from prokaryotes in the microbiome or from pathogenic infections regularly cross the kingdom barrier to the somatic cells of their eukaryotic hosts. It is proposed this horizontal transfer of TEs from microbe to host is a stochastic, ongoing catalyst of genome destabilization, resulting in structural and epigenetic variations, and activation of well-evolved host defense mechanisms contributing to inflammation, senescence, and biological ageing. It is proposed that innate immunity pathways defend against the horizontal acquisition of microbial TEs, and that activation of this pathway during horizontal transposon transfer promotes chronic inflammation during ageing. Finally, it is suggested that horizontal acquisition of prokaryotic TEs into mammalian genomes has been masked and subsequently under-reported due to flaws in current sequencing pipelines, and new strategies to uncover these events are proposed.
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Affiliation(s)
| | - Lindsay E Wu
- School of Medical Sciences, UNSW, Sydney, NSW, 2052, Australia
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17
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Perera BP, Faulk C, Svoboda LK, Goodrich JM, Dolinoy DC. The role of environmental exposures and the epigenome in health and disease. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:176-192. [PMID: 31177562 PMCID: PMC7252203 DOI: 10.1002/em.22311] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 05/02/2023]
Abstract
The genetic material of every organism exists within the context of regulatory networks that govern gene expression, collectively called the epigenome. Epigenetics has taken center stage in the study of diseases such as cancer and diabetes, but its integration into the field of environmental health is still emerging. As the Environmental Mutagenesis and Genomics Society (EMGS) celebrates its 50th Anniversary this year, we have come together to review and summarize the seminal advances in the field of environmental epigenomics. Specifically, we focus on the role epigenetics may play in multigenerational and transgenerational transmission of environmentally induced health effects. We also summarize state of the art techniques for evaluating the epigenome, environmental epigenetic analysis, and the emerging field of epigenome editing. Finally, we evaluate transposon epigenetics as they relate to environmental exposures and explore the role of noncoding RNA as biomarkers of environmental exposures. Although the field has advanced over the past several decades, including being recognized by EMGS with its own Special Interest Group, recently renamed Epigenomics, we are excited about the opportunities for environmental epigenetic science in the next 50 years. Environ. Mol. Mutagen. 61:176-192, 2020. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Bambarendage P.U. Perera
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Christopher Faulk
- Department of Animal Sciences, University of Minnesota, St. Paul, Minnesota
| | - Laurie K. Svoboda
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Jaclyn M. Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
- Correspondence to: Dana C. Dolinoy, Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan.
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18
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Ghanam AR, Cao J, Ouyang X, Song X. New Insights into Chronological Mobility of Retrotransposons In Vivo. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:2818415. [PMID: 31346359 PMCID: PMC6617872 DOI: 10.1155/2019/2818415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 06/03/2019] [Indexed: 12/17/2022]
Abstract
Tissue aging is the gradual decline of physiological homeostasis accompanied with accumulation of senescent cells, decreased clearance of unwanted biological compounds, and depletion of stem cells. Senescent cells were cell cycle arrested in response to various stimuli and identified using distinct phenotypes and changes in gene expression. Senescent cells that accumulate with aging can compromise normal tissue function and inhibit or stop repair and regeneration. Selective removal of senescent cells can slow the aging process and inhibits age-associated diseases leading to extended lifespans in mice and thus provides a possibility for developing antiaging therapy. To monitor the appearance of senescent cells in vivo and target them, a clearer understanding of senescent cell expression markers is needed. We investigated the age-associated expression of three molecular hallmarks of aging: SA-β-gal, P16INK4a, and retrotransposable elements (RTEs), in different mouse tissues during chronological aging. Our data showed that the expression of these markers is variable with aging in the different tissues. P16INK4a showed consistent increases with age in most tissues, while expression of RTEs was variable among different tissues examined. These data suggest that biological changes occurring with physiological aging may be useful in choosing the appropriate timing of therapeutic interventions to slow the aging process or keep more susceptible organs healthier in the aging process.
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Affiliation(s)
- Amr. R. Ghanam
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Neurodegenerative Disorder Research Center, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jun Cao
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Neurodegenerative Disorder Research Center, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xuan Ouyang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Neurodegenerative Disorder Research Center, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiaoyuan Song
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Neurodegenerative Disorder Research Center, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
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19
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Dubnau J. The Retrotransposon storm and the dangers of a Collyer's genome. Curr Opin Genet Dev 2018; 49:95-105. [PMID: 29705598 PMCID: PMC5975205 DOI: 10.1016/j.gde.2018.04.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 03/08/2018] [Accepted: 04/11/2018] [Indexed: 12/13/2022]
Abstract
Like the famous Collyer's mansion in NY, our genomes have accumulated vast quantities of sequences that have been referred to as 'junk DNA,' much of which consists of retrotransposons (RTEs). A recent literature establishes the phenomenology that many RTEs become expressed at progressively higher levels during the course of normal aging. This seems to reflect gradual loss of heterochromatin in old age. In addition, RTEs appear to be precociously expressed in brains of younger animals that are experiencing neurodegenerative decline. Although it is difficult to distinguish cause from consequence, several recent studies support the contention that RTE expression, and even perhaps transposition, causally contribute to both the normal deterioration seen with age and to the precipitous decline in some neurodegenerative disorders. This may reflect a two hit model in which normal age-dependent loss of heterochromatin synergizes with a disruption to posttranscriptional silencing of RTEs caused by genetic and environmental stress.
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Affiliation(s)
- Josh Dubnau
- Department of Anesthesiology, State University of New York at Stony Brook, Stony Brook, NY 11794-8480, United States; Department of Neurobiology & Behavior, Stony Brook University & Stony Brook School of Medicine, Stony Brook, NY 11794-8480, United States.
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20
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Cardelli M. The epigenetic alterations of endogenous retroelements in aging. Mech Ageing Dev 2018; 174:30-46. [PMID: 29458070 DOI: 10.1016/j.mad.2018.02.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/05/2018] [Accepted: 02/08/2018] [Indexed: 02/06/2023]
Abstract
Endogenous retroelements, transposons that mobilize through RNA intermediates, include some of the most abundant repetitive sequences of the human genome, such as Alu and LINE-1 sequences, and human endogenous retroviruses. Recent discoveries demonstrate that these mobile genetic elements not only act as intragenomic parasites, but also exert regulatory roles in living cells. The risk of genomic instability represented by endogenous retroelements is normally counteracted by a series of epigenetic control mechanisms which include, among the most important, CpG DNA methylation. Indeed, most of the genomic CpG sites subjected to DNA methylation in the nuclear DNA are carried by these repetitive elements. As other parts of the genome, endogenous retroelements and other transposable elements are subjected to deep epigenetic alterations during aging, repeatedly observed in the context of organismal and cellular senescence, in human and other species. This review summarizes the current status of knowledge about the epigenetic alterations occurring in this large, non-genic portion of the genome in aging and age-related conditions, with a focus on the causes and the possible functional consequences of these alterations.
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Affiliation(s)
- Maurizio Cardelli
- Advanced Technology Center for Aging Research, Scientific Technological Area, Italian National Research Center on Aging (INRCA), via Birarelli 8, 60121 Ancona, Italy.
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21
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Jasiulionis MG. Abnormal Epigenetic Regulation of Immune System during Aging. Front Immunol 2018; 9:197. [PMID: 29483913 PMCID: PMC5816044 DOI: 10.3389/fimmu.2018.00197] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 01/23/2018] [Indexed: 12/15/2022] Open
Abstract
Epigenetics refers to the study of mechanisms controlling the chromatin structure, which has fundamental role in the regulation of gene expression and genome stability. Epigenetic marks, such as DNA methylation and histone modifications, are established during embryonic development and epigenetic profiles are stably inherited during mitosis, ensuring cell differentiation and fate. Under the effect of intrinsic and extrinsic factors, such as metabolic profile, hormones, nutrition, drugs, smoke, and stress, epigenetic marks are actively modulated. In this sense, the lifestyle may affect significantly the epigenome, and as a result, the gene expression profile and cell function. Epigenetic alterations are a hallmark of aging and diseases, such as cancer. Among biological systems compromised with aging is the decline of immune response. Different regulators of immune response have their promoters and enhancers susceptible to the modulation by epigenetic marks, which is fundamental to the differentiation and function of immune cells. Consistent evidence has showed the regulation of innate immune cells, and T and B lymphocytes by epigenetic mechanisms. Therefore, age-dependent alterations in epigenetic marks may result in the decline of immune function and this might contribute to the increased incidence of diseases in old people. In order to maintain health, we need to better understand how to avoid epigenetic alterations related to immune aging. In this review, the contribution of epigenetic mechanisms to the loss of immune function during aging will be discussed, and the promise of new means of disease prevention and management will be pointed.
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Affiliation(s)
- Miriam G Jasiulionis
- Laboratory of Ontogeny and Epigenetics, Pharmacology Department, Universidade Federal de São Paulo, São Paulo, Brazil
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22
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Park JH, Yoo Y, Park YJ. Epigenetics: Linking Nutrition to Molecular Mechanisms in Aging. Prev Nutr Food Sci 2017; 22:81-89. [PMID: 28702424 PMCID: PMC5503416 DOI: 10.3746/pnf.2017.22.2.81] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/07/2017] [Indexed: 11/06/2022] Open
Abstract
Healthy aging has become a major goal of public health. Many studies have provided evidence and theories to explain molecular mechanisms of the aging process. Recent studies suggest that epigenetic mechanisms are responsible for life span and the progression of aging. Epigenetics is a fascinating field of molecular biology, which studies heritable modifications of DNA and histones that regulate gene expression without altering the DNA sequence. DNA methylation is a major epigenetic mark that shows progressive changes during aging. Recent studies have investigated aging-related DNA methylation as a biomarker that predicts cellular age. Interestingly, growing evidence proposes that nutrients play a crucial role in the regulation of epigenetic modifiers. Because various nutrients and their metabolites function as substrates or cofactors for epigenetic modifiers, nutrition can modulate or reverse epigenetic marks in the genome as well as expression patterns. Here, we will review the results on aging-associated epigenetic modifications and the possible mechanisms by which nutrition, including nutrient availability and bioactive compounds, regulate epigenetic changes and affect aging physiology.
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Affiliation(s)
- Joo Hyun Park
- Metabolism and Epigenetics Laboratory, Department of Nutritional Science and Food Management, Ewha Womans University, Seoul 03760, Korea
| | - Yeongran Yoo
- Metabolism and Epigenetics Laboratory, Department of Nutritional Science and Food Management, Ewha Womans University, Seoul 03760, Korea
| | - Yoon Jung Park
- Metabolism and Epigenetics Laboratory, Department of Nutritional Science and Food Management, Ewha Womans University, Seoul 03760, Korea
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23
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Blinov VM, Zverev VV, Krasnov GS, Filatov FP, Shargunov AV. Viral component of the human genome. Mol Biol 2017; 51:205-215. [PMID: 32214476 PMCID: PMC7089383 DOI: 10.1134/s0026893317020066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Revised: 04/27/2016] [Indexed: 12/17/2022]
Abstract
Relationships between viruses and their human host are traditionally described from the point of view taking into consideration hosts as victims of viral aggression, which results in infectious diseases. However, these relations are in fact two-sided and involve modifications of both the virus and host genomes. Mutations that accumulate in the populations of viruses and hosts may provide them advantages such as the ability to overcome defense barriers of host cells or to create more efficient barriers to deal with the attack of the viral agent. One of the most common ways of reinforcing anti-viral barriers is the horizontal transfer of viral genes into the host genome. Within the host genome, these genes may be modified and extensively expressed to compete with viral copies and inhibit the synthesis of their products or modulate their functions in other ways. This review summarizes the available data on the horizontal gene transfer between viral and human genomes and discusses related problems.
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Affiliation(s)
- V M Blinov
- 1Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064 Russia
| | - V V Zverev
- 1Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064 Russia
| | - G S Krasnov
- 1Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064 Russia.,2Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 111911 Russia.,3Orekhovich Research Institute of Biomedical Chemistry, Moscow, 119121 Russia
| | - F P Filatov
- 1Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064 Russia.,Gamaleya Research Center of Epidemiology and Microbiology, Moscow, 123098 Russia
| | - A V Shargunov
- 1Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064 Russia
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24
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Han Y, He X. Integrating Epigenomics into the Understanding of Biomedical Insight. Bioinform Biol Insights 2016; 10:267-289. [PMID: 27980397 PMCID: PMC5138066 DOI: 10.4137/bbi.s38427] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 11/01/2016] [Accepted: 11/06/2016] [Indexed: 12/13/2022] Open
Abstract
Epigenetics is one of the most rapidly expanding fields in biomedical research, and the popularity of the high-throughput next-generation sequencing (NGS) highlights the accelerating speed of epigenomics discovery over the past decade. Epigenetics studies the heritable phenotypes resulting from chromatin changes but without alteration on DNA sequence. Epigenetic factors and their interactive network regulate almost all of the fundamental biological procedures, and incorrect epigenetic information may lead to complex diseases. A comprehensive understanding of epigenetic mechanisms, their interactions, and alterations in health and diseases genome widely has become a priority in biological research. Bioinformatics is expected to make a remarkable contribution for this purpose, especially in processing and interpreting the large-scale NGS datasets. In this review, we introduce the epigenetics pioneering achievements in health status and complex diseases; next, we give a systematic review of the epigenomics data generation, summarize public resources and integrative analysis approaches, and finally outline the challenges and future directions in computational epigenomics.
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Affiliation(s)
- Yixing Han
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.; Present address: Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ximiao He
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.; Present address: Department of Medical Genetics, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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Kochmanski J, Marchlewicz EH, Savidge M, Montrose L, Faulk C, Dolinoy DC. Longitudinal effects of developmental bisphenol A and variable diet exposures on epigenetic drift in mice. Reprod Toxicol 2016; 68:154-163. [PMID: 27496716 DOI: 10.1016/j.reprotox.2016.07.021] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/18/2016] [Accepted: 07/31/2016] [Indexed: 12/13/2022]
Abstract
Environmental factors, including exogenous exposures and nutritional status, can affect DNA methylation across the epigenome, but effects of exposures on age-dependent epigenetic drift remain unclear. Here, we tested the hypothesis that early-life exposure to bisphenol A (BPA) and/or variable diet results in altered epigenetic drift, as measured longitudinally via target loci methylation in paired mouse tail tissue (3 wks/10 mos old). Methylation was quantified at two repetitive elements (LINE-1, IAP), two imprinted genes (Igf2, H19), and one non-imprinted gene (Esr1) in isogenic mice developmentally exposed to Control, Control+BPA (50μg/kg diet), Mediterranean, Western, Mediterranean+BPA, or Western+BPA diets. Across age, methylation levels significantly (p<0.050) decreased at LINE-1, IAP, and H19, and increased at Esr1. Igf2 demonstrated Western-specific changes in early-life methylation (p=0.027), and IAP showed marginal negative modification of drift in Western (p=0.058) and Western+BPA (p=0.051). Thus, DNA methylation drifts across age, and developmental nutritional exposures can alter age-related methylation patterns.
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Affiliation(s)
- Joseph Kochmanski
- Environmental Health Sciences, University of Michigan, School of Public Health, 1415 Washington Heights Ann Arbor, MI, 48109, USA.
| | - Elizabeth H Marchlewicz
- Environmental Health Sciences, University of Michigan, School of Public Health, 1415 Washington Heights Ann Arbor, MI, 48109, USA.
| | - Matthew Savidge
- Environmental Health Sciences, University of Michigan, School of Public Health, 1415 Washington Heights Ann Arbor, MI, 48109, USA.
| | - Luke Montrose
- Environmental Health Sciences, University of Michigan, School of Public Health, 1415 Washington Heights Ann Arbor, MI, 48109, USA.
| | - Christopher Faulk
- Environmental Health Sciences, University of Michigan, School of Public Health, 1415 Washington Heights Ann Arbor, MI, 48109, USA; Department of Animal Science, University of Minnesota, 1364 Eckles Ave, Falcon Heights, MN 55108, USA.
| | - Dana C Dolinoy
- Environmental Health Sciences, University of Michigan, School of Public Health, 1415 Washington Heights Ann Arbor, MI, 48109, USA; Nutritional Sciences, University of Michigan, School of Public Health, 1415 Washington Heights Ann Arbor, MI, 48109, USA.
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Canapa A, Barucca M, Biscotti MA, Forconi M, Olmo E. Transposons, Genome Size, and Evolutionary Insights in Animals. Cytogenet Genome Res 2016; 147:217-39. [PMID: 26967166 DOI: 10.1159/000444429] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2015] [Indexed: 11/19/2022] Open
Abstract
The relationship between genome size and the percentage of transposons in 161 animal species evidenced that variations in genome size are linked to the amplification or the contraction of transposable elements. The activity of transposable elements could represent a response to environmental stressors. Indeed, although with different trends in protostomes and deuterostomes, comprehensive changes in genome size were recorded in concomitance with particular periods of evolutionary history or adaptations to specific environments. During evolution, genome size and the presence of transposable elements have influenced structural and functional parameters of genomes and cells. Changes of these parameters have had an impact on morphological and functional characteristics of the organism on which natural selection directly acts. Therefore, the current situation represents a balance between insertion and amplification of transposons and the mechanisms responsible for their deletion or for decreasing their activity. Among the latter, methylation and the silencing action of small RNAs likely represent the most frequent mechanisms.
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Affiliation(s)
- Adriana Canapa
- Dipartimento di Scienze della Vita e dell'Ambiente, Universitx00E0; Politecnica delle Marche, Ancona, Italy
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Mendelsohn AR, Larrick JW. Systemic factors mediate reversible age-associated brain dysfunction. Rejuvenation Res 2015; 17:525-8. [PMID: 25400086 DOI: 10.1089/rej.2014.1643] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Brain function declines in aging mammals. Recent work has identified dysregulation of key blood-borne factors whose altered expression during aging diminishes brain function in mice. Increased C-C motif chemokine 11 (CCL11) expression with aging is detrimental to brain function. On the other hand, plasma levels of the trophic factor growth/differentiation factor 11 (GDF11) decrease with aging. Restoration of youthful levels of GDF11 by injection partially restores brain function and neurogenesis by improving endothelial cell function and vasculature. Moreover, GDF11 has a rejuvenative effect on cardiac and skeletal muscle. Decreased type II interferon (IFN-II) and increased type I interferon (IFN-I) signaling during aging at the choroid plexus (CP), which constitutes the brain-cerebrospinal fluid barrier (B-CSF-B), negatively effects brain function. Blood from young mice contains factors that restore IFN-II levels. IFN-II is required for maintenance of the CP, and low IFN-II levels are associated with decreased cognitive abilities. IFN-I levels appear to drive increased CCL11 expression through the CSF. Blood from young animals does not restore IFN-I levels. However, injecting anti-interferon-α/β receptor (IFNAR) antibodies into the CSF inhibits downstream IFN-I gene and protein expression and decreases expression of CCL11, partially restoring neurogenesis and cognitive function. These results suggest that IFN-I plays a critical role in increasing CCL11 during aging of the brain. An emerging theme is that aging-associated loss of function in mammals may involve a set of defined, potentially reversible changes in many tissues and organs, including the brain, permitting development of potential rejuvenative therapies.
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Affiliation(s)
- Andrew R Mendelsohn
- Panorama Research Institute and Regenerative Sciences Institute , Sunnyvale, California
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Mitochondrial Oxidative Stress, Mitochondrial DNA Damage and Their Role in Age-Related Vascular Dysfunction. Int J Mol Sci 2015; 16:15918-53. [PMID: 26184181 PMCID: PMC4519931 DOI: 10.3390/ijms160715918] [Citation(s) in RCA: 171] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 06/17/2015] [Accepted: 06/29/2015] [Indexed: 02/06/2023] Open
Abstract
The prevalence of cardiovascular diseases is significantly increased in the older population. Risk factors and predictors of future cardiovascular events such as hypertension, atherosclerosis, or diabetes are observed with higher frequency in elderly individuals. A major determinant of vascular aging is endothelial dysfunction, characterized by impaired endothelium-dependent signaling processes. Increased production of reactive oxygen species (ROS) leads to oxidative stress, loss of nitric oxide (•NO) signaling, loss of endothelial barrier function and infiltration of leukocytes to the vascular wall, explaining the low-grade inflammation characteristic for the aged vasculature. We here discuss the importance of different sources of ROS for vascular aging and their contribution to the increased cardiovascular risk in the elderly population with special emphasis on mitochondrial ROS formation and oxidative damage of mitochondrial DNA. Also the interaction (crosstalk) of mitochondria with nicotinamide adenosine dinucleotide phosphate (NADPH) oxidases is highlighted. Current concepts of vascular aging, consequences for the development of cardiovascular events and the particular role of ROS are evaluated on the basis of cell culture experiments, animal studies and clinical trials. Present data point to a more important role of oxidative stress for the maximal healthspan (healthy aging) than for the maximal lifespan.
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Sturm Á, Ivics Z, Vellai T. The mechanism of ageing: primary role of transposable elements in genome disintegration. Cell Mol Life Sci 2015; 72:1839-47. [PMID: 25837999 PMCID: PMC11113528 DOI: 10.1007/s00018-015-1896-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 03/16/2015] [Accepted: 03/25/2015] [Indexed: 01/11/2023]
Abstract
Understanding the molecular basis of ageing remains a fundamental problem in biology. In multicellular organisms, while the soma undergoes a progressive deterioration over the lifespan, the germ line is essentially immortal as it interconnects the subsequent generations. Genomic instability in somatic cells increases with age, and accumulating evidence indicates that the disintegration of somatic genomes is accompanied by the mobilisation of transposable elements (TEs) that, when mobilised, can be mutagenic by disrupting coding or regulatory sequences. In contrast, TEs are effectively silenced in the germ line by the Piwi-piRNA system. Here, we propose that TE repression transmits the persistent proliferation capacity and the non-ageing phenotype (e.g., preservation of genomic integrity) of the germ line. The Piwi-piRNA pathway also operates in tumorous cells and in somatic cells of certain organisms, including hydras, which likewise exhibit immortality. However, in somatic cells lacking the Piwi-piRNA pathway, gradual chromatin decondensation increasingly allows the mobilisation of TEs as the organism ages. This can explain why the mortality rate rises exponentially throughout the adult life in most animal species, including humans.
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Affiliation(s)
- Ádám Sturm
- Department of Genetics, Eötvös Loránd University, Pázmány Péter stny. 1/C, Budapest, Hungary
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, 63225 Langen, Germany
| | - Tibor Vellai
- Department of Genetics, Eötvös Loránd University, Pázmány Péter stny. 1/C, Budapest, Hungary
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Smith JA, Zagel AL, Sun YV, Dolinoy DC, Bielak LF, Peyser PA, Turner ST, Mosley TH, Kardia SL. Epigenomic Indicators of Age in African Americans. ACTA ACUST UNITED AC 2014; 3. [PMID: 26807331 PMCID: PMC4721639 DOI: 10.4172/2161-1041.1000137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Age is a well-established risk factor for chronic diseases. However, the cellular and molecular changes associated with aging processes that are related to chronic disease initiation and progression are not well-understood. Thus, there is an increased need to identify new markers of cellular and molecular changes that occur during aging processes. In this study, we use genome-wide DNA methylation from 26,428 CpG sites in 13,877 genes to investigate the relationship between age and epigenetic variation in the peripheral blood cells of 972 African American adults from the Genetic Epidemiology Network of Arteriopathy (GENOA) study (mean age=66.3 years, range=39-95). Age was significantly associated with 7,601 (28.8%) CpG sites after Bonferroni correction for α=0.05 (p<1.89×10-6). Due to the extraordinarily strong associations between age and many of the CpG sites (>7,000 sites with p-values ranging from 10-6 to 10-43), we investigated how well the DNA methylation markers predict age. We found that 2,095 (7.9%) CpG sites were significant predictors of age after Bonferroni correction. The top five principal components of the 2,095 age-associated CpG sites accounted for 69.3% of the variability in these CpG sites, and they explained 26.8% of the variation in age. The associations between methylation markers and adult age are so ubiquitous and strong that we hypothesize that DNA methylation patterns may be an important measure of cellular aging processes. Given the highly correlated nature of the age-associated epigenome (as evidenced by the principal components analysis), whole pathways may be regulated as a consequence of aging.
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Affiliation(s)
- Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan USA
| | - Alicia L Zagel
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan USA; Center for Health Statistics, Washington State Department of Health, Olympia, Washington USA
| | - Yan V Sun
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia USA
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan USA
| | - Stephen T Turner
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota USA
| | - Thomas H Mosley
- Department of Medicine and Neurology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Sharon Lr Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan USA
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Larger mammalian body size leads to lower retroviral activity. PLoS Pathog 2014; 10:e1004214. [PMID: 25033295 PMCID: PMC4102558 DOI: 10.1371/journal.ppat.1004214] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 05/15/2014] [Indexed: 02/07/2023] Open
Abstract
Retroviruses have been infecting mammals for at least 100 million years, leaving descendants in host genomes known as endogenous retroviruses (ERVs). The abundance of ERVs is partly determined by their mode of replication, but it has also been suggested that host life history traits could enhance or suppress their activity. We show that larger bodied species have lower levels of ERV activity by reconstructing the rate of ERV integration across 38 mammalian species. Body size explains 37% of the variance in ERV integration rate over the last 10 million years, controlling for the effect of confounding due to other life history traits. Furthermore, 68% of the variance in the mean age of ERVs per genome can also be explained by body size. These results indicate that body size limits the number of recently replicating ERVs due to their detrimental effects on their host. To comprehend the possible mechanistic links between body size and ERV integration we built a mathematical model, which shows that ERV abundance is favored by lower body size and higher horizontal transmission rates. We argue that because retroviral integration is tumorigenic, the negative correlation between body size and ERV numbers results from the necessity to reduce the risk of cancer, under the assumption that this risk scales positively with body size. Our model also fits the empirical observation that the lifetime risk of cancer is relatively invariant among mammals regardless of their body size, known as Peto's paradox, and indicates that larger bodied mammals may have evolved mechanisms to limit ERV activity. Retroviruses have been invading mammalian genomes for over 100 million years, leaving traces known as endogenous retroviruses (ERVs). Early genome sequencing studies revealed a marked difference in the activity of retroviruses among species, with humans largely containing inactive lineages of ERVs, while the mouse contains numerous lineages of active ERVs. We explore the hypothesis that life history traits determine the activity of ERVs in mammalian genomes, and show that larger mammals have fewer ERV copies over recent evolutionary time (the last 10 million years) compared to smaller mammals. This association is determined by body size independently of any confounding variables. We build a mathematical model that shows that ERV abundance in genomes decreases with larger body size and increases with horizontal transmission. Retroviral integration can cause cancer, and our analysis suggests that larger bodied animals control ERV replication in order to postpone cancer until a post-reproductive age. This is in line with a long-standing observation that cancer rates do not fluctuate among mammals of different body size, a phenomenon known as Peto's paradox, and opens up the possibility that larger animals have evolved mechanisms to limit ERV activity.
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Newman MR, Sykes PJ, Blyth BJ, Bezak E, Lawrence MD, Morel KL, Ormsby RJ. A single whole-body low dose X-irradiation does not affect L1, B1 and IAP repeat element DNA methylation longitudinally. PLoS One 2014; 9:e93016. [PMID: 24676381 PMCID: PMC3968115 DOI: 10.1371/journal.pone.0093016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 02/27/2014] [Indexed: 11/18/2022] Open
Abstract
The low dose radioadaptive response has been shown to be protective against high doses of radiation as well as aging-induced genomic instability. We hypothesised that a single whole-body exposure of low dose radiation would induce a radioadaptive response thereby reducing or abrogating aging-related changes in repeat element DNA methylation in mice. Following sham or 10 mGy X-irradiation, serial peripheral blood sampling was performed and differences in Long Interspersed Nucleic Element 1 (L1), B1 and Intracisternal-A-Particle (IAP) repeat element methylation between samples were assessed using high resolution melt analysis of PCR amplicons. By 420 days post-irradiation, neither radiation- or aging-related changes in the methylation of peripheral blood, spleen or liver L1, B1 and IAP elements were observed. Analysis of the spleen and liver tissues of cohorts of untreated aging mice showed that the 17-19 month age group exhibited higher repeat element methylation than younger or older mice, with no overall decline in methylation detected with age. This is the first temporal analysis of the effect of low dose radiation on repeat element methylation in mouse peripheral blood and the first to examine the long term effect of this dose on repeat element methylation in a radiosensitive tissue (spleen) and a tissue fundamental to the aging process (liver). Our data indicate that the methylation of murine DNA repeat elements can fluctuate with age, but unlike human studies, do not demonstrate an overall aging-related decline. Furthermore, our results indicate that a low dose of ionising radiation does not induce detectable changes to murine repeat element DNA methylation in the tissues and at the time-points examined in this study. This radiation dose is relevant to human diagnostic radiation exposures and suggests that a dose of 10 mGy X-rays, unlike high dose radiation, does not cause significant short or long term changes to repeat element or global DNA methylation.
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Affiliation(s)
- Michelle R. Newman
- Flinders Centre for Innovation in Cancer, Flinders University and Medical Centre, Bedford Park, South Australia, Australia
| | - Pamela J. Sykes
- Flinders Centre for Innovation in Cancer, Flinders University and Medical Centre, Bedford Park, South Australia, Australia
| | - Benjamin J. Blyth
- Flinders Centre for Innovation in Cancer, Flinders University and Medical Centre, Bedford Park, South Australia, Australia
| | - Eva Bezak
- Department of Medical Physics, Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Mark D. Lawrence
- Flinders Centre for Innovation in Cancer, Flinders University and Medical Centre, Bedford Park, South Australia, Australia
| | - Katherine L. Morel
- Flinders Centre for Innovation in Cancer, Flinders University and Medical Centre, Bedford Park, South Australia, Australia
| | - Rebecca J. Ormsby
- Flinders Centre for Innovation in Cancer, Flinders University and Medical Centre, Bedford Park, South Australia, Australia
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Moskalev AA, Aliper AM, Smit-McBride Z, Buzdin A, Zhavoronkov A. Genetics and epigenetics of aging and longevity. Cell Cycle 2014; 13:1063-77. [PMID: 24603410 PMCID: PMC4013158 DOI: 10.4161/cc.28433] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Evolutionary theories of aging predict the existence of certain genes that provide selective advantage early in life with adverse effect on lifespan later in life (antagonistic pleiotropy theory) or longevity insurance genes (disposable soma theory). Indeed, the study of human and animal genetics is gradually identifying new genes that increase lifespan when overexpressed or mutated: gerontogenes. Furthermore, genetic and epigenetic mechanisms are being identified that have a positive effect on longevity. The gerontogenes are classified as lifespan regulators, mediators, effectors, housekeeping genes, genes involved in mitochondrial function, and genes regulating cellular senescence and apoptosis. In this review we demonstrate that the majority of the genes as well as genetic and epigenetic mechanisms that are involved in regulation of longevity are highly interconnected and related to stress response.
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Affiliation(s)
- Alexey A Moskalev
- Moscow Institute of Physics and Technology; Moscow, Russian Federation; Institute of Biology; Komi Science Center of Russian Academy of Sciences; Syktyvkar, Russian Federation; Syktyvkar State University; Syktyvkar, Russian Federation
| | - Alexander M Aliper
- Moscow Institute of Physics and Technology; Moscow, Russian Federation; Institute of Biology; Komi Science Center of Russian Academy of Sciences; Syktyvkar, Russian Federation
| | - Zeljka Smit-McBride
- Department of Ophthalmology and Vision Science; School of Medicine; University of California at Davis; Davis, CA USA
| | - Anton Buzdin
- Moscow Institute of Physics and Technology; Moscow, Russian Federation; Federal Clinical Research Center of Pediatric Hematology, Oncology, and Immunology; Moscow, Russian Federation; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Moscow, Russian Federation; First Oncology Research and Advisory Center; Moscow, Russian Federation
| | - Alex Zhavoronkov
- Moscow Institute of Physics and Technology; Moscow, Russian Federation; Federal Clinical Research Center of Pediatric Hematology, Oncology, and Immunology; Moscow, Russian Federation; The Biogerontology Research Foundation; London, UK
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Bacalini MG, Friso S, Olivieri F, Pirazzini C, Giuliani C, Capri M, Santoro A, Franceschi C, Garagnani P. Present and future of anti-ageing epigenetic diets. Mech Ageing Dev 2014; 136-137:101-15. [DOI: 10.1016/j.mad.2013.12.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 12/06/2013] [Accepted: 12/20/2013] [Indexed: 12/13/2022]
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Sedivy JM, Kreiling JA, Neretti N, De Cecco M, Criscione SW, Hofmann JW, Zhao X, Ito T, Peterson AL. Death by transposition - the enemy within? Bioessays 2013; 35:1035-43. [PMID: 24129940 PMCID: PMC3922893 DOI: 10.1002/bies.201300097] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Here we present and develop the hypothesis that the derepression of endogenous retrotransposable elements (RTEs) – genomic parasites – is an important and hitherto under-unexplored molecular aging process that can potentially occur in most tissues. We further envision that the activation and continued presence of retrotransposition contribute to age-associated tissue degeneration and pathology. Chromatin is a complex and dynamic structure that needs to be maintained in a functional state throughout our lifetime. Studies of diverse species have revealed that chromatin undergoes extensive rearrangements during aging. Cellular senescence, an important component of mammalian aging, has recently been associated with decreased heterochromatinization of normally silenced regions of the genome. These changes lead to the expression of RTEs, culminating in their transposition. RTEs are common in all kingdoms of life, and comprise close to 50% of mammalian genomes. They are tightly controlled, as their activity is highly destabilizing and mutagenic to their resident genomes.
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Affiliation(s)
- John M Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
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36
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Magiorkinis G, Belshaw R, Katzourakis A. 'There and back again': revisiting the pathophysiological roles of human endogenous retroviruses in the post-genomic era. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120504. [PMID: 23938753 PMCID: PMC3758188 DOI: 10.1098/rstb.2012.0504] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Almost 8% of the human genome comprises endogenous retroviruses (ERVs). While they have been shown to cause specific pathologies in animals, such as cancer, their association with disease in humans remains controversial. The limited evidence is partly due to the physical and bioethical restrictions surrounding the study of transposons in humans, coupled with the major experimental and bioinformatics challenges surrounding the association of ERVs with disease in general. Two biotechnological landmarks of the past decade provide us with unprecedented research artillery: (i) the ultra-fine sequencing of the human genome and (ii) the emergence of high-throughput sequencing technologies. Here, we critically assemble research about potential pathologies of ERVs in humans. We argue that the time is right to revisit the long-standing questions of human ERV pathogenesis within a robust and carefully structured framework that makes full use of genomic sequence data. We also pose two thought-provoking research questions on potential pathophysiological roles of ERVs with respect to immune escape and regulation.
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37
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Fang X, Corrales J, Thornton C, Scheffler BE, Willett KL. Global and gene specific DNA methylation changes during zebrafish development. Comp Biochem Physiol B Biochem Mol Biol 2013; 166:99-108. [PMID: 23876386 DOI: 10.1016/j.cbpb.2013.07.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 07/16/2013] [Accepted: 07/17/2013] [Indexed: 02/06/2023]
Abstract
DNA methylation is dynamic through the life of an organism. Previous studies have primarily focused on DNA methylation changes during very early embryogenesis. In this study, global and gene specific DNA methylation in zebrafish (Danio rerio) embryos, larvae and adult livers were compared. The percent methylation of cytosines was low in 2 to 4.3h post fertilization (hpf) zebrafish embryos and was consistently higher in zebrafish older than 6 hpf. Furthermore, quantitative real-time PCR (qPCR) results showed relatively high DNA methyltransferase 1 (dnmt1) and low glycine N-methyltransferase (gnmt) mRNA expression in early embryogenesis. By studying methylation patterns and gene expression of five developmentally important genes, namely vasa, Ras-association domain family member 1 (rassf1), telomerase reverse transcriptase (tert), c-jun and c-myca, we found that the timing of changes in DNA methylation patterns was gene specific, and changes in gene expression were not necessarily correlated with the DNA methylation patterns.
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Affiliation(s)
- Xiefan Fang
- Department of Pharmacology and Environmental Toxicology Research Program, School of Pharmacy, University of Mississippi, University, MS 38677, USA
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Moskalev AA, Shaposhnikov MV, Plyusnina EN, Zhavoronkov A, Budovsky A, Yanai H, Fraifeld VE. The role of DNA damage and repair in aging through the prism of Koch-like criteria. Ageing Res Rev 2013; 12:661-84. [PMID: 22353384 DOI: 10.1016/j.arr.2012.02.001] [Citation(s) in RCA: 222] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 01/27/2012] [Accepted: 02/06/2012] [Indexed: 12/21/2022]
Abstract
Since the first publication on Somatic Mutation Theory of Aging (Szilárd, 1959), a great volume of knowledge in the field has been accumulated. Here we attempted to organize the evidence "for" and "against" the hypothesized causal role of DNA damage and mutation accumulation in aging in light of four Koch-like criteria. They are based on the assumption that some quantitative relationship between the levels of DNA damage/mutations and aging rate should exist, so that (i) the longer-lived individuals or species would have a lower rate of damage than the shorter-lived, and (ii) the interventions that modulate the level of DNA damage and repair capacity should also modulate the rate of aging and longevity and vice versa. The analysis of how the existing data meets the proposed criteria showed that many gaps should still be filled in order to reach a clear-cut conclusion. As a perspective, it seems that the main emphasis in future studies should be put on the role of DNA damage in stem cell aging.
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p53 cooperates with DNA methylation and a suicidal interferon response to maintain epigenetic silencing of repeats and noncoding RNAs. Proc Natl Acad Sci U S A 2012; 110:E89-98. [PMID: 23236145 DOI: 10.1073/pnas.1216922110] [Citation(s) in RCA: 191] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Large parts of mammalian genomes are transcriptionally inactive and enriched with various classes of interspersed and tandem repeats. Here we show that the tumor suppressor protein p53 cooperates with DNA methylation to maintain silencing of a large portion of the mouse genome. Massive transcription of major classes of short, interspersed nuclear elements (SINEs) B1 and B2, both strands of near-centromeric satellite DNAs consisting of tandem repeats, and multiple species of noncoding RNAs was observed in p53-deficient but not in p53 wild-type mouse fibroblasts treated with the DNA demethylating agent 5-aza-2'-deoxycytidine. The abundance of these transcripts exceeded the level of β-actin mRNA by more than 150-fold. Accumulation of these transcripts, which are capable of forming double-stranded RNA (dsRNA), was accompanied by a strong, endogenous, apoptosis-inducing type I IFN response. This phenomenon, which we named "TRAIN" (for "transcription of repeats activates interferon"), was observed in spontaneous tumors in two models of cancer-prone mice, presumably reflecting naturally occurring DNA hypomethylation and p53 inactivation in cancer. These observations suggest that p53 and IFN cooperate to prevent accumulation of cells with activated repeats and provide a plausible explanation for the deregulation of IFN function frequently seen in tumors. Overall, this work reveals roles for p53 and IFN that are key for genetic stability and therefore relevant to both tumorigenesis and the evolution of species.
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The influence of five monoamine genes on trajectories of depressive symptoms across adolescence and young adulthood. Dev Psychopathol 2012; 24:267-85. [PMID: 22293009 DOI: 10.1017/s0954579411000824] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The influence of five monoamine candidate genes on depressive symptom trajectories in adolescence and young adulthood were examined in the Add Health genetic sample. Results indicated that, for all respondents, carriers of the dopamine receptor D4 5-repeat allele were characterized by distinct depressive symptom trajectories across adolescence and early adulthood. Similarly, for males, individuals with the monoamine oxidase A 3.5-repeat allele exhibited unique depressive symptom trajectories. Specifically, the trajectories of those with the dopamine receptor D4 5-repeat allele were characterized by rising levels in the transition to adulthood, while their peers were experiencing a normative drop in depressive symptom frequency. Conversely, males with the monoamine oxidase A 3.5-repeat allele were shown to experience increased distress in late adolescence. An empirical method for examining a wide array of allelic combinations was employed, and false discovery rate methods were used to control the risk of false positives due to multiple testing. Special attention was given to thoroughly interrogate the robustness of the putative genetic effects. These results demonstrate the value of combining dynamic developmental perspectives with statistical genetic methods to optimize the search for genetic influences on psychopathology across the life course.
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Li CCY, Maloney CA, Cropley JE, Suter CM. Epigenetic programming by maternal nutrition: shaping future generations. Epigenomics 2012; 2:539-49. [PMID: 22121973 DOI: 10.2217/epi.10.33] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Within the Western world's aging and increasingly overweight population, we are seeing an increasing prevalence of adult-onset, lifestyle-related disease such as diabetes, hypertension and atherosclerosis. There is significant evidence that suboptimal nutrition in pregnancy can lead to an increased risk of these diseases developing in offspring, and that this increased risk can be heritable. Thus, poor in utero nutrition may be a major contributor to the current cycle of obesity. While the molecular basis of this phenomenon is unknown, available evidence suggests that it can be mediated by epigenetic changes to gene expression. Here, we discuss epigenetics as a mediator of disease risk in response to nutritional cues. The potential for maternal nutrition to heritably alter epigenetic states may have implications for population health and adaptive evolution.
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Affiliation(s)
- Cheryl Chui Ying Li
- Victor Chang Cardiac Research Institute, Lowy Packer Building, 405 Liverpool Street, Darlinghurst, NSW 2010, Australia
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Bellizzi D, D’Aquila P, Montesanto A, Corsonello A, Mari V, Mazzei B, Lattanzio F, Passarino G. Global DNA methylation in old subjects is correlated with frailty. AGE (DORDRECHT, NETHERLANDS) 2012; 34:169-79. [PMID: 21336567 PMCID: PMC3260357 DOI: 10.1007/s11357-011-9216-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 01/30/2011] [Indexed: 05/12/2023]
Abstract
Epigenetic variations have been widely described to occur during the aging process. To verify if these modifications are correlated with the inter-individual phenotypic variability of elderly people, we searched for a correlation between global DNA methylation levels and frailty. We found that the global DNA methylation levels were correlated to the frailty status in middle/advanced-aged subjects but not with age. A 7-year follow-up study also revealed that a worsening in the frailty status was associated to a significant decrease in the global DNA methylation levels. These results suggest that the relaxation of the epigenetic control in aging is specifically associated with the functional decline rather than with the chronological age of individuals. Thus, the modifications of DNA methylation, representing a drawbridge between the genetic and the environmental factors affecting the age-related decay of the organism, may play an important role in determining physiological changes over old age.
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Affiliation(s)
- Dina Bellizzi
- Department of Cell Biology, University of Calabria, 87036 Rende, Italy
| | - Patrizia D’Aquila
- Department of Cell Biology, University of Calabria, 87036 Rende, Italy
| | | | | | - Vincenzo Mari
- Italian National Research Center on Aging, 87100 Cosenza, Italy
| | - Bruno Mazzei
- Italian National Research Center on Aging, 87100 Cosenza, Italy
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Newman M, Blyth BJ, Hussey DJ, Jardine D, Sykes PJ, Ormsby RJ. Sensitive quantitative analysis of murine LINE1 DNA methylation using high resolution melt analysis. Epigenetics 2012; 7:92-105. [PMID: 22274612 DOI: 10.4161/epi.7.1.18815] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
We present here the first high resolution melt (HRM) assay to quantitatively analyze differences in murine DNA methylation levels utilizing CpG methylation of Long Interspersed Elements-1 (LINE1 or L1). By calculating the integral difference in melt temperature between samples and a methylated control, and biasing PCR primers for unmethylated CpGs, the assay demonstrates enhanced sensitivity to detect changes in methylation in a cell line treated with low doses of 5-aza-2'-deoxycytidine (5-aza). The L1 assay was confirmed to be a good marker of changes in DNA methylation of L1 elements at multiple regions across the genome when compared with total 5-methyl-cytosine content, measured by Liquid Chromatography-Mass Spectrometry (LC-MS). The assay design was also used to detect changes in methylation at other murine repeat elements (B1 and Intracisternal-A-particle Long-terminal Repeat elements). Pyrosequencing analysis revealed that L1 methylation changes were non-uniform across the CpGs within the L1-HRM target region, demonstrating that the L1 assay can detect small changes in CpG methylation among a large pool of heterogeneously methylated DNA templates. Application of the assay to various tissues from Balb/c and CBA mice, including previously unreported peripheral blood (PB), revealed a tissue hierarchy (from hypermethylated to hypomethylated) of PB > kidney > liver > prostate > spleen. CBA mice demonstrated overall greater methylation than Balb/c mice, and male mice demonstrated higher tissue methylation compared with female mice in both strains. Changes in DNA methylation have been reported to be an early and fundamental event in the pathogenesis of many human diseases, including cancer. Mouse studies designed to identify modulators of DNA methylation, the critical doses, relevant time points and the tissues affected are limited by the low throughput nature and exorbitant cost of many DNA methylation assays. The L1 assay provides a high throughput, inexpensive and sensitive screening tool for identifying and characterizing DNA methylation changes to L1 elements at multiple regions across the genome.
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Affiliation(s)
- Michelle Newman
- Haematology and Genetic Pathology, Flinders University and Medical Centre, Bedford Park, Adelaide, SA Australia
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On the role of low-dose effects and epigenetics in toxicology. EXPERIENTIA SUPPLEMENTUM (2012) 2012; 101:499-550. [PMID: 22945581 DOI: 10.1007/978-3-7643-8340-4_18] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
For a long time, scientists considered genotoxic effects as the major issue concerning the influence of environmental chemicals on human health. Over the last decades, a new layer superimposed the genome, i.e., the epigenome, tremendously changing this point of view. The term "epigenetics" comprises stable alterations in gene expression potential arising from variations in DNA methylation and a variety of histone modifications, without changing the underlying DNA sequence. Recently, also gene silencing by small noncoding RNAs (ncRNAs), in particular by microRNAs, was included in the list of epigenetic mechanisms. Multiple studies in vivo as well as in vitro have shown that a multitude of different environmental factors are capable of changing the epigenetic pattern as well as miRNA expression in certain cell types, leading to aberrant gene expression profiles in cells and tissues. These changes may have extensive effects concerning the proper gene expression necessary in a specified cell type and can even lead into a state of disease. Especially the roles of epigenetic modifications and miRNA alterations in tumorigenesis have been a major focus in research over the last years. This chapter will give an overview on epigenetic features and on the spectrum of epigenetic changes observed after exposure against environmental chemicals and pollutants.
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Retrotransposon-induced heterochromatin spreading in the mouse revealed by insertional polymorphisms. PLoS Genet 2011; 7:e1002301. [PMID: 21980304 PMCID: PMC3183085 DOI: 10.1371/journal.pgen.1002301] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Accepted: 08/04/2011] [Indexed: 12/13/2022] Open
Abstract
The "arms race" relationship between transposable elements (TEs) and their host has promoted a series of epigenetic silencing mechanisms directed against TEs. Retrotransposons, a class of TEs, are often located in repressed regions and are thought to induce heterochromatin formation and spreading. However, direct evidence for TE-induced local heterochromatin in mammals is surprisingly scarce. To examine this phenomenon, we chose two mouse embryonic stem (ES) cell lines that possess insertionally polymorphic retrotransposons (IAP, ETn/MusD, and LINE elements) at specific loci in one cell line but not the other. Employing ChIP-seq data for these cell lines, we show that IAP elements robustly induce H3K9me3 and H4K20me3 marks in flanking genomic DNA. In contrast, such heterochromatin is not induced by LINE copies and only by a minority of polymorphic ETn/MusD copies. DNA methylation is independent of the presence of IAP copies, since it is present in flanking regions of both full and empty sites. Finally, such spreading into genes appears to be rare, since the transcriptional start sites of very few genes are less than one Kb from an IAP. However, the B3galtl gene is subject to transcriptional silencing via IAP-induced heterochromatin. Hence, although rare, IAP-induced local heterochromatin spreading into nearby genes may influence expression and, in turn, host fitness.
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Maksakova IA, Goyal P, Bullwinkel J, Brown JP, Bilenky M, Mager DL, Singh PB, Lorincz MC. H3K9me3-binding proteins are dispensable for SETDB1/H3K9me3-dependent retroviral silencing. Epigenetics Chromatin 2011; 4:12. [PMID: 21774827 PMCID: PMC3169442 DOI: 10.1186/1756-8935-4-12] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 07/20/2011] [Indexed: 02/01/2023] Open
Abstract
Background Endogenous retroviruses (ERVs) are parasitic sequences whose derepression is associated with cancer and genomic instability. Many ERV families are silenced in mouse embryonic stem cells (mESCs) via SETDB1-deposited trimethylated lysine 9 of histone 3 (H3K9me3), but the mechanism of H3K9me3-dependent repression remains unknown. Multiple proteins, including members of the heterochromatin protein 1 (HP1) family, bind H3K9me2/3 and are involved in transcriptional silencing in model organisms. In this work, we address the role of such H3K9me2/3 "readers" in the silencing of ERVs in mESCs. Results We demonstrate that despite the reported function of HP1 proteins in H3K9me-dependent gene repression and the critical role of H3K9me3 in transcriptional silencing of class I and class II ERVs, the depletion of HP1α, HP1β and HP1γ, alone or in combination, is not sufficient for derepression of these elements in mESCs. While loss of HP1α or HP1β leads to modest defects in DNA methylation of ERVs or spreading of H4K20me3 into flanking genomic sequence, respectively, neither protein affects H3K9me3 or H4K20me3 in ERV bodies. Furthermore, using novel ERV reporter constructs targeted to a specific genomic site, we demonstrate that, relative to Setdb1, knockdown of the remaining known H3K9me3 readers expressed in mESCs, including Cdyl, Cdyl2, Cbx2, Cbx7, Mpp8, Uhrf1 and Jarid1a-c, leads to only modest proviral reactivation. Conclusion Taken together, these results reveal that each of the known H3K9me3-binding proteins is dispensable for SETDB1-mediated ERV silencing. We speculate that H3K9me3 might maintain ERVs in a silent state in mESCs by directly inhibiting deposition of active covalent histone marks.
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Affiliation(s)
- Irina A Maksakova
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada, V6T 1Z3.
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Hedges DJ, Belancio VP. Restless genomes humans as a model organism for understanding host-retrotransposable element dynamics. ADVANCES IN GENETICS 2011; 73:219-62. [PMID: 21310298 DOI: 10.1016/b978-0-12-380860-8.00006-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Since their initial discovery in maize, there have been various attempts to categorize the relationship between transposable elements (TEs) and their host organisms. These have ranged from TEs being selfish parasites to their role as essential, functional components of organismal biology. Research over the past several decades has, in many respects, only served to complicate the issue even further. On the one hand, investigators have amassed substantial evidence concerning the negative effects that TE-mutagenic activity can have on host genomes and organismal fitness. On the other hand, we find an increasing number of examples, across several taxa, of TEs being incorporated into functional biological roles for their host organism. Some 45% of our own genomes are comprised of TE copies. While many of these copies are dormant, having lost their ability to mobilize, several lineages continue to actively proliferate in modern human populations. With its complement of ancestral and active TEs, the human genome exhibits key aspects of the host-TE dynamic that has played out since early on in organismal evolution. In this review, we examine what insights the particularly well-characterized human system can provide regarding the nature of the host-TE interaction.
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Affiliation(s)
- Dale J Hedges
- Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, USA
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48
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Epigenetic mechanisms in Alzheimer's disease. Neurobiol Aging 2011; 32:1161-80. [PMID: 21482442 DOI: 10.1016/j.neurobiolaging.2010.08.017] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Revised: 07/20/2010] [Accepted: 08/07/2010] [Indexed: 12/20/2022]
Abstract
Epigenetic modifications help orchestrate sweeping developmental, aging, and disease-causing changes in phenotype by altering transcriptional activity in multiple genes spanning multiple biologic pathways. Although previous epigenetic research has focused primarily on dividing cells, particularly in cancer, recent studies have shown rapid, dynamic, and persistent epigenetic modifications in neurons that have significant neuroendocrine, neurophysiologic, and neurodegenerative consequences. Here, we provide a review of the major mechanisms for epigenetic modification and how they are reportedly altered in aging and Alzheimer's disease (AD). Because of their reach across the genome, epigenetic mechanisms may provide a unique integrative framework for the pathologic diversity and complexity of AD.
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49
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Hjelmeland LM. Dark matters in AMD genetics: epigenetics and stochasticity. Invest Ophthalmol Vis Sci 2011; 52:1622-31. [PMID: 21429863 DOI: 10.1167/iovs.10-6765] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Leonard M Hjelmeland
- Department of Ophthalmology and Vision Science, School of Medicine, University of California, Davis, California, USA.
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50
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