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Emerson FJ, Chiu C, Lin LY, Riedel CG, Zhu M, Lee SS. The chromatin factors SET-26 and HCF-1 oppose the histone deacetylase HDA-1 in longevity and gene regulation in C. elegans. Nat Commun 2024; 15:2320. [PMID: 38485937 PMCID: PMC10940595 DOI: 10.1038/s41467-024-46510-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 02/28/2024] [Indexed: 03/18/2024] Open
Abstract
SET-26, HCF-1, and HDA-1 are highly conserved chromatin factors with key roles in development and aging. Here we present mechanistic insights into how these factors regulate gene expression and modulate longevity in C. elegans. We show that SET-26 and HCF-1 cooperate to regulate a common set of genes, and both antagonize the histone deacetylase HDA-1 to limit longevity. HCF-1 localization at chromatin is largely dependent on functional SET-26, whereas SET-26 is only minorly affected by loss of HCF-1, suggesting that SET-26 could recruit HCF-1 to chromatin. HDA-1 opposes SET-26 and HCF-1 on the regulation of a subset of their common target genes and in longevity. Our findings suggest that SET-26, HCF-1, and HDA-1 comprise a mechanism to fine-tune gene expression and longevity and likely have important implications for the mechanistic understanding of how these factors function in diverse organisms, particularly in aging biology.
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Affiliation(s)
- Felicity J Emerson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Caitlin Chiu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Laura Y Lin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Christian G Riedel
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Ming Zhu
- National Institute of Biological Sciences, Beijing, China
| | - Siu Sylvia Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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2
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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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3
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Gaeta AL, Willicott K, Willicott CW, McKay LE, Keogh CM, Altman TJ, Kimble LC, Yarbrough AL, Caldwell KA, Caldwell GA. Mechanistic impacts of bacterial diet on dopaminergic neurodegeneration in a Caenorhabditis elegans α-synuclein model of Parkinson's disease. iScience 2023; 26:106859. [PMID: 37260751 PMCID: PMC10227375 DOI: 10.1016/j.isci.2023.106859] [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: 09/26/2022] [Revised: 04/03/2023] [Accepted: 05/08/2023] [Indexed: 06/02/2023] Open
Abstract
Failure of inherently protective cellular processes and misfolded protein-associated stress contribute to the progressive loss of dopamine (DA) neurons characteristic of Parkinson's disease (PD). A disease-modifying role for the microbiome has recently emerged in PD, representing an impetus to employ the soil-dwelling nematode, Caenorhabditis elegans, as a preclinical model to correlate changes in gene expression with neurodegeneration in transgenic animals grown on distinct bacterial food sources. Even under tightly controlled conditions, hundreds of differentially expressed genes and a robust neuroprotective response were discerned between clonal C. elegans strains overexpressing human alpha-synuclein in the DA neurons fed either one of only two subspecies of Escherichia coli. Moreover, this neuroprotection persisted in a transgenerational manner. Genetic analysis revealed a requirement for the double-stranded RNA (dsRNA)-mediated gene silencing machinery in conferring neuroprotection. In delineating the contribution of individual genes, evidence emerged for endopeptidase activity and heme-associated pathway(s) as mechanistic components for modulating dopaminergic neuroprotection.
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Affiliation(s)
- Anthony L. Gaeta
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Karolina Willicott
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Corey W. Willicott
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Luke E. McKay
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Candice M. Keogh
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Tyler J. Altman
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Logan C. Kimble
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Abigail L. Yarbrough
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Kim A. Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
- Center for Convergent Bioscience and Medicine, The University of Alabama, Tuscaloosa, AL 35487, USA
- Alabama Research Institute on Aging, The University of Alabama, Tuscaloosa, AL 35487, USA
- Department of Neurology, Center for Neurodegeneration and Experimental Therapeutics, Nathan Shock Center of Excellence for Basic Research in the Biology of Aging, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Guy A. Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
- Center for Convergent Bioscience and Medicine, The University of Alabama, Tuscaloosa, AL 35487, USA
- Department of Neurology, Center for Neurodegeneration and Experimental Therapeutics, Nathan Shock Center of Excellence for Basic Research in the Biology of Aging, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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4
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Xiao Y, Yee C, Zhao CZ, Martinez MAQ, Zhang W, Shen K, Matus DQ, Hammell C. An expandable FLP-ON::TIR1 system for precise spatiotemporal protein degradation in Caenorhabditis elegans. Genetics 2023; 223:iyad013. [PMID: 36722258 PMCID: PMC10319979 DOI: 10.1093/genetics/iyad013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/16/2023] [Indexed: 02/02/2023] Open
Abstract
The auxin-inducible degradation system has been widely adopted in the Caenorhabditis elegans research community for its ability to empirically control the spatiotemporal expression of target proteins. This system can efficiently degrade auxin-inducible degron (AID)-tagged proteins via the expression of a ligand-activatable AtTIR1 protein derived from A. thaliana that adapts target proteins to the endogenous C. elegans proteasome. While broad expression of AtTIR1 using strong, ubiquitous promoters can lead to rapid degradation of AID-tagged proteins, cell type-specific expression of AtTIR1 using spatially restricted promoters often results in less efficient target protein degradation. To circumvent this limitation, we have developed an FLP/FRT3-based system that functions to reanimate a dormant, high-powered promoter that can drive sufficient AtTIR1 expression in a cell type-specific manner. We benchmark the utility of this system by generating a number of tissue-specific FLP-ON::TIR1 drivers to reveal genetically separable cell type-specific phenotypes for several target proteins. We also demonstrate that the FLP-ON::TIR1 system is compatible with enhanced degron epitopes. Finally, we provide an expandable toolkit utilizing the basic FLP-ON::TIR1 system that can be adapted to drive optimized AtTIR1 expression in any tissue or cell type of interest.
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Affiliation(s)
- Yutong Xiao
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Callista Yee
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Chris Z Zhao
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Michael A Q Martinez
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Wan Zhang
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Kang Shen
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
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5
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Emerson FJ, Chiu C, Lin LY, Riedel CG, Zhu M, Lee SS. The chromatin factors SET-26 and HCF-1 oppose the histone deacetylase HDA-1 in longevity and gene regulation in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.531974. [PMID: 36993207 PMCID: PMC10055255 DOI: 10.1101/2023.03.20.531974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
SET-26, HCF-1, and HDA-1 are highly conserved chromatin factors with key roles in development and aging. Here we present mechanistic insights into how these factors regulate gene expression and modulate longevity in C. elegans. We show that SET-26 and HCF-1 cooperate to regulate a common set of genes, and both antagonize the histone deacetylase HDA-1 to limit longevity. We propose a model in which SET-26 recruits HCF-1 to chromatin in somatic cells, where they stabilize each other at the promoters of a subset of genes, particularly mitochondrial function genes, and regulate their expression. HDA-1 opposes SET-26 and HCF-1 on the regulation of a subset of their common target genes and in longevity. Our findings suggest that SET-26, HCF-1, and HDA-1 comprise a mechanism to fine-tune gene expression and longevity and likely have important implications for the mechanistic understanding of how these factors function in diverse organisms, particularly in aging biology.
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Affiliation(s)
- Felicity J. Emerson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Caitlin Chiu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Laura Y. Lin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Christian G. Riedel
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Ming Zhu
- National Institute of Biological Sciences, Beijing, China
| | - Siu Sylvia Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
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6
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Godbole AA, Gopalan S, Nguyen TK, Munden AL, Lui DS, Fanelli MJ, Vo P, Lewis CA, Spinelli JB, Fazzio TG, Walker AK. S-adenosylmethionine synthases specify distinct H3K4me3 populations and gene expression patterns during heat stress. eLife 2023; 12:e79511. [PMID: 36756948 PMCID: PMC9984191 DOI: 10.7554/elife.79511] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 02/07/2023] [Indexed: 02/10/2023] Open
Abstract
Methylation is a widely occurring modification that requires the methyl donor S-adenosylmethionine (SAM) and acts in regulation of gene expression and other processes. SAM is synthesized from methionine, which is imported or generated through the 1-carbon cycle (1 CC). Alterations in 1 CC function have clear effects on lifespan and stress responses, but the wide distribution of this modification has made identification of specific mechanistic links difficult. Exploiting a dynamic stress-induced transcription model, we find that two SAM synthases in Caenorhabditis elegans, SAMS-1 and SAMS-4, contribute differently to modification of H3K4me3, gene expression and survival. We find that sams-4 enhances H3K4me3 in heat shocked animals lacking sams-1, however, sams-1 cannot compensate for sams-4, which is required to survive heat stress. This suggests that the regulatory functions of SAM depend on its enzymatic source and that provisioning of SAM may be an important regulatory step linking 1 CC function to phenotypes in aging and stress.
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Affiliation(s)
- Adwait A Godbole
- Program in Molecular Medicine, UMASS Chan Medical SchoolWorcesterUnited States
| | - Sneha Gopalan
- Cancer Center, UMASS Chan Medical SchoolWorcesterUnited States
- Department of Molecular, Cell, and Cancer Biology, UMASS Chan Medical SchoolWorcesterUnited States
| | - Thien-Kim Nguyen
- Program in Molecular Medicine, UMASS Chan Medical SchoolWorcesterUnited States
| | - Alexander L Munden
- Program in Molecular Medicine, UMASS Chan Medical SchoolWorcesterUnited States
| | - Dominique S Lui
- Program in Molecular Medicine, UMASS Chan Medical SchoolWorcesterUnited States
| | - Matthew J Fanelli
- Program in Molecular Medicine, UMASS Chan Medical SchoolWorcesterUnited States
| | - Paula Vo
- Program in Molecular Medicine, UMASS Chan Medical SchoolWorcesterUnited States
| | - Caroline A Lewis
- Program in Molecular Medicine, UMASS Chan Medical SchoolWorcesterUnited States
| | - Jessica B Spinelli
- Program in Molecular Medicine, UMASS Chan Medical SchoolWorcesterUnited States
- Cancer Center, UMASS Chan Medical SchoolWorcesterUnited States
| | - Thomas G Fazzio
- Cancer Center, UMASS Chan Medical SchoolWorcesterUnited States
- Department of Molecular, Cell, and Cancer Biology, UMASS Chan Medical SchoolWorcesterUnited States
| | - Amy K Walker
- Program in Molecular Medicine, UMASS Chan Medical SchoolWorcesterUnited States
- Department of Molecular, Cell, and Cancer Biology, UMASS Chan Medical SchoolWorcesterUnited States
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7
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Fallet M, Blanc M, Di Criscio M, Antczak P, Engwall M, Guerrero Bosagna C, Rüegg J, Keiter SH. Present and future challenges for the investigation of transgenerational epigenetic inheritance. ENVIRONMENT INTERNATIONAL 2023; 172:107776. [PMID: 36731188 DOI: 10.1016/j.envint.2023.107776] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/18/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Epigenetic pathways are essential in different biological processes and in phenotype-environment interactions in response to different stressors and they can induce phenotypic plasticity. They encompass several processes that are mitotically and, in some cases, meiotically heritable, so they can be transferred to subsequent generations via the germline. Transgenerational Epigenetic Inheritance (TEI) describes the phenomenon that phenotypic traits, such as changes in fertility, metabolic function, or behavior, induced by environmental factors (e.g., parental care, pathogens, pollutants, climate change), can be transferred to offspring generations via epigenetic mechanisms. Investigations on TEI contribute to deciphering the role of epigenetic mechanisms in adaptation, adversity, and evolution. However, molecular mechanisms underlying the transmission of epigenetic changes between generations, and the downstream chain of events leading to persistent phenotypic changes, remain unclear. Therefore, inter-, (transmission of information between parental and offspring generation via direct exposure) and transgenerational (transmission of information through several generations with disappearance of the triggering factor) consequences of epigenetic modifications remain major issues in the field of modern biology. In this article, we review and describe the major gaps and issues still encountered in the TEI field: the general challenges faced in epigenetic research; deciphering the key epigenetic mechanisms in inheritance processes; identifying the relevant drivers for TEI and implement a collaborative and multi-disciplinary approach to study TEI. Finally, we provide suggestions on how to overcome these challenges and ultimately be able to identify the specific contribution of epigenetics in transgenerational inheritance and use the correct tools for environmental science investigation and biomarkers identification.
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Affiliation(s)
- Manon Fallet
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden; Department of Biochemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Rd, Oxford OX1 3QU, United Kingdom.
| | - Mélanie Blanc
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, INRAE, Palavas, France
| | - Michela Di Criscio
- Department of Organismal Biology, Uppsala University, Norbyv. 18A, 75236 Uppsala, Sweden
| | - Philipp Antczak
- University of Cologne, Faculty of Medicine and Cologne University Hospital, Center for Molecular Medicine Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, University of Cologne, Cologne, Germany
| | - Magnus Engwall
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden
| | | | - Joëlle Rüegg
- Department of Organismal Biology, Uppsala University, Norbyv. 18A, 75236 Uppsala, Sweden
| | - Steffen H Keiter
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden
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8
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Huang M, Hong M, Hou X, Zhu C, Chen D, Chen X, Guang S, Feng X. H3K9me1/2 methylation limits the lifespan of daf-2 mutants in C. elegans. eLife 2022; 11:74812. [PMID: 36125117 PMCID: PMC9514849 DOI: 10.7554/elife.74812] [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: 10/18/2021] [Accepted: 09/16/2022] [Indexed: 11/29/2022] Open
Abstract
Histone methylation plays crucial roles in the development, gene regulation, and maintenance of stem cell pluripotency in mammals. Recent work shows that histone methylation is associated with aging, yet the underlying mechanism remains unclear. In this work, we identified a class of putative histone 3 lysine 9 mono/dimethyltransferase genes (met-2, set-6, set-19, set-20, set-21, set-32, and set-33), mutations in which induce synergistic lifespan extension in the long-lived DAF-2 (insulin growth factor 1 [IGF-1] receptor) mutant in Caenorhabditis elegans. These putative histone methyltransferase plus daf-2 double mutants not only exhibited an average lifespan nearly three times that of wild-type animals and a maximal lifespan of approximately 100 days, but also significantly increased resistance to oxidative and heat stress. Synergistic lifespan extension depends on the transcription factor DAF-16 (FOXO). mRNA-seq experiments revealed that the mRNA levels of DAF-16 Class I genes, which are activated by DAF-16, were further elevated in the daf-2;set double mutants. Among these genes, tts-1, F35E8.7, ins-35, nhr-62, sod-3, asm-2, and Y39G8B.7 are required for the lifespan extension of the daf-2;set-21 double mutant. In addition, treating daf-2 animals with the H3K9me1/2 methyltransferase G9a inhibitor also extends lifespan and increases stress resistance. Therefore, investigation of DAF-2 and H3K9me1/2 deficiency-mediated synergistic longevity will contribute to a better understanding of the molecular mechanisms of aging and therapeutic applications.
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Affiliation(s)
- Meng Huang
- Department of Obstetrics and Gynecology, University of Science and Technology of China, Hefei, China
| | - Minjie Hong
- Department of Obstetrics and Gynecology, University of Science and Technology of China, Hefei, China
| | - Xinhao Hou
- Department of Obstetrics and Gynecology, University of Science and Technology of China, Hefei, China
| | - Chengming Zhu
- Department of Obstetrics and Gynecology, University of Science and Technology of China, Hefei, China
| | - Di Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Xiangyang Chen
- Department of Obstetrics and Gynecology, University of Science and Technology of China, Hefei, China
| | - Shouhong Guang
- Department of Obstetrics and Gynecology, University of Science and Technology of China, Hefei, China
| | - Xuezhu Feng
- Department of Obstetrics and Gynecology, University of Science and Technology of China, Hefei, China
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9
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Abstract
Cleavage under targets and release using nuclease (CUT&RUN) is a recently developed chromatin profiling technique that uses a targeted micrococcal nuclease cleavage strategy to obtain high-resolution binding profiles of protein factors or to map histones with specific post-translational modifications. Due to its high sensitivity, CUT&RUN allows quality binding profiles to be obtained with only a fraction of the starting material and sequencing depth typically required for other chromatin profiling techniques such as chromatin immunoprecipitation. Although CUT&RUN has been widely adopted in multiple model systems, it has rarely been utilized in Caenorhabditis elegans, a model system of great importance to genomic research. Cell dissociation techniques, which are required for this approach, can be challenging in C. elegans due to the toughness of the worm's cuticle and the sensitivity of the cells themselves. Here, we describe a robust CUT&RUN protocol for use in C. elegans to determine the genome-wide localization of protein factors and specific histone marks. With a simple protocol utilizing live, uncrosslinked tissue as the starting material, performing CUT&RUN in worms has the potential to produce physiologically relevant data at a higher resolution than chromatin immunoprecipitation. This protocol involves a simple dissociation step to uniformly permeabilize worms while avoiding sample loss or cell damage, resulting in high-quality CUT&RUN profiles with as few as 100 worms and detectable signal with as few as 10 worms. This represents a significant advancement over chromatin immunoprecipitation, which typically uses thousands or hundreds of thousands of worms for a single experiment. The protocols presented here provide a detailed description of worm growth, sample preparation, CUT&RUN workflow, library preparation for high-throughput sequencing, and a basic overview of data analysis, making CUT&RUN simple and accessible for any worm lab. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Growth and synchronization of C. elegans Basic Protocol 2: Worm dissociation, sample preparation, and optimization Basic Protocol 3: CUT&RUN chromatin profiling Alternate Protocol: Improving CUT&RUN signal using a secondary antibody Basic Protocol 4: CUT&RUN library preparation for Illumina high-throughput sequencing Basic Protocol 5: Basic data analysis using Linux.
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Affiliation(s)
- Felicity J. Emerson
- Department of Molecular Biology and Genetics, Cornell
University, Ithaca, NY, 14850
- Biomedical and Biological Sciences Ph.D. Program, Cornell
University, Ithaca, NY, 14850
| | - Siu Sylvia Lee
- Department of Molecular Biology and Genetics, Cornell
University, Ithaca, NY, 14850
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10
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Vogt G. Paradigm shifts in animal epigenetics: Research on non-model species leads to new insights into dependencies, functions and inheritance of DNA methylation. Bioessays 2022; 44:e2200040. [PMID: 35618444 DOI: 10.1002/bies.202200040] [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: 02/16/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/06/2022]
Abstract
Recent investigations with non-model species and whole-genome approaches have challenged several paradigms in animal epigenetics. They revealed that epigenetic variation in populations is not the mere consequence of genetic variation, but is a semi-independent or independent source of phenotypic variation, depending on mode of reproduction. DNA methylation is not positively correlated with genome size and phylogenetic position as earlier believed, but has evolved differently between and within higher taxa. Epigenetic marks are usually not completely erased in the zygote and germ cells as generalized from mouse, but often persist and can be transgenerationally inherited, making them evolutionarily relevant. Gene body methylation and promoter methylation are similar in vertebrates and invertebrates with well methylated genomes but transposon silencing through methylation is variable. The new data also suggest that animals use epigenetic mechanisms to cope with rapid environmental changes and to adapt to new environments. The main benefiters are asexual populations, invaders, sessile taxa and long-lived species.
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Affiliation(s)
- Günter Vogt
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
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11
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Takahashi Y, Shoura M, Fire A, Morishita S. Context-dependent DNA polymerization effects can masquerade as DNA modification signals. BMC Genomics 2022; 23:249. [PMID: 35361121 PMCID: PMC8973881 DOI: 10.1186/s12864-022-08471-2] [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: 05/13/2021] [Accepted: 03/15/2022] [Indexed: 11/23/2022] Open
Abstract
Background Single molecule measurements of DNA polymerization kinetics provide a sensitive means to detect both secondary structures in DNA and deviations from primary chemical structure as a result of modified bases. In one approach to such analysis, deviations can be inferred by monitoring the behavior of DNA polymerase using single-molecule, real-time sequencing with zero-mode waveguide. This approach uses a Single Molecule Real Time (SMRT)-sequencing measurement of time between fluorescence pulse signals from consecutive nucleosides incorporated during DNA replication, called the interpulse duration (IPD). Results In this paper we present an analysis of loci with high IPDs in two genomes, a bacterial genome (E. coli) and a eukaryotic genome (C. elegans). To distinguish the potential effects of DNA modification on DNA polymerization speed, we paired an analysis of native genomic DNA with whole-genome amplified (WGA) material in which DNA modifications were effectively removed. Adenine modification sites for E. coli are known and we observed the expected IPD shifts at these sites in the native but not WGA samples. For C. elegans, such differences were not observed. Instead, we found a number of novel sequence contexts where IPDs were raised relative to the average IPDs for each of the four nucleotides, but for which the raised IPD was present in both native and WGA samples. Conclusion The latter results argue strongly against DNA modification as the underlying driver for high IPD segments for C. elegans, and provide a framework for separating effects of DNA modification from context-dependent DNA polymerase kinetic patterns inherent in underlying DNA sequence for a complex eukaryotic genome. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08471-2.
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Affiliation(s)
- Yusuke Takahashi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Massa Shoura
- Departments of Pathology and Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Andrew Fire
- Departments of Pathology and Genetics, School of Medicine, Stanford University, Stanford, CA, USA.
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.
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12
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Zhang X, Jacobs D. OUP accepted manuscript. Genome Biol Evol 2022; 14:6519162. [PMID: 35104341 PMCID: PMC8857923 DOI: 10.1093/gbe/evab284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2021] [Indexed: 11/14/2022] Open
Abstract
DNA methylation, an important component of eukaryotic epigenetics, varies in pattern and function across Metazoa. Notably, bilaterian vertebrates and invertebrates differ dramatically in gene body methylation (GbM). Using the frequency of cytosine-phospho-guanines (CpGs), which are lost through mutation when methylated, we report the first broad survey of DNA methylation in Cnidaria, the ancient sister group to Bilateria. We find that: 1) GbM differentially relates to expression categories as it does in most bilaterian invertebrates, but distributions of GbM are less discretely bimodal. 2) Cnidarians generally have lower CpG frequencies on gene bodies than bilaterian invertebrates potentially suggesting a compensatory mechanism to replace CpG lost to mutation in Bilateria that is lacking in Cnidaria. 3) GbM patterns show some consistency within taxonomic groups such as the Scleractinian corals; however, GbM patterns variation across a range of taxonomic ranks in Cnidaria suggests active evolutionary change in GbM within Cnidaria. 4) Some but not all GbM variation is associated with life history change and genome expansion, whereas GbM loss is evident in endoparasitic cnidarians. 5) Cnidarian repetitive elements are less methylated than gene bodies, and methylation of both correlate with genome repeat content. 6) These observations reinforce claims that GbM evolved in stem Metazoa. Thus, this work supports overlap between DNA methylation processes in Cnidaria and Bilateria, provides a framework to compare methylation within and between Cnidaria and Bilateria, and demonstrates the previously unknown rapid evolution of cnidarian methylation.
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Affiliation(s)
- Xinhui Zhang
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
| | - David Jacobs
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
- Corresponding author: E-mail:
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13
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Hassanaly-Goulamhoussen R, De Carvalho Augusto R, Marteu-Garello N, Péré A, Favery B, Da Rocha M, Danchin EGJ, Abad P, Grunau C, Perfus-Barbeoch L. Chromatin Landscape Dynamics in the Early Development of the Plant Parasitic Nematode Meloidogyne incognita. Front Cell Dev Biol 2021; 9:765690. [PMID: 34938734 PMCID: PMC8685519 DOI: 10.3389/fcell.2021.765690] [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: 08/27/2021] [Accepted: 11/03/2021] [Indexed: 11/17/2022] Open
Abstract
In model organisms, epigenome dynamics underlies a plethora of biological processes. The role of epigenetic modifications in development and parasitism in nematode pests remains unknown. The root-knot nematode Meloidogyne incognita adapts rapidly to unfavorable conditions, despite its asexual reproduction. However, the mechanisms underlying this remarkable plasticity and their potential impact on gene expression remain unknown. This study provides the first insight into contribution of epigenetic mechanisms to this plasticity, by studying histone modifications in M. incognita. The distribution of five histone modifications revealed the existence of strong epigenetic signatures, similar to those found in the model nematode Caenorhabditis elegans. We investigated their impact on chromatin structure and their distribution relative to transposable elements (TE) loci. We assessed the influence of the chromatin landscape on gene expression at two developmental stages: eggs, and pre-parasitic juveniles. H3K4me3 histone modification was strongly correlated with high levels of expression for protein-coding genes implicated in stage-specific processes during M. incognita development. We provided new insights in the dynamic regulation of parasitism genes kept under histone modifications silencing. In this pioneering study, we establish a comprehensive framework for the importance of epigenetic mechanisms in the regulation of the genome expression and its stability in plant-parasitic nematodes.
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Affiliation(s)
| | - Ronaldo De Carvalho Augusto
- IHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, France.,Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard de Lyon, Université de Lyon, Lyon, France
| | | | - Arthur Péré
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Bruno Favery
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Martine Da Rocha
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | | | - Pierre Abad
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Christoph Grunau
- IHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, France
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14
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Li R, Tao M, Xu T, Pan S, Xu X, Wu T. Small berries as health-promoting ingredients: a review on anti-aging effects and mechanisms in Caenorhabditis elegans. Food Funct 2021; 13:478-500. [PMID: 34927654 DOI: 10.1039/d1fo02184b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Aging is an inevitable, irreversible, and complex process of damage accumulation and functional decline, increasing the risk of various chronic diseases. However, for now no drug can delay aging process nor cure aging-related diseases. Nutritional intervention is considered as a key and effective strategy to promote healthy aging and improve life quality. Small berries, as one of the most common and popular fruits, have been demonstrated to improve cognitive function and possess neuroprotective activities. However, the anti-aging effects of small berries have not been systematically elucidated yet. This review mainly focuses on small berries' anti-aging activity studies involving small berry types, active components, the utilized model organism Caenorhabditis elegans (C. elegans), related signaling pathways, and molecular mechanisms. The purpose of this review is to propose effective strategies to evaluate the anti-aging effects of small berries and provide guidance for the development of anti-aging supplements from small berries.
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Affiliation(s)
- Rong Li
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
| | - Mingfang Tao
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
| | - Tingting Xu
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
| | - Siyi Pan
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
| | - Xiaoyun Xu
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
| | - Ting Wu
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
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15
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Histone deacetylase HDA-4-mediated epigenetic regulation in space-flown C. elegans. NPJ Microgravity 2021; 7:33. [PMID: 34471121 PMCID: PMC8410859 DOI: 10.1038/s41526-021-00163-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/03/2021] [Indexed: 02/04/2023] Open
Abstract
Epigenetic changes during long-term spaceflight are beginning to be studied by NASA's twin astronauts and other model organisms. Here, we evaluate the epigenetic regulation of gene expression in space-flown C. elegans by comparing wild type and histone deacetylase (hda)-4 mutants. Expression levels of 39 genes were consistently upregulated in all four generations of adult hda-4 mutants grown under microgravity compared with artificial Earth-like gravity (1G). In contrast, in the wild type, microgravity-induced upregulation of these genes occurred a little. Among these genes, 11 contain the domain of unknown function 19 (DUF-19) and are located in a cluster on chromosome V. When compared with the 1G condition, histone H3 trimethylation at lysine 27 (H3K27me3) increased under microgravity in the DUF-19 containing genes T20D4.12 to 4.10 locus in wild-type adults. On the other hand, this increase was also observed in the hda-4 mutant, but the level was significantly reduced. The body length of wild-type adults decreased slightly but significantly when grown under microgravity. This decrease was even more pronounced with the hda-4 mutant. In ground-based experiments, one of the T20D4.11 overexpressing strains significantly reduced body length and also caused larval growth retardation and arrest. These results indicate that under microgravity, C. elegans activates histone deacetylase HDA-4 to suppress overregulation of several genes, including the DUF-19 family. In other words, the expression of certain genes, including negative regulators of growth and development, is epigenetically fine-tuned to adapt to the space microgravity.
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16
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Sen I, Kavšek A, Riedel CG. Chromatin Immunoprecipitation and Sequencing (ChIP-seq) Optimized for Application in Caenorhabditis elegans. Curr Protoc 2021; 1:e187. [PMID: 34242493 DOI: 10.1002/cpz1.187] [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] [Indexed: 11/07/2022]
Abstract
Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) has become one of the most popular methods to study protein-DNA interactions and can be used, for instance, to identify the binding sites of transcription factors or to determine the distributions of histones with specific post-translational modifications throughout the genome. Although standard ChIP-seq protocols work well in most experimental systems, there are exceptions, and one of these is the popular model organism Caenorhabditis elegans. Even though this system is very amenable to genetic and cytological methods, biochemical approaches are challenging. This is due to both the animals' cuticle, which impairs lysis as well as penetration by cross-linkers, and the rather low protein and chromatin content per body weight. These issues have rendered standard ChIP-seq protocols inefficient in C. elegans and raised a need for their improvement. Here, we describe improved protocols, with the most important advances being the efficient breakage of the C. elegans cuticle by freeze-grinding and the use of a very sensitive sequencing library construction procedure, optimized for the relatively low DNA content per body weight of C. elegans. The protocols should therefore improve the reproducibility, sensitivity, and uniformity across tissues of ChIP-seq in this organism. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Growth and harvesting of synchronized Caenorhabditis elegans Basic Protocol 2: Chromatin immunoprecipitation (ChIP) Basic Protocol 3: Library construction for Illumina sequencing.
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Affiliation(s)
- Ilke Sen
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Karolinska Institute, Huddinge, Sweden.,Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Alan Kavšek
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Karolinska Institute, Huddinge, Sweden.,Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Christian G Riedel
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Karolinska Institute, Huddinge, Sweden.,Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
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17
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Yu CW, Luk TC, Liao VHC. Long-term nanoplastics exposure results in multi and trans-generational reproduction decline associated with germline toxicity and epigenetic regulation in Caenorhabditis elegans. JOURNAL OF HAZARDOUS MATERIALS 2021; 412:125173. [PMID: 33517056 DOI: 10.1016/j.jhazmat.2021.125173] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/10/2021] [Accepted: 01/17/2021] [Indexed: 05/21/2023]
Abstract
The environmental risk from long-term plastic pollution is growing. We investigated the multi and trans-generational reproductive toxicity of nanoplastics (NPs) in Caenorhabditis elegans and the underlying mechanisms over five generations. Following a single maternal exposure (F0) to NPs (100 nm; 1, 10, 50, or 100 mg/L) for 72 h, the subsequent generations (F1-F4) were cultured under NPs-free conditions. We showed that the total brood size was significantly reduced across all offspring generations (F1-F4). NPs accumulated in the intestine of C. elegans in the F0 generation, but not in the germline system, and not observed in subsequent generations. Chromosomal aberrations in oocytes and germline cell apoptosis were significantly elevated in the NPs-exposed F0 generation and in subsequent unexposed generations. Likewise, the expression of ced-3 was increased across generations, regulated by hypomethylation in the promoter region of ced-3 after maternal NPs exposure. Finally, NPs exposure reduced the expression of epigenesis-related genes met-2, set-2, and spr-5 and the trans-generational effects of maternal NPs exposure were not observed in met-2, set-2, and spr-5 RNAi worms. We demonstrate that a single long-term maternal NPs exposure can cause multi and trans-generational reproduction decline in C. elegans, which may be associated with germline toxicity and epigenetic regulation.
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Affiliation(s)
- Chan-Wei Yu
- Department of Bioenvironmental Systems Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 106, Taiwan
| | - Tin Chi Luk
- Department of Bioenvironmental Systems Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 106, Taiwan
| | - Vivian Hsiu-Chuan Liao
- Department of Bioenvironmental Systems Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 106, Taiwan.
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18
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Kubota Y, Ohnishi Y, Hamasaki T, Yasui G, Ota N, Kitagawa H, Esaki A, Fahmi M, Ito M. Overlapping and non-overlapping roles of the class-I histone deacetylase-1 corepressors LET-418, SIN-3, and SPR-1 in Caenorhabditis elegans embryonic development. Genes Genomics 2021; 43:553-565. [PMID: 33740234 PMCID: PMC8110489 DOI: 10.1007/s13258-021-01076-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/01/2021] [Indexed: 01/15/2023]
Abstract
BACKGROUND Histone deacetylase (HDAC)-1, a Class-I HDAC family member, forms three types of complexes, the nucleosome remodeling deacetylase, Sin3, and CoREST complexes with the specific corepressor components chromodomain-helicase-DNA-binding protein 3 (Mi2/CHD-3), Sin3, and REST corepressor 1 (RCOR1), respectively, in humans. OBJECTIVE To elucidate the functional relationships among the three transcriptional corepressors during embryogenesis. METHODS The activities of HDA-1, LET-418, SIN-3, and SPR-1, the homologs of HDAC-1, Mi2, Sin3, and RCOR1 in Caenorhabditis elegans during embryogenesis were investigated through measurement of relative mRNA expression levels and embryonic lethality given either gene knockdown or deletion. Additionally, the terminal phenotypes of each knockdown and mutant embryo were observed using a differential-interference contrast microscope. Finally, the functional relationships among the three corepressors were examined through genetic interactions and transcriptome analyses. RESULTS Here, we report that each of the corepressors LET-418, SIN-3, and SPR-1 are expressed and have essential roles in C. elegans embryonic development. Our terminal phenotype observations of single mutants further implied that LET-418, SIN-3, and SPR-1 play similar roles in promoting advancement to the middle and late embryonic stages. Combined analysis of genetic interactions and gene ontology of these corepressors indicate a prominent overlapping role among SIN-3, SPR-1, and LET-418 and between SIN-3 and SPR-1. CONCLUSION Our findings suggest that the class-I HDAC-1 corepressors LET-418, SIN-3, and SPR-1 may cooperatively regulate the expression levels of some genes during C. elegans embryogenesis or may have some similar roles but functioning independently within a specific cell.
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Affiliation(s)
- Yukihiro Kubota
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Yuto Ohnishi
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Tasuku Hamasaki
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Gen Yasui
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Natsumi Ota
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Hiromu Kitagawa
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Arashi Esaki
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Muhamad Fahmi
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Masahiro Ito
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.
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19
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Nono M, Kishimoto S, Sato-Carlton A, Carlton PM, Nishida E, Uno M. Intestine-to-Germline Transmission of Epigenetic Information Intergenerationally Ensures Systemic Stress Resistance in C. elegans. Cell Rep 2021; 30:3207-3217.e4. [PMID: 32160530 DOI: 10.1016/j.celrep.2020.02.050] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 10/31/2019] [Accepted: 02/10/2020] [Indexed: 01/29/2023] Open
Abstract
Changes in epigenetic states affect organismal homeostasis, including stress resistance. However, the mechanisms coordinating epigenetic states and systemic stress resistance remain largely unknown. Here, we identify the intestine-to-germline communication of epigenetic states, which intergenerationally enhances stress resistance in C. elegans. The alterations in epigenetic states by deficiency of the histone H3K4me3 modifier ASH-2 in the intestine or germline increase organismal stress resistance, which is abrogated by knockdown of the H3K4 demethylase RBR-2. Remarkably, the increase in stress resistance induced by ASH-2 deficiency in the intestine is abrogated by RBR-2 knockdown in the germline, suggesting the intestine-to-germline transmission of epigenetic information. This communication from intestine to germline in the parental generation increases stress resistance in the next generation. Moreover, the intertissue communication is mediated partly by transcriptional regulation of F08F1.3. These results reveal that intertissue communication of epigenetic information provides mechanisms for intergenerational regulation of systemic stress resistance.
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Affiliation(s)
- Masanori Nono
- Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Saya Kishimoto
- Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Aya Sato-Carlton
- Laboratory of Chromosome Function and Inheritance, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Peter Mark Carlton
- Laboratory of Chromosome Function and Inheritance, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan; Laboratory of Chromosome Function and Inheritance, Radiation Biology Center, Kyoto University, Kyoto 606-8501, Japan
| | - Eisuke Nishida
- Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan.
| | - Masaharu Uno
- Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan.
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20
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Liu H, Kwak JI, Wang D, An YJ. Multigenerational effects of polyethylene terephthalate microfibers in Caenorhabditis elegans. ENVIRONMENTAL RESEARCH 2021; 193:110569. [PMID: 33275924 DOI: 10.1016/j.envres.2020.110569] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/25/2020] [Accepted: 11/28/2020] [Indexed: 06/12/2023]
Abstract
Microfibers (MFs) have recently become an increasingly prevalent pollutant in ecosystems and pose a direct threat to organisms and an indirect threat via adsorption of other pollutants. Here, we used Caenorhabditis elegans to study multigenerational effects of polyethylene terephthalate (PET) MFs (diameter 17.4 μm) by observing the maternal generation (P0) to the seventh offspring generation (F7) with continuous MF exposure. Exposure to 250-μm PET MFs decreased locomotion behavior and induced intestinal reactive oxygen species (ROS) in the P0 generation compared with other PET MF sizes. Moreover, no notably negative effects on survival were observed in any generation during continuous exposure to 250-μm PET MFs. However, the reproduction rate clearly decreased in the F2 and F3 generations but gradually recovered in the F4-F7 generations. Developmental abnormalities showed a close relationship with body length. Although some recovery was confirmed, there were significant decreases in body length in the F2-F5 generations. Interestingly, growth inhibition was also observed in the F6 generation without MF exposure. ROS production and dermal damage in the P0-F5 generations might have resulted in the toxicological responses. To the best of our knowledge, this is the first study to provide evidence of multigenerational toxicity of MFs in C. elegans.
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Affiliation(s)
- Huanliang Liu
- Key Laboratory of Environmental Medicine Engineering in Ministry of Education, Medical School, Southeast University, Nanjing, 210009, China
| | - Jin Il Kwak
- Department of Environmental Health Science, Konkuk University, Seoul, 05029, South Korea
| | - Dayong Wang
- Key Laboratory of Environmental Medicine Engineering in Ministry of Education, Medical School, Southeast University, Nanjing, 210009, China
| | - Youn-Joo An
- Department of Environmental Health Science, Konkuk University, Seoul, 05029, South Korea.
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21
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Tsurumi A, Li WX. Aging mechanisms-A perspective mostly from Drosophila. ADVANCED GENETICS (HOBOKEN, N.J.) 2020; 1:e10026. [PMID: 36619249 PMCID: PMC9744567 DOI: 10.1002/ggn2.10026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 04/04/2020] [Accepted: 04/08/2020] [Indexed: 01/11/2023]
Abstract
A mechanistic understanding of the natural aging process, which is distinct from aging-related disease mechanisms, is essential for developing interventions to extend lifespan or healthspan. Here, we discuss current trends in aging research and address conceptual and experimental challenges in the field. We examine various molecular markers implicated in aging with an emphasis on the role of heterochromatin and epigenetic changes. Studies in model organisms have been advantageous in elucidating conserved genetic and epigenetic mechanisms and assessing interventions that affect aging. We highlight the use of Drosophila, which allows controlled studies for evaluating genetic and environmental contributors to aging conveniently. Finally, we propose the use of novel methodologies and future strategies using Drosophila in aging research.
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Affiliation(s)
- Amy Tsurumi
- Department of SurgeryMassachusetts General Hospital, and Harvard Medical SchoolBostonMassachusettsUSA
- Department of Microbiology and ImmunologyHarvard Medical SchoolBostonMassachusettsUSA
- Shriners Hospitals for Children‐Boston®BostonMassachusettsUSA
| | - Willis X. Li
- Department of MedicineUniversity of California at San DiegoLa JollaCaliforniaUSA
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22
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Willis AR, Sukhdeo R, Reinke AW. Remembering your enemies: mechanisms of within-generation and multigenerational immune priming in Caenorhabditis elegans. FEBS J 2020; 288:1759-1770. [PMID: 32767821 DOI: 10.1111/febs.15509] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/17/2020] [Accepted: 07/30/2020] [Indexed: 12/12/2022]
Abstract
Pathogens are abundant and drive evolution of host immunity. Whilst immune memory is classically associated with adaptive immunity, studies in diverse species now show that priming of innate immune defences can also protect against secondary infection. Remarkably, priming may also be passed on to progeny to enhance pathogen resistance and promote survival in future generations. Phenotypic changes that occur independent of DNA sequence underlie both 'within-generation' priming and 'multigenerational' priming. However, the molecular mechanisms responsible for these phenomena are still poorly understood. Caenorhabditis elegans is a simple and genetically tractable model organism that has enabled key advances in immunity and environmental epigenetics. Using both natural and human pathogens, researchers have uncovered numerous examples of innate immune priming in this animal. Viral infection models have provided key evidence for a conserved antiviral RNA silencing mechanism that is inherited in progeny. Bacterial infection models have explored mechanisms of within-generation and multigenerational priming that span chromatin modification and transcriptional changes, small RNA pathways, maternal provisioning and pathogen avoidance strategies. Together, these studies are providing novel insight into the immune reactivity of the genome and have important consequences for our understanding of health and evolution. In this review, we present the current evidence for learned protection against pathogens in C. elegans, discuss the significance and limitations of these findings and highlight important avenues of future investigation.
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Affiliation(s)
| | - Ronesh Sukhdeo
- Department of Molecular Genetics, University of Toronto, ON, Canada
| | - Aaron W Reinke
- Department of Molecular Genetics, University of Toronto, ON, Canada
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23
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Barrere-Cain R, Allard P. An Understudied Dimension: Why Age Needs to Be Considered When Studying Epigenetic-Environment Interactions. Epigenet Insights 2020; 13:2516865720947014. [PMID: 32864568 PMCID: PMC7430070 DOI: 10.1177/2516865720947014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 07/06/2020] [Indexed: 02/02/2023] Open
Abstract
We live in a complex chemical environment where there are an estimated 350 000 chemical compounds or mixtures commercially produced. A strong body of literature shows that there are time points during early development when an organism’s epigenome is particularly sensitive to chemicals in its environment. What is less understood is how gene-environment and epigenetic-environment interactions change with age. This question is bidirectional: (1) how do chemicals in the environment affect the aging process and (2) how does aging affect an organism’s response to its chemical environment? The study of gene-environment interactions with age is especially important because, in many parts of the world, older individuals are a large and rapidly growing proportion of the population and because aging is a process universal to most of the animal kingdom. Epigenetics has emerged as a crucial framework for studying aging as epigenetic pathways, often triggered by environmental stimuli, have been shown to be essential regulators of the aging process. In this perspective article, we delineate the connection between aging, epigenetics, and environmental exposures. We discuss why it is essential to consider age when researching how an organism interacts with its environment. We describe recent advances in understanding how the chemical environment affects aging and the gap in research on how age affects an organism’s response to the environment. Finally, we highlight how model organisms and network approaches can help fill this crucial gap. Taken together, systemic changes that occur in the epigenome with age indicate that adult organisms cannot be treated as a homogeneous population and that there are discrete mechanisms modulating the aging epigenome that we do not yet understand.
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Affiliation(s)
- Rio Barrere-Cain
- Institute for Society & Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Patrick Allard
- Institute for Society & Genetics, University of California, Los Angeles, Los Angeles, CA, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
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24
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Mattout A, Gaidatzis D, Kalck V, Gasser SM. A Nuclear RNA Degradation Pathway Helps Silence Polycomb/H3K27me3-Marked Loci in Caenorhabditis elegans. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:141-153. [PMID: 32350050 DOI: 10.1101/sqb.2019.84.040238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In fission yeast and plants, RNA-processing pathways contribute to heterochromatin silencing, complementing well-characterized pathways of transcriptional repression. However, it was unclear whether this additional level of regulation occurs in metazoans. In a genetic screen, we uncovered a pathway of silencing in Caenorhabditis elegans somatic cells, whereby the highly conserved, RNA-binding complex LSM2-8 contributes to the repression of heterochromatic reporters and endogenous genes bearing the Polycomb mark H3K27me3. Importantly, the LSM2-8 complex works cooperatively with a 5'-3' exoribonuclease, XRN-2, and disruption of the pathway leads to selective mRNA stabilization. LSM2-8 complex-mediated RNA degradation does not target nor depend on H3K9me2/me3, unlike previously described pathways of heterochromatic RNA degradation. Up-regulation of lsm-8-sensitive loci coincides with a localized drop in H3K27me3 levels in the lsm-8 mutant. Put into the context of epigenetic control of gene expression, it appears that targeted RNA degradation helps repress a subset of H3K27me3-marked genes, revealing an unappreciated layer of regulation for facultative heterochromatin in animals.
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Affiliation(s)
- Anna Mattout
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Dimos Gaidatzis
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Véronique Kalck
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland.,University of Basel, Faculty of Science, CH-4056 Basel, Switzerland
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25
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LSM2-8 and XRN-2 contribute to the silencing of H3K27me3-marked genes through targeted RNA decay. Nat Cell Biol 2020; 22:579-590. [PMID: 32251399 PMCID: PMC7212045 DOI: 10.1038/s41556-020-0504-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 03/05/2020] [Indexed: 12/20/2022]
Abstract
In fission yeast and plants, RNA-processing and degradation contribute to
heterochromatin silencing, alongside conserved pathways of transcriptional
repression. It was unknown if similar pathways exist in metazoans. Here we
describe a pathway of silencing in C. elegans somatic cells, in
which the highly conserved RNA binding complex LSM2-8 contributes selectively to
the repression of heterochromatic reporters and endogenous genes bearing the
Polycomb mark, histone H3K27me3. It acts by degrading selected transcripts
through the XRN-2 exoribonuclease. Disruption of the LSM2-8 pathway leads to
mRNA stabilization. Unlike previously described pathways of heterochromatic RNA
degradation, LSM2-8-mediated RNA degradation does not require nor deposit H3K9
methylation. Rather, loss of this pathway coincides with a localized reduction
in H3K27me3 at lsm-8-sensitive loci. Thus, we have uncovered a
mechanism of RNA degradation that selectively contributes to the silencing of a
subset of H3K27me3-marked genes, revealing a previously unrecognized layer of
post-transcriptional control in metazoan heterochromatin.
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26
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Arsenite-induced transgenerational glycometabolism is associated with up-regulation of H3K4me2 via inhibiting spr-5 in caenorhabditis elegans. Toxicol Lett 2020; 326:11-17. [PMID: 32142838 DOI: 10.1016/j.toxlet.2020.03.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/28/2020] [Accepted: 03/02/2020] [Indexed: 11/23/2022]
Abstract
Arsenic (As) is a toxic element that is highly abundant in the environment. However, there has not been sufficient research into the mechanisms of arsenic-induced transgenerational effects. In biomedical and environmental toxicology research field, C. elegans are often used as the ideal model. In this study, F0 generation animals were cultured with arsenite, while subsequent generations animals (F1 - F6) were cultured in the absence of arsenic. Experiments were performed to examine the transgenerational glycometabolism and the associated mechanisms in all seven generations (F0 - F6) of C. elegans. Results show that arsenite exposure increased total glucose content but reduced glucose metabolites in F0 generation C. elegans. The total glucose content was also elevated in subsequent generations probably due to transgenerational downregulation of fgt-1. In addition, arsenite exposure induced transgenerational downregulation of histone demethyltransferase spr-5 and elevated histone dimethylation in F0 generation. This study highlights that single generation exposure to arsenite causes transgenerational changes in glycometabolism in C. elegans, which may be caused by downregulation of spr-5 and elevation of H3K4me2.
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27
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The Epigenetics of Aging in Invertebrates. Int J Mol Sci 2019; 20:ijms20184535. [PMID: 31540238 PMCID: PMC6769462 DOI: 10.3390/ijms20184535] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/03/2019] [Accepted: 09/12/2019] [Indexed: 12/16/2022] Open
Abstract
Aging is an unstoppable process coupled to the loss of physiological function and increased susceptibility to diseases. Epigenetic alteration is one of the hallmarks of aging, which involves changes in DNA methylation patterns, post-translational modification of histones, chromatin remodeling and non-coding RNA interference. Invertebrate model organisms, such as Drosophila melanogaster and Caenorhabditis elegans, have been used to investigate the biological mechanisms of aging because they show, evolutionarily, the conservation of many aspects of aging. In this review, we focus on recent advances in the epigenetic changes of aging with invertebrate models, providing insight into the relationship between epigenetic dynamics and aging.
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28
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Dall KB, Færgeman NJ. Metabolic regulation of lifespan from a C. elegans perspective. GENES & NUTRITION 2019; 14:25. [PMID: 31428207 PMCID: PMC6694653 DOI: 10.1186/s12263-019-0650-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/01/2019] [Indexed: 02/07/2023]
Abstract
Decline of cellular functions especially cognitive is a major deficit that arises with age in humans. Harnessing the strengths of small and genetic tractable model systems has revealed key conserved regulatory biochemical and signaling pathways that control aging. Here, we review some of the key signaling and biochemical pathways that coordinate aging processes with special emphasis on Caenorhabditis elegans as a model system and discuss how nutrients and metabolites can regulate lifespan by coordinating signaling and epigenetic programs. We focus on central nutrient-sensing pathways such as mTOR and insulin/insulin-like growth factor signaling and key transcription factors including the conserved basic helix-loop-helix transcription factor HLH-30/TFEB.
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Affiliation(s)
- Kathrine B. Dall
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Nils J. Færgeman
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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29
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Li Z, Zhao P, Xia Q. Epigenetic Methylations on N6-Adenine and N6-Adenosine with the same Input but Different Output. Int J Mol Sci 2019; 20:ijms20122931. [PMID: 31208067 PMCID: PMC6627651 DOI: 10.3390/ijms20122931] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 06/13/2019] [Accepted: 06/14/2019] [Indexed: 12/15/2022] Open
Abstract
Epigenetic modifications on individual bases in DNA and RNA can encode inheritable genetic information beyond the canonical bases. Among the nucleic acid modifications, DNA N6-methadenine (6mA) and RNA N6-methyladenosine (m6A) have recently been well-studied due to the technological development of detection strategies and the functional identification of modification enzymes. The current findings demonstrate a wide spectrum of 6mA and m6A distributions from prokaryotes to eukaryotes and critical roles in multiple cellular processes. It is interesting that the processes of modification in which the methyl group is added to adenine and adenosine are the same, but the outcomes of these modifications in terms of their physiological impacts in organisms are quite different. In this review, we summarize the latest progress in the study of enzymes involved in the 6mA and m6A methylation machinery, including methyltransferases and demethylases, and their functions in various biological pathways. In particular, we focus on the mechanisms by which 6mA and m6A regulate the expression of target genes, and we highlight the future challenges in epigenetic regulation.
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Affiliation(s)
- Zhiqing Li
- Biological Science Research Center, Southwest University, Chongqing 400715, China.
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China.
| | - Ping Zhao
- Biological Science Research Center, Southwest University, Chongqing 400715, China.
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China.
| | - Qingyou Xia
- Biological Science Research Center, Southwest University, Chongqing 400715, China.
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China.
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30
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Jabeena CA, Rajavelu A. Epigenetic Players of Chromatin Structure Regulation in Plasmodium falciparum. Chembiochem 2019; 20:1225-1230. [PMID: 30632244 DOI: 10.1002/cbic.201800718] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Indexed: 12/16/2022]
Abstract
The protozoan parasite Plasmodium has evolved to survive in different hosts and environments. The diverse strategies of adaptation to different niches involve differential gene expression mechanisms mediated by chromatin plasticity that are poorly characterized in Plasmodium. The parasite employs a wide variety of regulatory mechanisms to complete their life cycle and survive inside hosts. Among them, epigenetic-mediated mechanisms have been implicated for controlling chromatin organization, gene regulation, morphological differentiation, and antigenic variation. The differential gene expression in parasite is largely dependent on the nature of the chromatin structure. The histone core methylation marks and methyl mark readers contribute to chromatin dynamics. Here, we review the recent developments on various epigenetic marks and its enzymes in the Plasmodium falciparum, how these marks play a key role in the regulation of transcriptional activity of variable genes and coordinate the differential gene expression. We also discuss the possible roles of these epigenetic marks in chromatin structure regulation and plasticity at various stages of its development.
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Affiliation(s)
- C A Jabeena
- Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala, 695014, India.,Manipal Academy of Higher Education, Tiger Circle Road, Madhav Nagar, Manipal, Karnataka, 576104, India
| | - Arumugam Rajavelu
- Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala, 695014, India
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31
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Kako K, Kim JD, Fukamizu A. Emerging impacts of biological methylation on genetic information. J Biochem 2019; 165:9-18. [PMID: 30219914 DOI: 10.1093/jb/mvy075] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/13/2018] [Indexed: 12/13/2022] Open
Abstract
The central dogma of molecular biology explains the fundamental flow of genetic information for life. Although genome sequence (DNA) itself is a static chemical signature, it includes multiple layers of information composed of mRNA, tRNA, rRNA and small RNAs, all of which are involved in protein synthesis and is passing from parents to offspring via DNA. Methylation is a biologically important modification, because DNA, RNAs and proteins, components of the central dogma, are methylated by a set of methyltransferases. Recent works focused on understanding a variety of biological methylation have shed light on new regulation of cellular functions. In this review, we briefly discuss some of those recent findings of methylation, including DNA, RNAs and proteins.
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Affiliation(s)
- Koichiro Kako
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan.,Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan
| | - Jun-Dal Kim
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan
| | - Akiyoshi Fukamizu
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan.,International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan
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32
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Hajduskova M, Baytek G, Kolundzic E, Gosdschan A, Kazmierczak M, Ofenbauer A, Beato Del Rosal ML, Herzog S, Ul Fatima N, Mertins P, Seelk-Müthel S, Tursun B. MRG-1/MRG15 Is a Barrier for Germ Cell to Neuron Reprogramming in Caenorhabditis elegans. Genetics 2019; 211:121-139. [PMID: 30425042 PMCID: PMC6325694 DOI: 10.1534/genetics.118.301674] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 11/09/2018] [Indexed: 12/13/2022] Open
Abstract
Chromatin regulators play important roles in the safeguarding of cell identities by opposing the induction of ectopic cell fates and, thereby, preventing forced conversion of cell identities by reprogramming approaches. Our knowledge of chromatin regulators acting as reprogramming barriers in living organisms needs improvement as most studies use tissue culture. We used Caenorhabditis elegans as an in vivo gene discovery model and automated solid-phase RNA interference screening, by which we identified 10 chromatin-regulating factors that protect cells against ectopic fate induction. Specifically, the chromodomain protein MRG-1 safeguards germ cells against conversion into neurons. MRG-1 is the ortholog of mammalian MRG15 (MORF-related gene on chromosome 15) and is required during germline development in C. elegans However, MRG-1's function as a barrier for germ cell reprogramming has not been revealed previously. Here, we further provide protein-protein and genome interactions of MRG-1 to characterize its molecular functions. Conserved chromatin regulators may have similar functions in higher organisms, and therefore, understanding cell fate protection in C. elegans may also help to facilitate reprogramming of human cells.
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Affiliation(s)
- Martina Hajduskova
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Gülkiz Baytek
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Ena Kolundzic
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Alexander Gosdschan
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Marlon Kazmierczak
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Andreas Ofenbauer
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Maria Lena Beato Del Rosal
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Sergej Herzog
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Nida Ul Fatima
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Stefanie Seelk-Müthel
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Baris Tursun
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
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33
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Ding W, Higgins DP, Yadav DK, Godbole AA, Pukkila-Worley R, Walker AK. Stress-responsive and metabolic gene regulation are altered in low S-adenosylmethionine. PLoS Genet 2018; 14:e1007812. [PMID: 30485261 PMCID: PMC6287882 DOI: 10.1371/journal.pgen.1007812] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 12/10/2018] [Accepted: 11/06/2018] [Indexed: 12/31/2022] Open
Abstract
S-adenosylmethionine (SAM) is a donor which provides the methyl groups for histone or nucleic acid modification and phosphatidylcholine production. SAM is hypothesized to link metabolism and chromatin modification, however, its role in acute gene regulation is poorly understood. We recently found that Caenorhabditis elegans with reduced SAM had deficiencies in H3K4 trimethylation (H3K4me3) at pathogen-response genes, decreasing their expression and limiting pathogen resistance. We hypothesized that SAM may be generally required for stress-responsive transcription. Here, using genetic assays, we show that transcriptional responses to bacterial or xenotoxic stress fail in C. elegans with low SAM, but that expression of heat shock genes are unaffected. We also found that two H3K4 methyltransferases, set-2/SET1 and set-16/MLL, had differential responses to survival during stress. set-2/SET1 is specifically required in bacterial responses, whereas set-16/MLL is universally required. These results define a role for SAM in the acute stress-responsive gene expression. Finally, we find that modification of metabolic gene expression correlates with enhanced survival during stress.
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Affiliation(s)
- Wei Ding
- Program in Molecular Medicine, UMASS Medical School, Worcester, MA, United States of America
| | - Daniel P. Higgins
- Department of Computer Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Dilip K. Yadav
- Program in Molecular Medicine, UMASS Medical School, Worcester, MA, United States of America
| | - Adwait A. Godbole
- Program in Molecular Medicine, UMASS Medical School, Worcester, MA, United States of America
| | - Read Pukkila-Worley
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, UMASS Medical School, Worcester, MA, United States of America
| | - Amy K. Walker
- Program in Molecular Medicine, UMASS Medical School, Worcester, MA, United States of America
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34
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Singh A, Vancura A, Woycicki RK, Hogan DJ, Hendrick AG, Nowacki M. Determination of the presence of 5-methylcytosine in Paramecium tetraurelia. PLoS One 2018; 13:e0206667. [PMID: 30379964 PMCID: PMC6209305 DOI: 10.1371/journal.pone.0206667] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 10/17/2018] [Indexed: 11/19/2022] Open
Abstract
5-methylcytosine DNA methylation regulates gene expression and developmental programming in a broad range of eukaryotes. However, its presence and potential roles in ciliates, complex single-celled eukaryotes with germline-somatic genome specialization via nuclear dimorphism, are largely uncharted. While canonical cytosine methyltransferases have not been discovered in published ciliate genomes, recent studies performed in the stichotrichous ciliate Oxytricha trifallax suggest de novo cytosine methylation during macronuclear development. In this study, we applied bisulfite genome sequencing, DNA mass spectrometry and antibody-based fluorescence detection to investigate the presence of DNA methylation in Paramecium tetraurelia. While the antibody-based methods suggest cytosine methylation, DNA mass spectrometry and bisulfite sequencing reveal that levels are actually below the limit of detection. Our results suggest that Paramecium does not utilize 5-methylcytosine DNA methylation as an integral part of its epigenetic arsenal.
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Affiliation(s)
- Aditi Singh
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Freiestrasse 1, Bern, Switzerland
| | - Adrienne Vancura
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, Bern, Switzerland
| | - Rafal K. Woycicki
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, Bern, Switzerland
| | - Daniel J. Hogan
- Tocagen Incorporated, San Diego, California, United States of America
| | - Alan G. Hendrick
- Storm Therapeutics Limited, Moneta Building, Babraham Research Campus, Cambridge, United Kingdom
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, Bern, Switzerland
- * E-mail:
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35
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Yang J, Chatterjee N, Kim Y, Roh JY, Kwon JH, Park MS, Choi J. Histone methylation-associated transgenerational inheritance of reproductive defects in Caenorhabditis elegans exposed to crude oil under various exposure scenarios. CHEMOSPHERE 2018; 200:358-365. [PMID: 29494917 DOI: 10.1016/j.chemosphere.2018.02.080] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 02/11/2018] [Accepted: 02/13/2018] [Indexed: 06/08/2023]
Abstract
As part of a study to explore the long-term effects of the Hebei Spirit oil spill accident, transgenerational toxicity and associated epigenetic changes were investigated in the nematode Caenorhabditis elegans. Under experimental conditions, worms were exposed to Iranian heavy crude oil (IHC) under three different scenarios: partial early-life exposure (PE), partial late-life exposure (PL), and whole-life exposure (WE). Growth, reproduction, and histone methylation were monitored in the exposed parental worms (P0) and in three consecutive unexposed offspring generations (F1-3). Reproductive potential in the exposed P0 generation in the WE treatment group was reduced; additionally, it was inhibited in the unexposed offspring generations of the P0 worms. This suggests that there was transgenerational inheritance of defective reproduction. Comparison of developmental periods of exposure showed that IHC-treated worms in the PL group had a greater reduction in reproductive capacity than those in the PE group. Decreased methylation of histone H3 (H3K9) was found in the IHC-exposed parental generation. A heritable reduction in reproductive capacity occurred in wildtype N2 but was not found in a H3K9 histone methyltransferase (HMT) mutant, met-2(n4256), suggesting a potential role for HMT in transgenerational toxicity. Our results suggest that the reproductive toxicity after IHC exposure could be heritable and that histone methylation is associated with the transmission of the inherited phenotype.
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Affiliation(s)
- Jisu Yang
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul, 02504, Republic of Korea
| | - Nivedita Chatterjee
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul, 02504, Republic of Korea
| | - Youngho Kim
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul, 02504, Republic of Korea
| | - Ji-Yeon Roh
- Division of Environmental Science and Ecological Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Jung-Hwan Kwon
- Division of Environmental Science and Ecological Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Myung-Sook Park
- Taean Environmental Health Center, 1952-16 Seohae-ro, Taean-eup, Taean-gun, Chungcheongnam-do, 32148, Republic of Korea
| | - Jinhee Choi
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul, 02504, Republic of Korea.
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36
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Papaluca A, Wagner JR, Saragovi HU, Ramotar D. UNG-1 and APN-1 are the major enzymes to efficiently repair 5-hydroxymethyluracil DNA lesions in C. elegans. Sci Rep 2018; 8:6860. [PMID: 29717169 PMCID: PMC5931555 DOI: 10.1038/s41598-018-25124-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/13/2018] [Indexed: 11/16/2022] Open
Abstract
In Caenorhabditis elegans, two DNA glycosylases, UNG-1 and NTH-1, and two AP endonucleases, APN-1 and EXO-3, have been characterized from the base-excision repair (BER) pathway that repairs oxidatively modified DNA bases. UNG-1 removes uracil, while NTH-1 can remove 5-hydroxymethyluracil (5-hmU), an oxidation product of thymine, as well as other lesions. Both APN-1 and EXO-3 can incise AP sites and remove 3′-blocking lesions at DNA single strand breaks, and only APN-1 possesses 3′- to 5′-exonulease and nucleotide incision repair activities. We used C. elegans mutants to study the role of the BER pathway in processing 5-hmU. We observe that ung-1 mutants exhibited a decrease in brood size and lifespan, and an elevated level of germ cell apoptosis when challenged with 5-hmU. These phenotypes were exacerbated by RNAi downregulation of apn-1 in the ung-1 mutant. The nth-1 or exo-3 mutants displayed wild type phenotypes towards 5-hmU. We show that partially purified UNG-1 can act on 5-hmU lesion in vitro. We propose that UNG-1 removes 5-hmU incorporated into the genome and the resulting AP site is cleaved by APN-1 or EXO-3. In the absence of UNG-1, the 5-hmU is removed by NTH-1 creating a genotoxic 3′-blocking lesion that requires the action of APN-1.
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Affiliation(s)
- Arturo Papaluca
- Maisonneuve-Rosemont Hospital, Research Center, Université de Montréal, Department of Medicine, 5415 Boul. de l'Assomption, Montréal, Québec, H1T2M4, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Department of Pharmacology and Therapeutics, McGill University, Department of Pharmacology and Therapeutics, 3755 Chemin de la Côte Sainte-Catherine, Québec, Montréal, H3T1E2, Canada
| | - J Richard Wagner
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12 Avenue Nord, Sherbrooke, Québec, J1H5N4, Canada
| | - H Uri Saragovi
- Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Department of Pharmacology and Therapeutics, McGill University, Department of Pharmacology and Therapeutics, 3755 Chemin de la Côte Sainte-Catherine, Québec, Montréal, H3T1E2, Canada
| | - Dindial Ramotar
- Maisonneuve-Rosemont Hospital, Research Center, Université de Montréal, Department of Medicine, 5415 Boul. de l'Assomption, Montréal, Québec, H1T2M4, Canada.
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37
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Schultz CL, Wamucho A, Tsyusko OV, Unrine JM, Crossley A, Svendsen C, Spurgeon DJ. Multigenerational exposure to silver ions and silver nanoparticles reveals heightened sensitivity and epigenetic memory in Caenorhabditis elegans. Proc Biol Sci 2017; 283:rspb.2015.2911. [PMID: 27306046 DOI: 10.1098/rspb.2015.2911] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 05/17/2016] [Indexed: 11/12/2022] Open
Abstract
The effects from multigenerational exposures to engineered nanoparticles (ENPs) in their pristine and transformed states are currently unknown despite such exposures being an increasingly common scenario in natural environments. Here, we examine how exposure over 10 generations affects the sensitivity of the nematode Caenorhabditis elegans to pristine and sulfidized Ag ENPs and AgNO3 We also include populations that were initially exposed over six generations but kept unexposed for subsequent four generations to allow recovery from exposure. Toxicity of the different silver forms decreased in the order AgNO3, Ag ENPs and Ag2S ENPs. Continuous exposure to Ag ENPs and AgNO3 caused pronounced sensitization (approx. 10-fold) in the F2 generation, which was sustained until F10. This sensitization was less pronounced for Ag2S ENP exposures, indicating different toxicity mechanisms. Subtle changes in size and lifespan were also measured. In the recovery populations, the sensitivity to Ag ENPs and AgNO3 resulting from the initial multigenerational exposure persisted. Their response sensitivity for all endpoints was most closely related to the last ancestral exposed generation (F5), rather than unexposed controls. The mechanisms of transgenerational transfer of sensitivity are probably organized through the epigenome, and we encourage others to investigate such effects as a priority for mechanistic toxicology.
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Affiliation(s)
- Carolin L Schultz
- Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxon OX10 8BB, UK Department of Materials, Oxford University, Begbroke Science Park, Begbroke Hill, Yarnton, Oxford OX5 1PF, UK
| | - Anye Wamucho
- Department of Plant and Soil Sciences, University of Kentucky, 1100 S. Limestone St., Lexington, KY 40546, USA
| | - Olga V Tsyusko
- Department of Plant and Soil Sciences, University of Kentucky, 1100 S. Limestone St., Lexington, KY 40546, USA
| | - Jason M Unrine
- Department of Plant and Soil Sciences, University of Kentucky, 1100 S. Limestone St., Lexington, KY 40546, USA
| | - Alison Crossley
- Department of Materials, Oxford University, Begbroke Science Park, Begbroke Hill, Yarnton, Oxford OX5 1PF, UK
| | - Claus Svendsen
- Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxon OX10 8BB, UK
| | - David J Spurgeon
- Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxon OX10 8BB, UK
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Stern S, Kirst C, Bargmann CI. Neuromodulatory Control of Long-Term Behavioral Patterns and Individuality across Development. Cell 2017; 171:1649-1662.e10. [DOI: 10.1016/j.cell.2017.10.041] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 09/10/2017] [Accepted: 10/24/2017] [Indexed: 12/20/2022]
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39
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Parashar NC, Parashar G, Nayyar H, Sandhir R. N 6-adenine DNA methylation demystified in eukaryotic genome: From biology to pathology. Biochimie 2017; 144:56-62. [PMID: 29074394 DOI: 10.1016/j.biochi.2017.10.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 10/17/2017] [Indexed: 01/16/2023]
Abstract
N6-methyl-2'-deoxyadenosine (m6dA) is a well characterized DNA modification in prokaryotes. Its existence in eukaryotic DNA remained doubtful until recently. Evidence suggests that the m6dA levels decrease with the increasing complexity of eukaryotic genomes. Analysis of m6dA levels in genome of lower eukaryotes reveals its role in gene regulation, nucleosome positioning and early development. In higher eukaryotes m6dA is enriched in nongenic region compared to genic region, preferentially in chromosome X and 13 suggesting a chromosome bias. High levels of m6dA during embryogenesis as compared to adult tissues are indicative of its importance during development and possible association with regeneration capabilities. Further, decreased levels of m6dA in diabetic patients has been correlated with expression of Fat mass and obesity-associated (FTO) which acts as m6A demethylase. m6dA levels have also been reported to be decreased in different types of cancers. The present review highlights the role of m6dA modification in eukaryotic genomes and its functional importance in regulation of physiological and pathological processes.
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Affiliation(s)
| | - Gaurav Parashar
- Laboratory of Epigenetics and Diseases, Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar (Mohali), Punjab, 160062, India
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, 160014, India
| | - Rajat Sandhir
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India.
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40
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Shi DQ, Ali I, Tang J, Yang WC. New Insights into 5hmC DNA Modification: Generation, Distribution and Function. Front Genet 2017; 8:100. [PMID: 28769976 PMCID: PMC5515870 DOI: 10.3389/fgene.2017.00100] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 07/05/2017] [Indexed: 01/10/2023] Open
Abstract
Dynamic DNA modifications, such as methylation/demethylation on cytosine, are major epigenetic mechanisms to modulate gene expression in both eukaryotes and prokaryotes. In addition to the common methylation on the 5th position of the pyrimidine ring of cytosine (5mC), other types of modifications at the same position, such as 5-hydroxymethyl (5hmC), 5-formyl (5fC), and 5-carboxyl (5caC), are also important. Recently, 5hmC, a product of 5mC demethylation by the Ten-Eleven Translocation family proteins, was shown to regulate many cellular and developmental processes, including the pluripotency of embryonic stem cells, neuron development, and tumorigenesis in mammals. Here, we review recent advances on the generation, distribution, and function of 5hmC modification in mammals and discuss its potential roles in plants.
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Affiliation(s)
- Dong-Qiao Shi
- State Key Laboratory of Molecular Developmental Biology, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Iftikhar Ali
- State Key Laboratory of Molecular Developmental Biology, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Jun Tang
- State Key Laboratory of Molecular Developmental Biology, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Wei-Cai Yang
- State Key Laboratory of Molecular Developmental Biology, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, University of Chinese Academy of SciencesBeijing, China
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41
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DNA N 6-methyladenine in metazoans: functional epigenetic mark or bystander? Nat Struct Mol Biol 2017; 24:503-506. [PMID: 28586322 DOI: 10.1038/nsmb.3412] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 04/18/2017] [Indexed: 02/06/2023]
Abstract
The DNA-adenine modification N6-methyladenine (6mA), initially thought to be mainly restricted to prokaryotes and certain unicellular eukaryotes, has recently been found in metazoans. Proposed functions vary from gene activation to transposon suppression. However, since most metazoan genomes possess 5-methylcytosine (5mC) as a dominant epigenetic mark, it raises the question of why 6mA is required. This Perspective summarizes the latest discoveries and suggests potential functional roles for 6mA in metazoan genomes.
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42
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BLIMP-1/BLMP-1 and Metastasis-Associated Protein Regulate Stress Resistant Development in Caenorhabditis elegans. Genetics 2016; 203:1721-32. [PMID: 27334271 DOI: 10.1534/genetics.116.190793] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/14/2016] [Indexed: 01/17/2023] Open
Abstract
Environmental stress triggers multilevel adaptations in animal development that depend in part on epigenetic mechanisms. In response to harsh environmental conditions and pheromone signals, Caenorhabditis elegans larvae become the highly stress-resistant and long-lived dauer. Despite extensive studies of dauer formation pathways that integrate specific environmental cues and appear to depend on transcriptional reprogramming, the role of epigenetic regulation in dauer development has remained unclear. Here we report that BLMP-1, the BLIMP-1 ortholog, regulates dauer formation via epigenetic pathways; in the absence of TGF-β signaling (in daf-7 mutants), lack of blmp-1 caused lethality. Using this phenotype, we screened 283 epigenetic factors, and identified lin-40, a homolog of metastasis-associate protein 1 (MTA1) as an interactor of BLMP-1 The interaction between LIN-40 and BLMP-1 is conserved because mammalian homologs for both MTA1 and BLIMP-1 could also interact. From microarray studies, we identified several downstream target genes of blmp-1: npr-3, nhr-23, ptr-4, and sams-1 Among them S-adenosyl methionine synthase (SAMS-1), is the key enzyme for production of SAM used in histone methylation. Indeed, blmp-1 is necessary for controlling histone methylation level in daf-7 mutants, suggesting BLMP-1 regulates the expression of SAMS-1, which in turn may regulate histone methylation and dauer formation. Our results reveal a new interaction between BLMP-1/BLIMP-1 and LIN-40/MTA1, as well as potential epigenetic downstream pathways, whereby these proteins cooperate to regulate stress-specific developmental adaptations.
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43
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Ding W, Smulan LJ, Hou NS, Taubert S, Watts JL, Walker AK. s-Adenosylmethionine Levels Govern Innate Immunity through Distinct Methylation-Dependent Pathways. Cell Metab 2015; 22:633-45. [PMID: 26321661 PMCID: PMC4598287 DOI: 10.1016/j.cmet.2015.07.013] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/29/2015] [Accepted: 07/17/2015] [Indexed: 12/13/2022]
Abstract
s-adenosylmethionine (SAM) is the sole methyl donor modifying histones, nucleic acids, and phospholipids. Its fluctuation affects hepatic phosphatidylcholine (PC) synthesis or may be linked to variations in DNA or histone methylation. Physiologically, low SAM is associated with lipid accumulation, tissue injury, and immune responses in fatty liver disease. However, molecular connections among SAM limitation, methyltransferases, and disease-associated phenotypes are unclear. We find that low SAM can activate or attenuate Caenorhabditis elegans immune responses. Immune pathways are stimulated downstream of PC production on a non-pathogenic diet. In contrast, distinct SAM-dependent mechanisms limit survival on pathogenic Pseudomonas aeruginosa. C. elegans undertakes a broad transcriptional response to pathogens and we find that low SAM restricts H3K4me3 at Pseudomonas-responsive promoters, limiting their expression. Furthermore, this response depends on the H3K4 methyltransferase set-16/MLL. Thus, our studies provide molecular links between SAM and innate immune functions and suggest that SAM depletion may limit stress-induced gene expression.
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Affiliation(s)
- Wei Ding
- Program in Molecular Medicine, UMass Worcester, 373 Plantation Street, Worcester, MA 01605, USA
| | - Lorissa J Smulan
- Program in Molecular Medicine, UMass Worcester, 373 Plantation Street, Worcester, MA 01605, USA
| | - Nicole S Hou
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics (CMMT) and Child & Family Research Institute (CFRI), University of British Columbia (UBC), Vancouver, BC V5Z 4H4, Canada
| | - Stefan Taubert
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics (CMMT) and Child & Family Research Institute (CFRI), University of British Columbia (UBC), Vancouver, BC V5Z 4H4, Canada
| | - Jennifer L Watts
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-6340, USA
| | - Amy K Walker
- Program in Molecular Medicine, UMass Worcester, 373 Plantation Street, Worcester, MA 01605, USA.
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44
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Rankin CH. A review of transgenerational epigenetics for RNAi, longevity, germline maintenance and olfactory imprinting in Caenorhabditis elegans. ACTA ACUST UNITED AC 2015; 218:41-9. [PMID: 25568450 DOI: 10.1242/jeb.108340] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Inheritance of acquired characteristics without changes in DNA sequence has been called transgenerational epigenetics. This review looks at studies that used the model system Caenorhabditis elegans to uncover mechanisms of transgenerational epigenetics in studies of RNA interference, studies of longevity, studies of germline continuity and a study on olfactory imprinting. In each case, researchers have uncovered critical roles for small RNAs and for Argonaute proteins. They have revealed several different genetic pathways that mediate RNA silencing of foreign RNA for a few or for many generations, as well as identifying a related pathway responsible for recognized self-generated RNAs. Together, these studies have greatly advanced our understanding of trangenerational epigenetics.
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Affiliation(s)
- Catharine H Rankin
- Department of Psychology and Brain Research Centre, University of British Columbia, Vancouver, BC, Canada, V6T 2B5
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45
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Summerer D. N 6-Methyladenin: ein potentieller epigenetischer Marker in eukaryontischen Genomen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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46
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Abstract
N(6) -methyladenine (6mA) is known to be an epigenetic mark in bacterial genomes. Three studies have now demonstrated the existence of significant levels of 6mA in the genomes of several phylogenetically distinct eukaryotes, along with findings that suggest that 6mA may act as a dynamic epigenetic mark in the regulation of eukaryotic gene expression.
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Affiliation(s)
- Daniel Summerer
- Department of Chemistry and Konstanz Research School, Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz (Germany).
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47
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Stegemann R, Buchner DA. Transgenerational inheritance of metabolic disease. Semin Cell Dev Biol 2015; 43:131-140. [PMID: 25937492 PMCID: PMC4626440 DOI: 10.1016/j.semcdb.2015.04.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/20/2015] [Accepted: 04/22/2015] [Indexed: 02/05/2023]
Abstract
Metabolic disease encompasses several disorders including obesity, type 2 diabetes, and dyslipidemia. Recently, the incidence of metabolic disease has drastically increased, driven primarily by a worldwide obesity epidemic. Transgenerational inheritance remains controversial, but has been proposed to contribute to human metabolic disease risk based on a growing number of proof-of-principle studies in model organisms ranging from Caenorhabditis elegans to Mus musculus to Sus scrofa. Collectively, these studies demonstrate that heritable risk is epigenetically transmitted from parent to offspring over multiple generations in the absence of a continued exposure to the triggering stimuli. A diverse assortment of initial triggers can induce transgenerational inheritance including high-fat or high-sugar diets, low-protein diets, various toxins, and ancestral genetic variants. Although the mechanistic basis underlying the transgenerational inheritance of disease risk remains largely unknown, putative molecules mediating transmission include small RNAs, histone modifications, and DNA methylation. Due to the considerable impact of metabolic disease on human health, it is critical to better understand the role of transgenerational inheritance of metabolic disease risk to open new avenues for therapeutic intervention and improve upon the current methods for clinical diagnoses and treatment.
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Affiliation(s)
- Rachel Stegemann
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, United States
| | - David A Buchner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, United States; Department of Biological Chemistry, Case Western Reserve University, Cleveland, OH 44106, United States.
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48
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Leopold LE, Heestand BN, Seong S, Shtessel L, Ahmed S. Lack of pairing during meiosis triggers multigenerational transgene silencing in Caenorhabditis elegans. Proc Natl Acad Sci U S A 2015; 112:E2667-76. [PMID: 25941370 PMCID: PMC4443339 DOI: 10.1073/pnas.1501979112] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Single-copy transgenes in Caenorhabditis elegans can be subjected to a potent, irreversible silencing process termed small RNA-induced epigenetic silencing (RNAe). RNAe is promoted by the Piwi Argonaute protein PRG-1 and associated Piwi-interacting RNAs (piRNAs), as well as by proteins that promote and respond to secondary small interfering RNA (siRNA) production. Here we define a related siRNA-mediated silencing process, termed "multigenerational RNAe," which can occur for transgenes that are maintained in a hemizygous state for several generations. We found that transgenes that contain either GFP or mCherry epitope tags can be silenced via multigenerational RNAe, whereas a transgene that possesses GFP and a perfect piRNA target site can be rapidly and permanently silenced via RNAe. Although previous studies have shown that PRG-1 is typically dispensable for maintenance of RNAe, we found that both initiation and maintenance of multigenerational RNAe requires PRG-1 and the secondary siRNA biogenesis protein RDE-2. Although silencing via RNAe is irreversible, we found that transgene expression can be restored when hemizygous transgenes that were silenced via multigenerational RNAe become homozygous. Furthermore, multigenerational RNAe was accelerated when meiotic pairing of the chromosome possessing the transgene was abolished. We propose that persistent lack of pairing during meiosis elicits a reversible multigenerational silencing response, which can lead to permanent transgene silencing. Multigenerational RNAe may be broadly relevant to single-copy transgenes used in experimental biology and to shaping the epigenomic landscape of diverse species, where genomic polymorphisms between homologous chromosomes commonly result in unpaired DNA during meiosis.
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Affiliation(s)
| | - Bree N Heestand
- Department of Genetics, Lineberger Comprehensive Cancer Center, and
| | | | | | - Shawn Ahmed
- Department of Genetics, Lineberger Comprehensive Cancer Center, and Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280
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49
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Greer EL, Blanco MA, Gu L, Sendinc E, Liu J, Aristizábal-Corrales D, Hsu CH, Aravind L, He C, Shi Y. DNA Methylation on N6-Adenine in C. elegans. Cell 2015; 161:868-78. [PMID: 25936839 DOI: 10.1016/j.cell.2015.04.005] [Citation(s) in RCA: 457] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 03/02/2015] [Accepted: 03/31/2015] [Indexed: 02/02/2023]
Abstract
In mammalian cells, DNA methylation on the fifth position of cytosine (5mC) plays an important role as an epigenetic mark. However, DNA methylation was considered to be absent in C. elegans because of the lack of detectable 5mC, as well as homologs of the cytosine DNA methyltransferases. Here, using multiple approaches, we demonstrate the presence of adenine N(6)-methylation (6mA) in C. elegans DNA. We further demonstrate that this modification increases trans-generationally in a paradigm of epigenetic inheritance. Importantly, we identify a DNA demethylase, NMAD-1, and a potential DNA methyltransferase, DAMT-1, which regulate 6mA levels and crosstalk between methylations of histone H3K4 and adenines and control the epigenetic inheritance of phenotypes associated with the loss of the H3K4me2 demethylase spr-5. Together, these data identify a DNA modification in C. elegans and raise the exciting possibility that 6mA may be a carrier of heritable epigenetic information in eukaryotes.
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Affiliation(s)
- Eric Lieberman Greer
- Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
| | - Mario Andres Blanco
- Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Lei Gu
- Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Erdem Sendinc
- Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jianzhao Liu
- Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - David Aristizábal-Corrales
- Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Chih-Hung Hsu
- Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 208943, USA
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Yang Shi
- Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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50
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Trace analysis of methylated and hydroxymethylated cytosines in DNA by isotope-dilution LC–MS/MS: first evidence of DNA methylation in Caenorhabditis elegans. Biochem J 2014; 465:39-47. [DOI: 10.1042/bj20140844] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We developed an online solid-phase extraction LC–MS/MS method to simultaneously measure 5-methyl-2′-deoxycytidine and 5-hydroxymethyl-2′-deoxycytidine in DNA. We demonstrated that 5-methyl-2′-deoxycytidine is present in Caenorhabditis elegans and its level was regulated by decitabine or cadmium in a dose–response manner.
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