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Garambois C, Boulesteix M, Fablet M. Effects of Arboviral Infections on Transposable Element Transcript Levels in Aedes aegypti. Genome Biol Evol 2024; 16:evae092. [PMID: 38695057 PMCID: PMC11110940 DOI: 10.1093/gbe/evae092] [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] [Accepted: 04/22/2024] [Indexed: 05/23/2024] Open
Abstract
Transposable elements are mobile repeated sequences found in all genomes. Transposable elements are controlled by RNA interference pathways in most organisms, and this control involves the PIWI-interacting RNA pathway and the small interfering RNA pathway, which is also known to be the first line of antiviral defense in invertebrates. Using Drosophila, we recently showed that viral infections result in the modulation of transposable element transcript levels through modulation of the small RNA repertoire. The Aedes aegypti mosquito is of particular interest because almost half of its genome is made of transposable elements, and it is described as a major vector of viruses (such as the dengue [DENV], Zika [ZIKV], and chikungunya [CHIKV] arboviruses). Moreover, Aedes mosquitoes are unique among insects in that the PIWI-interacting RNA pathway is also involved in the somatic antiviral response, in addition to the transposable element control and PIWI-interacting RNA pathway genes expanded in the mosquito genome. For these reasons, we studied the impacts of viral infections on transposable element transcript levels in A. aegypti samples. We retrieved public datasets corresponding to RNA-seq data obtained from viral infections by DENV, ZIKV, and CHIKV in various tissues. We found that transposable element transcripts are moderately modulated following viral infection and that the direction of the modulation varies greatly across tissues and viruses. These results highlight the need for an in-depth investigation of the tightly intertwined interactions between transposable elements and viruses.
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Affiliation(s)
- Chloé Garambois
- Universite Claude Bernard Lyon 1, Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, CNRS, VAS, Villeurbanne 69622, France
| | - Matthieu Boulesteix
- Universite Claude Bernard Lyon 1, Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, CNRS, VAS, Villeurbanne 69622, France
| | - Marie Fablet
- Universite Claude Bernard Lyon 1, Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, CNRS, VAS, Villeurbanne 69622, France
- Institut Universitaire de France (IUF), Paris, France
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2
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Crawford BI, Talley MJ, Russman J, Riddle J, Torres S, Williams T, Longworth MS. Condensin-mediated restriction of retrotransposable elements facilitates brain development in Drosophila melanogaster. Nat Commun 2024; 15:2716. [PMID: 38548759 PMCID: PMC10978865 DOI: 10.1038/s41467-024-47042-9] [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: 12/22/2022] [Accepted: 03/18/2024] [Indexed: 04/01/2024] Open
Abstract
Neural stem and progenitor cell (NSPC) maintenance is essential for ensuring that organisms are born with proper brain volumes and head sizes. Microcephaly is a disorder in which babies are born with significantly smaller head sizes and cortical volumes. Mutations in subunits of the DNA organizing complex condensin have been identified in microcephaly patients. However, the molecular mechanisms by which condensin insufficiency causes microcephaly remain elusive. We previously identified conserved roles for condensins in repression of retrotransposable elements (RTEs). Here, we show that condensin subunit knockdown in NSPCs of the Drosophila larval central brain increases RTE expression and mobility which causes cell death, and significantly decreases adult head sizes and brain volumes. These findings suggest that unrestricted RTE expression and activity may lead to improper brain development in condensin insufficient organisms, and lay the foundation for future exploration of causative roles for RTEs in other microcephaly models.
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Affiliation(s)
- Bert I Crawford
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Mary Jo Talley
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Joshua Russman
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - James Riddle
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Sabrina Torres
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Troy Williams
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Michelle S Longworth
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, 44195, USA.
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3
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Hassan AH, Mokhtar MM, El Allali A. Transposable elements: multifunctional players in the plant genome. FRONTIERS IN PLANT SCIENCE 2024; 14:1330127. [PMID: 38239225 PMCID: PMC10794571 DOI: 10.3389/fpls.2023.1330127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/06/2023] [Indexed: 01/22/2024]
Abstract
Transposable elements (TEs) are indispensable components of eukaryotic genomes that play diverse roles in gene regulation, recombination, and environmental adaptation. Their ability to mobilize within the genome leads to gene expression and DNA structure changes. TEs serve as valuable markers for genetic and evolutionary studies and facilitate genetic mapping and phylogenetic analysis. They also provide insight into how organisms adapt to a changing environment by promoting gene rearrangements that lead to new gene combinations. These repetitive sequences significantly impact genome structure, function and evolution. This review takes a comprehensive look at TEs and their applications in biotechnology, particularly in the context of plant biology, where they are now considered "genomic gold" due to their extensive functionalities. The article addresses various aspects of TEs in plant development, including their structure, epigenetic regulation, evolutionary patterns, and their use in gene editing and plant molecular markers. The goal is to systematically understand TEs and shed light on their diverse roles in plant biology.
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Affiliation(s)
- Asmaa H. Hassan
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- Agricultural Genetic Engineering Research Institute, Agriculture Research Center, Giza, Egypt
| | - Morad M. Mokhtar
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- Agricultural Genetic Engineering Research Institute, Agriculture Research Center, Giza, Egypt
| | - Achraf El Allali
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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4
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Scopa C, Barnada SM, Cicardi ME, Singer M, Trotti D, Trizzino M. JUN upregulation drives aberrant transposable element mobilization, associated innate immune response, and impaired neurogenesis in Alzheimer's disease. Nat Commun 2023; 14:8021. [PMID: 38049398 PMCID: PMC10696058 DOI: 10.1038/s41467-023-43728-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 11/06/2023] [Indexed: 12/06/2023] Open
Abstract
Adult neurogenic decline, inflammation, and neurodegeneration are phenotypic hallmarks of Alzheimer's disease (AD). Mobilization of transposable elements (TEs) in heterochromatic regions was recently reported in AD, but the underlying mechanisms are still underappreciated. Combining functional genomics with the differentiation of familial and sporadic AD patient derived-iPSCs into hippocampal progenitors, CA3 neurons, and cerebral organoids, we found that the upregulation of the AP-1 subunit, c-Jun, triggers decondensation of genomic regions containing TEs. This leads to the cytoplasmic accumulation of HERVK-derived RNA-DNA hybrids, the activation of the cGAS-STING cascade, and increased levels of cleaved caspase-3, suggesting the initiation of programmed cell death in AD progenitors and neurons. Notably, inhibiting c-Jun effectively blocks all these downstream molecular processes and rescues neuronal death and the impaired neurogenesis phenotype in AD progenitors. Our findings open new avenues for identifying therapeutic strategies and biomarkers to counteract disease progression and diagnose AD in the early, pre-symptomatic stages.
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Affiliation(s)
- Chiara Scopa
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA.
- Jefferson Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA.
| | - Samantha M Barnada
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Maria E Cicardi
- Jefferson Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - Mo Singer
- Jefferson Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - Davide Trotti
- Jefferson Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA.
| | - Marco Trizzino
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA.
- Department of Life Sciences, Imperial College London, London, UK.
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5
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Wodrich APK, Scott AW, Giniger E. What do we mean by "aging"?: Questions and perspectives revealed by studies in Drosophila. Mech Ageing Dev 2023:111839. [PMID: 37354919 DOI: 10.1016/j.mad.2023.111839] [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: 05/01/2023] [Revised: 06/14/2023] [Accepted: 06/21/2023] [Indexed: 06/26/2023]
Abstract
What is the nature of aging, and how best can we study it? Here, using a series of questions that highlight differing perspectives about the nature of aging, we ask how data from Drosophila melanogaster at the organismal, tissue, cellular, and molecular levels shed light on the complex interactions among the phenotypes associated with aging. Should aging be viewed as an individual's increasing probability of mortality over time or as a progression of physiological states? Are all age-correlated changes in physiology detrimental to vigor or are some compensatory changes that maintain vigor? Why do different age-correlated functions seem to change at different rates in a single individual as it ages? Should aging be considered as a single, integrated process across the scales of biological resolution, from organismal to molecular, or must we consider each level of biological scale as a separate, distinct entity? Viewing aging from these differing perspectives yields distinct but complementary interpretations about the properties and mechanisms of aging and may offer a path through the complexities related to understanding the nature of aging.
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Affiliation(s)
- Andrew P K Wodrich
- National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, United States; Interdisciplinary Program in Neuroscience, Georgetown University, Washington, DC, United States; College of Medicine, University of Kentucky, Lexington, KY, United States
| | - Andrew W Scott
- National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Edward Giniger
- National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, United States.
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6
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Schneider BK, Sun S, Lee M, Li W, Skvir N, Neretti N, Vijg J, Secombe J. Expression of retrotransposons contributes to aging in Drosophila. Genetics 2023; 224:iyad073. [PMID: 37084379 PMCID: PMC10213499 DOI: 10.1093/genetics/iyad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/12/2022] [Accepted: 04/11/2023] [Indexed: 04/23/2023] Open
Abstract
Retrotransposons are a class of transposable elements capable of self-replication and insertion into new genomic locations. Across species, the mobilization of retrotransposons in somatic cells has been suggested to contribute to the cell and tissue functional decline that occurs during aging. Retrotransposons are broadly expressed across cell types, and de novo insertions have been observed to correlate with tumorigenesis. However, the extent to which new retrotransposon insertions occur during normal aging and their effect on cellular and animal function remains understudied. Here, we use a single nucleus whole genome sequencing approach in Drosophila to directly test whether transposon insertions increase with age in somatic cells. Analyses of nuclei from thoraces and indirect flight muscles using a newly developed pipeline, Retrofind, revealed no significant increase in the number of transposon insertions with age. Despite this, reducing the expression of two different retrotransposons, 412 and Roo, extended lifespan, but did not alter indicators of health such as stress resistance. This suggests a key role for transposon expression and not insertion in regulating longevity. Transcriptomic analyses revealed similar changes to gene expression in 412 and Roo knockdown flies and highlighted changes to genes involved in proteolysis and immune function as potential contributors to the observed changes in longevity. Combined, our data show a clear link between retrotransposon expression and aging.
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Affiliation(s)
- Blair K Schneider
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Ullmann 809 Bronx, NY 10461, USA
| | - Shixiang Sun
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave., Price 468 Bronx, NY 10461, USA
| | - Moonsook Lee
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave., Price 468 Bronx, NY 10461, USA
| | - Wenge Li
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Ullmann 909 Bronx, NY 10461, USA
| | - Nicholas Skvir
- Department of Molecular biology, Cell biology and Biochemistry, Brown University, 70 Ship St., Providence 02903, USA
| | - Nicola Neretti
- Department of Molecular biology, Cell biology and Biochemistry, Brown University, 70 Ship St., Providence 02903, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave., Price 468 Bronx, NY 10461, USA
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Ullmann 809 Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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7
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Copley KE, Shorter J. Repetitive elements in aging and neurodegeneration. Trends Genet 2023; 39:381-400. [PMID: 36935218 PMCID: PMC10121923 DOI: 10.1016/j.tig.2023.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 03/19/2023]
Abstract
Repetitive elements (REs), such as transposable elements (TEs) and satellites, comprise much of the genome. Here, we review how TEs and (peri)centromeric satellite DNA may contribute to aging and neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS). Alterations in RE expression, retrotransposition, and chromatin microenvironment may shorten lifespan, elicit neurodegeneration, and impair memory and movement. REs may cause these phenotypes via DNA damage, protein sequestration, insertional mutagenesis, and inflammation. We discuss several TE families, including gypsy, HERV-K, and HERV-W, and how TEs interact with various factors, including transactive response (TAR) DNA-binding protein 43 kDa (TDP-43) and the siRNA and piwi-interacting (pi)RNA systems. Studies of TEs in neurodegeneration have focused on Drosophila and, thus, further examination in mammals is needed. We suggest that therapeutic silencing of REs could help mitigate neurodegenerative disorders.
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Affiliation(s)
- Katie E Copley
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Neuroscience Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Neuroscience Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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8
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Yushkova E, Moskalev A. Transposable elements and their role in aging. Ageing Res Rev 2023; 86:101881. [PMID: 36773759 DOI: 10.1016/j.arr.2023.101881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/16/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023]
Abstract
Transposable elements (TEs) are an important part of eukaryotic genomes. The role of somatic transposition in aging, carcinogenesis, and other age-related diseases has been determined. This review discusses the fundamental properties of TEs and their complex interactions with cellular processes, which are crucial for understanding the diverse effects of their activity on the genetics and epigenetics of the organism. The interactions of TEs with recombination, replication, repair, and chromosomal regulation; the ability of TEs to maintain a balance between their own activity and repression, the involvement of TEs in the creation of new or alternative genes, the expression of coding/non-coding RNA, and the role in DNA damage and modification of regulatory networks are reviewed. The contribution of the derepressed TEs to age-dependent effects in individual cells/tissues in different organisms was assessed. Conflicting information about TE activity under stress as well as theories of aging mechanisms related to TEs is discussed. On the one hand, transposition activity in response to stressors can lead to organisms acquiring adaptive innovations of great importance for evolution at the population level. On the other hand, the TE expression can cause decreased longevity and stress tolerance at the individual level. The specific features of TE effects on aging processes in germline and soma and the ways of their regulation in cells are highlighted. Recent results considering somatic mutations in normal human and animal tissues are indicated, with the emphasis on their possible functional consequences. In the context of aging, the correlation between somatic TE activation and age-related changes in the number of proteins required for heterochromatin maintenance and longevity regulation was analyzed. One of the original features of this review is a discussion of not only effects based on the TEs insertions and the associated consequences for the germline cell dynamics and somatic genome, but also the differences between transposon- and retrotransposon-mediated structural genome changes and possible phenotypic characteristics associated with aging and various age-related pathologies. Based on the analysis of published data, a hypothesis about the influence of the species-specific features of number, composition, and distribution of TEs on aging dynamics of different animal genomes was formulated.
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Affiliation(s)
- Elena Yushkova
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Center, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya st., 167982 Syktyvkar, Russian Federation
| | - Alexey Moskalev
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Center, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya st., 167982 Syktyvkar, Russian Federation; Laboratory of Genetics and Epigenetics of Aging, Russian Clinical Research Center for Gerontology, Pirogov Russian National Research Medical University, Moscow 129226, Russian Federation; Longaevus Technologies, London, UK.
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9
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Endogenous retroviruses and TDP-43 proteinopathy form a sustaining feedback driving intercellular spread of Drosophila neurodegeneration. Nat Commun 2023; 14:966. [PMID: 36810738 PMCID: PMC9944888 DOI: 10.1038/s41467-023-36649-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 02/09/2023] [Indexed: 02/23/2023] Open
Abstract
Inter-cellular movement of "prion-like" proteins is thought to explain propagation of neurodegeneration between cells. For example, propagation of abnormally phosphorylated cytoplasmic inclusions of TAR-DNA-Binding protein (TDP-43) is proposed to underlie progression of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). But unlike transmissible prion diseases, ALS and FTD are not infectious and injection of aggregated TDP-43 is not sufficient to cause disease. This suggests a missing component of a positive feedback necessary to sustain disease progression. We demonstrate that endogenous retrovirus (ERV) expression and TDP-43 proteinopathy are mutually reinforcing. Expression of either Drosophila mdg4-ERV (gypsy) or the human ERV, HERV-K (HML-2) are each sufficient to stimulate cytoplasmic aggregation of human TDP-43. Viral ERV transmission also triggers TDP-43 pathology in recipient cells that express physiological levels of TDP-43, whether they are in contact or at a distance. This mechanism potentially underlies the TDP-43 proteinopathy-caused neurodegenerative propagation through neuronal tissue.
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Ochoa E, Ramirez P, Gonzalez E, De Mange J, Ray WJ, Bieniek KF, Frost B. Pathogenic tau-induced transposable element-derived dsRNA drives neuroinflammation. SCIENCE ADVANCES 2023; 9:eabq5423. [PMID: 36608133 PMCID: PMC9821943 DOI: 10.1126/sciadv.abq5423] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Deposition of tau protein aggregates in the brain of affected individuals is a defining feature of "tauopathies," including Alzheimer's disease. Studies of human brain tissue and various model systems of tauopathy report that toxic forms of tau negatively affect nuclear and genomic architecture, identifying pathogenic tau-induced heterochromatin decondensation and consequent retrotransposon activation as a causal mediator of neurodegeneration. On the basis of their similarity to retroviruses, retrotransposons drive neuroinflammation via toxic intermediates, including double-stranded RNA (dsRNA). We find that dsRNA and dsRNA sensing machinery are elevated in astrocytes of postmortem brain tissue from patients with Alzheimer's disease and progressive supranuclear palsy and in brains of tau transgenic mice. Using a Drosophila model of tauopathy, we identify specific tau-induced retrotransposons that form dsRNA and find that pathogenic tau and heterochromatin decondensation causally drive dsRNA-mediated neurodegeneration and neuroinflammation. Our study suggests that pathogenic tau-induced heterochromatin decondensation and retrotransposon activation cause elevation of inflammatory, transposable element-derived dsRNA in the adult brain.
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Affiliation(s)
- Elizabeth Ochoa
- Sam and Ann Barshop Institute for Longevity and Aging Studies, San Antonio, TX, USA
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, San Antonio, TX, USA
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Paulino Ramirez
- Sam and Ann Barshop Institute for Longevity and Aging Studies, San Antonio, TX, USA
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, San Antonio, TX, USA
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Elias Gonzalez
- Sam and Ann Barshop Institute for Longevity and Aging Studies, San Antonio, TX, USA
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, San Antonio, TX, USA
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Jasmine De Mange
- Sam and Ann Barshop Institute for Longevity and Aging Studies, San Antonio, TX, USA
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, San Antonio, TX, USA
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA
| | - William J. Ray
- The Neurodegeneration Consortium, Therapeutics Discovery Division, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kevin F. Bieniek
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, San Antonio, TX, USA
- Department of Pathology and Laboratory Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Bess Frost
- Sam and Ann Barshop Institute for Longevity and Aging Studies, San Antonio, TX, USA
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, San Antonio, TX, USA
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA
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11
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Ramakrishnan M, Papolu PK, Mullasseri S, Zhou M, Sharma A, Ahmad Z, Satheesh V, Kalendar R, Wei Q. The role of LTR retrotransposons in plant genetic engineering: how to control their transposition in the genome. PLANT CELL REPORTS 2023; 42:3-15. [PMID: 36401648 DOI: 10.1007/s00299-022-02945-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
We briefly discuss that the similarity of LTR retrotransposons to retroviruses is a great opportunity for the development of a genetic engineering tool that exploits intragenic elements in the plant genome for plant genetic improvement. Long terminal repeat (LTR) retrotransposons are very similar to retroviruses but do not have the property of being infectious. While spreading between its host cells, a retrovirus inserts a DNA copy of its genome into the cells. The ability of retroviruses to cause infection with genome integration allows genes to be delivered to cells and tissues. Retrovirus vectors are, however, only specific to animals and insects, and, thus, are not relevant to plant genetic engineering. However, the similarity of LTR retrotransposons to retroviruses is an opportunity to explore the former as a tool for genetic engineering. Although recent long-read sequencing technologies have advanced the knowledge about transposable elements (TEs), the integration of TEs is still unable either to control them or to direct them to specific genomic locations. The use of existing intragenic elements to achieve the desired genome composition is better than using artificial constructs like vectors, but it is not yet clear how to control the process. Moreover, most LTR retrotransposons are inactive and unable to produce complete proteins. They are also highly mutable. In addition, it is impossible to find a full active copy of a LTR retrotransposon out of thousands of its own copies. Theoretically, if these elements were directly controlled and turned on or off using certain epigenetic mechanisms (inducing by stress or infection), LTR retrotransposons could be a great opportunity to develop a genetic engineering tool using intragenic elements in the plant genome. In this review, the recent developments in uncovering the nature of LTR retrotransposons and the possibility of using these intragenic elements as a tool for plant genetic engineering are briefly discussed.
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Affiliation(s)
- Muthusamy Ramakrishnan
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Pradeep K Papolu
- State Key Laboratory of Subtropical Silviculture, Institute of Bamboo Research, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Sileesh Mullasseri
- Department of Zoology, St. Albert's College (Autonomous), Kochi, 682018, Kerala, India
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Institute of Bamboo Research, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture, Institute of Bamboo Research, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Zishan Ahmad
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Viswanathan Satheesh
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Ruslan Kalendar
- Helsinki Institute of Life Science HiLIFE, University of Helsinki, Biocenter 3, Viikinkaari 1, F1-00014, Helsinki, Finland.
- Institute of Plant Biology and Biotechnology (IPBB), Timiryazev Street 45, 050040, Almaty, Kazakhstan.
| | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
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12
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van den Beek M, Rubanova N, Siudeja K. Experimental Approaches to Study Somatic Transposition in Drosophila Using Whole-Genome DNA Sequencing. Methods Mol Biol 2023; 2607:311-327. [PMID: 36449168 DOI: 10.1007/978-1-0716-2883-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The extent of transposable element (TE) mobilization in different somatic tissues and throughout diverse species is not well understood. Somatic transposition is often challenging to study as it generates de novo TE insertions that represent rare genetic variants present in heterogenous tissues. Here, we describe experimental approaches that can be applied to address TE mobility in somatic tissues with the use of short- and long-read whole-genome DNA sequencing. Focusing on the analysis of the Drosophila melanogaster intestinal and head tissues, we provide instructions on how to design, perform, and validate experiments that aim at detecting somatic transposition. In addition to providing examples of protocols, this chapter intends to deliver general experimental guidelines that may be adapted to other fly tissues or to other species.
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Affiliation(s)
- Marius van den Beek
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Paris, France
- The Pennsylvania State University, University Park, PA, USA
| | - Natalia Rubanova
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Paris, France
| | - Katarzyna Siudeja
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Paris, France.
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13
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Angileri KM, Bagia NA, Feschotte C. Transposon control as a checkpoint for tissue regeneration. Development 2022; 149:dev191957. [PMID: 36440631 PMCID: PMC10655923 DOI: 10.1242/dev.191957] [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: 03/11/2022] [Accepted: 10/03/2022] [Indexed: 11/29/2022]
Abstract
Tissue regeneration requires precise temporal control of cellular processes such as inflammatory signaling, chromatin remodeling and proliferation. The combination of these processes forms a unique microenvironment permissive to the expression, and potential mobilization of, transposable elements (TEs). Here, we develop the hypothesis that TE activation creates a barrier to tissue repair that must be overcome to achieve successful regeneration. We discuss how uncontrolled TE activity may impede tissue restoration and review mechanisms by which TE activity may be controlled during regeneration. We posit that the diversification and co-evolution of TEs and host control mechanisms may contribute to the wide variation in regenerative competency across tissues and species.
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Affiliation(s)
- Krista M. Angileri
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, NY 14850, USA
| | - Nornubari A. Bagia
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, NY 14850, USA
| | - Cedric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, NY 14850, USA
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14
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Benoit I, Di Curzio D, Civetta A, Douville RN. Drosophila as a Model for Human Viral Neuroinfections. Cells 2022; 11:cells11172685. [PMID: 36078091 PMCID: PMC9454636 DOI: 10.3390/cells11172685] [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] [Received: 08/02/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
The study of human neurological infection faces many technical and ethical challenges. While not as common as mammalian models, the use of Drosophila (fruit fly) in the investigation of virus–host dynamics is a powerful research tool. In this review, we focus on the benefits and caveats of using Drosophila as a model for neurological infections and neuroimmunity. Through the examination of in vitro, in vivo and transgenic systems, we highlight select examples to illustrate the use of flies for the study of exogenous and endogenous viruses associated with neurological disease. In each case, phenotypes in Drosophila are compared to those in human conditions. In addition, we discuss antiviral drug screening in flies and how investigating virus–host interactions may lead to novel antiviral drug targets. Together, we highlight standardized and reproducible readouts of fly behaviour, motor function and neurodegeneration that permit an accurate assessment of neurological outcomes for the study of viral infection in fly models. Adoption of Drosophila as a valuable model system for neurological infections has and will continue to guide the discovery of many novel virus–host interactions.
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Affiliation(s)
- Ilena Benoit
- Department of Biology, University of Winnipeg, 599 Portage Avenue, Winnipeg, MB R3B 2G3, Canada
- Division of Neurodegenerative Disorders, St. Boniface Hospital Albrechtsen Research Centre, 351 Taché Ave, Winnipeg, MB R2H 2A6, Canada
| | - Domenico Di Curzio
- Division of Neurodegenerative Disorders, St. Boniface Hospital Albrechtsen Research Centre, 351 Taché Ave, Winnipeg, MB R2H 2A6, Canada
| | - Alberto Civetta
- Department of Biology, University of Winnipeg, 599 Portage Avenue, Winnipeg, MB R3B 2G3, Canada
| | - Renée N. Douville
- Department of Biology, University of Winnipeg, 599 Portage Avenue, Winnipeg, MB R3B 2G3, Canada
- Division of Neurodegenerative Disorders, St. Boniface Hospital Albrechtsen Research Centre, 351 Taché Ave, Winnipeg, MB R2H 2A6, Canada
- Correspondence:
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15
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Rigal J, Martin Anduaga A, Bitman E, Rivellese E, Kadener S, Marr MT. Artificially stimulating retrotransposon activity increases mortality and accelerates a subset of aging phenotypes in Drosophila. eLife 2022; 11:80169. [PMID: 35980024 PMCID: PMC9427105 DOI: 10.7554/elife.80169] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/17/2022] [Indexed: 11/19/2022] Open
Abstract
Transposable elements (TEs) are mobile sequences of DNA that can become transcriptionally active as an animal ages. Whether TE activity is simply a by-product of heterochromatin breakdown or can contribute toward the aging process is not known. Here, we place the TE gypsy under the control of the UAS GAL4 system to model TE activation during aging. We find that increased TE activity shortens the life span of male Drosophila melanogaster. The effect is only apparent in middle-aged animals. The increase in mortality is not seen in young animals. An intact reverse transcriptase is necessary for the decrease in life span, implicating a DNA-mediated process in the effect. The decline in life span in the active gypsy flies is accompanied by the acceleration of a subset of aging phenotypes. TE activity increases sensitivity to oxidative stress and promotes a decline in circadian rhythmicity. The overexpression of the Forkhead-box O family (FOXO) stress response transcription factor can partially rescue the detrimental effects of increased TE activity on life span. Our results provide evidence that active TEs can behave as effectors in the aging process and suggest a potential novel role for dFOXO in its promotion of longevity in D. melanogaster.
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Affiliation(s)
- Joyce Rigal
- Department of Biology, Brandeis University, Waltham, United States
| | | | - Elena Bitman
- Department of Biology, Brandeis University, Waltham, United States
| | - Emma Rivellese
- Department of Biology, Brandeis University, Waltham, United States
| | | | - Michael T Marr
- Department of Biology, Brandeis University, Waltham, United States
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16
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Lee Y, Ha U, Moon S. Ongoing endeavors to detect mobilization of transposable elements. BMB Rep 2022. [PMID: 35725016 PMCID: PMC9340088 DOI: 10.5483/bmbrep.2022.55.7.088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transposable elements (TEs) are DNA sequences capable of mobilization from one location to another in the genome. Since the discovery of ‘Dissociation (Dc) locus’ by Barbara McClintock in maize (1), mounting evidence in the era of genomics indicates that a significant fraction of most eukaryotic genomes is composed of TE sequences, involving in various aspects of biological processes such as development, physiology, diseases and evolution. Although technical advances in genomics have discovered numerous functional impacts of TE across species, our understanding of TEs is still ongoing process due to challenges resulted from complexity and abundance of TEs in the genome. In this mini-review, we briefly summarize biology of TEs and their impacts on the host genome, emphasizing importance of understanding TE landscape in the genome. Then, we introduce recent endeavors especially in vivo retrotransposition assays and long read sequencing technology for identifying de novo insertions/TE polymorphism, which will broaden our knowledge of extraordinary relationship between genomic cohabitants and their host.
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Affiliation(s)
- Yujeong Lee
- Department of Biological Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Una Ha
- Department of Biological Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Sungjin Moon
- Department of Biological Sciences, Kangwon National University, Chuncheon 24341, Korea
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17
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Yang N, Srivastav SP, Rahman R, Ma Q, Dayama G, Li S, Chinen M, Lei EP, Rosbash M, Lau NC. Transposable element landscapes in aging Drosophila. PLoS Genet 2022; 18:e1010024. [PMID: 35239675 PMCID: PMC8893327 DOI: 10.1371/journal.pgen.1010024] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/10/2022] [Indexed: 11/28/2022] Open
Abstract
Genetic mechanisms that repress transposable elements (TEs) in young animals decline during aging, as reflected by increased TE expression in aged animals. Does increased TE expression during aging lead to more genomic TE copies in older animals? To address this question, we quantified TE Landscapes (TLs) via whole genome sequencing of young and aged Drosophila strains of wild-type and mutant backgrounds. We quantified TLs in whole flies and dissected brains and validated the feasibility of our approach in detecting new TE insertions in aging Drosophila genomes when small RNA and RNA interference (RNAi) pathways are compromised. We also describe improved sequencing methods to quantify extra-chromosomal DNA circles (eccDNAs) in Drosophila as an additional source of TE copies that accumulate during aging. Lastly, to combat the natural progression of aging-associated TE expression, we show that knocking down PAF1, a conserved transcription elongation factor that antagonizes RNAi pathways, may bolster suppression of TEs during aging and extend lifespan. Our study suggests that in addition to a possible influence by different genetic backgrounds, small RNA and RNAi mechanisms may mitigate genomic TL expansion despite the increase in TE transcripts during aging. Transposable elements, also called transposons, are genetic parasites found in all animal genomes. Normally, transposons are compacted away in silent chromatin in young animals. But, as animals age and transposon-silencing defense mechanisms break down, transposon RNAs accumulate to significant levels in old animals like fruit flies. An open question is whether the increased levels of transposon RNAs in older animals also correspond to increased genomic copies of transposons. This study approached this question by sequencing the whole genomes of young and old wild-type and mutant flies lacking a functional RNA interference (RNAi) pathway, which naturally silences transposon RNAs. Although the wild-type flies with intact RNAi activity had little new accumulation of transposon copies, the sequencing approach was able to detect several transposon accumulation occurrences in some RNAi mutants. In addition, we found that some fly transposon families can also accumulate as extra-chromosomal circular DNA copies. Lastly, we showed that genetically augmenting the expression of RNAi factors can counteract the rising transposon RNA levels in aging and promote longevity. This study improves our understanding of the animal host genome relationship with transposons during natural aging processes.
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Affiliation(s)
- Nachen Yang
- Boston University School of Medicine, Department of Biochemistry, Boston, Massachusetts, United States of America
| | - Satyam P. Srivastav
- Boston University School of Medicine, Department of Biochemistry, Boston, Massachusetts, United States of America
| | - Reazur Rahman
- Brandeis University, Department of Biology and Howard Hughes Medical Institute, Waltham, Massachusetts, United States of America
| | - Qicheng Ma
- Boston University School of Medicine, Department of Biochemistry, Boston, Massachusetts, United States of America
| | - Gargi Dayama
- Boston University School of Medicine, Department of Biochemistry, Boston, Massachusetts, United States of America
| | - Sizheng Li
- Boston University School of Medicine, Department of Biochemistry, Boston, Massachusetts, United States of America
| | - Madoka Chinen
- Nuclear Organization and Gene Expression Section, NIDDK, NIH, Bethesda, Maryland, United States of America
| | - Elissa P. Lei
- Nuclear Organization and Gene Expression Section, NIDDK, NIH, Bethesda, Maryland, United States of America
| | - Michael Rosbash
- Brandeis University, Department of Biology and Howard Hughes Medical Institute, Waltham, Massachusetts, United States of America
| | - Nelson C. Lau
- Boston University School of Medicine, Department of Biochemistry, Boston, Massachusetts, United States of America
- Boston University Genome Science Institute, Boston, Massachusetts, United States of America
- * E-mail:
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18
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Roy M, Viginier B, Mayeux CA, Ratinier M, Fablet M. Infections by Transovarially Transmitted DMelSV in Drosophila Have No Impact on Ovarian Transposable Element Transcripts but Increase Their Amounts in the Soma. Genome Biol Evol 2021; 13:evab207. [PMID: 34498066 PMCID: PMC8459167 DOI: 10.1093/gbe/evab207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2021] [Indexed: 12/21/2022] Open
Abstract
Transposable elements (TEs) are genomic parasites, which activity is tightly controlled in germline cells. Using Sindbis virus, it was recently demonstrated that viral infections affect TE transcript amounts in somatic tissues. However, the strongest evolutionary impacts are expected in gonads, because that is where the genomes of the next generations lie. Here, we investigated this aspect using the Drosophila melanogaster Sigma virus. It is particularly relevant in the genome/TE interaction given its tropism to ovaries, which is the organ displaying the more sophisticated TE control pathways. Our results in Drosophila simulans flies allowed us to confirm the existence of a strong homeostasis of the TE transcriptome in ovaries upon infection, which, however, rely on TE-derived small RNA modulations. In addition, we performed a meta-analysis of RNA-seq data and propose that the immune pathway that is triggered upon viral infection determines the direction of TE transcript modulation in somatic tissues.
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Affiliation(s)
- Marlène Roy
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, UMR 5558, Villeurbanne, France
- EPHE, PSL Research University, INRA, Université de Lyon, Université Claude Bernard Lyon1, UMR754, IVPC, Lyon, France
| | - Barbara Viginier
- EPHE, PSL Research University, INRA, Université de Lyon, Université Claude Bernard Lyon1, UMR754, IVPC, Lyon, France
| | - Camille A Mayeux
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, UMR 5558, Villeurbanne, France
| | - Maxime Ratinier
- EPHE, PSL Research University, INRA, Université de Lyon, Université Claude Bernard Lyon1, UMR754, IVPC, Lyon, France
| | - Marie Fablet
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, UMR 5558, Villeurbanne, France
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19
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Allen AM, B Sokolowski M. Expression of the foraging gene in adult Drosophila melanogaster. J Neurogenet 2021; 35:192-212. [PMID: 34382904 PMCID: PMC8846931 DOI: 10.1080/01677063.2021.1941946] [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] [Indexed: 10/25/2022]
Abstract
The foraging gene in Drosophila melanogaster, which encodes a cGMP-dependent protein kinase, is a highly conserved, complex gene with multiple pleiotropic behavioral and physiological functions in both the larval and adult fly. Adult foraging expression is less well characterized than in the larva. We characterized foraging expression in the brain, gastric system, and reproductive systems using a T2A-Gal4 gene-trap allele. In the brain, foraging expression appears to be restricted to multiple sub-types of glia. This glial-specific cellular localization of foraging was supported by single-cell transcriptomic atlases of the adult brain. foraging is extensively expressed in most cell types in the gastric and reproductive systems. We then mapped multiple cis-regulatory elements responsible for parts of the observed expression patterns by a nested cloned promoter-Gal4 analysis. The mapped cis-regulatory elements were consistently modular when comparing the larval and adult expression patterns. These new data using the T2A-Gal4 gene-trap and cloned foraging promoter fusion GAL4's are discussed with respect to previous work using an anti-FOR antibody, which we show here to be non-specific. Future studies of foraging's function will consider roles for glial subtypes and peripheral tissues (gastric and reproductive systems) in foraging's pleiotropic behavioral and physiological effects.
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Affiliation(s)
- Aaron M Allen
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada.,Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, UK
| | - Marla B Sokolowski
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada.,Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Canada
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20
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Nandakumar S, Rozich E, Buttitta L. Cell Cycle Re-entry in the Nervous System: From Polyploidy to Neurodegeneration. Front Cell Dev Biol 2021; 9:698661. [PMID: 34249947 PMCID: PMC8264763 DOI: 10.3389/fcell.2021.698661] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 05/19/2021] [Indexed: 12/15/2022] Open
Abstract
Terminally differentiated cells of the nervous system have long been considered to be in a stable non-cycling state and are often considered to be permanently in G0. Exit from the cell cycle during development is often coincident with the differentiation of neurons, and is critical for neuronal function. But what happens in long lived postmitotic tissues that accumulate cell damage or suffer cell loss during aging? In other contexts, cells that are normally non-dividing or postmitotic can or re-enter the cell cycle and begin replicating their DNA to facilitate cellular growth in response to cell loss. This leads to a state called polyploidy, where cells contain multiple copies of the genome. A growing body of literature from several vertebrate and invertebrate model organisms has shown that polyploidy in the nervous system may be more common than previously appreciated and occurs under normal physiological conditions. Moreover, it has been found that neuronal polyploidization can play a protective role when cells are challenged with DNA damage or oxidative stress. By contrast, work over the last two and a half decades has discovered a link between cell-cycle reentry in neurons and several neurodegenerative conditions. In this context, neuronal cell cycle re-entry is widely considered to be aberrant and deleterious to neuronal health. In this review, we highlight historical and emerging reports of polyploidy in the nervous systems of various vertebrate and invertebrate organisms. We discuss the potential functions of polyploidization in the nervous system, particularly in the context of long-lived cells and age-associated polyploidization. Finally, we attempt to reconcile the seemingly disparate associations of neuronal polyploidy with both neurodegeneration and neuroprotection.
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Affiliation(s)
| | | | - Laura Buttitta
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
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21
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Siudeja K, van den Beek M, Riddiford N, Boumard B, Wurmser A, Stefanutti M, Lameiras S, Bardin AJ. Unraveling the features of somatic transposition in the Drosophila intestine. EMBO J 2021; 40:e106388. [PMID: 33634906 PMCID: PMC8090852 DOI: 10.15252/embj.2020106388] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 01/20/2021] [Accepted: 01/27/2021] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) play a significant role in evolution, contributing to genetic variation. However, TE mobilization in somatic cells is not well understood. Here, we address the prevalence of transposition in a somatic tissue, exploiting the Drosophila midgut as a model. Using whole-genome sequencing of in vivo clonally expanded gut tissue, we have mapped hundreds of high-confidence somatic TE integration sites genome-wide. We show that somatic retrotransposon insertions are associated with inactivation of the tumor suppressor Notch, likely contributing to neoplasia formation. Moreover, applying Oxford Nanopore long-read sequencing technology we provide evidence for tissue-specific differences in retrotransposition. Comparing somatic TE insertional activity with transcriptomic and small RNA sequencing data, we demonstrate that transposon mobility cannot be simply predicted by whole tissue TE expression levels or by small RNA pathway activity. Finally, we reveal that somatic TE insertions in the adult fly intestine are enriched in genic regions and in transcriptionally active chromatin. Together, our findings provide clear evidence of ongoing somatic transposition in Drosophila and delineate previously unknown features underlying somatic TE mobility in vivo.
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Affiliation(s)
- Katarzyna Siudeja
- Institut CurieCNRSUMR 3215INSERM U934Stem Cells and Tissue Homeostasis GroupPSL Research UniversityParisFrance
- Sorbonne UniversitésUPMC Univ Paris 6ParisFrance
| | - Marius van den Beek
- Institut CurieCNRSUMR 3215INSERM U934Stem Cells and Tissue Homeostasis GroupPSL Research UniversityParisFrance
- Sorbonne UniversitésUPMC Univ Paris 6ParisFrance
| | - Nick Riddiford
- Institut CurieCNRSUMR 3215INSERM U934Stem Cells and Tissue Homeostasis GroupPSL Research UniversityParisFrance
- Sorbonne UniversitésUPMC Univ Paris 6ParisFrance
| | - Benjamin Boumard
- Institut CurieCNRSUMR 3215INSERM U934Stem Cells and Tissue Homeostasis GroupPSL Research UniversityParisFrance
- Sorbonne UniversitésUPMC Univ Paris 6ParisFrance
| | - Annabelle Wurmser
- Institut CurieCNRSUMR 3215INSERM U934Stem Cells and Tissue Homeostasis GroupPSL Research UniversityParisFrance
- Sorbonne UniversitésUPMC Univ Paris 6ParisFrance
| | - Marine Stefanutti
- Institut CurieCNRSUMR 3215INSERM U934Stem Cells and Tissue Homeostasis GroupPSL Research UniversityParisFrance
- Sorbonne UniversitésUPMC Univ Paris 6ParisFrance
| | - Sonia Lameiras
- ICGex Next‐Generation Sequencing PlatformInstitut CuriePSL Research UniversityParisFrance
| | - Allison J Bardin
- Institut CurieCNRSUMR 3215INSERM U934Stem Cells and Tissue Homeostasis GroupPSL Research UniversityParisFrance
- Sorbonne UniversitésUPMC Univ Paris 6ParisFrance
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22
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Keegan RM, Talbot LR, Chang YH, Metzger MJ, Dubnau J. Intercellular viral spread and intracellular transposition of Drosophila gypsy. PLoS Genet 2021; 17:e1009535. [PMID: 33886543 PMCID: PMC8096092 DOI: 10.1371/journal.pgen.1009535] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 05/04/2021] [Accepted: 04/06/2021] [Indexed: 01/12/2023] Open
Abstract
It has become increasingly clear that retrotransposons (RTEs) are more widely expressed in somatic tissues than previously appreciated. RTE expression has been implicated in a myriad of biological processes ranging from normal development and aging, to age related diseases such as cancer and neurodegeneration. Long Terminal Repeat (LTR)-RTEs are evolutionary ancestors to, and share many features with, exogenous retroviruses. In fact, many organisms contain endogenous retroviruses (ERVs) derived from exogenous retroviruses that integrated into the germ line. These ERVs are inherited in Mendelian fashion like RTEs, and some retain the ability to transmit between cells like viruses, while others develop the ability to act as RTEs. The process of evolutionary transition between LTR-RTE and retroviruses is thought to involve multiple steps by which the element loses or gains the ability to transmit copies between cells versus the ability to replicate intracellularly. But, typically, these two modes of transmission are incompatible because they require assembly in different sub-cellular compartments. Like murine IAP/IAP-E elements, the gypsy family of retroelements in arthropods appear to sit along this evolutionary transition. Indeed, there is some evidence that gypsy may exhibit retroviral properties. Given that gypsy elements have been found to actively mobilize in neurons and glial cells during normal aging and in models of neurodegeneration, this raises the question of whether gypsy replication in somatic cells occurs via intracellular retrotransposition, intercellular viral spread, or some combination of the two. These modes of replication in somatic tissues would have quite different biological implications. Here, we demonstrate that Drosophila gypsy is capable of both cell-associated and cell-free viral transmission between cultured S2 cells of somatic origin. Further, we demonstrate that the ability of gypsy to move between cells is dependent upon a functional copy of its viral envelope protein. This argues that the gypsy element has transitioned from an RTE into a functional endogenous retrovirus with the acquisition of its envelope gene. On the other hand, we also find that intracellular retrotransposition of the same genomic copy of gypsy can occur in the absence of the Env protein. Thus, gypsy exhibits both intracellular retrotransposition and intercellular viral transmission as modes of replicating its genome.
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Affiliation(s)
- Richard M. Keegan
- Program in Neuroscience, Department of Neurobiology and Behavior, Stony Brook University, New York City, New York, United States of America
| | - Lillian R. Talbot
- Medical Scientist Training Program, Department of Neurobiology and Behavior, Stony Brook University, New York City, New York, United States of America
| | - Yung-Heng Chang
- Department of Anesthesiology, Stony Brook School of Medicine, New York City, New York, United States of America
| | - Michael J. Metzger
- Pacific Northwest Research Institute, Seattle, Washington, United States of America
| | - Josh Dubnau
- Program in Neuroscience, Department of Neurobiology and Behavior, Stony Brook University, New York City, New York, United States of America
- Department of Anesthesiology, Stony Brook School of Medicine, New York City, New York, United States of America
- Pacific Northwest Research Institute, Seattle, Washington, United States of America
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23
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Fort-Aznar L, Ugbode C, Sweeney ST. Retrovirus reactivation in CHMP2BIntron5 models of frontotemporal dementia. Hum Mol Genet 2020; 29:2637-2646. [PMID: 32628265 PMCID: PMC7530534 DOI: 10.1093/hmg/ddaa142] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 12/13/2022] Open
Abstract
Frontotemporal dementia (FTD) is the second most prevalent form of pre-senile dementia after Alzheimer's disease. Amyotrophic lateral sclerosis (ALS) can overlap genetically, pathologically and clinically with FTD indicating the two conditions are ends of a spectrum and may share common pathological mechanisms. FTD-ALS causing mutations are known to be involved in endosomal trafficking and RNA regulation. Using an unbiased genome-wide genetic screen to identify mutations affecting an FTD-ALS-related phenotype in Drosophila caused by CHMP2BIntron5 expression, we have uncovered repressors of retrovirus (RV) activity as modifiers of CHMP2BIntron5 toxicity. We report that neuronal expression of CHMP2BIntron5 causes an increase in the activity of the endogenous Drosophila RV, gypsy, in the nervous system. Genetically blocking Drosophila gypsy activation and pharmacologically inhibiting viral reverse transcriptase activity prevents degenerative phenotypes observed in fly and rat neurons. These findings directly link endosomal dysfunction to RV de-repression in an FTD-ALS model without TDP-43 pathology. These observations may contribute an understanding to previous discoveries of RV activation in ALS affected patients.
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Affiliation(s)
- Laura Fort-Aznar
- Department of Biology, University of York, York YO10 5DD, UK
- York Biomedical Research Institute, University of York, York YO10 5DD, UK
| | - Chris Ugbode
- Department of Biology, University of York, York YO10 5DD, UK
- York Biomedical Research Institute, University of York, York YO10 5DD, UK
| | - Sean T Sweeney
- Department of Biology, University of York, York YO10 5DD, UK
- York Biomedical Research Institute, University of York, York YO10 5DD, UK
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24
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Abstract
Transposable elements (TEs) are genomic parasites that are found in all genomes, some of which display sequence similarity to certain viruses. In insects, TEs are controlled by the Piwi-interacting small interfering RNA (piRNA) pathway in gonads, while the small interfering RNA (siRNA) pathway is dedicated to TE somatic control and defense against viruses. So far, these two small interfering RNA pathways are considered to involve distinct molecular effectors and are described as independent. Using Sindbis virus (SINV) in Drosophila, here we show that viral infections affect TE transcript amounts via modulations of the piRNA and siRNA repertoires, with the clearest effects in somatic tissues. These results suggest that viral acute or chronic infections may impact TE activity and, thus, the tempo of genetic diversification. In addition, these results deserve further evolutionary considerations regarding potential benefits to the host, the virus, or the TEs.
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Allen AM, Neville MC, Birtles S, Croset V, Treiber CD, Waddell S, Goodwin SF. A single-cell transcriptomic atlas of the adult Drosophila ventral nerve cord. eLife 2020; 9:e54074. [PMID: 32314735 PMCID: PMC7173974 DOI: 10.7554/elife.54074] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 04/03/2020] [Indexed: 02/07/2023] Open
Abstract
The Drosophila ventral nerve cord (VNC) receives and processes descending signals from the brain to produce a variety of coordinated locomotor outputs. It also integrates sensory information from the periphery and sends ascending signals to the brain. We used single-cell transcriptomics to generate an unbiased classification of cellular diversity in the VNC of five-day old adult flies. We produced an atlas of 26,000 high-quality cells, representing more than 100 transcriptionally distinct cell types. The predominant gene signatures defining neuronal cell types reflect shared developmental histories based on the neuroblast from which cells were derived, as well as their birth order. The relative position of cells along the anterior-posterior axis could also be assigned using adult Hox gene expression. This single-cell transcriptional atlas of the adult fly VNC will be a valuable resource for future studies of neurodevelopment and behavior.
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Affiliation(s)
- Aaron M Allen
- Centre for Neural Circuits and Behaviour, University of OxfordOxfordUnited Kingdom
| | - Megan C Neville
- Centre for Neural Circuits and Behaviour, University of OxfordOxfordUnited Kingdom
| | - Sebastian Birtles
- Centre for Neural Circuits and Behaviour, University of OxfordOxfordUnited Kingdom
| | - Vincent Croset
- Centre for Neural Circuits and Behaviour, University of OxfordOxfordUnited Kingdom
| | | | - Scott Waddell
- Centre for Neural Circuits and Behaviour, University of OxfordOxfordUnited Kingdom
| | - Stephen F Goodwin
- Centre for Neural Circuits and Behaviour, University of OxfordOxfordUnited Kingdom
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26
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Ochoa Thomas E, Zuniga G, Sun W, Frost B. Awakening the dark side: retrotransposon activation in neurodegenerative disorders. Curr Opin Neurobiol 2020; 61:65-72. [PMID: 32092528 PMCID: PMC7198348 DOI: 10.1016/j.conb.2020.01.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 01/07/2020] [Accepted: 01/23/2020] [Indexed: 12/30/2022]
Abstract
Nearly half (45%) of the human genome is composed of transposable elements, or 'jumping genes'. Since Barbara McClintock's original discovery of transposable elements in 1950, we have come to appreciate that transposable element mobilization is a major driver of evolution that transposons are active in the germline and the soma, and that transposable element dysregulation is causally associated with many human disorders. In the present review, we highlight recent studies investigating transposable element activation in the adult brain and in the context of neurodegeneration. Collectively, these studies contribute to a greater understanding of the frequency of complete retrotransposition in the adult brain as well as the presence of transposable element-derived RNA and protein in brain and fluids of patients with neurodegenerative disorders. We discuss therapeutic opportunities and speculate on the larger implications of transposable element activation in regard to current hot topics in the field of neurodegeneration.
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Affiliation(s)
- Elizabeth Ochoa Thomas
- Sam & Ann Barshop Institute for Longevity and Aging Studies, Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX, United States
| | - Gabbe Zuniga
- Sam & Ann Barshop Institute for Longevity and Aging Studies, Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX, United States
| | - Wenyan Sun
- Sam & Ann Barshop Institute for Longevity and Aging Studies, Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX, United States
| | - Bess Frost
- Sam & Ann Barshop Institute for Longevity and Aging Studies, Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX, United States.
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27
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Terry DM, Devine SE. Aberrantly High Levels of Somatic LINE-1 Expression and Retrotransposition in Human Neurological Disorders. Front Genet 2020; 10:1244. [PMID: 31969897 PMCID: PMC6960195 DOI: 10.3389/fgene.2019.01244] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/11/2019] [Indexed: 12/31/2022] Open
Abstract
Retrotransposable elements (RTEs) have actively multiplied over the past 80 million years of primate evolution, and as a consequence, such elements collectively occupy ∼ 40% of the human genome. As RTE activity can have detrimental effects on the human genome and transcriptome, silencing mechanisms have evolved to restrict retrotransposition. The brain is the only known somatic tissue where RTEs are de-repressed throughout the life of a healthy human and each neuron in specific brain regions accumulates up to ∼13.7 new somatic L1 insertions (and perhaps more). However, even higher levels of somatic RTE expression and retrotransposition have been found in a number of human neurological disorders. This review is focused on how RTE expression and retrotransposition in neuronal tissues might contribute to the initiation and progression of these disorders. These disorders are discussed in three broad and sometimes overlapping categories: 1) disorders such as Rett syndrome, Aicardi-Goutières syndrome, and ataxia–telangiectasia, where expression/retrotransposition is increased due to mutations in genes that play a role in regulating RTEs in healthy cells, 2) disorders such as autism spectrum disorder, schizophrenia, and substance abuse disorders, which are thought to be caused by a combination of genetic and environmental stress factors, and 3) disorders associated with age, such as frontotemporal lobar degeneration (FTLD), amyotrophic lateral sclerosis (ALS), and normal aging, where there is a time-dependent accumulation of neurological degeneration, RTE copy number, and phenotypes. Research has revealed increased levels of RTE activity in many neurological disorders, but in most cases, a clear causal link between RTE activity and these disorders has not been well established. At the same time, even if increased RTE activity is a passenger and not a driver of disease, a detrimental effect is more likely than a beneficial one. Thus, a better understanding of the role of RTEs in neuronal tissues likely is an important part of understanding, preventing, and treating these disorders.
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Affiliation(s)
- Diane M Terry
- Molecular Medicine Graduate Program, University of Maryland School of Medicine, Baltimore, MD, United States.,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Scott E Devine
- Molecular Medicine Graduate Program, University of Maryland School of Medicine, Baltimore, MD, United States.,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States.,Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States.,Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, United States
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28
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Chang YH, Dubnau J. The Gypsy Endogenous Retrovirus Drives Non-Cell-Autonomous Propagation in a Drosophila TDP-43 Model of Neurodegeneration. Curr Biol 2019; 29:3135-3152.e4. [PMID: 31495585 PMCID: PMC6783360 DOI: 10.1016/j.cub.2019.07.071] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/11/2019] [Accepted: 07/23/2019] [Indexed: 12/16/2022]
Abstract
A hallmark of neurodegenerative disease is focal onset of pathological protein aggregation, followed by progressive spread of pathology to connected brain regions. In amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), pathology is often associated with aggregation of TAR DNA-binding protein 43 (TDP-43). Although aggregated TDP-43 protein moves between cells, it is not clear whether and how this movement propagates the degeneration. Here, we have established a Drosophila model of human TDP-43 in which we initiated toxic expression of human TDP-43 focally within small groups of glial cells. We found that this focal onset kills adjacent neurons. Surprisingly, we show that this spreading death is caused by an endogenous retrovirus within the glia, which leads to DNA damage and death in adjacent neurons. These findings suggest a possible mechanism by which human retroviruses such as HERV-K might contribute to TDP-43-mediated propagation of neurodegeneration.
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Affiliation(s)
- Yung-Heng Chang
- Department of Anesthesiology, Stony Brook School of Medicine, NY 11794, USA
| | - Josh Dubnau
- Department of Anesthesiology, Stony Brook School of Medicine, NY 11794, USA; Department of Neurobiology and Behavior, Stony Brook University, NY 11794, USA.
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