1
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Weavers H. Biological resilience in health and disease. Dis Model Mech 2024; 17:dmm050799. [PMID: 39051470 DOI: 10.1242/dmm.050799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024] Open
Abstract
All living organisms - from single-celled prokaryotes through to invertebrates and humans - are frequently exposed to numerous challenges during their lifetime, which could damage their molecular and cellular contents and threaten their survival. Nevertheless, these diverse organisms are, on the whole, remarkably resilient to potential threats. Recent years have seen rapid advances in our mechanistic understanding of this emerging phenomenon of biological resilience, which enables cells, tissues and whole organisms to bounce back from challenges or stress. In this At a Glance article, I discuss current knowledge on the diverse molecular mechanisms driving biological resilience across scales, with particular focus on its dynamic and adaptive nature. I highlight emerging evidence that loss of biological resilience could underly numerous pathologies, including age-related frailty and degenerative disease. Finally, I present the multi-disciplinary experimental approaches that are helping to unravel the causal mechanisms of resilience and how this emerging knowledge could be harnessed therapeutically in the clinic.
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Affiliation(s)
- Helen Weavers
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences, University of Bristol, Bristol BS8 1TD, UK
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2
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Khan S, Mishra RK. Multigenerational Effect of Heat Stress on the Drosophila melanogaster Sperm Proteome. J Proteome Res 2024. [PMID: 38743012 DOI: 10.1021/acs.jproteome.4c00205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The effect of the parental environment on offspring through non-DNA sequence-based mechanisms, such as DNA methylation, chromatin modifications, noncoding RNAs, and proteins, could only be established after the conception of "epigenetics". These effects are now broadly referred to as multigenerational epigenetic effects. Despite accumulating evidence of male gamete-mediated multigenerational epigenetic inheritance, little is known about the factors that underlie heat stress-induced multigenerational epigenetic inheritance via the male germline in Drosophila. In this study, we address this gap by utilizing an established heat stress paradigm in Drosophila and investigating its multigenerational effect on the sperm proteome. Our findings indicate that multigenerational heat stress during the early embryonic stage significantly influences proteins in the sperm associated with translation, chromatin organization, microtubule-based processes, and the generation of metabolites and energy. Assessment of life-history traits revealed that reproductive fitness and stress tolerance remained unaffected by multigenerational heat stress. Our study offers initial insights into the chromatin-based epigenetic mechanisms as a plausible means of transmitting heat stress memory through the male germline in Drosophila. Furthermore, it sheds light on the repercussions of early embryonic heat stress on male reproductive potential. The data sets from this study are available at the ProteomeXchange Consortium under the identifier PXD037488.
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Affiliation(s)
- Shagufta Khan
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad-500 007, Telangana, India
| | - Rakesh K Mishra
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad-500 007, Telangana, India
- Tata Institute for Genetics and Society, Bengaluru-560 065, Karnataka, India
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3
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Zhang Y, Wang B, Sun W, Wang G, Liu Z, Zhang X, Ding J, Han Y, Zhang H. Paternal exposures to endocrine-disrupting chemicals induce intergenerational epigenetic influences on offspring: A review. ENVIRONMENT INTERNATIONAL 2024; 187:108689. [PMID: 38688236 DOI: 10.1016/j.envint.2024.108689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/28/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024]
Abstract
Endocrine-disrupting chemicals (EDCs) are ubiquitous in ecological environments and have become a great issue of public health concern since the 1990 s. There is a deep scientific understanding of the toxicity of EDCs. However, recent studies have found that the abnormal physiological functions of the parents caused by EDCs could be transmitted to their unexposed offspring, leading to intergenerational toxicity. We questioned whether sustained epigenetic changes occur through the male germline. In this review, we (1) systematically searched the available research on the intergenerational impacts of EDCs in aquatic and mammal organisms, including 42 articles, (2) summarized the intergenerational genetic effects, such as decreased offspring survival, abnormal reproductive dysfunction, metabolic disorders, and behavioral abnormalities, (3) summarized the mechanisms of intergenerational toxicity through paternal interactions, and (4) propose suggestions on future research directions to develop a deeper understanding of the ecological risk of EDCs.
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Affiliation(s)
- Yinan Zhang
- Hangzhou Normal University, Hangzhou 310018, China
| | - Bingyi Wang
- Hangzhou Normal University, Hangzhou 310018, China
| | - Wenhui Sun
- Hangzhou Normal University, Hangzhou 310018, China
| | | | - Zhiquan Liu
- Hangzhou Normal University, Hangzhou 310018, China; Hangzhou International Urbanology Research Center, Hangzhou 311121, China
| | | | - Jiafeng Ding
- Hangzhou Normal University, Hangzhou 310018, China
| | - Yu Han
- Hangzhou Normal University, Hangzhou 310018, China
| | - Hangjun Zhang
- Hangzhou Normal University, Hangzhou 310018, China; Hangzhou International Urbanology Research Center, Hangzhou 311121, China.
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4
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Martinez-Feduchi P, Jin P, Yao B. Epigenetic modifications of DNA and RNA in Alzheimer's disease. Front Mol Neurosci 2024; 17:1398026. [PMID: 38726308 PMCID: PMC11079283 DOI: 10.3389/fnmol.2024.1398026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
Alzheimer's disease (AD) is a complex neurodegenerative disorder and the most common form of dementia. There are two main types of AD: familial and sporadic. Familial AD is linked to mutations in amyloid precursor protein (APP), presenilin-1 (PSEN1), and presenilin-2 (PSEN2). On the other hand, sporadic AD is the more common form of the disease and has genetic, epigenetic, and environmental components that influence disease onset and progression. Investigating the epigenetic mechanisms associated with AD is essential for increasing understanding of pathology and identifying biomarkers for diagnosis and treatment. Chemical covalent modifications on DNA and RNA can epigenetically regulate gene expression at transcriptional and post-transcriptional levels and play protective or pathological roles in AD and other neurodegenerative diseases.
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Affiliation(s)
| | | | - Bing Yao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
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5
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Wu Z, Zhang W, Qu J, Liu GH. Emerging epigenetic insights into aging mechanisms and interventions. Trends Pharmacol Sci 2024; 45:157-172. [PMID: 38216430 DOI: 10.1016/j.tips.2023.12.002] [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: 11/21/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Epigenetic dysregulation emerges as a critical hallmark and driving force of aging. Although still an evolving field with much to explore, it has rapidly gained significance by providing valuable insights into the mechanisms of aging and potential therapeutic opportunities for age-related diseases. Recent years have witnessed remarkable strides in our understanding of the epigenetic landscape of aging, encompassing pivotal elements, such as DNA methylation, histone modifications, RNA modifications, and noncoding (nc) RNAs. Here, we review the latest discoveries that shed light on new epigenetic mechanisms and critical targets for predicting and intervening in aging and related disorders. Furthermore, we explore burgeoning interventions and exemplary clinical trials explicitly designed to foster healthy aging, while contemplating the potential ramifications of epigenetic influences.
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Affiliation(s)
- 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; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Weiqi Zhang
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jing Qu
- 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; State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Guang-Hui Liu
- 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; Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
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6
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Sands B, Yun SR, Oshima J, Mendenhall AR. Maternal histone methyltransferases antagonistically regulate monoallelic expression in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576748. [PMID: 38328214 PMCID: PMC10849558 DOI: 10.1101/2024.01.22.576748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Undefined epigenetic programs act to probabilistically silence individual autosomal alleles, generating unique individuals, even from genetic clones. This sort of random monoallelic expression can explain variation in traits and diseases that differences in genes and environments cannot. Here, we developed the nematode Caenorhabditis elegans to study monoallelic expression in whole tissues, and defined a developmental genetic regulation pathway. We found maternal H3K9 histone methyltransferase (HMT) SET-25/SUV39/G9a works with HPL-2/HP1 and LIN-61/L3MBTL2 to randomly silence alleles in the intestinal progenitor E-cell of 8-cell embryos to cause monoallelic expression. SET-25 was antagonized by another maternal H3K9 HMT, MET-2/SETDB1, which works with LIN-65/ATF7ZIP and ARLE-14/ARL14EP to prevent monoallelic expression. The HMT-catalytic SET domains of both MET-2 and SET-25 were required for regulating monoallelic expression. Our data support a model wherein SET-25 and MET-2 regulate histones during development to generate patterns of somatic monoallelic expression that are persistent but not heritable.
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Wu Z, Qu J, Zhang W, Liu GH. Stress, epigenetics, and aging: Unraveling the intricate crosstalk. Mol Cell 2024; 84:34-54. [PMID: 37963471 DOI: 10.1016/j.molcel.2023.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 11/16/2023]
Abstract
Aging, as a complex process involving multiple cellular and molecular pathways, is known to be exacerbated by various stresses. Because responses to these stresses, such as oxidative stress and genotoxic stress, are known to interplay with the epigenome and thereby contribute to the development of age-related diseases, investigations into how such epigenetic mechanisms alter gene expression and maintenance of cellular homeostasis is an active research area. In this review, we highlight recent studies investigating the intricate relationship between stress and aging, including its underlying epigenetic basis; describe different types of stresses that originate from both internal and external stimuli; and discuss potential interventions aimed at alleviating stress and restoring epigenetic patterns to combat aging or age-related diseases. Additionally, we address the challenges currently limiting advancement in this burgeoning field.
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Affiliation(s)
- 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; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Jing Qu
- 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; State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Weiqi Zhang
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; The Fifth People's Hospital of Chongqing, Chongqing 400062, China.
| | - Guang-Hui Liu
- 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; Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
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8
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Ow MC, Hall SE. Inheritance of Stress Responses via Small Non-Coding RNAs in Invertebrates and Mammals. EPIGENOMES 2023; 8:1. [PMID: 38534792 DOI: 10.3390/epigenomes8010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 03/28/2024] Open
Abstract
While reports on the generational inheritance of a parental response to stress have been widely reported in animals, the molecular mechanisms behind this phenomenon have only recently emerged. The booming interest in epigenetic inheritance has been facilitated in part by the discovery that small non-coding RNAs are one of its principal conduits. Discovered 30 years ago in the Caenorhabditis elegans nematode, these small molecules have since cemented their critical roles in regulating virtually all aspects of eukaryotic development. Here, we provide an overview on the current understanding of epigenetic inheritance in animals, including mice and C. elegans, as it pertains to stresses such as temperature, nutritional, and pathogenic encounters. We focus on C. elegans to address the mechanistic complexity of how small RNAs target their cohort mRNAs to effect gene expression and how they govern the propagation or termination of generational perdurance in epigenetic inheritance. Presently, while a great amount has been learned regarding the heritability of gene expression states, many more questions remain unanswered and warrant further investigation.
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Affiliation(s)
- Maria C Ow
- Department of Biology, Syracuse University, Syracuse, NY 13210, USA
| | - Sarah E Hall
- Department of Biology and Program in Neuroscience, Syracuse University, Syracuse, NY 13210, USA
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9
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Erofeeva EA. Environmental hormesis in living systems: The role of hormetic trade-offs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:166022. [PMID: 37541518 DOI: 10.1016/j.scitotenv.2023.166022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/22/2023] [Accepted: 08/01/2023] [Indexed: 08/06/2023]
Abstract
Hormesis (low-dose stimulation and high-dose inhibition) can be accompanied by hormetic trade-offs, that is, stimulation of some traits and inhibition (trade-off 1) or invariability (trade-off 2) of others. Currently, trade-off options and their biological significance are insufficiently studied. Therefore, the review analyses trade-off types, their relationship with asynchronous stress responses of indicators, the importance of trade-offs for preconditioning, hormesis transgenerational effects, fitness, and evolution. The analysis has shown that hormetic trade-offs 1 and 2 can be observed in evolutionarily distant groups of organisms and at different biological levels (cells, individuals, populations, and communities) with abiotic and biotic stressors, as well as various pollutants. Trade-offs 1 and 2 are found both between different functional traits (e.g., self-maintenance and reproduction in animals, growth and defense in plants), and between the endpoints of the same functional trait (e.g., seed weight and seed number in plants). Asynchronous responses of indicators to a low-dose stressor can lead to hormetic trade-offs in two cases: 1) these indicators have different responses (hormesis, inhibition or zero reaction) in the same dose range; 2) these indicators have hormetic responses with different hormetic zones. Trade-offs can have a positive, negative or zero effect on preconditioning, offspring, and fitness of the population. Trade-offs can potentially affect evolution in two ways: 1) the creation of trends in genotype selection; 2) participation in the assimilation of phenotypic adaptations in the genotype through the Baldwin effect (selection of mutations copying adaptive phenotypes).
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Affiliation(s)
- Elena A Erofeeva
- Department of Ecology, Institute of Biology and Biomedicine, Lobachevsky State University of Nizhni Novgorod, 23 Gagarina Pr, Nizhni Novgorod 603950, Russian Federation.
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10
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Zhang J, Peng Q, Ma C, Wang J, Xiao C, Li T, Liu X, Zhou L, Xu X, Zhou WZ, Ding W, An NA, Zhang L, Liu Y, Li CY. 6mA-Sniper: Quantifying 6mA sites in eukaryotes at single-nucleotide resolution. SCIENCE ADVANCES 2023; 9:eadh7912. [PMID: 37862411 PMCID: PMC10588941 DOI: 10.1126/sciadv.adh7912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 09/18/2023] [Indexed: 10/22/2023]
Abstract
While N6-methyldeoxyadenine (6mA) modification is a fundamental regulation in prokaryotes, its prevalence and functions in eukaryotes are controversial. Here, we report 6mA-Sniper to quantify 6mA sites in eukaryotes at single-nucleotide resolution, and delineate a 6mA profile in Caenorhabditis elegans with 2034 sites. Twenty-six of 39 events with Mnl I restriction endonuclease sites were verified, demonstrating the feasibility of this method. The levels of 6mA sites pinpointed by 6mA-Sniper are generally increased after Pseudomonas aeruginosa infection, but decreased in strains with the removal of METL-9, the dominant 6mA methyltransferase. The enrichment of these sites on specific motif of [GC]GAG, the selective constrains on them, and their coordinated changes with METL-9 levels thus support an active shaping of the 6mA profile by methyltransferase. Moreover, for regions marked by 6mA sites that emerged after infection, an enrichment of up-regulated genes was detected, possibly mediated through a mutual exclusive cross-talk between 6mA and H3K27me3 modification. We thus highlight 6mA regulation as a previously neglected regulator in eukaryotes.
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Affiliation(s)
- Jie Zhang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Qi Peng
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Chengchuan Ma
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Beijing Advanced Innovation Center for Genomics, Beijing 100871, China
| | - Jiaxin Wang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Chunfu Xiao
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Ting Li
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Xiaoge Liu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Liankui Zhou
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xinwei Xu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Wei-Zhen Zhou
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wanqiu Ding
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
- Bioinformatics Core, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Ni A. An
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Li Zhang
- Chinese Institute for Brain Research, Beijing, China
| | - Ying Liu
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Beijing Advanced Innovation Center for Genomics, Beijing 100871, China
| | - Chuan-Yun Li
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
- Chinese Institute for Brain Research, Beijing, China
- Southwest United Graduate School, Kunming 650092, China
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11
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Emerson FJ, Lee SS. Chromatin: the old and young of it. Front Mol Biosci 2023; 10:1270285. [PMID: 37877123 PMCID: PMC10591336 DOI: 10.3389/fmolb.2023.1270285] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/20/2023] [Indexed: 10/26/2023] Open
Abstract
Aging affects nearly all aspects of our cells, from our DNA to our proteins to how our cells handle stress and communicate with each other. Age-related chromatin changes are of particular interest because chromatin can dynamically respond to the cellular and organismal environment, and many modifications at chromatin are reversible. Changes at chromatin occur during aging, and evidence from model organisms suggests that chromatin factors could play a role in modulating the aging process itself, as altering proteins that work at chromatin often affect the lifespan of yeast, worms, flies, and mice. The field of chromatin and aging is rapidly expanding, and high-resolution genomics tools make it possible to survey the chromatin environment or track chromatin factors implicated in longevity with precision that was not previously possible. In this review, we discuss the state of chromatin and aging research. We include examples from yeast, Drosophila, mice, and humans, but we particularly focus on the commonly used aging model, the worm Caenorhabditis elegans, in which there are many examples of chromatin factors that modulate longevity. We include evidence of both age-related changes to chromatin and evidence of specific chromatin factors linked to longevity in core histones, nuclear architecture, chromatin remodeling, and histone modifications.
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Affiliation(s)
| | - Siu Sylvia Lee
- Lee Lab, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
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12
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Ma C, Xue T, Peng Q, Zhang J, Guan J, Ding W, Li Y, Xia P, Zhou L, Zhao T, Wang S, Quan L, Li CY, Liu Y. A novel N 6-Deoxyadenine methyltransferase METL-9 modulates C. elegans immunity via dichotomous mechanisms. Cell Res 2023; 33:628-639. [PMID: 37271765 PMCID: PMC10397248 DOI: 10.1038/s41422-023-00826-y] [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: 10/27/2022] [Accepted: 05/09/2023] [Indexed: 06/06/2023] Open
Abstract
N6-Methyldeoxyadenine (6mA) has been rediscovered as a DNA modification with potential biological function in metazoans. However, the physiological function and regulatory mechanisms regarding the establishment, maintenance and removal of 6mA in eukaryotes are still poorly understood. Here we show that genomic 6mA levels change in response to pathogenic infection in Caenorhabditis elegans (C. elegans). We further identify METL-9 as the methyltransferase that catalyzes DNA 6mA modifications upon pathogen infection. Deficiency of METL-9 impairs the induction of innate immune response genes and renders the animals more susceptible to pathogen infection. Interestingly, METL-9 functions through both 6mA-dependent and -independent mechanisms to transcriptionally regulate innate immunity. Our findings reveal that 6mA is a functional DNA modification in immunomodulation in C. elegans.
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Affiliation(s)
- Chengchuan Ma
- State Key Laboratory of Membrane Biology, New Cornerstone Science Laboratory, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- Beijing Advanced Innovation Center for Genomics, Beijing, China.
- Research Center for Stem Cell and Regenerative Medicine, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan, China.
| | - Tingling Xue
- State Key Laboratory of Membrane Biology, New Cornerstone Science Laboratory, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Qi Peng
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jie Zhang
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jialiang Guan
- State Key Laboratory of Membrane Biology, New Cornerstone Science Laboratory, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- PKU-Tsinghua-NIBS Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Wanqiu Ding
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Yi Li
- State Key Laboratory of Membrane Biology, New Cornerstone Science Laboratory, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Peixue Xia
- State Key Laboratory of Membrane Biology, New Cornerstone Science Laboratory, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Liankui Zhou
- State Key Laboratory of Membrane Biology, New Cornerstone Science Laboratory, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Tianyu Zhao
- State Key Laboratory of Membrane Biology, New Cornerstone Science Laboratory, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Sheng Wang
- Shanghai Zelixir Biotech Company Ltd., Shanghai, China
| | - Li Quan
- State Key Laboratory of Membrane Biology, New Cornerstone Science Laboratory, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Chuan-Yun Li
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China.
| | - Ying Liu
- State Key Laboratory of Membrane Biology, New Cornerstone Science Laboratory, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- Beijing Advanced Innovation Center for Genomics, Beijing, China.
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13
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Mc Auley MT. An evolutionary perspective of lifespan and epigenetic inheritance. Exp Gerontol 2023; 179:112256. [PMID: 37460026 DOI: 10.1016/j.exger.2023.112256] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 07/04/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023]
Abstract
In the last decade epigenetics has come to the fore as a discipline which is central to biogerontology. Age associated epigenetic changes are routinely linked with pathologies, including cardiovascular disease, cancer, and Alzheimer's disease; moreover, epigenetic clocks are capable of correlating biological age with chronological age in many species including humans. Recent intriguing empirical observations also suggest that inherited epigenetic effects could influence lifespan/longevity in a variety of organisms. If this is the case, an imperative exists to reconcile lifespan/longevity associated inherited epigenetic processes with the evolution of ageing. This review will critically evaluate inherited epigenetic effects from an evolutionary perspective. The overarching aim is to integrate the evidence which suggests epigenetic inheritance modulates lifespan/longevity with the main evolutionary theories of ageing.
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Xu F, Li R, von Gromoff ED, Drepper F, Knapp B, Warscheid B, Baumeister R, Qi W. Reprogramming of the transcriptome after heat stress mediates heat hormesis in Caenorhabditis elegans. Nat Commun 2023; 14:4176. [PMID: 37443152 PMCID: PMC10345090 DOI: 10.1038/s41467-023-39882-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Transient stress experiences not only trigger acute stress responses, but can also have long-lasting effects on cellular functions. In Caenorhabditis elegans, a brief exposure to heat shock during early adulthood extends lifespan and improves stress resistance, a phenomenon known as heat hormesis. Here, we investigated the prolonged effect of hormetic heat stress on the transcriptome of worms and found that the canonical heat shock response is followed by a profound transcriptional reprogramming in the post-stress period. This reprogramming relies on the endoribonuclease ENDU-2 but not the heat shock factor 1. ENDU-2 co-localizes with chromatin and interacts with RNA polymerase II, enabling specific regulation of transcription after the stress period. Failure to activate the post-stress response does not affect the resistance of animals to heat shock but eliminates the beneficial effects of hormetic heat stress. In summary, our work discovers that the RNA-binding protein ENDU-2 mediates the long-term impacts of transient heat stress via reprogramming transcriptome after stress exposure.
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Affiliation(s)
- Fan Xu
- Bioinformatics and Molecular Genetics (Faculty of Biology), Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
| | - Ruoyao Li
- Bioinformatics and Molecular Genetics (Faculty of Biology), Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
| | - Erika D von Gromoff
- Bioinformatics and Molecular Genetics (Faculty of Biology), Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
| | - Friedel Drepper
- Biochemistry-Functional Proteomics, Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
| | - Bettina Knapp
- Biochemistry-Functional Proteomics, Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
| | - Bettina Warscheid
- Biochemistry-Functional Proteomics, Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
- Signalling Research Centers BIOSS and CIBSS, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
- Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, 97074, Würzburg, Germany
| | - Ralf Baumeister
- Bioinformatics and Molecular Genetics (Faculty of Biology), Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
- Signalling Research Centers BIOSS and CIBSS, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
- Center for Biochemistry and Molecular Cell Research (Faculty of Medicine), Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
| | - Wenjing Qi
- Bioinformatics and Molecular Genetics (Faculty of Biology), Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany.
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15
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Zheng J, Luo Z, Chiu K, Li Y, Yang J, Zhou Q, So KF, Wan QL. Lycium barbarum glycopetide prolong lifespan and alleviate Parkinson's disease in Caenorhabditis elegans. Front Aging Neurosci 2023; 15:1156265. [PMID: 37469953 PMCID: PMC10353607 DOI: 10.3389/fnagi.2023.1156265] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/20/2023] [Indexed: 07/21/2023] Open
Abstract
Introduction Lycium barbarum glycopeptide (LbGp) is the main bioactive compound extracted from the traditional Chinese medicine. L. barbarum berries and has been proven to have numerous health benefits, including antioxidative, anti-inflammatory, anticancer, and cytoprotective activities. However, the antiaging effect of LbGp remains unknown. Methods The lifespan and body movement of C. elegans were used to evaluate the effect of LbGp on lifespan and health span. The thrashing assay was used to determine the role of LbGp in Parkinson's disease. To investigate the mechanisms of LbGp-induced antiaging effects, we analyzed changes in lifespan, movement, and the expression of longevity-related genes in a series of worm mutants after LbGp treatment. Results We found that LbGp treatment prolonged the lifespan and health span of C. elegans. Mechanistically, we found that LbGp could activate the transcription factors DAF-16/FOXO, SKN-1/Nrf2, and HSF-1, as well as the nuclear receptor DAF-12, thereby upregulating longevity-related genes to achieve lifespan extension. In addition, we found that the lifespan extension induced by LbGp partially depends on mitochondrial function. Intriguingly, LbGp also ameliorated neurodegenerative diseases such as Parkinson's disease in a DAF-16-, SKN-1-, and HSF-1-dependent manner. Conclusion Our work suggests that LbGp might be a viable candidate for the treatment and prevention of aging and age-related diseases.
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Affiliation(s)
- Jingming Zheng
- Department of Pathogen Biology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Zhenhuan Luo
- Department of Pathogen Biology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Kin Chiu
- State Key Lab of Brain and Cognitive Sciences, Department of Psychology, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Yimin Li
- Department of Pathogen Biology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Jing Yang
- Faculty of Medical Science, The Biomedical Translational Research Institute, Jinan University, Guangzhou, Guangdong, China
| | - Qinghua Zhou
- Faculty of Medical Science, The Biomedical Translational Research Institute, Jinan University, Guangzhou, Guangdong, China
| | - Kwok-Fai So
- Guangdong-Hongkong-Macau Institute of Central Nervous System (CNS) Regeneration, Ministry of Education Central Nervous System (CNS) Regeneration Collaborative Joint Laboratory, Jinan University, Guangzhou, Guangdong, China
| | - Qin-Li Wan
- Department of Pathogen Biology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
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16
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Wu T, He C. 6mA-METL-9 axis regulates innate immunity in C. elegans. Cell Res 2023:10.1038/s41422-023-00837-9. [PMID: 37337028 PMCID: PMC10397307 DOI: 10.1038/s41422-023-00837-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Affiliation(s)
- Tong Wu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
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17
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Mao F, Xie H, Shi Y, Jiang S, Wang S, Wu Y. The Global Changes of N6-methyldeoxyadenosine in Response to Low Temperature in Arabidopsis thaliana and Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:2373. [PMID: 37375998 DOI: 10.3390/plants12122373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023]
Abstract
N6-methyldeoxyadenosine (6mA) is a recently discovered DNA modification involved in regulating plant adaptation to abiotic stresses. However, the mechanisms and changes of 6mA under cold stress in plants are not yet fully understood. Here, we conducted a genome-wide analysis of 6mA and observed that 6mA peaks were predominantly present within the gene body regions under both normal and cold conditions. In addition, the global level of 6mA increased both in Arabidopsis and rice after the cold treatment. The genes that exhibited an up-methylation showed enrichment in various biological processes, whereas there was no significant enrichment observed among the down-methylated genes. The association analysis revealed a positive correlation between the 6mA level and the gene expression level. Joint analysis of the 6mA methylome and transcriptome of Arabidopsis and rice unraveled that fluctuations in 6mA levels caused by cold exposure were not correlated to changes in transcript levels. Furthermore, we discovered that orthologous genes modified by 6mA showed high expression levels; however, only a minor amount of differentially 6mA-methylated orthologous genes were shared between Arabidopsis and rice under low-temperature conditions. In conclusion, our study provides information on the role of 6mA in response to cold stress and reveals its potential for regulating the expression of stress-related genes.
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Affiliation(s)
- Fei Mao
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Hairong Xie
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Yucheng Shi
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Shasha Jiang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuai Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Yufeng Wu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
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18
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Zhang Y, Zhou Y, Kan D, Yang Y, Shen J, Han C, Liu X, Yang J. m6A-mediated nonhomologous end joining (NHEJ) pathway regulates senescence in Brachionus plicatilis (Rotifera). Arch Gerontol Geriatr 2023; 111:104994. [PMID: 36963346 DOI: 10.1016/j.archger.2023.104994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/23/2023] [Accepted: 03/06/2023] [Indexed: 03/14/2023]
Abstract
Epigenetic modifications play an important role in the regulation of senescence. N6-methyladenosine (m6A) is the most abundant modification of mRNA. However, the impact of m6A on senescence remains largely unknown at the animal individual level. Standard model organisms Caenorhabditis elegans and Drosophila melanogaster lack many gene homologs of vertebrate m6A system that are present in other invertebrates. In this study, we employed a small aquatic invertebrate Brachionus plicatilis which has been used in aging studies for nearly 100 years to study how m6A affects aging. Phylogenetic analysis confirmed that rotifers' m6A pathway has a conserved methyltransferase complex but no demethylases and the m6A reading system was more akin to that of vertebrates than that of D. melanogaster. m6A methyltransferases are highly expressed during development but reduces dramatically during aging. Knockdown of METTL3 results in decreased fecundity and premature senescence of rotifers. Furthermore, RT-qPCR analysis indicates a role for m6A in the nonhomologous end joining (NHEJ) pathway of DNA double-strand breaks (DSBs) repair. Altogether, our work reveals a senescence regulatory model for the rotifer METTL3-m6A-NHEJ pathway.
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Affiliation(s)
- Yu Zhang
- School of Marine Science and Engineering, Nanjing Normal University, No. 2 Xuelin Rd, Nanjing 210023, People's Republic of China
| | - Yang Zhou
- School of Marine Science and Engineering, Nanjing Normal University, No. 2 Xuelin Rd, Nanjing 210023, People's Republic of China
| | - Dongqi Kan
- School of Marine Science and Engineering, Nanjing Normal University, No. 2 Xuelin Rd, Nanjing 210023, People's Republic of China
| | - Yunhong Yang
- School of Marine Science and Engineering, Nanjing Normal University, No. 2 Xuelin Rd, Nanjing 210023, People's Republic of China
| | - Jing Shen
- School of Marine Science and Engineering, Nanjing Normal University, No. 2 Xuelin Rd, Nanjing 210023, People's Republic of China
| | - Cui Han
- School of Marine Science and Engineering, Nanjing Normal University, No. 2 Xuelin Rd, Nanjing 210023, People's Republic of China
| | - Xiaojie Liu
- School of Marine Science and Engineering, Nanjing Normal University, No. 2 Xuelin Rd, Nanjing 210023, People's Republic of China
| | - Jiaxin Yang
- School of Marine Science and Engineering, Nanjing Normal University, No. 2 Xuelin Rd, Nanjing 210023, People's Republic of China.
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19
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Zhao Y, Hua X, Rui Q, Wang D. Exposure to multi-walled carbon nanotubes causes suppression in octopamine signal associated with transgenerational toxicity induction in C.elegans. CHEMOSPHERE 2023; 318:137986. [PMID: 36716936 DOI: 10.1016/j.chemosphere.2023.137986] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/26/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Multi-walled carbon nanotube (MWCNT), a kind of carbon-based nanomaterials, has been extensively utilized in a variety of fields. In Caenorhabditis elegans, MWCNT exposure can result in toxicity not only at parental generation (P0-G) but also in the offspring. However, the underlying mechanisms remain still largely unknown. DAF-12, a transcriptional factor (TF), was previously found to be activated and involved in transgenerational toxicity control after MWCNT exposure. In this study, we observed that exposure to 0.1-10 μg/L MWCNTs caused the significant decrease in expression of tbh-1 encoding a tyramine beta-hydroxylase with the function to govern the octopamine synthesis, suggesting the inhibition in octopamine signal. After exposure to 0.1 μg/L MWCNT, the decrease in tbh-1 expression could be also detected in F1-G and F2-G. Moreover, in germline cells, the TF DAF-12 regulated transgenerational MWCNT toxicity by suppressing expression and function of TBH-1. Meanwhile, exposure to 0.1-10 μg/L MWCNTs induced the increase in octr-1 expression and the decrease in ser-6 expression. After exposure to 0.1 μg/L MWCNT, the increased octr-1 expression and the decreased ser-6 expression were further observed in F1-G and F2-G. Germline TBH-1 controlled transgenerational MWCNT toxicity by regulating the activity of octopamine receptors (SER-6 and OCTR-1) in offspring. Furthermore, in the offspring, SER-6 and OCTR-1 affected the induction of MWCNT toxicity by upregulating or downregulating the level of ELT-2, a GATA TF. Taken together, these findings suggested possible link between alteration in octopamine related signals and MWCNT toxicity induction in offspring in organisms.
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Affiliation(s)
- Yingyue Zhao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xin Hua
- Medical School, Southeast University, Nanjing, China
| | - Qi Rui
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China.
| | - Dayong Wang
- Medical School, Southeast University, Nanjing, China
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20
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Croft JC, Colunga A, Solh L, Dillon MK, Lee TWS. Pharyngeal pumping rate does not reflect lifespan extension in C. elegans transgenerational longevity mutants. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000719. [PMID: 36793895 PMCID: PMC9923420 DOI: 10.17912/micropub.biology.000719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/22/2023] [Accepted: 01/25/2023] [Indexed: 02/17/2023]
Abstract
Epigenetic modifications must be reprogrammed with each new generation. In Caenorhabditis elegans , defects in histone methylation reprogramming allow for the transgenerational acquisition of longevity. For example, mutations in the putative H3K9 demethylase JHDM-1 extend lifespan after six to ten generations. We noticed that long-lived jhdm-1 mutants appear healthier than wild-type animals from the same generation. To quantify health, we compared the common metric of pharyngeal pumping rate at specific adult ages between early-gen populations with normal lifespans and late-gen populations with long lifespans. Longevity did not affect pumping rate, but long-lived mutants stop pumping at a younger age, suggesting a possible conservation of energy to extend lifespan.
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Affiliation(s)
- Jaime C. Croft
- Department of Biological Sciences, University of Massachusetts Lowell, MA, USA
| | - Arthur Colunga
- Department of Biological Sciences, University of Massachusetts Lowell, MA, USA
| | - Lea Solh
- Department of Biological Sciences, University of Massachusetts Lowell, MA, USA
| | - Michaela K. Dillon
- Department of Biological Sciences, University of Massachusetts Lowell, MA, USA
| | - Teresa Wei-sy Lee
- Department of Biological Sciences, University of Massachusetts Lowell, MA, USA
,
Correspondence to: Teresa Wei-sy Lee (
)
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21
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Jiang Z, El-Brolosy MA, Serobyan V, Welker JM, Retzer N, Dooley CM, Jakutis G, Juan T, Fukuda N, Maischein HM, Balciunas D, Stainier DY. Parental mutations influence wild-type offspring via transcriptional adaptation. SCIENCE ADVANCES 2022; 8:eabj2029. [PMID: 36427314 PMCID: PMC9699682 DOI: 10.1126/sciadv.abj2029] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Transgenerational epigenetic inheritance (TEI) is mostly discussed in the context of physiological or environmental factors. Here, we show intergenerational and transgenerational inheritance of transcriptional adaptation (TA), a process whereby mutant messenger RNA (mRNA) degradation affects gene expression, in nematodes and zebrafish. Wild-type offspring of animals heterozygous for mRNA-destabilizing alleles display increased expression of adapting genes. Notably, offspring of animals heterozygous for nontranscribing alleles do not display this response. Germline-specific mutations are sufficient to induce TA in wild-type offspring, indicating that, at least for some genes, mutations in somatic tissues are not necessary for this process. Microinjecting total RNA from germ cells of TA-displaying heterozygous zebrafish can trigger TA in wild-type embryos and in their progeny, suggesting a model whereby mutant mRNAs in the germline trigger a TA response that can be epigenetically inherited. In sum, this previously unidentified mode of TEI reveals a means by which parental mutations can modulate the offspring's transcriptome.
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Affiliation(s)
- Zhen Jiang
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
| | - Mohamed A. El-Brolosy
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany
| | - Vahan Serobyan
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
| | - Jordan M. Welker
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany
| | - Nicholas Retzer
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany
| | - Christopher M. Dooley
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany
| | - Gabrielius Jakutis
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany
| | - Thomas Juan
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany
| | - Nana Fukuda
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany
| | - Hans-Martin Maischein
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany
| | - Darius Balciunas
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, USA
- Life Sciences Centre, Vilnius University, Vilnius, Lithuania
| | - Didier Y.R. Stainier
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
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22
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Murray KO, Clanton TL, Horowitz M. Epigenetic responses to heat: From adaptation to maladaptation. Exp Physiol 2022; 107:1144-1158. [PMID: 35413138 PMCID: PMC9529784 DOI: 10.1113/ep090143] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 03/25/2022] [Indexed: 11/08/2022]
Abstract
NEW FINDINGS What is the topic of this review? This review outlines the history of research on epigenetic adaptations to heat exposure. The perspective taken is that adaptations reflect properties of hormesis, whereby low, repeated doses of heat induce adaptation (acclimation/acclimatization); whereas brief, life-threatening exposures can induce maladaptive responses. What advances does it highlight? The epigenetic mechanisms underlying acclimation/acclimatization comprise specific molecular programmes on histones that regulate heat shock proteins transcriptionally and protect the organism from subsequent heat exposures, even after long delays. The epigenetic signalling underlying maladaptive responses might rely, in part, on extensive changes in DNA methylation that are sustained over time and might contribute to later health challenges. ABSTRACT Epigenetics plays a strong role in molecular adaptations to heat by producing a molecular memory of past environmental exposures. Moderate heat, over long periods of time, induces an 'adaptive' epigenetic memory, resulting in a condition of 'resilience' to future heat exposures or cross-tolerance to other forms of toxic stress. In contrast, intense, life-threatening heat exposures, such as severe heat stroke, can result in a 'maladaptive' epigenetic memory that can place an organism at risk of later health complications. These cellular memories are coded by post-translational modifications of histones on the nucleosomes and/or by changes in DNA methylation. They operate by inducing changes in the level of gene transcription and therefore phenotype. The adaptive response to heat acclimation functions, in part, by facilitating transcription of essential heat shock proteins and exhibits a biphasic short programme (maintaining DNA integrity, followed by a long-term consolidation). The latter accelerates acclimation responses after de-acclimation. Although less studied, the maladaptive responses to heat stroke appear to be coded in long-lasting changes in DNA methylation near the promoter region of genes involved with basic cell function. Whether these memories are also encoded in histone modifications is not yet known. There is considerable evidence that both adaptive and maladaptive epigenetic responses to heat can be inherited, although most evidence comes from lower organisms. Future challenges include understanding the signalling mechanisms responsible and discovering new ways to promote adaptive responses while suppressing maladaptive responses to heat, as all life forms adapt to life on a warming planet.
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Affiliation(s)
- Kevin O. Murray
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Thomas L. Clanton
- Department of Applied Physiology and Kinesiology, University of Florida, Gainesville, FL, USA
| | - Michal Horowitz
- Laboratory of Environmental Physiology, Faculty of Dentistry, The Hebrew University of Jerusalem, Jerusalem, Israel
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23
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Luo Z, Dai W, Wang C, Ye Q, Zhou Q, Wan QL. Gene activation in Caenorhabditis elegans using the Campylobacter jejuni CRISPR-Cas9 feeding system. G3 (BETHESDA, MD.) 2022; 12:6563187. [PMID: 35377421 PMCID: PMC9157054 DOI: 10.1093/g3journal/jkac068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 03/18/2022] [Indexed: 11/30/2022]
Abstract
Clustered regularly interspaced palindromic repeats-based activation system, a powerful genetic manipulation technology, can modulate endogenous gene transcription in various organisms through fusing nuclease-deficient Cas9 to transcriptional regulatory domains. At present, this clustered regularly interspaced palindromic repeats-based activation system has been applied to activate gene expression by microinjection manner in Caenorhabditis elegans. However, this complicated and time-consuming injection manner is not suitable for efficient and high-throughput gene regulation with clustered regularly interspaced palindromic repeats-Cas9 system. Here, we engineered a Campylobacter jejun clustered regularly interspaced palindromic repeats-Cas9-based gene activation system through bacteria feeding technique to delivering gene-specific sgRNA in C. elegans. It enables to activate various endogenous genes efficiently, as well as induce the corresponding phenotypes with a more efficient and labor-saving manner. Collectively, our results demonstrated that our novel dCjCas9-based activation feeding system holds great promise and potential in C. elegans.
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Affiliation(s)
- Zhenhuan Luo
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital Affiliated with Jinan University), Jinan University, Guangzhou 510632, China
| | - Wenyu Dai
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital Affiliated with Jinan University), Jinan University, Guangzhou 510632, China
| | - Chongyang Wang
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital Affiliated with Jinan University), Jinan University, Guangzhou 510632, China
| | - Qunshan Ye
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital Affiliated with Jinan University), Jinan University, Guangzhou 510632, China
| | - Qinghua Zhou
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital Affiliated with Jinan University), Jinan University, Guangzhou 510632, China
| | - Qin-Li Wan
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital Affiliated with Jinan University), Jinan University, Guangzhou 510632, China
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24
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Pioglitazone Hydrochloride Extends the Lifespan of Caenorhabditis elegans by Activating DAF-16/FOXO- and SKN-1/NRF2-Related Signaling Pathways. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:8496063. [PMID: 35677109 PMCID: PMC9168093 DOI: 10.1155/2022/8496063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 05/10/2022] [Indexed: 11/17/2022]
Abstract
Pioglitazone hydrochloride (PGZ), a nuclear receptor peroxisome proliferator-activated receptor gamma (PPAR-γ) agonist, is a universally adopted oral agent for the treatment of type 2 diabetes (T2D). Previous studies reported that PGZ could ameliorate the symptoms of aging-related diseases and Alzheimer's disease. However, whether PGZ participates in aging regulation and the underlying mechanism remain undetermined. Here, we found that PGZ significantly prolonged the lifespan and healthspan of Caenorhabditis elegans (C. elegans). We found that a variety of age-related pathways and age-related genes are required for PGZ-induced lifespan extension. The transcription factors DAF-16/FOXO, HSF-1, and SKN-1/NRF2, as well as the nuclear receptors DAF-12 and NHR-49, all functioned in the survival advantage conferred by PGZ. Moreover, our results demonstrated that PGZ induced lifespan extension through the inhibition of insulin/insulin-like signaling (IIS) and reproductive signaling pathways, as well as the activation of dietary restriction- (DR-) related pathways. Additionally, our results also indicated that beneficial longevity mediated by PGZ is linked to its antioxidative activity. Our research may provide a basis for further research on PGZ, as an anti-T2D drug, to interfere with aging and reduce the incidence of age-related diseases in diabetic patients.
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25
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Sheng Y, Zhou M, You C, Dai X. Dynamics and biological relevance of epigenetic N6-methyladenine DNA modification in eukaryotic cells. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.08.109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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26
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Holcombe J, Weavers H. The role of preconditioning in the development of resilience: mechanistic insights. CURRENT OPINION IN TOXICOLOGY 2022. [DOI: 10.1016/j.cotox.2022.02.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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27
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Wan QL, Meng X, Wang C, Dai W, Luo Z, Yin Z, Ju Z, Fu X, Yang J, Ye Q, Zhang ZH, Zhou Q. Histone H3K4me3 modification is a transgenerational epigenetic signal for lipid metabolism in Caenorhabditis elegans. Nat Commun 2022; 13:768. [PMID: 35140229 PMCID: PMC8828817 DOI: 10.1038/s41467-022-28469-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/20/2022] [Indexed: 11/09/2022] Open
Abstract
As a major risk factor to human health, obesity presents a massive burden to people and society. Interestingly, the obese status of parents can cause progeny's lipid accumulation through epigenetic inheritance in multiple species. To date, many questions remain as to how lipid accumulation leads to signals that are transmitted across generations. In this study, we establish a nematode model of C. elegans raised on a high-fat diet (HFD) that leads to measurable lipid accumulation, which can transmit the lipid accumulation signal to their multigenerational progeny. Using this model, we find that transcription factors DAF-16/FOXO and SBP-1/SREBP, nuclear receptors NHR-49 and NHR-80, and delta-9 desaturases (fat-5, fat-6, and fat-7) are required for transgenerational lipid accumulation. Additionally, histone H3K4 trimethylation (H3K4me3) marks lipid metabolism genes and increases their transcription response to multigenerational obesogenic effects. In summary, this study establishes an interaction between a network of lipid metabolic genes and chromatin modifications, which work together to achieve transgenerational epigenetic inheritance of obesogenic effects.
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Affiliation(s)
- Qin-Li Wan
- The Sixth Affiliated Hospital of Jinan University, Jinan University, Dongguan, 523560, Guangdong, China.,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, 510632, Guangdong, China.,Department of Pathogen Biology, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Xiao Meng
- The Sixth Affiliated Hospital of Jinan University, Jinan University, Dongguan, 523560, Guangdong, China.,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Chongyang Wang
- The Sixth Affiliated Hospital of Jinan University, Jinan University, Dongguan, 523560, Guangdong, China.,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Wenyu Dai
- The Sixth Affiliated Hospital of Jinan University, Jinan University, Dongguan, 523560, Guangdong, China.,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Zhenhuan Luo
- The Sixth Affiliated Hospital of Jinan University, Jinan University, Dongguan, 523560, Guangdong, China.,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Zhinan Yin
- The Sixth Affiliated Hospital of Jinan University, Jinan University, Dongguan, 523560, Guangdong, China.,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Zhenyu Ju
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regeneration Medicine, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Xiaodie Fu
- The Sixth Affiliated Hospital of Jinan University, Jinan University, Dongguan, 523560, Guangdong, China.,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Jing Yang
- The Sixth Affiliated Hospital of Jinan University, Jinan University, Dongguan, 523560, Guangdong, China.,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Qunshan Ye
- The Sixth Affiliated Hospital of Jinan University, Jinan University, Dongguan, 523560, Guangdong, China.,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Zhan-Hui Zhang
- The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Qinghua Zhou
- The Sixth Affiliated Hospital of Jinan University, Jinan University, Dongguan, 523560, Guangdong, China. .,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, 510632, Guangdong, China.
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28
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Actin Contributes to the Hyperexpression of Baculovirus Polyhedrin (polh) and p10 as a Component of Transcription Initiation Complex (TIC). Viruses 2022; 14:v14010153. [PMID: 35062357 PMCID: PMC8779803 DOI: 10.3390/v14010153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/30/2021] [Accepted: 01/06/2022] [Indexed: 11/16/2022] Open
Abstract
Hyperexpression of polh and p10, two very late genes, is one of the remarkable characteristics in the baculovirus life cycle. However, the mechanisms underlying the hyperexpression of these two genes are still incompletely understood. In this study, actin was identified as a highly potential binding partner of polh and p10 promoters by conducting DNA pull-down and LC–MS/MS analyses. Inhibiting actin dynamics delayed and decreased the transcription of polh and p10. Actin interacted with viral RNA polymerase and transcription regulators, and the nuclear import of viral polymerase was inhibited with the disruption of actin dynamics. Simultaneously, the high enrichment of actin in polh and p10 promoters discovered via a chromatin immunoprecipitation (ChIP) assay indicated that actin was a component of the viral polymerase TIC. Moreover, overexpression of actin surprisingly upregulated the expression of luciferase (Luc) under the control of polh and p10 promoters. Taken together, actin participated in the hyperexpression of polh and p10 as a component of TIC. These results facilitate the promotion of the expression efficiency of foreign genes in the baculovirus expression vector system (BEVS).
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29
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Molecular insights into transgenerational inheritance of stress memory. J Genet Genomics 2021; 49:89-95. [PMID: 34923165 DOI: 10.1016/j.jgg.2021.11.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 11/23/2022]
Abstract
There is accumulating evidence to show that environmental stressors can regulate a variety of phenotypes in descendants through germline-mediated epigenetic inheritance. Studies of model organisms exposed to environmental cues (e.g., diet, heat stress, toxins) indicate that altered DNA methylations, histone modifications, or non-coding RNAs in the germ cells are responsible for the transgenerational effects. In addition, it has also become evident that maternal provision could provide a mechanism for the transgenerational inheritance of stress adaptations that result from ancestral environmental cues. However, how the signal of environmentally-induced stress response transmits from the soma to the germline, which may influence offspring fitness, remains largely elusive. Small RNAs could serve as signaling molecules that transmit between tissues and even across generations. Furthermore, a recent study revealed that neuronal mitochondrial perturbations induce a transgenerational induction of the mitochondrial unfolded protein response mediated by a Wnt-dependent increase in mitochondrial DNA levels. Here, we review recent work on the molecular mechanism by which parental experience can affect future generations and the importance of soma-to-germline signaling for transgenerational inheritance.
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30
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Le NQK, Ho QT. Deep transformers and convolutional neural network in identifying DNA N6-methyladenine sites in cross-species genomes. Methods 2021; 204:199-206. [PMID: 34915158 DOI: 10.1016/j.ymeth.2021.12.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 11/30/2021] [Accepted: 12/09/2021] [Indexed: 12/19/2022] Open
Abstract
As one of the most common post-transcriptional epigenetic modifications, N6-methyladenine (6 mA), plays an essential role in various cellular processes and disease pathogenesis. Therefore, accurately identifying 6 mA modifications is necessary for a deep understanding of cellular processes and other possible functional mechanisms. Although a few computational methods have been proposed, their respective models were developed with small training datasets. Hence, their practical application is quite limited in genome-wide detection. To overcome the existing limitations, we present a novel model based on transformer architecture and deep learning to identify DNA 6 mA sites from the cross-species genome. The model is constructed on a benchmark dataset and explored a feature derived from pre-trained transformer word embedding approaches. Subsequently, a convolutional neural network was employed to learn the generated features and generate the prediction outcomes. As a result, our predictor achieved excellent performance during independent test with the accuracy and Matthews correlation coefficient (MCC) of 79.3% and 0.58, respectively. Overall, its performance achieved better accuracy than the baseline models and significantly outperformed the existing predictors, demonstrating the effectiveness of our proposed hybrid framework. Furthermore, our model is expected to assist biologists in accurately identifying 6mAs and formulate the novel testable biological hypothesis. We also release source codes and datasets freely at https://github.com/khanhlee/bert-dna for front-end users.
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Affiliation(s)
- Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei 106, Taiwan; Research Center for Artificial Intelligence in Medicine, Taipei Medical University, Taipei 106, Taiwan; Translational Imaging Research Center, Taipei Medical University Hospital, Taipei 110, Taiwan.
| | - Quang-Thai Ho
- College of Information & Communication Technology, Can Tho University, Viet Nam; Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, 32003, Taiwan
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31
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Das S, Min S, Prahlad V. Gene bookmarking by the heat shock transcription factor programs the insulin-like signaling pathway. Mol Cell 2021; 81:4843-4860.e8. [PMID: 34648748 PMCID: PMC8642288 DOI: 10.1016/j.molcel.2021.09.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/09/2021] [Accepted: 09/17/2021] [Indexed: 12/13/2022]
Abstract
Maternal stress can have long-lasting epigenetic effects on offspring. To examine how epigenetic changes are triggered by stress, we examined the effects of activating the universal stress-responsive heat shock transcription factor HSF-1 in the germline of Caenorhabditis elegans. We show that, when activated in germ cells, HSF-1 recruits MET-2, the putative histone 3 lysine 9 (H3K9) methyltransferase responsible for repressive H3K9me2 (H3K9 dimethyl) marks in chromatin, and negatively bookmarks the insulin receptor daf-2 and other HSF-1 target genes. Increased H3K9me2 at these genes persists in adult progeny and shifts their stress response strategy away from inducible chaperone expression as a mechanism to survive stress and instead rely on decreased insulin/insulin growth factor (IGF-1)-like signaling (IIS). Depending on the duration of maternal heat stress exposure, this epigenetic memory is inherited by the next generation. Thus, paradoxically, HSF-1 recruits the germline machinery normally responsible for erasing transcriptional memory but, instead, establishes a heritable epigenetic memory of prior stress exposure.
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Affiliation(s)
- Srijit Das
- Department of Biology, Aging Mind and Brain Initiative, 143 Biology Building, Iowa City, IA 52242-1324, USA
| | - Sehee Min
- Department of Biology, Aging Mind and Brain Initiative, 143 Biology Building, Iowa City, IA 52242-1324, USA
| | - Veena Prahlad
- Department of Biology, Aging Mind and Brain Initiative, 143 Biology Building, Iowa City, IA 52242-1324, USA; Department of Biology, 143 Biology Building, Iowa City, IA 52242-1324, USA; Iowa Neuroscience Institute, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, Iowa City, IA 52242, USA.
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32
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Burton NO, Greer EL. Multigenerational epigenetic inheritance: Transmitting information across generations. Semin Cell Dev Biol 2021; 127:121-132. [PMID: 34426067 DOI: 10.1016/j.semcdb.2021.08.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 01/07/2023]
Abstract
Inherited epigenetic information has been observed to regulate a variety of complex organismal phenotypes across diverse taxa of life. This continually expanding body of literature suggests that epigenetic inheritance plays a significant, and potentially fundamental, role in inheritance. Despite the important role these types of effects play in biology, the molecular mediators of this non-genetic transmission of information are just now beginning to be deciphered. Here we provide an intellectual framework for interpreting these findings and how they can interact with each other. We also define the different types of mechanisms that have been found to mediate epigenetic inheritance and to regulate whether epigenetic information persists for one or many generations. The field of epigenetic inheritance is entering an exciting phase, in which we are beginning to understand the mechanisms by which non-genetic information is transmitted to, and deciphered by, subsequent generations to maintain essential environmental information without permanently altering the genetic code. A more complete understanding of how and when epigenetic inheritance occurs will advance our understanding of numerous different aspects of biology ranging from how organisms cope with changing environments to human pathologies influenced by a parent's environment.
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Affiliation(s)
- Nicholas O Burton
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK; Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
| | - Eric L Greer
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA.
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33
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Zhang X, Lv S, Luo Z, Hu Y, Peng X, Lv J, Zhao S, Feng J, Huang G, Wan QL, Liu J, Huang H, Luan B, Wang D, Zhao X, Lin Y, Zhou Q, Zhang ZN, Rong Z. MiniCAFE, a CRISPR/Cas9-based compact and potent transcriptional activator, elicits gene expression in vivo. Nucleic Acids Res 2021; 49:4171-4185. [PMID: 33751124 PMCID: PMC8053112 DOI: 10.1093/nar/gkab174] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/28/2021] [Accepted: 03/04/2021] [Indexed: 12/23/2022] Open
Abstract
CRISPR-mediated gene activation (CRISPRa) is a promising therapeutic gene editing strategy without inducing DNA double-strand breaks (DSBs). However, in vivo implementation of these CRISPRa systems remains a challenge. Here, we report a compact and robust miniCas9 activator (termed miniCAFE) for in vivo activation of endogenous target genes. The system relies on recruitment of an engineered minimal nuclease-null Cas9 from Campylobacter jejuni and potent transcriptional activators to a target locus by a single guide RNA. It enables robust gene activation in human cells even with a single DNA copy and is able to promote lifespan of Caenorhabditis elegans through activation of longevity-regulating genes. As proof-of-concept, delivered within an all-in-one adeno-associated virus (AAV), miniCAFE can activate Fgf21 expression in the liver and regulate energy metabolism in adult mice. Thus, miniCAFE holds great therapeutic potential against human diseases.
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Affiliation(s)
- Xin Zhang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Sihan Lv
- Department of Endocrinology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, China
| | - Zhenhuan Luo
- Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai 519000, China
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, China
| | - Yongfei Hu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Xin Peng
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jie Lv
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Shanshan Zhao
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jianqi Feng
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Guanjie Huang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Qin-Li Wan
- Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai 519000, China
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, China
| | - Jun Liu
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Hongxin Huang
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Bing Luan
- Department of Endocrinology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, China
| | - Dong Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Xiaoyang Zhao
- Department of Development, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Ying Lin
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Qinghua Zhou
- Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai 519000, China
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, China
| | - Zhen-Ning Zhang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zhili Rong
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
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