1
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Senft AD, Macfarlan TS. Transposable elements shape the evolution of mammalian development. Nat Rev Genet 2021; 22:691-711. [PMID: 34354263 DOI: 10.1038/s41576-021-00385-1] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2021] [Indexed: 02/06/2023]
Abstract
Transposable elements (TEs) promote genetic innovation but also threaten genome stability. Despite multiple layers of host defence, TEs actively shape mammalian-specific developmental processes, particularly during pre-implantation and extra-embryonic development and at the maternal-fetal interface. Here, we review how TEs influence mammalian genomes both directly by providing the raw material for genetic change and indirectly via co-evolving TE-binding Krüppel-associated box zinc finger proteins (KRAB-ZFPs). Throughout mammalian evolution, individual activities of ancient TEs were co-opted to enable invasive placentation that characterizes live-born mammals. By contrast, the widespread activity of evolutionarily young TEs may reflect an ongoing co-evolution that continues to impact mammalian development.
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Affiliation(s)
- Anna D Senft
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, MD, USA.
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, MD, USA.
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2
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Lou C, Goodier JL, Qiang R. A potential new mechanism for pregnancy loss: considering the role of LINE-1 retrotransposons in early spontaneous miscarriage. Reprod Biol Endocrinol 2020; 18:6. [PMID: 31964400 PMCID: PMC6971995 DOI: 10.1186/s12958-020-0564-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 01/07/2020] [Indexed: 12/14/2022] Open
Abstract
LINE1 retrotransposons are mobile DNA elements that copy and paste themselves into new sites in the genome. To ensure their evolutionary success, heritable new LINE-1 insertions accumulate in cells that can transmit genetic information to the next generation (i.e., germ cells and embryonic stem cells). It is our hypothesis that LINE1 retrotransposons, insertional mutagens that affect expression of genes, may be causal agents of early miscarriage in humans. The cell has evolved various defenses restricting retrotransposition-caused mutation, but these are occasionally relaxed in certain somatic cell types, including those of the early embryo. We predict that reduced suppression of L1s in germ cells or early-stage embryos may lead to excessive genome mutation by retrotransposon insertion, or to the induction of an inflammatory response or apoptosis due to increased expression of L1-derived nucleic acids and proteins, and so disrupt gene function important for embryogenesis. If correct, a novel threat to normal human development is revealed, and reverse transcriptase therapy could be one future strategy for controlling this cause of embryonic damage in patients with recurrent miscarriages.
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Affiliation(s)
- Chao Lou
- Department of Genetics, Northwest Women’s and Children’s Hospital, 1616 Yanxiang Road, Xi’an, Shaanxi Province People’s Republic of China
| | - John L. Goodier
- 0000 0001 2171 9311grid.21107.35McKusick-Nathans Deartment of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Rong Qiang
- Department of Genetics, Northwest Women’s and Children’s Hospital, 1616 Yanxiang Road, Xi’an, Shaanxi Province People’s Republic of China
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3
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Adney EM, Ochmann MT, Sil S, Truong DM, Mita P, Wang X, Kahler DJ, Fenyö D, Holt LJ, Boeke JD. Comprehensive Scanning Mutagenesis of Human Retrotransposon LINE-1 Identifies Motifs Essential for Function. Genetics 2019; 213:1401-1414. [PMID: 31666291 PMCID: PMC6893370 DOI: 10.1534/genetics.119.302601] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 10/22/2019] [Indexed: 12/19/2022] Open
Abstract
Long Interspersed Nuclear Element-1 (LINE-1, L1) is the only autonomous active transposable element in the human genome. The L1-encoded proteins ORF1p and ORF2p enable the element to jump from one locus to another via a "copy-and-paste" mechanism. ORF1p is an RNA-binding protein, and ORF2p has endonuclease and reverse transcriptase activities. The huge number of truncated L1 remnants in the human genome suggests that the host has likely evolved mechanisms to prevent full L1 replication, and thereby decrease the proliferation of active elements and reduce the mutagenic potential of L1. In turn, L1 appears to have a minimized length to increase the probability of successful full-length replication. This streamlining would be expected to lead to high information density. Here, we describe the construction and initial characterization of a library of 538 consecutive trialanine substitutions that scan along ORF1p and ORF2p to identify functionally important regions. In accordance with the streamlining hypothesis, retrotransposition was overall very sensitive to mutations in ORF1p and ORF2p; only 16% of trialanine mutants retained near-wild-type (WT) activity. All ORF1p mutants formed near-WT levels of mRNA transcripts and 75% formed near-WT levels of protein. Two ORF1p mutants presented a unique nucleolar-relocalization phenotype. Regions of ORF2p that are sensitive to mutagenesis but lack phylogenetic conservation were also identified. We provide comprehensive information on the regions most critical to retrotransposition. This resource will guide future studies of intermolecular interactions that form with RNA, proteins, and target DNA throughout the L1 life cycle.
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Affiliation(s)
- Emily M Adney
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Matthias T Ochmann
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen 63225, Germany
| | - Srinjoy Sil
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
| | - David M Truong
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
| | - Paolo Mita
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
| | - Xuya Wang
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
| | - David J Kahler
- High Throughput Biology Laboratory, NYU Langone Health, New York 10016
| | - David Fenyö
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
| | - Liam J Holt
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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4
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Romero MA, Mumford PW, Roberson PA, Osburn SC, Parry HA, Kavazis AN, Gladden LB, Schwartz TS, Baker BA, Toedebusch RG, Childs TE, Booth FW, Roberts MD. Five months of voluntary wheel running downregulates skeletal muscle LINE-1 gene expression in rats. Am J Physiol Cell Physiol 2019; 317:C1313-C1323. [PMID: 31618076 DOI: 10.1152/ajpcell.00301.2019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Transposable elements (TEs) are mobile DNA and constitute approximately half of the human genome. LINE-1 (L1) is the only active autonomous TE in the mammalian genome and has been implicated in a number of diseases as well as aging. We have previously reported that skeletal muscle L1 expression is lower following acute and chronic exercise training in humans. Herein, we used a rodent model of voluntary wheel running to determine whether long-term exercise training affects markers of skeletal muscle L1 regulation. Selectively bred high-running female Wistar rats (n = 11 per group) were either given access to a running wheel (EX) or not (SED) at 5 wk of age, and these conditions were maintained until 27 wk of age. Thereafter, mixed gastrocnemius tissue was harvested and analyzed for L1 mRNA expression and DNA content along with other L1 regulation markers. We observed significantly (P < 0.05) lower L1 mRNA expression, higher L1 DNA methylation, and less L1 DNA in accessible chromatin regions in EX versus SED rats. We followed these experiments with 3-h in vitro drug treatments in L6 myotubes to mimic transient exercise-specific signaling events. The AMP-activated protein kinase (AMPK) agonist 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR; 4 mM) significantly decreased L1 mRNA expression in L6 myotubes. However, this effect was not facilitated through increased L1 DNA methylation. Collectively, these data suggest that long-term voluntary wheel running downregulates skeletal muscle L1 mRNA, and this may occur through chromatin modifications. Enhanced AMPK signaling with repetitive exercise bouts may also decrease L1 mRNA expression, although the mechanism of action remains unknown.
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Affiliation(s)
| | | | | | | | - Hailey A Parry
- School of Kinesiology, Auburn University, Auburn, Alabama
| | | | | | - Tonia S Schwartz
- Department of Biological Sciences, Auburn University, Auburn, Alabama
| | - Brent A Baker
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, West Virginia
| | - Ryan G Toedebusch
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri
| | - Thomas E Childs
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri
| | - Frank W Booth
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri
| | - Michael D Roberts
- School of Kinesiology, Auburn University, Auburn, Alabama.,Edward Via College of Osteopathic Medicine-Auburn Campus, Auburn, Alabama
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5
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Jiang H, Taylor MS, Molloy KR, Altukhov I, LaCava J. Identification of RNase-sensitive LINE-1 Ribonucleoprotein Interactions by Differential Affinity Immobilization. Bio Protoc 2019; 9:e3200. [PMID: 31106238 PMCID: PMC6519465 DOI: 10.21769/bioprotoc.3200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/26/2019] [Accepted: 03/12/2019] [Indexed: 01/19/2023] Open
Abstract
Long Interspersed Nuclear Element-1 (LINE-1, L1) constitutes a family of autonomous, self-replicating genetic elements known as retrotransposons. Although most are inactive, copious L1 sequences populate the human genome. L1s proliferate in a 'copy-and-paste' fashion through an RNA intermediate; a full-length L1 transcript is ~6,000 nucleotides long and functions as a bicistronic mRNA that encodes and assembles in cis with two main polypeptides, ORF1p and ORF2p, forming a ribonucleoprotein (RNP); L1 RNPs also interact with a wide range of host factors in positive and negative regulatory capacities. The following protocol describes an approach to affinity enrich ectopically expressed L1 RNPs and, using RNases, release the fraction of protein that depends upon the presence of intact RNA for retention in the immobilized macromolecules.
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Affiliation(s)
- Hua Jiang
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, USA
| | - Martin S. Taylor
- Department of Pathology, Massachusetts General Hospital, Boston, USA
| | - Kelly R. Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, USA
| | - Ilya Altukhov
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, USA
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6
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O'Donnell KA. Advances in functional genetic screening with transposons and CRISPR/Cas9 to illuminate cancer biology. Curr Opin Genet Dev 2018; 49:85-94. [PMID: 29587177 PMCID: PMC6312197 DOI: 10.1016/j.gde.2018.03.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 02/27/2018] [Accepted: 03/08/2018] [Indexed: 12/18/2022]
Abstract
Large-scale genome sequencing studies have identified a wealth of mutations in human tumors and have dramatically advanced the field of cancer genetics. However, the functional consequences of an altered gene in tumor progression cannot always be inferred from mutation status alone. This underscores the critical need for complementary methods to assign functional significance to mutated genes in cancer. Transposons are mobile genetic elements that serve as powerful tools for insertional mutagenesis. Over the last decade, investigators have employed mouse models with ondemand transposon-mediated mutagenesis to perform unbiased genetic screens to identify clinically relevant genes that participate in the pathogenesis of human cancer. Two distinct DNA transposon mutagenesis systems, Sleeping Beauty (SB) and PiggyBac (PB), have been applied extensively in vivo and more recently, in ex vivo settings. These studies have informed our understanding of the genes and pathways that drive cancer initiation, progression, and metastasis. This review highlights the latest progress on cancer gene identification for specific cancer subtypes, as well as new technological advances and incorporation of the CRISPR/Cas9 toolbox into transposon-mediated functional genetic studies.
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Affiliation(s)
- Kathryn A O'Donnell
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390-9148, United States; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390-9148, United States; Hamon Center for Regenerative Science and Medicine, UT Southwestern Medical Center, Dallas, TX 75390-9148, United States.
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7
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Achleitner M, Kleefisch M, Hennig A, Peschke K, Polikarpova A, Oertel R, Gabriel B, Schulze L, Lindeman D, Gerbaulet A, Fiebig U, Lee-Kirsch MA, Roers A, Behrendt R. Lack of Trex1 Causes Systemic Autoimmunity despite the Presence of Antiretroviral Drugs. THE JOURNAL OF IMMUNOLOGY 2017; 199:2261-2269. [PMID: 28835460 DOI: 10.4049/jimmunol.1700714] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/26/2017] [Indexed: 01/25/2023]
Abstract
Biallelic mutations of three prime repair exonuclease 1 (TREX1) cause the lupus-like disease Aicardi-Goutières syndrome in which accumulation of a yet unknown endogenous DNA substrate of TREX1 triggers a cyclic GMP-AMP synthase-dependent type I IFN response and systemic autoimmunity. Products of reverse transcription originating from endogenous retroelements have been suggested to be a major substrate for TREX1, and reverse transcriptase inhibitors (RTIs) were proposed as a therapeutic option in autoimmunity ensuing from defects of TREX1. In this study, we treated Trex1-/- mice with RTIs. The serum RTI levels reached were sufficient to block retrotransposition of endogenous retroelements. However, the treatment did not reduce the spontaneous type I IFN response and did not ameliorate lethal inflammation. Furthermore, long interspersed nuclear elements 1 retrotransposition was not enhanced in the absence of Trex1. Our data do not support the concept of retroelement-derived cDNA as key triggers of systemic autoimmunity in Trex1-deficient humans and mice and motivate the continuing search for the pathogenic IFN-inducing Trex1 substrate.
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Affiliation(s)
- Martin Achleitner
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Martin Kleefisch
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Alexander Hennig
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Katrin Peschke
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Anastasia Polikarpova
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Reinhard Oertel
- Institute of Clinical Pharmacology, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Benjamin Gabriel
- Division for HIV and Other Retroviruses, Department of Infectious Diseases, Robert Koch Institute, 13353 Berlin, Germany
| | - Livia Schulze
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Dirk Lindeman
- Institute of Virology, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany; and
| | - Alexander Gerbaulet
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Uwe Fiebig
- Division for HIV and Other Retroviruses, Department of Infectious Diseases, Robert Koch Institute, 13353 Berlin, Germany
| | - Min Ae Lee-Kirsch
- Molecular Pediatrics, Department of Pediatrics, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Axel Roers
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Rayk Behrendt
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany;
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8
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Horn AV, Celic I, Dong C, Martirosyan I, Han JS. A conserved role for the ESCRT membrane budding complex in LINE retrotransposition. PLoS Genet 2017; 13:e1006837. [PMID: 28586350 PMCID: PMC5478143 DOI: 10.1371/journal.pgen.1006837] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 06/20/2017] [Accepted: 05/23/2017] [Indexed: 11/18/2022] Open
Abstract
Long interspersed nuclear element-1s (LINE-1s, or L1s) are an active family of retrotransposable elements that continue to mutate mammalian genomes. Despite the large contribution of L1 to mammalian genome evolution, we do not know where active L1 particles (particles in the process of retrotransposition) are located in the cell, or how they move towards the nucleus, the site of L1 reverse transcription. Using a yeast model of LINE retrotransposition, we identified ESCRT (endosomal sorting complex required for transport) as a critical complex for LINE retrotransposition, and verified that this interaction is conserved for human L1. ESCRT interacts with L1 via a late domain motif, and this interaction facilitates L1 replication. Loss of the L1/ESCRT interaction does not impair RNP formation or enzymatic activity, but leads to loss of retrotransposition and reduced L1 endonuclease activity in the nucleus. This study highlights the importance of the ESCRT complex in the L1 life cycle and suggests an unusual mode for L1 RNP trafficking. Long interspersed nuclear elements (LINEs) are a class of retrotransposable elements that mutate mammalian genomes. LINEs have been highly successful in the human genome, multiplying to over 800,000 copies. The LINE-encoded replication machinery is also used by other retrotransposons, and in total, has been responsible for the generation of over 1/3 of human DNA sequence. To replicate, a LINE mRNA forms a ribonucleoprotein particle (RNP) with its proteins. This RNP eventually enters the nucleus to integrate a cDNA copy of itself into chromosomes. The events between RNP formation and successful integration are difficult to study and largely unknown. Here we show that the ESCRT complex plays a conserved role in LINE retrotransposition in both yeast and humans. ESCRT is a membrane budding complex involved in cellular trafficking and membrane budding/fusion. Our results imply that membranes play an integral part of LINE replication, and ESCRT may be required for RNP trafficking towards the nucleus.
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Affiliation(s)
- Axel V. Horn
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, United States of America
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, United States of America
| | - Ivana Celic
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, United States of America
| | - Chun Dong
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, United States of America
| | - Irena Martirosyan
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, United States of America
| | - Jeffrey S. Han
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, United States of America
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, United States of America
- * E-mail:
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9
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Kühnel E, Kleff V, Stojanovska V, Kaiser S, Waldschütz R, Herse F, Plösch T, Winterhager E, Gellhaus A. Placental-Specific Overexpression of sFlt-1 Alters Trophoblast Differentiation and Nutrient Transporter Expression in an IUGR Mouse Model. J Cell Biochem 2017; 118:1316-1329. [PMID: 27859593 DOI: 10.1002/jcb.25789] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/07/2016] [Indexed: 12/25/2022]
Abstract
Since it is known that placental overexpression of the human anti-angiogenic molecule sFlt-1, the main candidate in the progression of preeclampsia, lead to intrauterine growth restriction (IUGR) in mice by lentiviral transduction of mouse blastocysts, we hypothesize that sFlt-1 influence placental morphology and physiology resulting in fetal IUGR. We therefore examined the effect of sFlt-1 on placental morphology and physiology at embryonic day 18.5 with histologic and morphometric analyses, transcript analyses, immunoblotting, and methylation studies. Interestingly, placental overexpression of sFlt-1 leads to IUGR in the fetus and results in lower placental weights. Moreover, we observed altered trophoblast differentiation with reduced expression of IGF2, resulting in a smaller placenta, a smaller labyrinth, and the loss of glycogen cells in the junctional zone. Changes in IGF2 are accompanied by small changes in its DNA methylation, whereas overall DNA methylation is unaffected. In addition, the expression of placental nutrient transporters, such as the glucose diffusion channel Cx26, is decreased. In contrast, the expression of the fatty acid transporter CD36 and the cholesterol transporter ABCA1 is significantly increased. In conclusion, placental sFlt-1 overexpression resulted in a reduction in the differentiation of the spongiotrophoblast into glycogen cells. These findings of a reduced exchange area of the labyrinth and glycogen stores, as well as decreased expression of glucose transporter, could contribute to the intrauterine growth restriction phenotype. All of these factors change the intrauterine availability of nutrients. Thus, we speculate that the alterations triggered by increased anti-angiogenesis strongly affect fetal outcome and programming. J. Cell. Biochem. 118: 1316-1329, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Elisabeth Kühnel
- Department of Gynecology and Obstetrics, University Hospital Essen, Essen, Germany
| | - Veronika Kleff
- Institute of Molecular Biology, University of Duisburg-Essen, Essen, Germany
| | - Violeta Stojanovska
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Stephanie Kaiser
- Institute of Molecular Biology, University of Duisburg-Essen, Essen, Germany
| | - Ralph Waldschütz
- Central Animal Laboratory, University of Duisburg-Essen, Essen, Germany
| | - Florian Herse
- Experimental and Clinical Research Center, a joint cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité Medical Faculty, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Torsten Plösch
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Elke Winterhager
- Institute of Molecular Biology, University of Duisburg-Essen, Essen, Germany
| | - Alexandra Gellhaus
- Department of Gynecology and Obstetrics, University Hospital Essen, Essen, Germany
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10
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Ardeljan D, Taylor MS, Burns KH, Boeke JD, Espey MG, Woodhouse EC, Howcroft TK. Meeting Report: The Role of the Mobilome in Cancer. Cancer Res 2016; 76:4316-9. [PMID: 27527733 DOI: 10.1158/0008-5472.can-15-3421] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/13/2016] [Indexed: 11/16/2022]
Abstract
Approximately half of the human genome consists of repetitive sequence attributed to the activities of mobile DNAs, including DNA transposons, RNA transposons, and endogenous retroviruses. Of these, only long interspersed elements (LINE-1 or L1) and sequences copied by LINE-1 remain mobile in our species today. Although cells restrict L1 activity by both transcriptional and posttranscriptional mechanisms, L1 derepression occurs in developmental and pathologic contexts, including many types of cancers. However, we have limited knowledge of the extent and consequences of L1 expression in premalignancies and cancer. Participants in this NIH strategic workshop considered key questions to enhance our understanding of mechanisms and roles the mobilome may play in cancer biology. Cancer Res; 76(15); 4316-9. ©2016 AACR.
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Affiliation(s)
- Daniel Ardeljan
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland. Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Martin S Taylor
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Kathleen H Burns
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland. Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jef D Boeke
- Institute for Systems Genetics, New York University Langone Medical Center, New York, New York
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11
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Parrish NF, Tomonaga K. Endogenized viral sequences in mammals. Curr Opin Microbiol 2016; 31:176-183. [PMID: 27128186 DOI: 10.1016/j.mib.2016.03.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 03/15/2016] [Accepted: 03/15/2016] [Indexed: 12/13/2022]
Abstract
Reverse-transcribed RNA molecules compose a significant portion of the human genome. Many of these RNA molecules were retrovirus genomes either infecting germline cells or having done so in a previous generation but retaining transcriptional activity. This mechanism itself accounts for a quarter of the genomic sequence information of mammals for which there is data. We understand relatively little about the causes and consequences of retroviral endogenization. This review highlights functions ascribed to sequences of viral origin endogenized into mammalian genomes and suggests some of the most pressing questions raised by these observations.
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Affiliation(s)
- Nicholas F Parrish
- Section of Surgical Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, United States.
| | - Keizo Tomonaga
- Department of Viral Oncology, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan; Department of Tumor Viruses, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan; Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto 606-8507, Japan.
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12
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LaCava J, Molloy KR, Taylor MS, Domanski M, Chait BT, Rout MP. Affinity proteomics to study endogenous protein complexes: pointers, pitfalls, preferences and perspectives. Biotechniques 2015; 58:103-19. [PMID: 25757543 PMCID: PMC4465938 DOI: 10.2144/000114262] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 02/17/2015] [Indexed: 01/13/2023] Open
Abstract
Dissecting and studying cellular systems requires the ability to specifically isolate distinct proteins along with the co-assembled constituents of their associated complexes. Affinity capture techniques leverage high affinity, high specificity reagents to target and capture proteins of interest along with specifically associated proteins from cell extracts. Affinity capture coupled to mass spectrometry (MS)-based proteomic analyses has enabled the isolation and characterization of a wide range of endogenous protein complexes. Here, we outline effective procedures for the affinity capture of protein complexes, highlighting best practices and common pitfalls.
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Affiliation(s)
- John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York
- Institute for Systems Genetics, New York University School of Medicine, New York, NY
| | - Kelly R. Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY
| | - Martin S. Taylor
- High Throughput Biology Center and Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Michal Domanski
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York
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13
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Exploiting the power of LINE-1 retrotransposon mutagenesis for identification of genes involved in embryonic stem cell differentiation. Stem Cell Rev Rep 2014; 10:408-16. [PMID: 24610122 PMCID: PMC4008784 DOI: 10.1007/s12015-014-9500-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Identifying the genes or epigenetic factors that control the self-renewal and differentiation of stem cells is critical to understanding the molecular basis of cell commitment. Although a number of insertional mutagenesis vectors have been developed for identifying gene functions in animal models, the L1 retrotransposition system offers additional advantages as a tool to disrupt genes in embryonic stem cells in order to identify their functions and the phenotypes associated with them. Recent advances in producing synthetic versions of L1 retrotransposon vector system and the optimization of techniques to accurately identify retrotransposon integration sites have increased their utility for gene discovery applications. We have developed a novel episomal, nonviral L1 retrotransposon vector using scaffold/matrix attachment regions that provides stable, sustained levels of retrotransposition in cell cultures without being affected by epigenetic silencing or from some of the common problems of vector integration. This modified vector contains a GFP marker whose expression occurs only after successful gene disruption events and thus the cells with disrupted genes can be easily picked for functional analysis. Here we present a method to disrupt gene function in embryonic stem cells that aid in the identification of genes involved in stem cell differentiation processes. The methods presented here can be easily adapted to the study of other types of cancer stem cells or induced pluripotent stem cells using the L1 retrotransposon as an insertional mutagen.
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14
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Malki S, van der Heijden GW, O'Donnell KA, Martin SL, Bortvin A. A role for retrotransposon LINE-1 in fetal oocyte attrition in mice. Dev Cell 2014; 29:521-533. [PMID: 24882376 DOI: 10.1016/j.devcel.2014.04.027] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 03/31/2014] [Accepted: 04/23/2014] [Indexed: 11/24/2022]
Abstract
Fetal oocyte attrition (FOA) is a conserved but poorly understood process of elimination of more than two-thirds of meiotic prophase I (MPI) oocytes before birth. We now implicate retrotransposons LINE-1 (L1), activated during epigenetic reprogramming of the embryonic germline, in FOA in mice. We show that wild-type fetal oocytes possess differential nuclear levels of L1ORF1p, an L1-encoded protein essential for L1 ribonucleoprotein particle (L1RNP) formation and L1 retrotransposition. We demonstrate that experimental elevation of L1 expression correlates with increased MPI defects, FOA, oocyte aneuploidy, and embryonic lethality. Conversely, reverse transcriptase (RT) inhibitor AZT has a profound effect on the FOA dynamics and meiotic recombination, and it implicates an RT-dependent trigger in oocyte elimination in early MPI. We propose that FOA serves to select oocytes with limited L1 activity that are therefore best suited for the next generation.
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Affiliation(s)
- Safia Malki
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA
| | | | - Kathryn A O'Donnell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sandra L Martin
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Alex Bortvin
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA.
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15
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Affinity proteomics reveals human host factors implicated in discrete stages of LINE-1 retrotransposition. Cell 2014; 155:1034-48. [PMID: 24267889 DOI: 10.1016/j.cell.2013.10.021] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 08/25/2013] [Accepted: 09/30/2013] [Indexed: 11/21/2022]
Abstract
LINE-1s are active human DNA parasites that are agents of genome dynamics in evolution and disease. These streamlined elements require host factors to complete their life cycles, whereas hosts have developed mechanisms to combat retrotransposition's mutagenic effects. As such, endogenous L1 expression levels are extremely low, creating a roadblock for detailed interactomic analyses. Here, we describe a system to express and purify highly active L1 RNP complexes from human suspension cell culture and characterize the copurified proteome, identifying 37 high-confidence candidate interactors. These data sets include known interactors PABPC1 and MOV10 and, with in-cell imaging studies, suggest existence of at least three types of compositionally and functionally distinct L1 RNPs. Among the findings, UPF1, a key nonsense-mediated decay factor, and PCNA, the polymerase-delta-associated sliding DNA clamp, were identified and validated. PCNA interacts with ORF2p via a PIP box motif; mechanistic studies suggest that this occurs during or immediately after target-primed reverse transcription.
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