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Li CY, Boldt H, Parent E, Ficklin J, James A, Anlage TJ, Boyer LM, Pierce BR, Siegfried KR, Harris MP, Haag ES. Genetic tools for the study of the mangrove killifish, Kryptolebias marmoratus, an emerging vertebrate model for phenotypic plasticity. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024; 342:164-177. [PMID: 37553824 DOI: 10.1002/jez.b.23216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/04/2023] [Accepted: 07/21/2023] [Indexed: 08/10/2023]
Abstract
Kryptolebias marmoratus (Kmar), a teleost fish of the order Cyprinodontiformes, has a suite of unique phenotypes and behaviors not observed in other fishes. Many of these phenotypes are discrete and highly plastic-varying over time within an individual, and in some cases reversible. Kmar and its interfertile sister species, K. hermaphroditus, are the only known self-fertile vertebrates. This unusual sexual mode has the potential to provide unique insights into the regulation of vertebrate sexual development, and also lends itself to genetics. Kmar is easily adapted to the lab and requires little maintenance. However, its internal fertilization and small clutch size limits its experimental use. To support Kmar as a genetic model, we compared alternative husbandry techniques to maximize recovery of early cleavage-stage embryos. We find that frequent egg collection enhances yield, and that protease treatment promotes the greatest hatching success. We completed a forward mutagenesis screen and recovered several mutant lines that serve as important tools for genetics in this model. Several will serve as useful viable recessive markers for marking crosses. Importantly, the mutant kissylips lays embryos at twice the rate of wild-type. Combining frequent egg collection with the kissylips mutant background allows for a substantial enhancement of early embryo yield. These improvements were sufficient to allow experimental analysis of early development and the successful mono- and bi-allelic targeted knockout of an endogenous tyrosinase gene with CRISPR/Cas9 nucleases. Collectively, these tools will facilitate modern developmental genetics in this fascinating fish, leading to future insights into the regulation of plasticity.
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Affiliation(s)
- Cheng-Yu Li
- Department of Biology, University of Maryland, College Park, Maryland, USA
| | - Helena Boldt
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Department of Orthopaedic Surgery, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Emily Parent
- Department of Biology, University of Maryland, College Park, Maryland, USA
| | - Jax Ficklin
- Department of Biology, University of Maryland, College Park, Maryland, USA
- College of Computer, Mathematical, and Natural Sciences, Biological Sciences Graduate Program, University of Maryland, College Park, Maryland, USA
| | - Althea James
- Department of Orthopaedic Surgery, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Troy J Anlage
- Department of Biology, University of Maryland, College Park, Maryland, USA
| | - Lena M Boyer
- Department of Biology, University of Maryland, College Park, Maryland, USA
| | - Brianna R Pierce
- Department of Biology, University of Maryland, College Park, Maryland, USA
| | - Kellee R Siegfried
- Department of Biology, University of Massachusetts, Boston, Massachusetts, USA
| | - Matthew P Harris
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Department of Orthopaedic Surgery, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Eric S Haag
- Department of Biology, University of Maryland, College Park, Maryland, USA
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2
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Singh M, Leddy SM, Iñiguez LP, Bendall ML, Nixon DF, Feschotte C. Transposable elements may enhance antiviral resistance in HIV-1 elite controllers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.11.571123. [PMID: 38168352 PMCID: PMC10760019 DOI: 10.1101/2023.12.11.571123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Less than 0.5% of people living with HIV-1 are elite controllers (ECs) - individuals who have a replication-competent viral reservoir in their CD4+ T cells but maintain undetectable plasma viremia without the help of antiretroviral therapy. While the EC CD4+ T cell transcriptome has been investigated for gene expression signatures associated with disease progression (or, in this case, a lack thereof), the expression and regulatory activity of transposable elements (TEs) in ECs has not been explored. Yet previous studies have established that TEs can directly impact the immune response to pathogens, including HIV-1. Thus, we hypothesize that the regulatory activities of TEs could contribute to the natural resistance of ECs against HIV-1. We perform a TE-centric analysis of previously published multi-omics data derived from EC individuals and other populations. We find that the CD4+ T cell transcriptome and retrotranscriptome of ECs are distinct from healthy controls, treated patients, and viremic progressors. However, there is a substantial level of transcriptomic heterogeneity among ECs. We categorize individuals with distinct chromatin accessibility and expression profiles into four clusters within the EC group, each possessing unique repertoires of TEs and antiviral factors. Notably, several TE families with known immuno-regulatory activity are differentially expressed among ECs. Their transcript levels in ECs positively correlate with their chromatin accessibility and negatively correlate with the expression of their KRAB zinc-finger (KZNF) repressors. This coordinated variation is seen at the level of individual TE loci likely acting or, in some cases, known to act as cis-regulatory elements for nearby genes involved in the immune response and HIV-1 restriction. Based on these results, we propose that the EC phenotype is driven in part by the reduced availability of specific KZNF proteins to repress TE-derived cis-regulatory elements for antiviral genes, thereby heightening their basal level of resistance to HIV-1 infection. Our study reveals considerable heterogeneity in the CD4+ T cell transcriptome of ECs, including variable expression of TEs and their KZNF controllers, that must be taken into consideration to decipher the mechanisms enabling HIV-1 control.
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Affiliation(s)
- Manvendra Singh
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Clinical Neuroscience, Max Planck Institute for Multidisciplinary Sciences, City Campus, Göttingen, Germany
| | - Sabrina M Leddy
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Luis Pedro Iñiguez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Matthew L Bendall
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Douglas F Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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3
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Panzeri I, Fagnocchi L, Apostle S, Tompkins M, Wolfrum E, Madaj Z, Hostetter G, Liu Y, Schaefer K, Chih-Hsiang Y, Bergsma A, Drougard A, Dror E, Chandler D, Schramek D, Triche TJ, Pospisilik JA. Developmental priming of cancer susceptibility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557446. [PMID: 37745326 PMCID: PMC10515831 DOI: 10.1101/2023.09.12.557446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
DNA mutations are necessary drivers of cancer, yet only a small subset of mutated cells go on to cause the disease. To date, the mechanisms that determine which rare subset of cells transform and initiate tumorigenesis remain unclear. Here, we take advantage of a unique model of intrinsic developmental heterogeneity (Trim28+/D9) and demonstrate that stochastic early life epigenetic variation can trigger distinct cancer-susceptibility 'states' in adulthood. We show that these developmentally primed states are characterized by differential methylation patterns at typically silenced heterochromatin, and that these epigenetic signatures are detectable as early as 10 days of age. The differentially methylated loci are enriched for genes with known oncogenic potential. These same genes are frequently mutated in human cancers, and their dysregulation correlates with poor prognosis. These results provide proof-of-concept that intrinsic developmental heterogeneity can prime individual, life-long cancer risk.
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Affiliation(s)
- Ilaria Panzeri
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Luca Fagnocchi
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Stefanos Apostle
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Megan Tompkins
- Vivarium and Transgenics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Emily Wolfrum
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Zachary Madaj
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Galen Hostetter
- Pathology and Biorepository Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Yanqing Liu
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Kristen Schaefer
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Department of Genetics and Genome Science, Case Western Reserve University, Cleveland, Ohio, USA
| | - Yang Chih-Hsiang
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Alexis Bergsma
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Parkinson’s Disease Center, Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Anne Drougard
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Erez Dror
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Darrell Chandler
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Daniel Schramek
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Timothy J. Triche
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - J. Andrew Pospisilik
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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4
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Hay AD, Kessler NJ, Gebert D, Takahashi N, Tavares H, Teixeira FK, Ferguson-Smith AC. Epigenetic inheritance is unfaithful at intermediately methylated CpG sites. Nat Commun 2023; 14:5336. [PMID: 37660134 PMCID: PMC10475082 DOI: 10.1038/s41467-023-40845-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/12/2023] [Indexed: 09/04/2023] Open
Abstract
DNA methylation at the CpG dinucleotide is considered a stable epigenetic mark due to its presumed long-term inheritance through clonal expansion. Here, we perform high-throughput bisulfite sequencing on clonally derived somatic cell lines to quantitatively measure methylation inheritance at the nucleotide level. We find that although DNA methylation is generally faithfully maintained at hypo- and hypermethylated sites, this is not the case at intermediately methylated CpGs. Low fidelity intermediate methylation is interspersed throughout the genome and within genes with no or low transcriptional activity, and is not coordinately maintained between neighbouring sites. We determine that the probabilistic changes that occur at intermediately methylated sites are likely due to DNMT1 rather than DNMT3A/3B activity. The observed lack of clonal inheritance at intermediately methylated sites challenges the current epigenetic inheritance model and has direct implications for both the functional relevance and general interpretability of DNA methylation as a stable epigenetic mark.
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Affiliation(s)
- Amir D Hay
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Noah J Kessler
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Daniel Gebert
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Nozomi Takahashi
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Hugo Tavares
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Felipe K Teixeira
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK.
| | - Anne C Ferguson-Smith
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
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Gerdes P, Chan D, Lundberg M, Sanchez-Luque FJ, Bodea GO, Ewing AD, Faulkner GJ, Richardson SR. Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development. Genome Res 2023; 33:1465-1481. [PMID: 37798118 PMCID: PMC10620060 DOI: 10.1101/gr.278003.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/21/2023] [Indexed: 10/07/2023]
Abstract
Mice harbor ∼2800 intact copies of the retrotransposon Long Interspersed Element 1 (L1). The in vivo retrotransposition capacity of an L1 copy is defined by both its sequence integrity and epigenetic status, including DNA methylation of the monomeric units constituting young mouse L1 promoters. Locus-specific L1 methylation dynamics during development may therefore elucidate and explain spatiotemporal niches of endogenous retrotransposition but remain unresolved. Here, we interrogate the retrotransposition efficiency and epigenetic fate of source (donor) L1s, identified as mobile in vivo. We show that promoter monomer loss consistently attenuates the relative retrotransposition potential of their offspring (daughter) L1 insertions. We also observe that most donor/daughter L1 pairs are efficiently methylated upon differentiation in vivo and in vitro. We use Oxford Nanopore Technologies (ONT) long-read sequencing to resolve L1 methylation genome-wide and at individual L1 loci, revealing a distinctive "smile" pattern in methylation levels across the L1 promoter region. Using Pacific Biosciences (PacBio) SMRT sequencing of L1 5' RACE products, we then examine DNA methylation dynamics at the mouse L1 promoter in parallel with transcription start site (TSS) distribution at locus-specific resolution. Together, our results offer a novel perspective on the interplay between epigenetic repression, L1 evolution, and genome stability.
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Affiliation(s)
- Patricia Gerdes
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland 4102, Australia
| | - Dorothy Chan
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland 4102, Australia
| | - Mischa Lundberg
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland 4102, Australia
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Queensland 4102, Australia
- Translational Bioinformatics, Commonwealth Scientific and Industrial Research Organisation, Sydney, New South Wales 2113, Australia
| | - Francisco J Sanchez-Luque
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland 4102, Australia
- GENYO. Centre for Genomics and Oncological Research (Pfizer-University of Granada-Andalusian Regional Government), PTS Granada, 18016, Spain
- MRC Human Genetics Unit, Institute of Genetics and Cancer (IGC), University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Gabriela O Bodea
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland 4102, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Adam D Ewing
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland 4102, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland 4102, Australia;
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sandra R Richardson
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland 4102, Australia;
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6
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Liu ZW, Liu J, Liu F, Zhong X. Depositing centromere repeats induces heritable intragenic heterochromatin establishment and spreading in Arabidopsis. Nucleic Acids Res 2023; 51:6039-6054. [PMID: 37094065 PMCID: PMC10325890 DOI: 10.1093/nar/gkad306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 04/10/2023] [Accepted: 04/19/2023] [Indexed: 04/26/2023] Open
Abstract
Stable transmission of non-DNA-sequence-based epigenetic information contributes to heritable phenotypic variants and thus to biological diversity. While studies on spontaneous natural epigenome variants have revealed an association of epialleles with a wide range of biological traits in both plants and animals, the function, transmission mechanism, and stability of an epiallele over generations in a locus-specific manner remain poorly investigated. Here, we invented a DNA sequence deposition strategy to generate a locus-specific epiallele by depositing CEN180 satellite repeats into a euchromatic target locus in Arabidopsis. Using CRISPR/Cas9-mediated knock-in system, we demonstrated that depositing CEN180 repeats can induce heterochromatin nucleation accompanied by DNA methylation, H3K9me2, and changes in the nucleosome occupancy at the insertion sites. Interestingly, both DNA methylation and H3K9me2 are restricted within the depositing sites and depletion of an H3K9me2 demethylase IBM1 enables the outward heterochromatin propagation into the neighboring regions, leading to inheritable target gene silencing to persist for at least five generations. Together, these results demonstrate the promise of employing a cis-engineering system for the creation of stable and site-specific epialleles and provide important insights into functional epigenome studies and locus-specific transgenerational epigenetic inheritance.
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Affiliation(s)
- Zhang-Wei Liu
- Department of Biology, Washington University in St Louis, St Louis, MO 63130, USA
- Wisconsin Institute for Discovery & Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jie Liu
- Department of Biology, Washington University in St Louis, St Louis, MO 63130, USA
- Wisconsin Institute for Discovery & Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Xuehua Zhong
- Department of Biology, Washington University in St Louis, St Louis, MO 63130, USA
- Wisconsin Institute for Discovery & Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
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7
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Gentilini D, Muzza M, de Filippis T, Vigone MC, Weber G, Calzari L, Cassio A, Di Frenna M, Bartolucci M, Grassi ES, Carbone E, Olivieri A, Persani L. Stochastic epigenetic mutations as possible explanation for phenotypical discordance among twins with congenital hypothyroidism. J Endocrinol Invest 2023; 46:393-404. [PMID: 36071330 PMCID: PMC9859866 DOI: 10.1007/s40618-022-01915-2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 08/29/2022] [Indexed: 01/27/2023]
Abstract
PURPOSE The elevated frequency of discordance for congenital hypothyroidism (CH) phenotype between monozygotic twins suggests the involvement of non-mendelian mechanisms. The aim of the study was to investigate the role of epigenetics in CH pathogenesis. METHODS A genome-wide DNA methylation analysis was performed on the peripheral blood of 23 twin pairs (10 monozygotic and 13 dizygotic), 4 concordant and 19 discordant pairs for CH at birth. RESULTS Differential methylation analysis did not show significant differences in methylation levels between CH cases and controls, but a different methylation status of several genes may explain the CH discordance of a monozygotic twin couple carrying a monoallelic nonsense mutation of DUOX2. In addition, the median number of hypo-methylated Stochastic Epigenetic Mutations (SEMs) resulted significantly increased in cases compared to controls. The prioritization analysis for CH performed on the genes epimutated exclusively in the cases identified SLC26A4, FOXI1, NKX2-5 and TSHB as the genes with the highest score. The analysis of significantly SEMs-enriched regions led to the identification of two genes (FAM50B and MEG8) that resulted epigenetically dysregulated in cases. CONCLUSION Epigenetic modifications may potentially account for CH pathogenesis and explain discordance among monozygotic twins.
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Affiliation(s)
- D Gentilini
- Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, Cusano Milanino, 20095, Milan, Italy
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - M Muzza
- Laboratory of Endocrine and Metabolic Research, Department of Endocrine and Metabolic Diseases, Istituto Auxologico Italiano IRCCS, Piazzale Brescia 20, 20149, Milan, Italy
| | - T de Filippis
- Laboratory of Endocrine and Metabolic Research, Department of Endocrine and Metabolic Diseases, Istituto Auxologico Italiano IRCCS, Piazzale Brescia 20, 20149, Milan, Italy
| | - M C Vigone
- Department of Pediatrics, Endocrine Unit, IRCCS San Raffaele Hospital, Milan, Italy
| | - G Weber
- Department of Pediatrics, Endocrine Unit, IRCCS San Raffaele Hospital, Milan, Italy
| | - L Calzari
- Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, Cusano Milanino, 20095, Milan, Italy
| | - A Cassio
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - M Di Frenna
- Department of Pediatrics, Endocrine Unit, IRCCS San Raffaele Hospital, Milan, Italy
| | - M Bartolucci
- Department of Maternal and Child Sciences and Urology, University "La Sapienza", Rome, Italy
| | - E S Grassi
- Department of Medical Biotechnology and Experimental Medicine, University of Milan, 20122, Milan, Italy
| | - E Carbone
- Laboratory of Endocrine and Metabolic Research, Department of Endocrine and Metabolic Diseases, Istituto Auxologico Italiano IRCCS, Piazzale Brescia 20, 20149, Milan, Italy
| | - A Olivieri
- Department of Cardiovascular and Endocrine-Metabolic Diseases and Aging, Italian National Institute of Health, 00161, Rome, Italy
| | - L Persani
- Laboratory of Endocrine and Metabolic Research, Department of Endocrine and Metabolic Diseases, Istituto Auxologico Italiano IRCCS, Piazzale Brescia 20, 20149, Milan, Italy.
- Department of Medical Biotechnology and Experimental Medicine, University of Milan, 20122, Milan, Italy.
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8
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Švorcová J. Transgenerational Epigenetic Inheritance of Traumatic Experience in Mammals. Genes (Basel) 2023; 14:120. [PMID: 36672861 PMCID: PMC9859285 DOI: 10.3390/genes14010120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023] Open
Abstract
In recent years, we have seen an increasing amount of evidence pointing to the existence of a non-genetic heredity of the effects of events such as separation from parents, threat to life, or other traumatising experiences such as famine. This heredity is often mediated by epigenetic regulations of gene expression and may be transferred even across several generations. In this review, we focus on studies which involve transgenerational epigenetic inheritance (TEI), with a short detour to intergenerational studies focused on the inheritance of trauma or stressful experiences. The reviewed studies show a plethora of universal changes which stress exposure initiates on multiple levels of organisation ranging from hormonal production and the hypothalamic-pituitary-adrenal (HPA) axis modulation all the way to cognition, behaviour, or propensity to certain psychiatric or metabolic disorders. This review will also provide an overview of relevant methodology and difficulties linked to implementation of epigenetic studies. A better understanding of these processes may help us elucidate the evolutionary pathways which are at work in the course of emergence of the diseases and disorders associated with exposure to trauma, either direct or in a previous generation.
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Affiliation(s)
- Jana Švorcová
- Department of Philosophy and History of Science, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
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9
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Fueyo R, Judd J, Feschotte C, Wysocka J. Roles of transposable elements in the regulation of mammalian transcription. Nat Rev Mol Cell Biol 2022; 23:481-497. [PMID: 35228718 PMCID: PMC10470143 DOI: 10.1038/s41580-022-00457-y] [Citation(s) in RCA: 110] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2022] [Indexed: 12/16/2022]
Abstract
Transposable elements (TEs) comprise about half of the mammalian genome. TEs often contain sequences capable of recruiting the host transcription machinery, which they use to express their own products and promote transposition. However, the regulatory sequences carried by TEs may affect host transcription long after the TEs have lost the ability to transpose. Recent advances in genome analysis and engineering have facilitated systematic interrogation of the regulatory activities of TEs. In this Review, we discuss diverse mechanisms by which TEs contribute to transcription regulation. Notably, TEs can donate enhancer and promoter sequences that influence the expression of host genes, modify 3D chromatin architecture and give rise to novel regulatory genes, including non-coding RNAs and transcription factors. We discuss how TEs spur regulatory evolution and facilitate the emergence of genetic novelties in mammalian physiology and development. By virtue of their repetitive and interspersed nature, TEs offer unique opportunities to dissect the effects of mutation and genomic context on the function and evolution of cis-regulatory elements. We argue that TE-centric studies hold the key to unlocking general principles of transcription regulation and evolution.
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Affiliation(s)
- Raquel Fueyo
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julius Judd
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Cedric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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10
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Carlini V, Policarpi C, Hackett JA. Epigenetic inheritance is gated by naïve pluripotency and Dppa2. EMBO J 2022; 41:e108677. [PMID: 35199868 PMCID: PMC8982627 DOI: 10.15252/embj.2021108677] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 12/14/2022] Open
Abstract
Environmental factors can trigger cellular responses that propagate across mitosis or even generations. Perturbations to the epigenome could underpin such acquired changes, however, the extent and contexts in which modified chromatin states confer heritable memory in mammals is unclear. Here, we exploit a precision epigenetic editing strategy and forced Xist activity to programme de novo heterochromatin domains (epialleles) at endogenous loci and track their inheritance in a developmental model. We find that naïve pluripotent phases systematically erase ectopic domains of heterochromatin via active mechanisms, which likely acts as an intergenerational safeguard against transmission of epialleles. Upon lineage specification, however, acquired chromatin states can be probabilistically inherited under selectively favourable conditions, including propagation of p53 silencing through in vivo development. Using genome‐wide CRISPR screening, we identify molecular factors that restrict heritable memory of epialleles in naïve pluripotent cells, and demonstrate that removal of chromatin factor Dppa2 unlocks the potential for epigenetic inheritance uncoupled from DNA sequence. Our study outlines a mechanistic basis for how epigenetic inheritance is constrained in mammals, and reveals genomic and developmental contexts in which heritable memory is feasible.
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Affiliation(s)
- Valentina Carlini
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy.,Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Cristina Policarpi
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
| | - Jamie A Hackett
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
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11
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Abstract
Increasing evidence indicates that non-DNA sequence-based epigenetic information can be inherited across several generations in organisms ranging from yeast to plants to humans. This raises the possibility of heritable 'epimutations' contributing to heritable phenotypic variation and thus to evolution. Recent work has shed light on both the signals that underpin these epimutations, including DNA methylation, histone modifications and non-coding RNAs, and the mechanisms by which they are transmitted across generations at the molecular level. These mechanisms can vary greatly among species and have a more limited effect in mammals than in plants and other animal species. Nevertheless, common principles are emerging, with transmission occurring either via direct replicative mechanisms or indirect reconstruction of the signal in subsequent generations. As these processes become clearer we continue to improve our understanding of the distinctive features and relative contribution of DNA sequence and epigenetic variation to heritable differences in phenotype.
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12
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Ghai M, Kader F. A Review on Epigenetic Inheritance of Experiences in Humans. Biochem Genet 2021; 60:1107-1140. [PMID: 34792705 DOI: 10.1007/s10528-021-10155-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 11/04/2021] [Indexed: 12/13/2022]
Abstract
If genetics defines the inheritance of DNA, epigenetics aims to regulate and make it adaptable. Epigenetic alterations include DNA methylation, chromatin remodelling, post-translational modifications of histone proteins and activity of non-coding RNAs. Several studies, especially in animal models, have reported transgenerational inheritance of epigenetic marks. However, evidence of transgenerational inheritance in humans via germline in the absence of any direct exposure to the driving external stimulus remains controversial. Most of the epimutations exist in relation with genetic variants. The present review looks at intergenerational and transgenerational inheritance in humans, (both father and mother) in response to diet, exposure to chemicals, stress, exercise, and disease status. If not transgenerational, at least intergenerational human studies could help to understand early processes of inheritance. In humans, female and male germline development follow separate paths of epigenetic events and both oocyte and sperm possess their own unique epigenomes. While DNA methylation alterations are reset during epigenetic reprogramming, non-coding RNAs via human sperm provide evidence of being reliable carriers for transgenerational inheritance. Human studies reveal that one mechanism of epigenetic inheritance cannot be applied to the complete human genome. Multiple factors including time, type, and tissue of exposure determine if the modified epigenetic mark could be transmissible and till which generation. Population-specific differences should also be taken into consideration while associating inheritance to an environmental exposure. A longitudinal study targeting one environmental factor, but different population groups should be conducted at a specific geographical location to pinpoint heritable epigenetic changes.
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Affiliation(s)
- Meenu Ghai
- Discipline of Genetics, School of Life Sciences, Westville Campus, University of KwaZulu-Natal, Private Bag X54001, Durban, KwaZulu Natal, South Africa.
| | - Farzeen Kader
- Discipline of Genetics, School of Life Sciences, Westville Campus, University of KwaZulu-Natal, Private Bag X54001, Durban, KwaZulu Natal, South Africa
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13
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14
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Luperchio TR, Boukas L, Zhang L, Pilarowski G, Jiang J, Kalinousky A, Hansen KD, Bjornsson HT. Leveraging the Mendelian disorders of the epigenetic machinery to systematically map functional epigenetic variation. eLife 2021; 10:65884. [PMID: 34463256 PMCID: PMC8443249 DOI: 10.7554/elife.65884] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 08/27/2021] [Indexed: 12/12/2022] Open
Abstract
Although each Mendelian Disorder of the Epigenetic Machinery (MDEM) has a different causative gene, there are shared disease manifestations. We hypothesize that this phenotypic convergence is a consequence of shared epigenetic alterations. To identify such shared alterations, we interrogate chromatin (ATAC-seq) and expression (RNA-seq) states in B cells from three MDEM mouse models (Kabuki [KS] type 1 and 2 and Rubinstein-Taybi type 1 [RT1] syndromes). We develop a new approach for the overlap analysis and find extensive overlap primarily localized in gene promoters. We show that disruption of chromatin accessibility at promoters often disrupts downstream gene expression, and identify 587 loci and 264 genes with shared disruption across all three MDEMs. Subtle expression alterations of multiple, IgA-relevant genes, collectively contribute to IgA deficiency in KS1 and RT1, but not in KS2. We propose that the joint study of MDEMs offers a principled approach for systematically mapping functional epigenetic variation in mammals.
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Affiliation(s)
- Teresa Romeo Luperchio
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Leandros Boukas
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Li Zhang
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Genay Pilarowski
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Jenny Jiang
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Allison Kalinousky
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Kasper D Hansen
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Hans T Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Landspitali University Hospital, Reykjavik, Iceland
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15
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Bertozzi TM, Becker JL, Blake GET, Bansal A, Nguyen DK, Fernandez-Twinn DS, Ozanne SE, Bartolomei MS, Simmons RA, Watson ED, Ferguson-Smith AC. Variably methylated retrotransposons are refractory to a range of environmental perturbations. Nat Genet 2021; 53:1233-1242. [PMID: 34326545 PMCID: PMC7611517 DOI: 10.1038/s41588-021-00898-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 06/18/2021] [Indexed: 12/27/2022]
Abstract
The agouti viable yellow (Avy) allele is an insertional mutation in the mouse genome caused by a variably methylated intracisternal A particle (VM-IAP) retrotransposon. Avy expressivity is sensitive to a range of early-life chemical exposures and nutritional interventions, suggesting that environmental perturbations can have long-lasting effects on the methylome. However, the extent to which VM-IAP elements are environmentally labile with phenotypic implications is unknown. Using a recently identified repertoire of VM-IAPs, we assessed the epigenetic effects of different environmental contexts. A longitudinal aging analysis indicated that VM-IAPs are stable across the murine lifespan, with only small increases in DNA methylation detected for a subset of loci. No significant effects were observed after maternal exposure to the endocrine disruptor bisphenol A, an obesogenic diet or methyl donor supplementation. A genetic mouse model of abnormal folate metabolism exhibited shifted VM-IAP methylation levels and altered VM-IAP-associated gene expression, yet these effects are likely largely driven by differential targeting by polymorphic KRAB zinc finger proteins. We conclude that epigenetic variability at retrotransposons is not predictive of environmental susceptibility.
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Affiliation(s)
| | | | - Georgina E T Blake
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Amita Bansal
- Center for Research on Reproduction and Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Australian National University Medical School, John Curtin School of Medical Research, College of Health and Medicine, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Duy K Nguyen
- Department of Cell and Developmental Biology, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Denise S Fernandez-Twinn
- University of Cambridge Metabolic Research Laboratories and Medical Research Council Metabolic Diseases Unit, Wellcome Trust Medical Research Council Institute of Metabolic Science, Cambridge, UK
| | - Susan E Ozanne
- University of Cambridge Metabolic Research Laboratories and Medical Research Council Metabolic Diseases Unit, Wellcome Trust Medical Research Council Institute of Metabolic Science, Cambridge, UK
| | - Marisa S Bartolomei
- Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Rebecca A Simmons
- Center for Research on Reproduction and Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Erica D Watson
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Anne C Ferguson-Smith
- Department of Genetics, University of Cambridge, Cambridge, UK.
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
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16
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Bertozzi TM, Takahashi N, Hanin G, Kazachenka A, Ferguson-Smith AC. A spontaneous genetically induced epiallele at a retrotransposon shapes host genome function. eLife 2021; 10:e65233. [PMID: 33755012 PMCID: PMC8084528 DOI: 10.7554/elife.65233] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/22/2021] [Indexed: 12/14/2022] Open
Abstract
Intracisternal A-particles (IAPs) are endogenous retroviruses (ERVs) responsible for most insertional mutations in the mouse. Full-length IAPs harbour genes flanked by long terminal repeats (LTRs). Here, we identify a solo LTR IAP variant (Iap5-1solo) recently formed in the inbred C57BL/6J mouse strain. In contrast to the C57BL/6J full-length IAP at this locus (Iap5-1full), Iap5-1solo lacks DNA methylation and H3K9 trimethylation. The distinct DNA methylation levels between the two alleles are established during preimplantation development, likely due to loss of KRAB zinc finger protein binding at the Iap5-1solo variant. Iap5-1solo methylation increases and becomes more variable in a hybrid genetic background yet is unresponsive to maternal dietary methyl supplementation. Differential epigenetic modification of the two variants is associated with metabolic differences and tissue-specific changes in adjacent gene expression. Our characterisation of Iap5-1 as a genetically induced epiallele with functional consequences establishes a new model to study transposable element repression and host-element co-evolution.
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Affiliation(s)
- Tessa M Bertozzi
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Nozomi Takahashi
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Geula Hanin
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
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17
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Elmer JL, Hay AD, Kessler NJ, Bertozzi TM, Ainscough EAC, Ferguson-Smith AC. Genomic properties of variably methylated retrotransposons in mouse. Mob DNA 2021; 12:6. [PMID: 33612119 PMCID: PMC7898769 DOI: 10.1186/s13100-021-00235-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/02/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are enriched in cytosine methylation, preventing their mobility within the genome. We previously identified a genome-wide repertoire of candidate intracisternal A particle (IAP) TEs in mice that exhibit inter-individual variability in this methylation (VM-IAPs) with implications for genome function. RESULTS Here we validate these metastable epialleles and discover a novel class that exhibit tissue specificity (tsVM-IAPs) in addition to those with uniform methylation in all tissues (constitutive- or cVM-IAPs); both types have the potential to regulate genes in cis. Screening for variable methylation at other TEs shows that this phenomenon is largely limited to IAPs, which are amongst the youngest and most active endogenous retroviruses. We identify sequences enriched within cVM-IAPs, but determine that these are not sufficient to confer epigenetic variability. CTCF is enriched at VM-IAPs with binding inversely correlated with DNA methylation. We uncover dynamic physical interactions between cVM-IAPs with low methylation ranges and other genomic loci, suggesting that VM-IAPs have the potential for long-range regulation. CONCLUSION Our findings indicate that a recently evolved interplay between genetic sequence, CTCF binding, and DNA methylation at young TEs can result in inter-individual variability in transcriptional outcomes with implications for phenotypic variation.
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Affiliation(s)
- Jessica L. Elmer
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
| | - Amir D. Hay
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
| | - Noah J. Kessler
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
| | - Tessa M. Bertozzi
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
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18
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Wu HJ, Kuchtey J, Kuchtey RW. Increased Susceptibility to Glaucomatous Damage in Microfibril Deficient Mice. Invest Ophthalmol Vis Sci 2021; 61:28. [PMID: 32797197 PMCID: PMC7441341 DOI: 10.1167/iovs.61.10.28] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Purpose To test whether mice with microfibril deficiency due to the Tsk mutation of fibrillin-1 (Fbn1Tsk/+) have increased susceptibility to pressure-induced retinal ganglion cell (RGC) degeneration. Methods Intraocular pressure (IOP) elevation was induced in Fbn1Tsk/+ and wild type (wt) mice by injecting microbeads into the anterior chamber. Mice were then followed up for four months, with IOP measurements every three to six days. Retinas were stained for Brn3a to determine RGC number. Optic nerve cross-sections were stained with p-phenylene diamine to determine nerve area, axon number, and caliber and thickness of the pia mater. Results Microbead injection induced significant IOP elevation that was significantly less for Fbn1Tsk/+ mice compared with wt. The optic nerves and optic nerve axons were larger, and the elastic fiber-rich pia mater was thinner in Fbn1Tsk/+ mice. Microbead injection resulted in reduced optic nerve size, thicker pia mater, and a slight decrease in axon size. Fbn1Tsk/+ mice had significantly greater loss of RGCs and optic nerve axons compared with wt (14.8% vs. 5.8%, P = 0.002, and 17.0% vs. 7.5%, P = 0.002, respectively). Conclusions Fbn1Tsk/+mice had altered optic nerve structure as indicated by larger optic nerves, larger optic nerve axons and thinner pia mater, consistent with our previous findings. Despite lower IOP elevation, Fbn1Tsk/+mice had greater loss of RGCs and optic nerve axons, suggesting increased susceptibility to IOP-induced optic nerve degeneration in microfibril-deficient mice.
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Affiliation(s)
- Hang-Jing Wu
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - John Kuchtey
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Rachel W Kuchtey
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States.,Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States
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19
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Bertozzi TM, Elmer JL, Macfarlan TS, Ferguson-Smith AC. KRAB zinc finger protein diversification drives mammalian interindividual methylation variability. Proc Natl Acad Sci U S A 2020; 117:31290-31300. [PMID: 33239447 PMCID: PMC7733849 DOI: 10.1073/pnas.2017053117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Most transposable elements (TEs) in the mouse genome are heavily modified by DNA methylation and repressive histone modifications. However, a subset of TEs exhibit variable methylation levels in genetically identical individuals, and this is associated with epigenetically conferred phenotypic differences, environmental adaptability, and transgenerational epigenetic inheritance. The evolutionary origins and molecular mechanisms underlying interindividual epigenetic variability remain unknown. Using a repertoire of murine variably methylated intracisternal A-particle (VM-IAP) epialleles as a model, we demonstrate that variable DNA methylation states at TEs are highly susceptible to genetic background effects. Taking a classical genetics approach coupled with genome-wide analysis, we harness these effects and identify a cluster of KRAB zinc finger protein (KZFP) genes that modifies VM-IAPs in trans in a sequence-specific manner. Deletion of the cluster results in decreased DNA methylation levels and altered histone modifications at the targeted VM-IAPs. In some cases, these effects are accompanied by dysregulation of neighboring genes. We find that VM-IAPs cluster together phylogenetically and that this is linked to differential KZFP binding, suggestive of an ongoing evolutionary arms race between TEs and this large family of epigenetic regulators. These findings indicate that KZFP divergence and concomitant evolution of DNA binding capabilities are mechanistically linked to methylation variability in mammals, with implications for phenotypic variation and putative paradigms of mammalian epigenetic inheritance.
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Affiliation(s)
- Tessa M Bertozzi
- Department of Genetics, University of Cambridge, CB2 3EH Cambridge, United Kingdom
| | - Jessica L Elmer
- Department of Genetics, University of Cambridge, CB2 3EH Cambridge, United Kingdom
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, MD 20892
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20
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Nätt D, Öst A. Male reproductive health and intergenerational metabolic responses from a small RNA perspective. J Intern Med 2020; 288:305-320. [PMID: 32415866 DOI: 10.1111/joim.13096] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/10/2020] [Accepted: 04/23/2020] [Indexed: 02/06/2023]
Abstract
The world has recently experienced a decline in male reproductive (e.g. sperm counts and motility) and metabolic (e.g. obesity and diabetes) health. Accumulated evidence from animal models also shows that the metabolic health of the father may influence the metabolic health in his offspring. Vectors for such paternal intergenerational metabolic responses (IGMRs) involve small noncoding RNAs (sncRNAs) that often increase in spermatozoa during the last days of maturation in the epididymis. We and others have shown that the metabolic state - depending on factors such as diet, obesity and physical exercise - may affect sperm quality and sperm sncRNA. Together, this suggests that there are overlapping aetiologies between the male metabolic syndrome, male factor infertility and intergenerational responses. In this review, we present a theoretical framework for an overlap of these aetiologies by exploring the advances in our understanding of the roles of sncRNA in spermatogenesis and offspring development. A special focus will lie on novel findings about tRNA-derived small RNA (tsRNA), rRNA-derived small RNA (rsRNA) and small mitochondrial RNA (mitoRNA), and their emerging roles in intergenerational metabolic and reproductive health.
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Affiliation(s)
- D Nätt
- From the, Department of Clinical and Experimental Medicine, Linköping University, Linkoping, Sweden
| | - A Öst
- From the, Department of Clinical and Experimental Medicine, Linköping University, Linkoping, Sweden
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21
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Strain-Specific Epigenetic Regulation of Endogenous Retroviruses: The Role of Trans-Acting Modifiers. Viruses 2020; 12:v12080810. [PMID: 32727076 PMCID: PMC7472028 DOI: 10.3390/v12080810] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/21/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023] Open
Abstract
Approximately 10 percent of the mouse genome consists of endogenous retroviruses (ERVs), relics of ancient retroviral infections that are classified based on their relatedness to exogenous retroviral genera. Because of the ability of ERVs to retrotranspose, as well as their cis-acting regulatory potential due to functional elements located within the elements, mammalian ERVs are generally subject to epigenetic silencing by DNA methylation and repressive histone modifications. The mobilisation and expansion of ERV elements is strain-specific, leading to ERVs being highly polymorphic between inbred mouse strains, hinting at the possibility of the strain-specific regulation of ERVs. In this review, we describe the existing evidence of mouse strain-specific epigenetic control of ERVs and discuss the implications of differential ERV regulation on epigenetic inheritance models. We consider Krüppel-associated box domain (KRAB) zinc finger proteins as likely candidates for strain-specific ERV modifiers, drawing on insights gained from the study of the strain-specific behaviour of transgenes. We conclude by considering the coevolution of KRAB zinc finger proteins and actively transposing ERV elements, and highlight the importance of cross-strain studies in elucidating the mechanisms and consequences of strain-specific ERV regulation.
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22
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Cullen H, Schorn AJ. Endogenous Retroviruses Walk a Fine Line between Priming and Silencing. Viruses 2020; 12:v12080792. [PMID: 32718022 PMCID: PMC7472051 DOI: 10.3390/v12080792] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/31/2022] Open
Abstract
Endogenous retroviruses (ERVs) in mammals are closely related to infectious retroviruses and utilize host tRNAs as a primer for reverse transcription and replication, a hallmark of long terminal repeat (LTR) retroelements. Their dependency on tRNA makes these elements vulnerable to targeting by small RNAs derived from the 3′-end of mature tRNAs (3′-tRFs), which are highly expressed during epigenetic reprogramming and potentially protect many tissues in eukaryotes. Here, we review some key functions of ERV reprogramming during mouse and human development and discuss how small RNA-mediated silencing maintains genome stability when ERVs are temporarily released from heterochromatin repression. In particular, we take a closer look at the tRNA primer binding sites (PBS) of two highly active ERV families in mice and their sequence variation that is shaped by the conflict of successful tRNA priming for replication versus evasion of silencing by 3′-tRFs.
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