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Cristofari G. Snapshots of genetic copy-and-paste machinery in action. Nature 2024; 626:40-42. [PMID: 38287184 DOI: 10.1038/d41586-024-00112-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
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Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sánchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Işik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, Riento K, Halls-Kass R, Augustin M, Lammens A, Jestel A, Upla P, Xibinaku K, Congreve S, Hennink M, Rogala KB, Schneider AM, Fairman JE, Christensen SM, Desrosiers B, Bisacchi GS, Saunders OL, Hafeez N, Miao W, Kapeller R, Zaller DM, Sali A, Weichenrieder O, Burns KH, Götte M, Rout MP, Arnold E, Greenbaum BD, Romero DL, LaCava J, Taylor MS. Structures, functions and adaptations of the human LINE-1 ORF2 protein. Nature 2024; 626:194-206. [PMID: 38096902 PMCID: PMC10830420 DOI: 10.1038/s41586-023-06947-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024]
Abstract
The LINE-1 (L1) retrotransposon is an ancient genetic parasite that has written around one-third of the human genome through a 'copy and paste' mechanism catalysed by its multifunctional enzyme, open reading frame 2 protein (ORF2p)1. ORF2p reverse transcriptase (RT) and endonuclease activities have been implicated in the pathophysiology of cancer2,3, autoimmunity4,5 and ageing6,7, making ORF2p a potential therapeutic target. However, a lack of structural and mechanistic knowledge has hampered efforts to rationally exploit it. We report structures of the human ORF2p 'core' (residues 238-1061, including the RT domain) by X-ray crystallography and cryo-electron microscopy in several conformational states. Our analyses identified two previously undescribed folded domains, extensive contacts to RNA templates and associated adaptations that contribute to unique aspects of the L1 replication cycle. Computed integrative structural models of full-length ORF2p show a dynamic closed-ring conformation that appears to open during retrotransposition. We characterize ORF2p RT inhibition and reveal its underlying structural basis. Imaging and biochemistry show that non-canonical cytosolic ORF2p RT activity can produce RNA:DNA hybrids, activating innate immune signalling through cGAS/STING and resulting in interferon production6-8. In contrast to retroviral RTs, L1 RT is efficiently primed by short RNAs and hairpins, which probably explains cytosolic priming. Other biochemical activities including processivity, DNA-directed polymerization, non-templated base addition and template switching together allow us to propose a revised L1 insertion model. Finally, our evolutionary analysis demonstrates structural conservation between ORF2p and other RNA- and DNA-dependent polymerases. We therefore provide key mechanistic insights into L1 polymerization and insertion, shed light on the evolutionary history of L1 and enable rational drug development targeting L1.
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Affiliation(s)
| | - Trevor van Eeuwen
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - David Hoyos
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arthur Zalevsky
- Department of Bioengineering and Therapeutic Sciences University of California, San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biology Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Egor P Tchesnokov
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | | | - Bryant D Miller
- Department of Pathology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Luciano H Di Stefano
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, The Netherlands
| | - Francesc Xavier Ruiz
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Matthew Hancock
- Department of Bioengineering and Therapeutic Sciences University of California, San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biology Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Esin Işik
- Department of Pathology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Carlos Mendez-Dorantes
- Department of Pathology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Thomas Walpole
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | - Charles Nichols
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | - Paul Wan
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | - Kirsi Riento
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | - Rowan Halls-Kass
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | | | - Alfred Lammens
- Proteros Biostructures GmbH, Martinsried, Planegg, Germany
| | - Anja Jestel
- Proteros Biostructures GmbH, Martinsried, Planegg, Germany
| | - Paula Upla
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - Kera Xibinaku
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | | | | | - Kacper B Rogala
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Anna M Schneider
- Structural Biology of Selfish RNA, Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | | | | | | | | | | | | | | | | | | | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences University of California, San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biology Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Oliver Weichenrieder
- Structural Biology of Selfish RNA, Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | - Kathleen H Burns
- Department of Pathology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada.
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA.
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA.
| | - Benjamin D Greenbaum
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA.
| | | | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA.
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, The Netherlands.
| | - Martin S Taylor
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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Mathavarajah S, Dellaire G. LINE-1: an emerging initiator of cGAS-STING signalling and inflammation that is dysregulated in disease. Biochem Cell Biol 2024; 102:38-46. [PMID: 37643478 DOI: 10.1139/bcb-2023-0134] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023] Open
Abstract
The cGAS-STING (cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING)) axis integrates DNA damage and cellular stress with type I interferon (IFN) signalling to facilitate transcriptional changes underlying inflammatory stress responses. The cGAS-STING pathway responds to cytosolic DNA in the form of double-stranded DNA, micronuclei, and long interspersed nuclear element 1 (L1) retroelements. L1 retroelements are a class of self-propagating non-long terminal repeat transposons that have remained highly active in mammalian genomes. L1 retroelements are emerging as important inducers of cGAS-STING and IFN signalling, which are often dysregulated in several diseases, including cancer. A key repressor of cGAS-STING and L1 activity is the exonuclease three prime repair exonuclease 1 (TREX1), and loss of TREX1 promotes the accumulation of L1. In addition, L1 dysregulation is a common theme among diseases with chronic induction of type I IFN signalling through cGAS-STING, such as Aicardi-Goutières syndrome, Fanconi anemia, and dermatomyositis. Although TREX1 is highly conserved in tetrapod species, other suppressor proteins exist that inhibit L1 retrotransposition. These suppressor genes when mutated are often associated with diseases characterized by unchecked inflammation that is associated with high cGAS-STING activity and elevated levels of L1 expression. In this review, we discuss these interconnected pathways of L1 suppression and their role in the regulation of cGAS-STING and inflammation in disease.
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Affiliation(s)
| | - Graham Dellaire
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
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Luqman-Fatah A, Miyoshi T. Human LINE-1 retrotransposons: impacts on the genome and regulation by host factors. Genes Genet Syst 2023; 98:121-154. [PMID: 36436935 DOI: 10.1266/ggs.22-00038] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Genome sequencing revealed that nearly half of the human genome is comprised of transposable elements. Although most of these elements have been rendered inactive due to mutations, full-length intact long interspersed element-1 (LINE-1 or L1) copies retain the ability to mobilize through RNA intermediates by a so-called "copy-and-paste" mechanism, termed retrotransposition. L1 is the only known autonomous mobile genetic element in the genome, and its retrotransposition contributes to inter- or intra-individual genetic variation within the human population. However, L1 retrotransposition also poses a threat to genome integrity due to gene disruption and chromosomal instability. Moreover, recent studies suggest that aberrant L1 expression can impact human health by causing diseases such as cancer and chronic inflammation that might lead to autoimmune disorders. To counteract these adverse effects, the host cells have evolved multiple layers of defense mechanisms at the epigenetic, RNA and protein levels. Intriguingly, several host factors have also been reported to facilitate L1 retrotransposition, suggesting that there is competition between negative and positive regulation of L1 by host factors. Here, we summarize the known host proteins that regulate L1 activity at different stages of the replication cycle and discuss how these factors modulate disease-associated phenotypes caused by L1.
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Affiliation(s)
- Ahmad Luqman-Fatah
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University
- Department of Stress Response, Radiation Biology Center, Graduate School of Biostudies, Kyoto University
| | - Tomoichiro Miyoshi
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University
- Department of Stress Response, Radiation Biology Center, Graduate School of Biostudies, Kyoto University
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Luqman-Fatah A, Watanabe Y, Uno K, Ishikawa F, Moran JV, Miyoshi T. The interferon stimulated gene-encoded protein HELZ2 inhibits human LINE-1 retrotransposition and LINE-1 RNA-mediated type I interferon induction. Nat Commun 2023; 14:203. [PMID: 36639706 PMCID: PMC9839780 DOI: 10.1038/s41467-022-35757-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 12/23/2022] [Indexed: 01/15/2023] Open
Abstract
Some interferon stimulated genes (ISGs) encode proteins that inhibit LINE-1 (L1) retrotransposition. Here, we use immunoprecipitation followed by liquid chromatography-tandem mass spectrometry to identify proteins that associate with the L1 ORF1-encoded protein (ORF1p) in ribonucleoprotein particles. Three ISG proteins that interact with ORF1p inhibit retrotransposition: HECT and RLD domain containing E3 ubiquitin-protein ligase 5 (HERC5); 2'-5'-oligoadenylate synthetase-like (OASL); and helicase with zinc finger 2 (HELZ2). HERC5 destabilizes ORF1p, but does not affect its cellular localization. OASL impairs ORF1p cytoplasmic foci formation. HELZ2 recognizes sequences and/or structures within the L1 5'UTR to reduce L1 RNA, ORF1p, and ORF1p cytoplasmic foci levels. Overexpression of WT or reverse transcriptase-deficient L1s lead to a modest induction of IFN-α expression, which is abrogated upon HELZ2 overexpression. Notably, IFN-α expression is enhanced upon overexpression of an ORF1p RNA binding mutant, suggesting ORF1p binding might protect L1 RNA from "triggering" IFN-α induction. Thus, ISG proteins can inhibit retrotransposition by different mechanisms.
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Affiliation(s)
- Ahmad Luqman-Fatah
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - Yuzo Watanabe
- Proteomics Facility, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - Kazuko Uno
- Division of Basic Research, Louis Pasteur Center for Medical Research, Kyoto, 606-8225, Japan
| | - Fuyuki Ishikawa
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Tomoichiro Miyoshi
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan.
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan.
- Laboratory for Retrotransposon Dynamics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
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Martin MD, Brown DN, Ramos KS. Computational modeling of RNase, antisense ORF0 RNA, and intracellular compartmentation and their impact on the life cycle of the line retrotransposon. Comput Struct Biotechnol J 2021; 19:5667-5677. [PMID: 34765087 PMCID: PMC8554170 DOI: 10.1016/j.csbj.2021.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/10/2021] [Accepted: 10/01/2021] [Indexed: 11/08/2022] Open
Abstract
Nearly half of the human genome is occupied by repetitive sequences of ancient virus-like genetic elements. The largest class, comprising 17% of the genome, belong to the type 1 Long INterspersed Elements (LINE-1) and are the only class capable of autonomous propagation in the genome. When epigenetic silencing mechanisms of LINE-1 fail, the proteins encoded by LINE-1 engage in reverse transcription to make new copies of their own or other DNAs that are pasted back into the genome. To elucidate how LINE-1 is dysregulated as a result of carcinogen exposure, we developed a computational model of key elements in the LINE-1 lifecycle, namely, the role of cytosolic ribonuclease (RNase), RNA interference (RNAi) by the antisense ORF0 RNA, and sequestration of LINE-1 products into stress granules and multivesicular structures. The model showed that when carcinogen exposure is represented as either a sudden increase in LINE-1 mRNA count, or as an increase in mRNA transcription rate, the retrotransposon copy number exhibits a distinct threshold behavior above which LINE-1 enters a positive feedback loop that allows the cDNA copy number to grow exponentially. We also found that most of the LINE-1 RNA was degraded via the RNAase pathway and that neither ORF0 RNAi, nor the sequestration of LINE-1 products into granules and multivesicular structures, played a significant role in regulating the retrotransposon’s life cycle. Several aspects of the prediction agree with experimental results and indicate that the model has significant potential to inform future experiments related to LINE-1 activation.
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Affiliation(s)
| | - David N Brown
- Western Kentucky University, 1906 College Heights Blvd, Bowling Green, Kentucky 42101, United States
| | - Kenneth S Ramos
- Center for Genomic and Precision Medicine, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX 77030, United States
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Miller I, Totrov M, Korotchkina L, Kazyulkin DN, Gudkov AV, Korolev S. Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease. Nucleic Acids Res 2021; 49:11350-11366. [PMID: 34554261 PMCID: PMC8565326 DOI: 10.1093/nar/gkab826] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 11/12/2022] Open
Abstract
Long interspersed nuclear element-1 (L1) is an autonomous non-LTR retrotransposon comprising ∼20% of the human genome. L1 self-propagation causes genomic instability and is strongly associated with aging, cancer and other diseases. The endonuclease domain of L1’s ORFp2 protein (L1-EN) initiates de novo L1 integration by nicking the consensus sequence 5′-TTTTT/AA-3′. In contrast, related nucleases including structurally conserved apurinic/apyrimidinic endonuclease 1 (APE1) are non-sequence specific. To investigate mechanisms underlying sequence recognition and catalysis by L1-EN, we solved crystal structures of L1-EN complexed with DNA substrates. This showed that conformational properties of the preferred sequence drive L1-EN’s sequence-specificity and catalysis. Unlike APE1, L1-EN does not bend the DNA helix, but rather causes ‘compression’ near the cleavage site. This provides multiple advantages for L1-EN’s role in retrotransposition including facilitating use of the nicked poly-T DNA strand as a primer for reverse transcription. We also observed two alternative conformations of the scissile bond phosphate, which allowed us to model distinct conformations for a nucleophilic attack and a transition state that are likely applicable to the entire family of nucleases. This work adds to our mechanistic understanding of L1-EN and related nucleases and should facilitate development of L1-EN inhibitors as potential anticancer and antiaging therapeutics.
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Affiliation(s)
- Ian Miller
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | | | | | | | - Andrei V Gudkov
- Genome Protection, Inc., Buffalo, NY 14203, USA.,Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Sergey Korolev
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
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Ramos KS, Bojang P, Bowers E. Role of long interspersed nuclear element-1 in the regulation of chromatin landscapes and genome dynamics. Exp Biol Med (Maywood) 2021; 246:2082-2097. [PMID: 34304633 PMCID: PMC8524765 DOI: 10.1177/15353702211031247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 12/27/2022] Open
Abstract
LINE-1 retrotransposon, the most active mobile element of the human genome, is subject to tight regulatory control. Stressful environments and disease modify the recruitment of regulatory proteins leading to unregulated activation of LINE-1. The activation of LINE-1 influences genome dynamics through altered chromatin landscapes, insertion mutations, deletions, and modulation of cellular plasticity. To date, LINE-1 retrotransposition has been linked to various cancer types and may in fact underwrite the genetic basis of various other forms of chronic human illness. The occurrence of LINE-1 polymorphisms in the human population may define inter-individual differences in susceptibility to disease. This review is written in honor of Dr Peter Stambrook, a friend and colleague who carried out highly impactful cancer research over many years of professional practice. Dr Stambrook devoted considerable energy to helping others live up to their full potential and to navigate the complexities of professional life. He was an inspirational leader, a strong advocate, a kind mentor, a vocal supporter and cheerleader, and yes, a hard critic and tough friend when needed. His passionate stand on issues, his witty sense of humor, and his love for humanity have left a huge mark in our lives. We hope that that the knowledge summarized here will advance our understanding of the role of LINE-1 in cancer biology and expedite the development of innovative cancer diagnostics and treatments in the ways that Dr Stambrook himself had so passionately envisioned.
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Affiliation(s)
- Kenneth S Ramos
- Institute of Biosciences and Technology, Texas A&M Health, Houston, TX 77030, USA
| | - Pasano Bojang
- University of Kentucky College of Medicine, Lexington, KY 40506, USA
| | - Emma Bowers
- Institute of Biosciences and Technology, Texas A&M Health, Houston, TX 77030, USA
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Banuelos-Sanchez G, Sanchez L, Benitez-Guijarro M, Sanchez-Carnerero V, Salvador-Palomeque C, Tristan-Ramos P, Benkaddour-Boumzaouad M, Morell S, Garcia-Puche JL, Heras SR, Franco-Montalban F, Tamayo JA, Garcia-Perez JL. Synthesis and Characterization of Specific Reverse Transcriptase Inhibitors for Mammalian LINE-1 Retrotransposons. Cell Chem Biol 2019; 26:1095-1109.e14. [DOI: 10.1016/j.chembiol.2019.04.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/29/2019] [Accepted: 04/19/2019] [Indexed: 12/24/2022]
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Schumann GG, Fuchs NV, Tristán-Ramos P, Sebe A, Ivics Z, Heras SR. The impact of transposable element activity on therapeutically relevant human stem cells. Mob DNA 2019; 10:9. [PMID: 30899334 PMCID: PMC6408843 DOI: 10.1186/s13100-019-0151-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/27/2019] [Indexed: 12/11/2022] Open
Abstract
Human stem cells harbor significant potential for basic and clinical translational research as well as regenerative medicine. Currently ~ 3000 adult and ~ 30 pluripotent stem cell-based, interventional clinical trials are ongoing worldwide, and numbers are increasing continuously. Although stem cells are promising cell sources to treat a wide range of human diseases, there are also concerns regarding potential risks associated with their clinical use, including genomic instability and tumorigenesis concerns. Thus, a deeper understanding of the factors and molecular mechanisms contributing to stem cell genome stability are a prerequisite to harnessing their therapeutic potential for degenerative diseases. Chemical and physical factors are known to influence the stability of stem cell genomes, together with random mutations and Copy Number Variants (CNVs) that accumulated in cultured human stem cells. Here we review the activity of endogenous transposable elements (TEs) in human multipotent and pluripotent stem cells, and the consequences of their mobility for genomic integrity and host gene expression. We describe transcriptional and post-transcriptional mechanisms antagonizing the spread of TEs in the human genome, and highlight those that are more prevalent in multipotent and pluripotent stem cells. Notably, TEs do not only represent a source of mutations/CNVs in genomes, but are also often harnessed as tools to engineer the stem cell genome; thus, we also describe and discuss the most widely applied transposon-based tools and highlight the most relevant areas of their biomedical applications in stem cells. Taken together, this review will contribute to the assessment of the risk that endogenous TE activity and the application of genetically engineered TEs constitute for the biosafety of stem cells to be used for substitutive and regenerative cell therapies.
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Affiliation(s)
- Gerald G Schumann
- 1Division of Medical Biotechnology, Paul-Ehrlich-Institut, Paul-Ehrlich-Str.51-59, 63225 Langen, Germany
| | - Nina V Fuchs
- 2Host-Pathogen Interactions, Paul-Ehrlich-Institut, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany
| | - Pablo Tristán-Ramos
- 3GENYO. Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada-Avenida de la Ilustración, 114, 18016 Granada, Spain.,4Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, 18071 Granada, Spain
| | - Attila Sebe
- 1Division of Medical Biotechnology, Paul-Ehrlich-Institut, Paul-Ehrlich-Str.51-59, 63225 Langen, Germany
| | - Zoltán Ivics
- 1Division of Medical Biotechnology, Paul-Ehrlich-Institut, Paul-Ehrlich-Str.51-59, 63225 Langen, Germany
| | - Sara R Heras
- 3GENYO. Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada-Avenida de la Ilustración, 114, 18016 Granada, Spain.,4Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, 18071 Granada, Spain
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11
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Benitez-Guijarro M, Lopez-Ruiz C, Tarnauskaitė Ž, Murina O, Mian Mohammad M, Williams TC, Fluteau A, Sanchez L, Vilar-Astasio R, Garcia-Canadas M, Cano D, Kempen MJH, Sanchez-Pozo A, Heras SR, Jackson AP, Reijns MA, Garcia-Perez JL. RNase H2, mutated in Aicardi-Goutières syndrome, promotes LINE-1 retrotransposition. EMBO J 2018; 37:e98506. [PMID: 29959219 PMCID: PMC6068448 DOI: 10.15252/embj.201798506] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 05/23/2018] [Accepted: 05/28/2018] [Indexed: 12/03/2022] Open
Abstract
Long INterspersed Element class 1 (LINE-1) elements are a type of abundant retrotransposons active in mammalian genomes. An average human genome contains ~100 retrotransposition-competent LINE-1s, whose activity is influenced by the combined action of cellular repressors and activators. TREX1, SAMHD1 and ADAR1 are known LINE-1 repressors and when mutated cause the autoinflammatory disorder Aicardi-Goutières syndrome (AGS). Mutations in RNase H2 are the most common cause of AGS, and its activity was proposed to similarly control LINE-1 retrotransposition. It has therefore been suggested that increased LINE-1 activity may be the cause of aberrant innate immune activation in AGS Here, we establish that, contrary to expectations, RNase H2 is required for efficient LINE-1 retrotransposition. As RNase H1 overexpression partially rescues the defect in RNase H2 null cells, we propose a model in which RNase H2 degrades the LINE-1 RNA after reverse transcription, allowing retrotransposition to be completed. This also explains how LINE-1 elements can retrotranspose efficiently without their own RNase H activity. Our findings appear to be at odds with LINE-1-derived nucleic acids driving autoinflammation in AGS.
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Affiliation(s)
- Maria Benitez-Guijarro
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
| | - Cesar Lopez-Ruiz
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
| | - Žygimantė Tarnauskaitė
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Olga Murina
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Mahwish Mian Mohammad
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Thomas C Williams
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Adeline Fluteau
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Laura Sanchez
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
| | - Raquel Vilar-Astasio
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
| | - Marta Garcia-Canadas
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
| | - David Cano
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
| | - Marie-Jeanne Hc Kempen
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Antonio Sanchez-Pozo
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Sara R Heras
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Andrew P Jackson
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Martin Am Reijns
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Jose L Garcia-Perez
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
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12
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Zhao C, Liu F, Pyle AM. An ultraprocessive, accurate reverse transcriptase encoded by a metazoan group II intron. RNA (NEW YORK, N.Y.) 2018; 24:183-195. [PMID: 29109157 PMCID: PMC5769746 DOI: 10.1261/rna.063479.117] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/31/2017] [Indexed: 05/24/2023]
Abstract
Group II introns and non-LTR retrotransposons encode a phylogenetically related family of highly processive reverse transcriptases (RTs) that are essential for mobility and persistence of these retroelements. Recent crystallographic studies on members of this RT family have revealed that they are structurally distinct from the retroviral RTs that are typically used in biotechnology. However, quantitative, structure-guided analysis of processivity, efficiency, and accuracy of this alternate RT family has been lacking. Here, we characterize the processivity of a group II intron maturase RT from Eubacterium rectale (E.r), for which high-resolution structural information is available. We find that the E.r. maturase RT (MarathonRT) efficiently copies transcripts at least 10 kb in length and displays superior intrinsic RT processivity compared to commercial enzymes such as Superscript IV (SSIV). The elevated processivity of MarathonRT is at least partly mediated by a loop structure in the finger subdomain that acts as a steric guard (the α-loop). Additionally, we find that a positively charged secondary RNA binding site on the surface of the RT diminishes the primer utilization efficiency of the enzyme, and that reengineering of this surface enhances capabilities of the MarathonRT. Finally, using single-molecule sequencing, we show that the error frequency of MarathonRT is comparable to that of other high-performance RTs, such as SSIV, which were tested in parallel. Our results provide a structural framework for understanding the enhanced processivity of retroelement RTs, and they demonstrate the potential for engineering a powerful new generation of RT tools for application in biotechnology and research.
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Affiliation(s)
- Chen Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Fei Liu
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
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13
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Feng Y, Goubran MH, Follack TB, Chelico L. Deamination-independent restriction of LINE-1 retrotransposition by APOBEC3H. Sci Rep 2017; 7:10881. [PMID: 28883657 PMCID: PMC5589869 DOI: 10.1038/s41598-017-11344-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 08/18/2017] [Indexed: 12/16/2022] Open
Abstract
The APOBEC3 family of cytosine deaminase enzymes are able to restrict replication of retroelements, such as LINE-1. However, each of the seven APOBEC3 enzymes have been reported to act differentially to prevent LINE-1 retrotransposition and the mechanisms of APOBEC3-mediated LINE-1 inhibition has not been well understood. The prevailing view for many years was that APOBEC3-mediated LINE-1 inhibition was deamination-independent and relied on APOBEC3s blocking the LINE-1 reverse transcriptase DNA polymerization or transport of the LINE-1 RNA into the nucleus. However, recently it was shown that APOBEC3A can deaminate cytosine, to form uracil, on transiently exposed single-stranded LINE-1 cDNA and this leads to LINE-1 cDNA degradation. In this study, we confirmed that APOBEC3A is a potent deamination-dependent inhibitor of LINE-1 retrotransposition, but show that in contrast, A3H haplotype II and haplotype V restrict LINE-1 activity using a deamination-independent mechanism. Our study supports the model that different APOBEC3 proteins have evolved to inhibit LINE-1 retrotransposition through distinct mechanisms.
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Affiliation(s)
- Yuqing Feng
- Department of Microbiology & Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Mariam H Goubran
- Department of Microbiology & Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Tyson B Follack
- Department of Microbiology & Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Linda Chelico
- Department of Microbiology & Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5, Canada.
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14
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Involvement of Conserved Amino Acids in the C-Terminal Region of LINE-1 ORF2p in Retrotransposition. Genetics 2017; 205:1139-1149. [PMID: 28100588 DOI: 10.1534/genetics.116.191403] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 12/10/2016] [Indexed: 01/09/2023] Open
Abstract
Long interspersed element 1 (L1) is the only currently active autonomous retroelement in the human genome. Along with the parasitic SVA and short interspersed element Alu, L1 is the source of DNA damage induced by retrotransposition: a copy-and-paste process that has the potential to disrupt gene function and cause human disease. The retrotransposition process is dependent upon the ORF2 protein (ORF2p). However, it is unknown whether most of the protein is important for retrotransposition. In particular, other than the Cys motif, the C terminus of the protein has not been intensely examined in the context of retrotransposition. Using evolutionary analysis and the Alu retrotransposition assay, we sought to identify additional amino acids in the C terminus important for retrotransposition. Here, we demonstrate that Gal4-tagged and untagged C-terminally truncated ORF2p fragments possess residual potential to drive Alu retrotransposition. Using sight-directed mutagenesis we identify that while the Y1180 amino acid is important for ORF2p- and L1-driven Alu retrotransposition, a mutation at this position improves L1 retrotransposition. Even though the mechanism of the contribution of Y1180 to Alu and L1 mobilization remains unknown, experimental evidence rules out its direct involvement in the ability of the ORF2p reverse transcriptase to generate complementary DNA. Additionally, our data support that ORF2p amino acids 1180 and 1250-1262 may be involved in the reported ORF1p-mediated increase in ORF2p-driven Alu retrotransposition.
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15
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Hancks DC, Kazazian HH. Roles for retrotransposon insertions in human disease. Mob DNA 2016; 7:9. [PMID: 27158268 PMCID: PMC4859970 DOI: 10.1186/s13100-016-0065-9] [Citation(s) in RCA: 421] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/14/2016] [Indexed: 12/12/2022] Open
Abstract
Over evolutionary time, the dynamic nature of a genome is driven, in part, by the activity of transposable elements (TE) such as retrotransposons. On a shorter time scale it has been established that new TE insertions can result in single-gene disease in an individual. In humans, the non-LTR retrotransposon Long INterspersed Element-1 (LINE-1 or L1) is the only active autonomous TE. In addition to mobilizing its own RNA to new genomic locations via a "copy-and-paste" mechanism, LINE-1 is able to retrotranspose other RNAs including Alu, SVA, and occasionally cellular RNAs. To date in humans, 124 LINE-1-mediated insertions which result in genetic diseases have been reported. Disease causing LINE-1 insertions have provided a wealth of insight and the foundation for valuable tools to study these genomic parasites. In this review, we provide an overview of LINE-1 biology followed by highlights from new reports of LINE-1-mediated genetic disease in humans.
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Affiliation(s)
- Dustin C. Hancks
- />Eccles Institute of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Haig H. Kazazian
- />McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins School of Medicine, Baltimore, MD USA
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16
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Christian CM, deHaro D, Kines KJ, Sokolowski M, Belancio VP. Identification of L1 ORF2p sequence important to retrotransposition using Bipartile Alu retrotransposition (BAR). Nucleic Acids Res 2016; 44:4818-34. [PMID: 27095191 PMCID: PMC4889948 DOI: 10.1093/nar/gkw277] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 04/06/2016] [Indexed: 01/14/2023] Open
Abstract
Long Interspersed Element 1 (LINE-1 or L1) is capable of causing genomic instability through the activity of the L1 ORF2 protein (ORF2p). This protein contains endonuclease (EN) and reverse transcriptase (RT) domains that are necessary for the retrotransposition of L1 and the Short Interspersed Element (SINE) Alu. The functional importance of approximately 50% of the ORF2p molecule remains unknown, but some of these sequences could play a role in retrotransposition, or be necessary for the enzymatic activities of the EN and/or RT domains. Conventional approaches using the full-length, contiguous ORF2p make it difficult to study the involvement of these unannotated sequences in the function of L1 ORF2p. Our lab has developed a Bipartile Alu Retrotransposition (BAR) assay that relies on separate truncated ORF2p fragments: an EN-containing and an RT-containing fragment. We validated the utility of this method for studying the ORF2p function in retrotransposition by assessing the effect of expression levels and previously characterized mutations on BAR. Using BAR, we identified two pairs of amino acids important for retrotransposition, an FF and a WD. The WD appears to play a role in cDNA synthesis by the ORF2p molecule, despite being outside the canonical RT domain.
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Affiliation(s)
- Claiborne M Christian
- Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70130, USA
| | - Dawn deHaro
- Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70130, USA
| | - Kristine J Kines
- Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70130, USA
| | - Mark Sokolowski
- Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70130, USA
| | - Victoria P Belancio
- Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70130, USA
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17
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Abstract
Transposable elements have had a profound impact on the structure and function of mammalian genomes. The retrotransposon Long INterspersed Element-1 (LINE-1 or L1), by virtue of its replicative mobilization mechanism, comprises ∼17% of the human genome. Although the vast majority of human LINE-1 sequences are inactive molecular fossils, an estimated 80-100 copies per individual retain the ability to mobilize by a process termed retrotransposition. Indeed, LINE-1 is the only active, autonomous retrotransposon in humans and its retrotransposition continues to generate both intra-individual and inter-individual genetic diversity. Here, we briefly review the types of transposable elements that reside in mammalian genomes. We will focus our discussion on LINE-1 retrotransposons and the non-autonomous Short INterspersed Elements (SINEs) that rely on the proteins encoded by LINE-1 for their mobilization. We review cases where LINE-1-mediated retrotransposition events have resulted in genetic disease and discuss how the characterization of these mutagenic insertions led to the identification of retrotransposition-competent LINE-1s in the human and mouse genomes. We then discuss how the integration of molecular genetic, biochemical, and modern genomic technologies have yielded insight into the mechanism of LINE-1 retrotransposition, the impact of LINE-1-mediated retrotransposition events on mammalian genomes, and the host cellular mechanisms that protect the genome from unabated LINE-1-mediated retrotransposition events. Throughout this review, we highlight unanswered questions in LINE-1 biology that provide exciting opportunities for future research. Clearly, much has been learned about LINE-1 and SINE biology since the publication of Mobile DNA II thirteen years ago. Future studies should continue to yield exciting discoveries about how these retrotransposons contribute to genetic diversity in mammalian genomes.
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18
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Kopera HC, Flasch DA, Nakamura M, Miyoshi T, Doucet AJ, Moran JV. LEAP: L1 Element Amplification Protocol. Methods Mol Biol 2016; 1400:339-55. [PMID: 26895063 DOI: 10.1007/978-1-4939-3372-3_21] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Long INterspersed Element-1 (LINE-1 or L1) retrotransposons encode two proteins (ORF1p and ORF2p) that are required for retrotransposition. The L1 element amplification protocol (LEAP) assays the ability of L1 ORF2p to reverse transcribe L1 RNA in vitro. Ultracentrifugation or immunoprecipitation is used to isolate L1 ribonucleoprotein particle (RNP) complexes from cultured human cells transfected with an engineered L1 expression construct. The isolated RNPs are incubated with an oligonucleotide that contains a unique sequence at its 5' end and a thymidine-rich sequence at its 3' end. The addition of dNTPs to the reaction allows L1 ORF2p bound to L1 RNA to generate L1 cDNA. The resultant L1 cDNAs then are amplified using polymerase chain reaction (PCR) and the products are visualized by gel electrophoresis. Sequencing the resultant PCR products then allows product verification. The LEAP assay has been instrumental in determining how mutations in L1 ORF1p and ORF2p affect L1 reverse transcriptase (RT) activity. Furthermore, the LEAP assay has revealed that the L1 ORF2p RT can extend a DNA primer with mismatched 3' terminal bases when it is annealed to an L1 RNA template. As the LINE-1 biology field gravitates toward studying cellular proteins that regulate LINE-1, molecular genetic and biochemical approaches such as LEAP, in conjunction with the LINE-1-cultured cell retrotransposition assay, are essential to dissect the molecular mechanism of L1 retrotransposition.
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Affiliation(s)
- Huira C Kopera
- Department of Human Genetics, University of Michigan Medical School, 1241 E. Catherine Street, Ann Arbor, MI, 48109, USA.
| | - Diane A Flasch
- Department of Human Genetics, University of Michigan Medical School, 1241 E. Catherine Street, Ann Arbor, MI, 48109, USA
| | - Mitsuhiro Nakamura
- Department of Human Genetics, University of Michigan Medical School, 1241 E. Catherine Street, Ann Arbor, MI, 48109, USA
| | - Tomoichiro Miyoshi
- Department of Human Genetics, University of Michigan Medical School, 1241 E. Catherine Street, Ann Arbor, MI, 48109, USA
| | - Aurélien J Doucet
- Department of Human Genetics, University of Michigan Medical School, 1241 E. Catherine Street, Ann Arbor, MI, 48109, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, 1241 E. Catherine Street, Ann Arbor, MI, 48109, USA. .,Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, USA. .,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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19
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Wildschutte JH, Baron A, Diroff NM, Kidd JM. Discovery and characterization of Alu repeat sequences via precise local read assembly. Nucleic Acids Res 2015; 43:10292-307. [PMID: 26503250 PMCID: PMC4666360 DOI: 10.1093/nar/gkv1089] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 10/08/2015] [Indexed: 12/03/2022] Open
Abstract
Alu insertions have contributed to >11% of the human genome and ∼30–35 Alu subfamilies remain actively mobile, yet the characterization of polymorphic Alu insertions from short-read data remains a challenge. We build on existing computational methods to combine Alu detection and de novo assembly of WGS data as a means to reconstruct the full sequence of insertion events from Illumina paired end reads. Comparison with published calls obtained using PacBio long-reads indicates a false discovery rate below 5%, at the cost of reduced sensitivity due to the colocation of reference and non-reference repeats. We generate a highly accurate call set of 1614 completely assembled Alu variants from 53 samples from the Human Genome Diversity Project (HGDP) panel. We utilize the reconstructed alternative insertion haplotypes to genotype 1010 fully assembled insertions, obtaining >99% agreement with genotypes obtained by PCR. In our assembled sequences, we find evidence of premature insertion mechanisms and observe 5′ truncation in 16% of AluYa5 and AluYb8 insertions. The sites of truncation coincide with stem-loop structures and SRP9/14 binding sites in the Alu RNA, implicating L1 ORF2p pausing in the generation of 5′ truncations. Additionally, we identified variable AluJ and AluS elements that likely arose due to non-retrotransposition mechanisms.
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Affiliation(s)
- Julia H Wildschutte
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Alayna Baron
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Nicolette M Diroff
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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20
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Zhou K, Kuo A, Grigoriev IV. Reverse transcriptase and intron number evolution. Stem Cell Investig 2014; 1:17. [PMID: 27358863 DOI: 10.3978/j.issn.2306-9759.2014.08.01] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 08/04/2014] [Indexed: 11/14/2022]
Abstract
BACKGROUND Introns are universal in eukaryotic genomes and play important roles in transcriptional regulation, mRNA export to the cytoplasm, nonsense-mediated decay as both a regulatory and a splicing quality control mechanism, R-loop avoidance, alternative splicing, chromatin structure, and evolution by exon-shuffling. METHODS Sixteen complete fungal genomes were used 13 of which were sequenced and annotated by JGI. Ustilago maydis, Cryptococcus neoformans, and Coprinus cinereus (also named Coprinopsis cinerea) were from the Broad Institute. Gene models from JGI-annotated genomes were taken from the GeneCatalog track that contained the best representative gene models. Varying fractions of the GeneCatalog were manually curated by external users. For clarity, we used the JGI unique database identifier. RESULTS The last common ancestor of eukaryotes (LECA) has an estimated 6.4 coding exons per gene (EPG) and evolved into the diverse eukaryotic life forms, which is recapitulated by the development of a stem cell. We found a parallel between the simulated reverse transcriptase (RT)-mediated intron loss and the comparative analysis of 16 fungal genomes that spanned a wide range of intron density. Although footprints of RT (RTF) were dynamic, relative intron location (RIL) to the 5'-end of mRNA faithfully traced RT-mediated intron loss and revealed 7.7 EPG for LECA. The mode of exon length distribution was conserved in simulated intron loss, which was exemplified by the shared mode of 75 nt between fungal and Chlamydomonas genomes. The dominant ancient exon length was corroborated by the average exon length of the most intron-rich genes in fungal genomes and consistent with ancient protein modules being ~25 aa. Combined with the conservation of a protein length of 400 aa, the earliest ancestor of eukaryotes could have 16 EPG. During earlier evolution, Ascomycota's ancestor had significantly more 3'-biased RT-mediated intron loss that was followed by dramatic RTF loss. There was a down trend of EPG from more conserved to less conserved genes. Moreover, species-specific genes have higher exon-densities, shorter exons, and longer introns when compared to genes conserved at the phylum level. However, intron length in species-specific genes became shorter than that of genes conserved in all species after genomes experiencing drastic intron loss. The estimated EPG from the most frequent exon length is more than double that from the RIL method. CONCLUSIONS This implies significant intron loss during the very early period of eukaryotic evolution. De novo gene-birth contributes to shorter exons, longer introns, and higher exon-density in species-specific genes relative to conserved genes.
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Affiliation(s)
- Kemin Zhou
- 1 Computational Genomics, Bristol-Myers Squibb, 311 Pennington Rocky Hill Road, Pennington, NJ 08534, USA ; 2 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Alan Kuo
- 1 Computational Genomics, Bristol-Myers Squibb, 311 Pennington Rocky Hill Road, Pennington, NJ 08534, USA ; 2 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Igor V Grigoriev
- 1 Computational Genomics, Bristol-Myers Squibb, 311 Pennington Rocky Hill Road, Pennington, NJ 08534, USA ; 2 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
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21
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Piskareva O, Ernst C, Higgins N, Schmatchenko V. The carboxy-terminal segment of the human LINE-1 ORF2 protein is involved in RNA binding. FEBS Open Bio 2013; 3:433-7. [PMID: 24251107 PMCID: PMC3821027 DOI: 10.1016/j.fob.2013.09.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 09/18/2013] [Indexed: 10/27/2022] Open
Abstract
The human LINE-1/L1 ORF2 protein is a multifunctional enzyme which plays a vital role in the life cycle of the human L1 retrotransposon. The protein consists of an endonuclease domain, followed by a central reverse transcriptase domain and a carboxy-terminal C-domain with unknown function. Here, we explore the nucleic acid binding properties of the 180-amino acid carboxy-terminal segment (CTS) of the human L1 ORF2p in vitro. In a series of experiments involving gel shift assay, we demonstrate that the CTS of L1 ORF2p binds RNA in non-sequence-specific manner. Finally, we report that mutations destroying the putative Zn-knuckle structure of the protein do not significantly affect the level of RNA binding and discuss the possible functional role of the CTS in L1 retrotransposition.
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Affiliation(s)
- Olga Piskareva
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
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22
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Belan E. LINEs of evidence: noncanonical DNA replication as an epigenetic determinant. Biol Direct 2013; 8:22. [PMID: 24034780 PMCID: PMC3868326 DOI: 10.1186/1745-6150-8-22] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 09/06/2013] [Indexed: 12/17/2022] Open
Abstract
LINE-1 (L1) retrotransposons are repetitive elements in mammalian genomes. They are
capable of synthesizing DNA on their own RNA templates by harnessing reverse
transcriptase (RT) that they encode. Abundantly expressed full-length L1s and their
RT are found to globally influence gene expression profiles, differentiation state,
and proliferation capacity of early embryos and many types of cancer, albeit by yet
unknown mechanisms. They are essential for the progression of early development and
the establishment of a cancer-related undifferentiated state. This raises important
questions regarding the functional significance of L1 RT in these cell systems.
Massive nuclear L1-linked reverse transcription has been shown to occur in mouse
zygotes and two-cell embryos, and this phenomenon is purported to be DNA replication
independent. This review argues against this claim with the goal of understanding the
nature of this phenomenon and the role of L1 RT in early embryos and cancers.
Available L1 data are revisited and integrated with relevant findings accumulated in
the fields of replication timing, chromatin organization, and epigenetics, bringing
together evidence that strongly supports two new concepts. First, noncanonical
replication of a portion of genomic full-length L1s by means of L1 RNP-driven reverse
transcription is proposed to co-exist with DNA polymerase-dependent replication of
the rest of the genome during the same round of DNA replication in embryonic and
cancer cell systems. Second, the role of this mechanism is thought to be epigenetic;
it might promote transcriptional competence of neighboring genes linked to
undifferentiated states through the prevention of tethering of involved L1s to the
nuclear periphery. From the standpoint of these concepts, several hitherto
inexplicable phenomena can be explained. Testing methods for the model are
proposed.
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Affiliation(s)
- Ekaterina Belan
- Genetics Laboratory, Royal University Hospital, Saskatoon, SK S7N 0W8, Canada.
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23
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Monot C, Kuciak M, Viollet S, Mir AA, Gabus C, Darlix JL, Cristofari G. The specificity and flexibility of l1 reverse transcription priming at imperfect T-tracts. PLoS Genet 2013; 9:e1003499. [PMID: 23675310 PMCID: PMC3649969 DOI: 10.1371/journal.pgen.1003499] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 03/22/2013] [Indexed: 01/18/2023] Open
Abstract
L1 retrotransposons have a prominent role in reshaping mammalian genomes. To replicate, the L1 ribonucleoprotein particle (RNP) first uses its endonuclease (EN) to nick the genomic DNA. The newly generated DNA end is subsequently used as a primer to initiate reverse transcription within the L1 RNA poly(A) tail, a process known as target-primed reverse transcription (TPRT). Prior studies demonstrated that most L1 insertions occur into sequences related to the L1 EN consensus sequence (degenerate 5′-TTTT/A-3′ sites) and frequently preceded by imperfect T-tracts. However, it is currently unclear whether—and to which degree—the liberated 3′-hydroxyl extremity on the genomic DNA needs to be accessible and complementary to the poly(A) tail of the L1 RNA for efficient priming of reverse transcription. Here, we employed a direct assay for the initiation of L1 reverse transcription to define the molecular rules that guide this process. First, efficient priming is detected with as few as 4 matching nucleotides at the primer 3′ end. Second, L1 RNP can tolerate terminal mismatches if they are compensated within the 10 last bases of the primer by an increased number of matching nucleotides. All terminal mismatches are not equally detrimental to DNA extension, a C being extended at higher levels than an A or a G. Third, efficient priming in the context of duplex DNA requires a 3′ overhang. This suggests the possible existence of additional DNA processing steps, which generate a single-stranded 3′ end to allow L1 reverse transcription. Based on these data we propose that the specificity of L1 reverse transcription initiation contributes, together with the specificity of the initial EN cleavage, to the distribution of new L1 insertions within the human genome. Jumping genes are DNA sequences present in the genome of most living organisms. They contribute to genome dynamics and occasionally result in hereditary genetic diseases or cancer. L1 elements are the only autonomously active jumping genes in the human genome. They replicate through an RNA–mediated copy-and-paste mechanism by cleaving the host genome and then using this new DNA end as a primer to reverse transcribe its own RNA, generating a new L1 DNA copy. The molecular determinants that influence L1 target site choice are not fully understood. Here we present a quantitative assay to measure the influence of DNA target site sequence and structure on the reverse transcription step. By testing more than 65 potential DNA primers, we observe that not all sites are equally extended by the L1 machinery, and we define the rules guiding this process. In particular, we highlight the importance of partial sequence complementarity between the target site and the L1 RNA extremity, but also the high level of flexibility of this process, since detrimental terminal mismatches can be compensated by an increasing number of interacting nucleotides. We propose that this mechanism contributes to the distribution of new L1 insertions within the human genome.
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Affiliation(s)
- Clément Monot
- INSERM, U1081, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- CNRS, UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- University of Nice-Sophia-Antipolis, Faculty of Medicine, Nice, France
| | - Monika Kuciak
- INSERM, U1081, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- CNRS, UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- University of Nice-Sophia-Antipolis, Faculty of Medicine, Nice, France
| | - Sébastien Viollet
- INSERM, U1081, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- CNRS, UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- University of Nice-Sophia-Antipolis, Faculty of Medicine, Nice, France
| | - Ashfaq Ali Mir
- INSERM, U1081, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- CNRS, UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- University of Nice-Sophia-Antipolis, Faculty of Medicine, Nice, France
| | - Caroline Gabus
- Ecole Normale Supérieure de Lyon, Human Virology Department, INSERM U758, Lyon, France
| | - Jean-Luc Darlix
- Ecole Normale Supérieure de Lyon, Human Virology Department, INSERM U758, Lyon, France
| | - Gaël Cristofari
- INSERM, U1081, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- CNRS, UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- University of Nice-Sophia-Antipolis, Faculty of Medicine, Nice, France
- * E-mail:
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Bojang P, Roberts RA, Anderton MJ, Ramos KS. Reprogramming of the HepG2 genome by long interspersed nuclear element-1. Mol Oncol 2013; 7:812-25. [PMID: 23648019 DOI: 10.1016/j.molonc.2013.04.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 04/05/2013] [Accepted: 04/08/2013] [Indexed: 10/26/2022] Open
Abstract
Long Interspersed Nuclear Element-1 (LINE-1 or L1) is an autonomous, mobile element within the human genome that transposes via a "copy and paste" mechanism and relies upon L1-encoded endonuclease and reverse transcriptase (RT) activities to compromise genome integrity. L1 has been implicated in various forms of cancer, but its role in the regulation of the oncogenic phenotype is not understood. The present studies were conducted to evaluate mechanisms of genetic regulatory control in HepG2 cells by human L1, or a D702Y mutant deficient in RT activity, and their influence on cellular phenotype. Forced expression of synthetic L1 ORF1p and ORF2p was associated with formation of cytoplasmic foci and minor association with the nuclear compartment. While de novo L1 mobilizations were only identified in cells expressing wild type L1, and were absent in the D702Y mutant, changes in gene expression profiles involved RT dependent as well as RT independent mechanisms. Synthetic L1 altered the expression of 24 in silico predicted genetic targets; ten of which showed RT-dependence, ten RT-independence, and four reciprocal regulatory control by both wild type and RT mutant. Of five targets examined, only VCAM1 and PTPRB colocalized with newly retrotransposed wild type L1. Biological discretization to partition patterns of gene expression into unique frequencies identified adhesion, inflammation, and cellular metabolism as key processes targeted for molecular interference with disruption of epithelial-to-mesenchymal programming seen irrespective of the RT phenotype. These findings establish L1 as a key regulator of genome plasticity and EMT via mechanisms independent of RT activity.
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Affiliation(s)
- Pasano Bojang
- Department of Biochemistry and Molecular Biology, University of Louisville, Louisville, KY 40202, USA
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25
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Ataxia telangiectasia mutated (ATM) modulates long interspersed element-1 (L1) retrotransposition in human neural stem cells. Proc Natl Acad Sci U S A 2011; 108:20382-7. [PMID: 22159035 DOI: 10.1073/pnas.1100273108] [Citation(s) in RCA: 172] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Long interspersed element-1 (L1) retrotransposons compose ∼20% of the mammalian genome, and ongoing L1 retrotransposition events can impact genetic diversity by various mechanisms. Previous studies have demonstrated that endogenous L1 retrotransposition can occur in the germ line and during early embryonic development. In addition, recent data indicate that engineered human L1s can undergo somatic retrotransposition in human neural progenitor cells and that an increase in human-specific L1 DNA content can be detected in the brains of normal controls, as well as in Rett syndrome patients. Here, we demonstrate an increase in the retrotransposition efficiency of engineered human L1s in cells that lack or contain severely reduced levels of ataxia telangiectasia mutated, a serine/threonine kinase involved in DNA damage signaling and neurodegenerative disease. We demonstrate that the increase in L1 retrotransposition in ataxia telangiectasia mutated-deficient cells most likely occurs by conventional target-site primed reverse transcription and generate either longer, or perhaps more, L1 retrotransposition events per cell. Finally, we provide evidence suggesting an increase in human-specific L1 DNA copy number in postmortem brain tissue derived from ataxia telangiectasia patients compared with healthy controls. Together, these data suggest that cellular proteins involved in the DNA damage response may modulate L1 retrotransposition.
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26
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Hedges DJ, Belancio VP. Restless genomes humans as a model organism for understanding host-retrotransposable element dynamics. ADVANCES IN GENETICS 2011; 73:219-62. [PMID: 21310298 DOI: 10.1016/b978-0-12-380860-8.00006-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Since their initial discovery in maize, there have been various attempts to categorize the relationship between transposable elements (TEs) and their host organisms. These have ranged from TEs being selfish parasites to their role as essential, functional components of organismal biology. Research over the past several decades has, in many respects, only served to complicate the issue even further. On the one hand, investigators have amassed substantial evidence concerning the negative effects that TE-mutagenic activity can have on host genomes and organismal fitness. On the other hand, we find an increasing number of examples, across several taxa, of TEs being incorporated into functional biological roles for their host organism. Some 45% of our own genomes are comprised of TE copies. While many of these copies are dormant, having lost their ability to mobilize, several lineages continue to actively proliferate in modern human populations. With its complement of ancestral and active TEs, the human genome exhibits key aspects of the host-TE dynamic that has played out since early on in organismal evolution. In this review, we examine what insights the particularly well-characterized human system can provide regarding the nature of the host-TE interaction.
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Affiliation(s)
- Dale J Hedges
- Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, USA
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27
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Dai L, Huang Q, Boeke JD. Effect of reverse transcriptase inhibitors on LINE-1 and Ty1 reverse transcriptase activities and on LINE-1 retrotransposition. BMC BIOCHEMISTRY 2011; 12:18. [PMID: 21545744 PMCID: PMC3103432 DOI: 10.1186/1471-2091-12-18] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2011] [Accepted: 05/05/2011] [Indexed: 11/10/2022]
Abstract
BACKGROUND LINE-1s (L1, Long Interspersed Element-1) are the most abundant autonomous non-LTR retrotransposons in the human genome and replicate by reverse transcription of an RNA intermediate. Full-length L1 encodes two open reading frames (ORF1, ORF2) and ORF2 has reverse transcriptase activity. RESULTS Here we expressed human L1 RT in E. coli and the purified protein displayed the same RT activity as that of ORF2p expressed in insect cells. We tested the effect of different reverse transcriptase inhibitors on L1 RT and found that all four tested nucleoside inhibitors efficiently inhibited L1 RT activity competitively. The Ki values of NRTIs were calculated (AZTTP, 16.4 ± 4.21 nM; d4TTP, 0.73 ± 0.22 nM; ddCTP, 0.72 ± 0.16 nM; 3TCTP, 12.9 ± 2.07 nM). L1 RT was less sensitive to non-nucleoside reverse transcriptase inhibitors, among these nevirapine had no effect, even at concentrations up to 500 μM. We also examined the effect of RT inhibitors on L1 retrotransposition efficiency in vivo using a cell-based retrotransposition assay. Similarly, all analog inhibitors decreased L1 retrotransposition frequency with different potencies whereas nevirapine had little or no effect on L1 retrotransposition. For comparison, we also tested the same inhibitors to highly purified RT of an LTR-retrotransposon (Ty1) and found it was less sensitive to NRTIs than L1 RT and has the same inhibition profile as L1 RT to NNRTIs. CONCLUSIONS These data indicate that bacterially expressed L1 RT is an active reverse transcriptase sensitive to nucleoside RT inhibitors but not to non-nucleoside inhibitors.
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Affiliation(s)
- Lixin Dai
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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28
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Blackburn EH, Collins K. Telomerase: an RNP enzyme synthesizes DNA. Cold Spring Harb Perspect Biol 2011; 3:cshperspect.a003558. [PMID: 20660025 DOI: 10.1101/cshperspect.a003558] [Citation(s) in RCA: 229] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Telomerase is a eukaryotic ribonucleoprotein (RNP) whose specialized reverse transcriptase action performs de novo synthesis of one strand of telomeric DNA. The resulting telomerase-mediated elongation of telomeres, which are the protective end-caps for eukaryotic chromosomes, counterbalances the inevitable attrition from incomplete DNA replication and nuclease action. The telomerase strategy to maintain telomeres is deeply conserved among eukaryotes, yet the RNA component of telomerase, which carries the built-in template for telomeric DNA repeat synthesis, has evolutionarily diverse size and sequence. Telomerase shows a distribution of labor between RNA and protein in aspects of the polymerization reaction. This article first describes the underlying conservation of a core set of structural features of telomerase RNAs important for the fundamental polymerase activity of telomerase. These include a pseudoknot-plus-template domain and at least one other RNA structural motif separate from the template-containing domain. The principles driving the diversity of telomerase RNAs are then explored. Much of the diversification of telomerase RNAs has come from apparent gain-of-function elaborations, through inferred evolutionary acquisitions of various RNA motifs used for telomerase RNP biogenesis, cellular trafficking of enzyme components, and regulation of telomerase action at telomeres. Telomerase offers broadly applicable insights into the interplay of protein and RNA functions in the context of an RNP enzyme.
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29
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Martin SL. Nucleic acid chaperone properties of ORF1p from the non-LTR retrotransposon, LINE-1. RNA Biol 2010; 7:706-11. [PMID: 21045547 DOI: 10.4161/rna.7.6.13766] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Long interspersed element-1 (LINE-1, or L1) is a non-long terminal repeat (LTR) retrotransposon that has amplified to hundreds of thousands of copies in mammalian evolution. A small number of the individual copies of L1 are active retrotransposons which are presently replicating in most species, including humans and mice. L1 retrotransposition begins with transcription of an active element and ends with a newly inserted cDNA copy, a process which requires the two element-encoded proteins to act in cis on the L1 RNA. The ORF1 protein (ORF1p) is a high-affinity, non-sequence-specific RNA binding protein with nucleic acid chaperone activity, whereas the ORF2 protein (ORF2p) supplies the enzymatic activities for cDNA synthesis. This article reviews the nucleic acid chaperone properties of ORF1p in the context of L1 retrotransposition.
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Affiliation(s)
- Sandra L Martin
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO, USA.
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30
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Beauregard A, Curcio MJ, Belfort M. The take and give between retrotransposable elements and their hosts. Annu Rev Genet 2009; 42:587-617. [PMID: 18680436 DOI: 10.1146/annurev.genet.42.110807.091549] [Citation(s) in RCA: 140] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Retrotransposons mobilize via RNA intermediates and usually carry with them the agent of their mobility, reverse transcriptase. Retrotransposons are streamlined, and therefore rely on host factors to proliferate. However, retrotransposons are exposed to cellular forces that block their paths. For this review, we have selected for our focus elements from among target-primed (TP) retrotransposons, also called non-LTR retrotransposons, and extrachromosomally-primed (EP) retrotransposons, also called LTR retrotransposons. The TP retrotransposons considered here are group II introns, LINEs and SINEs, whereas the EP elements considered are the Ty and Tf retrotransposons, with a brief comparison to retroviruses. Recurring themes for these elements, in hosts ranging from bacteria to humans, are tie-ins of the retrotransposons to RNA metabolism, DNA replication and repair, and cellular stress. Likewise, there are parallels among host-cell defenses to combat rampant retrotransposon spread. The interactions between the retrotransposon and the host, and their coevolution to balance the tension between retrotransposon proliferation and host survival, form the basis of this review.
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Affiliation(s)
- Arthur Beauregard
- New York State Department of Health, Center for Medical Sciences, Albany, New York 12208, 12201-2002, USA.
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31
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Eickbush TH, Jamburuthugoda VK. The diversity of retrotransposons and the properties of their reverse transcriptases. Virus Res 2008; 134:221-34. [PMID: 18261821 DOI: 10.1016/j.virusres.2007.12.010] [Citation(s) in RCA: 171] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Revised: 12/14/2007] [Accepted: 12/14/2007] [Indexed: 11/30/2022]
Abstract
A number of abundant mobile genetic elements called retrotransposons reverse transcribe RNA to generate DNA for insertion into eukaryotic genomes. Four major classes of retrotransposons are described here. First, the long-terminal-repeat (LTR) retrotransposons have similar structures and mechanisms to those of the vertebrate retroviruses. Genes that may enable these retrotransposons to leave a cell have been acquired by these elements in a number of animal and plant lineages. Second, the tyrosine recombinase retrotransposons are similar to the LTR retrotransposons except that they have substituted a recombinase for the integrase and recombine into the host chromosomes. Third, the non-LTR retrotransposons use a cleaved chromosomal target site generated by an encoded endonuclease to prime reverse transcription. Finally, the Penelope-like retrotransposons are not well understood but appear to also use cleaved DNA or the ends of chromosomes as primer for reverse transcription. Described in the second part of this review are the enzymatic properties of the reverse transcriptases (RTs) encoded by retrotransposons. The RTs of the LTR retrotransposons are highly divergent in sequence but have similar enzymatic activities to those of retroviruses. The RTs of the non-LTR retrotransposons have several unique properties reflecting their adaptation to a different mechanism of retrotransposition.
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Affiliation(s)
- Thomas H Eickbush
- Department of Biology, University of Rochester, Rochester, NY 14627, USA.
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32
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Gogvadze E, Barbisan C, Lebrun MH, Buzdin A. Tripartite chimeric pseudogene from the genome of rice blast fungus Magnaporthe grisea suggests double template jumps during long interspersed nuclear element (LINE) reverse transcription. BMC Genomics 2007; 8:360. [PMID: 17922896 PMCID: PMC2104539 DOI: 10.1186/1471-2164-8-360] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2007] [Accepted: 10/08/2007] [Indexed: 01/26/2023] Open
Abstract
Background A systematic survey of loci carrying retrotransposons in the genome of the rice blast fungus Magnaporthe grisea allowed the identification of novel non-canonical retropseudogenes. These elements are chimeric retrogenes composed of DNA copies from different cellular transcripts directly fused to each other. Their components are copies of a non protein-coding highly expressed RNA of unknown function termed WEIRD and of two fungal retrotransposons: MGL and Mg-SINE. Many of these chimeras are transcribed in various M. grisea tissues and during plant infection. Chimeric retroelements with a similar structure were recently found in three mammalian genomes. All these chimeras are likely formed by RNA template switches during the reverse transcription of diverse LINE elements. Results We have shown that in M. grisea template switching occurs at specific sites within the initial template RNA which contains a characteristic consensus sequence. We also provide evidence that both single and double template switches may occur during LINE retrotransposition, resulting in the fusion of three different transcript copies. In addition to the 33 bipartite elements, one tripartite chimera corresponding to the fusion of three retrotranscripts (WEIRD, Mg-SINE, MGL-LINE) was identified in the M. grisea genome. Unlike the previously reported two human tripartite elements, this fungal retroelement is flanked by identical 14 bp-long direct repeats. The presence of these short terminal direct repeats demonstrates that the LINE enzymatic machinery was involved in the formation of this chimera and its integration in the M. grisea genome. Conclusion A survey of mammalian genomic databases also revealed two novel tripartite chimeric retroelements, suggesting that double template switches occur during reverse transcription of LINE retrotransposons in different eukaryotic organisms.
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Affiliation(s)
- Elena Gogvadze
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117871, Russia.
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DNA-directed DNA polymerase and strand displacement activity of the reverse transcriptase encoded by the R2 retrotransposon. J Mol Biol 2007; 374:322-33. [PMID: 17936300 DOI: 10.1016/j.jmb.2007.09.047] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Revised: 09/10/2007] [Accepted: 09/17/2007] [Indexed: 11/24/2022]
Abstract
R2 elements are non-long terminal repeat (non-LTR) retrotransposons with a single open reading-frame encoding reverse transcriptase, DNA endonuclease and nucleic acid-binding domains. The elements are specialized for insertion into the 28 S rRNA genes of many animal phyla. The R2-encoded activities initiate retrotransposition by sequence-specific cleavage of the 28 S gene target site and the utilization of the released DNA 3' end to prime reverse transcription (target primed reverse transcription). The activity of the R2 polymerase on RNA templates has been shown to differ from retroviral reverse transcriptases (RTs) in a number of properties. We demonstrate that the R2-RT is capable of efficiently utilizing single-stranded DNA (ssDNA) as a template. The processivity of the enzyme on ssDNA templates is higher than its processivity on RNA templates. This finding suggests that R2-RT is also capable of synthesizing the second DNA strand during retrotransposition. However, R2-RT lacks the RNAse H activity that is typically used by retroviral and LTR-retrotransposon RTs to remove the RNA strand before the first DNA strand is used as template. Remarkably, R2-RT can displace RNA strands that are annealed to ssDNA templates with essentially no loss of processivity. Such strand displacement activity is highly unusual for a DNA polymerase. Thus the single R2 protein contains all the activities needed to make a double-stranded DNA product from an RNA transcript. Finally, during these studies we found an unexpected property of the highly sequence-specific R2 endonuclease domain. The endonuclease can non-specifically cleave ssDNA at a junction with double-stranded DNA. This activity suggests that second-strand cleavage of the target site may not be sequence specific, but rather is specified by a single-stranded region generated when the first DNA strand is used to prime reverse transcription.
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Abstract
Long interspersed nucleotide element (LINE)-1 retrotransposon (L1) has emerged as the largest contributor to mammalian genome mass, responsible for over 35% of the human genome. Differences in the number and activity levels of L1s contribute to interindividual variation in humans, both by affecting an individual's likelihood of acquiring new L1-mediated mutations, as well as by differentially modifying gene expression. Here, we report on recent progress in understanding L1 biology, with a focus on mechanisms of L1-mediated disease. We discuss known details of L1 life cycle, including L1 structure, transcriptional regulation, and the mechanisms of translation and retrotransposition. Current views on cell type specificity, timing, and control of retrotransposition are put forth. Finally, we discuss the role of L1 as a mutagen, using the latest findings in L1 biology to illuminate molecular mechanisms of L1-mediated gene disruption.
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Affiliation(s)
- Daria V Babushok
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6145, USA
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35
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Buzdin A, Gogvadze E, Lebrun MH. Chimeric retrogenes suggest a role for the nucleolus in LINE amplification. FEBS Lett 2007; 581:2877-82. [DOI: 10.1016/j.febslet.2007.05.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Revised: 05/03/2007] [Accepted: 05/16/2007] [Indexed: 01/21/2023]
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36
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Detection and cloning of LINE-1 elements in CHO cells. Cytotechnology 2007; 53:75-80. [PMID: 19003192 DOI: 10.1007/s10616-007-9051-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Accepted: 01/25/2007] [Indexed: 10/23/2022] Open
Abstract
Long interspersed elements (LINEs, L1s) are non-long terminal repeat (LTR) retrotransposons found in mammalian genomes and account up to 20% of genomic DNA. It has been shown that active L1 elements can cause mutation resulting in disease, genetic variation and polymorphisms and their inactive copies seem to be involved in recombination and rearrangement. L1-encoded products have been detected in a number of tissues including mammalian germ cell tumours, breast carcinomas and a large variety of transformed mouse and human cell lines.Chinese Hamster Ovary (CHO) cells are widely used in the manufacture of recombinant proteins for biopharmaceuticals. Here, we investigated the transcriptional activity of hamster L1 elements in CHO-K1 cells. These cells were analysed for the presence of L1 RNA transcripts. The sequence, which is homologous to mammalian L1 elements, was cloned from hamster genomic DNA and used to design primers for RT-PCR. L1 transcripts were detected in CHO-K1 RNA.
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37
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Kulpa DA, Moran JV. Cis-preferential LINE-1 reverse transcriptase activity in ribonucleoprotein particles. Nat Struct Mol Biol 2006; 13:655-60. [PMID: 16783376 DOI: 10.1038/nsmb1107] [Citation(s) in RCA: 219] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Accepted: 05/11/2006] [Indexed: 11/09/2022]
Abstract
LINE-1 retrotransposons (L1s) constitute approximately 17% of human DNA, and their activity continues to affect genome evolution. Retrotransposition-competent human L1s encode two proteins required for their mobility (ORF1p and ORF2p); however, biochemical activities associated with ORF2p have been difficult to detect in cells. Here, we show for the first time the colocalization of L1 RNA, ORF1p and ORF2p to a putative ribonucleoprotein retrotransposition intermediate. We further demonstrate that ORF2p preferentially uses its encoding RNA as a template for reverse transcription. Thus, our data provide the first biochemical evidence supporting the cis-preferential action of the L1 reverse transcriptase.
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Affiliation(s)
- Deanna A Kulpa
- Department of Human Genetics 1241 E. Catherine St., University of Michigan Medical School, Ann Arbor, Michigan 48109-0618, USA.
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