1
|
Kong L, Saha K, Hu Y, Tschetter JN, Habben CE, Whitmore LS, Yao C, Ge X, Ye P, Newkirk SJ, An W. Subfamily-specific differential contribution of individual monomers and the tether sequence to mouse L1 promoter activity. Mob DNA 2022; 13:13. [PMID: 35443687 PMCID: PMC9022269 DOI: 10.1186/s13100-022-00269-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/28/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The internal promoter in L1 5'UTR is critical for autonomous L1 transcription and initiating retrotransposition. Unlike the human genome, which features one contemporarily active subfamily, four subfamilies (A_I, Gf_I and Tf_I/II) have been amplifying in the mouse genome in the last one million years. Moreover, mouse L1 5'UTRs are organized into tandem repeats called monomers, which are separated from ORF1 by a tether domain. In this study, we aim to compare promoter activities across young mouse L1 subfamilies and investigate the contribution of individual monomers and the tether sequence. RESULTS We observed an inverse relationship between subfamily age and the average number of monomers among evolutionarily young mouse L1 subfamilies. The youngest subgroup (A_I and Tf_I/II) on average carry 3-4 monomers in the 5'UTR. Using a single-vector dual-luciferase reporter assay, we compared promoter activities across six L1 subfamilies (A_I/II, Gf_I and Tf_I/II/III) and established their antisense promoter activities in a mouse embryonic fibroblast cell line and a mouse embryonal carcinoma cell line. Using consensus promoter sequences for three subfamilies (A_I, Gf_I and Tf_I), we dissected the differential roles of individual monomers and the tether domain in L1 promoter activity. We validated that, across multiple subfamilies, the second monomer consistently enhances the overall promoter activity. For individual promoter components, monomer 2 is consistently more active than the corresponding monomer 1 and/or the tether for each subfamily. Importantly, we revealed intricate interactions between monomer 2, monomer 1 and tether domains in a subfamily-specific manner. Furthermore, using three-monomer 5'UTRs, we established a complex nonlinear relationship between the length of the outmost monomer and the overall promoter activity. CONCLUSIONS The laboratory mouse is an important mammalian model system for human diseases as well as L1 biology. Our study extends previous findings and represents an important step toward a better understanding of the molecular mechanism controlling mouse L1 transcription as well as L1's impact on development and disease.
Collapse
Affiliation(s)
- Lingqi Kong
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, USA
| | - Karabi Saha
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, USA
| | - Yuchi Hu
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, USA
| | - Jada N Tschetter
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, USA
| | - Chase E Habben
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, USA
| | - Leanne S Whitmore
- Department of Immunology, University of Washington, Seattle, WA, 98109, USA
| | - Changfeng Yao
- Anhui University of Traditional Chinese Medicine, Hefei, 230012, Anhui, China
| | - Xijin Ge
- Department of Mathematics & Statistics, South Dakota State University, Brookings, SD, 57007, USA
| | - Ping Ye
- Department of Pharmacy Practice, South Dakota State University, Brookings, SD, 57007, USA
| | - Simon J Newkirk
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, USA
| | - Wenfeng An
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, USA.
| |
Collapse
|
2
|
Freeman BT, Sokolowski M, Roy-Engel AM, Smither ME, Belancio VP. Identification of charged amino acids required for nuclear localization of human L1 ORF1 protein. Mob DNA 2019; 10:20. [PMID: 31080522 PMCID: PMC6501352 DOI: 10.1186/s13100-019-0159-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 04/10/2019] [Indexed: 01/10/2023] Open
Abstract
Background Long Interspersed Element 1 (LINE-1) is a retrotransposon that is present in 500,000 copies in the human genome. Along with Alu and SVA elements, these three retrotransposons account for more than a third of the human genome sequence. These mobile elements are able to copy themselves within the genome via an RNA intermediate, a process that can promote genome instability. LINE-1 encodes two proteins, ORF1p and ORF2p. Association of ORF1p, ORF2p and a full-length L1 mRNA in a ribonucleoprotein (RNP) particle, L1 RNP, is required for L1 retrotransposition. Previous studies have suggested that fusion of a tag to L1 proteins can interfere with L1 retrotransposition. Results Using antibodies detecting untagged human ORF1p, western blot analysis and manipulation of ORF1 sequence and length, we have identified a set of charged amino acids in the C-terminal region of ORF1p that are important in determining its subcellular localization. Mutation of 7 non-identical lysine residues is sufficient to make the resulting ORF1p to be predominantly cytoplasmic, demonstrating intrinsic redundancy of this requirement. These residues are also necessary for ORF1p to retain its association with KPNA2 nuclear pore protein. We demonstrate that this interaction is significantly reduced by RNase treatment. Using co-IP, we have also determined that human ORF1p associates with all members of the KPNA subfamily. Conclusions The prediction of NLS sequences suggested that specific sequences within ORF1p could be responsible for its subcellular localization by interacting with nuclear binding proteins. We have found that multiple charged amino acids in the C-terminus of ORF1p are involved in ORF1 subcellular localization and interaction with KPNA2 nuclear pore protein. Our data demonstrate that different amino acids can be mutated to have the same phenotypic effect on ORF1p subcellular localization, demonstrating that the net number of charged residues or protein structure, rather than their specific location, is important for the ORF1p nuclear localization. We also identified that human ORF1p interacts with all members of the KPNA family of proteins and that multiple KPNA family genes are expressed in human cell lines. Electronic supplementary material The online version of this article (10.1186/s13100-019-0159-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- B T Freeman
- 1Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112 USA
| | - M Sokolowski
- 1Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112 USA
| | - A M Roy-Engel
- 2Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane Cancer Center, Tulane University, New Orleans, Louisiana 70112 USA
| | - M E Smither
- 1Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112 USA
| | - V P Belancio
- 1Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112 USA
| |
Collapse
|
3
|
Pereira GC, Sanchez L, Schaughency PM, Rubio-Roldán A, Choi JA, Planet E, Batra R, Turelli P, Trono D, Ostrow LW, Ravits J, Kazazian HH, Wheelan SJ, Heras SR, Mayer J, García-Pérez JL, Goodier JL. Properties of LINE-1 proteins and repeat element expression in the context of amyotrophic lateral sclerosis. Mob DNA 2018; 9:35. [PMID: 30564290 PMCID: PMC6295051 DOI: 10.1186/s13100-018-0138-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 11/15/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease involving loss of motor neurons and having no known cure and uncertain etiology. Several studies have drawn connections between altered retrotransposon expression and ALS. Certain features of the LINE-1 (L1) retrotransposon-encoded ORF1 protein (ORF1p) are analogous to those of neurodegeneration-associated RNA-binding proteins, including formation of cytoplasmic aggregates. In this study we explore these features and consider possible links between L1 expression and ALS. RESULTS We first considered factors that modulate aggregation and subcellular distribution of LINE-1 ORF1p, including nuclear localization. Changes to some ORF1p amino acid residues alter both retrotransposition efficiency and protein aggregation dynamics, and we found that one such polymorphism is present in endogenous L1s abundant in the human genome. We failed, however, to identify CRM1-mediated nuclear export signals in ORF1p nor strict involvement of cell cycle in endogenous ORF1p nuclear localization in human 2102Ep germline teratocarcinoma cells. Some proteins linked with ALS bind and colocalize with L1 ORF1p ribonucleoprotein particles in cytoplasmic RNA granules. Increased expression of several ALS-associated proteins, including TAR DNA Binding Protein (TDP-43), strongly limits cell culture retrotransposition, while some disease-related mutations modify these effects. Using quantitative reverse transcription PCR (RT-qPCR) of ALS tissues and reanalysis of publicly available RNA-Seq datasets, we asked if changes in expression of retrotransposons are associated with ALS. We found minimal altered expression in sporadic ALS tissues but confirmed a previous report of differential expression of many repeat subfamilies in C9orf72 gene-mutated ALS patients. CONCLUSIONS Here we extended understanding of the subcellular localization dynamics of the aggregation-prone LINE-1 ORF1p RNA-binding protein. However, we failed to find compelling evidence for misregulation of LINE-1 retrotransposons in sporadic ALS nor a clear effect of ALS-associated TDP-43 protein on L1 expression. In sum, our study reveals that the interplay of active retrotransposons and the molecular features of ALS are more complex than anticipated. Thus, the potential consequences of altered retrotransposon activity for ALS and other neurodegenerative disorders are worthy of continued investigation.
Collapse
Affiliation(s)
- Gavin C. Pereira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Laura Sanchez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Paul M. Schaughency
- Oncology Center-Cancer Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Alejandro Rubio-Roldán
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Jungbin A. Choi
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Evarist Planet
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ranjan Batra
- Department of Neurosciences, School of Medicine, University of California at San Diego, San Diego, California USA
| | - Priscilla Turelli
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Lyle W. Ostrow
- Neuromuscular Division, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - John Ravits
- Department of Neurosciences, School of Medicine, University of California at San Diego, San Diego, California USA
| | - Haig H. Kazazian
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Sarah J. Wheelan
- Oncology Center-Cancer Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Sara R. Heras
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Jens Mayer
- Department of Human Genetics, Medical Faculty, University of Saarland, Homburg/Saar, Germany
| | - Jose Luis García-Pérez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - John L. Goodier
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| |
Collapse
|
4
|
Richardson SR, Faulkner GJ. Heritable L1 Retrotransposition Events During Development: Understanding Their Origins: Examination of heritable, endogenous L1 retrotransposition in mice opens up exciting new questions and research directions. Bioessays 2018; 40:e1700189. [PMID: 29709066 PMCID: PMC6681178 DOI: 10.1002/bies.201700189] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 03/04/2018] [Indexed: 01/08/2023]
Abstract
The retrotransposon Long Interspersed Element 1 (LINE-1 or L1) has played a major role in shaping the sequence composition of the mammalian genome. In our recent publication, "Heritable L1 retrotransposition in the mouse primordial germline and early embryo," we systematically assessed the rate and developmental timing of de novo, heritable endogenous L1 insertions in mice. Such heritable retrotransposition events allow L1 to exert an ongoing influence upon genome evolution. Here, we place our findings in the context of earlier studies, and highlight how our results corroborate, and depart from, previous research based on human patient samples and transgenic mouse models harboring engineered L1 reporter genes. In parallel, we outline outstanding questions regarding the stage-specificity, regulation, and functional impact of embryonic and germline L1 retrotransposition, and propose avenues for future research in this field.
Collapse
Affiliation(s)
- Sandra R. Richardson
- Mater Research Institute–University of QueenslandWoolloongabbaQueensland 4102Australia
| | - Geoffrey J. Faulkner
- Mater Research Institute–University of QueenslandWoolloongabbaQueensland 4102Australia
- Queensland Brain InstituteUniversity of QueenslandBrisbaneQueensland 4072Australia
- School of Biomedical SciencesUniversity of QueenslandBrisbaneQueensland 4072Australia
| |
Collapse
|
5
|
Barbieri D, Elvira-Matelot E, Pelinski Y, Genève L, de Laval B, Yogarajah G, Pecquet C, Constantinescu SN, Porteu F. Thrombopoietin protects hematopoietic stem cells from retrotransposon-mediated damage by promoting an antiviral response. J Exp Med 2018; 215:1463-1480. [PMID: 29615469 PMCID: PMC5940259 DOI: 10.1084/jem.20170997] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 12/28/2017] [Accepted: 03/02/2018] [Indexed: 12/13/2022] Open
Abstract
Propagation of retrotransposons induces genomic instability. Their roles in HSCs remain poorly studied. Barbieri et al. show that retrotransposon expression and mobilization are involved in long-lasting HSC impairment upon irradiation. These effects are counteracted by the self-renewal cytokine THPO through induction of interferon-like response. Maintenance of genomic integrity is crucial for the preservation of hematopoietic stem cell (HSC) potential. Retrotransposons, spreading in the genome through an RNA intermediate, have been associated with loss of self-renewal, aging, and DNA damage. However, their role in HSCs has not been addressed. Here, we show that mouse HSCs express various retroelements (REs), including long interspersed element-1 (L1) recent family members that further increase upon irradiation. Using mice expressing an engineered human L1 retrotransposition reporter cassette and reverse transcription inhibitors, we demonstrate that L1 retransposition occurs in vivo and is involved in irradiation-induced persistent γH2AX foci and HSC loss of function. Thus, RE represents an important intrinsic HSC threat. Furthermore, we show that RE activity is restrained by thrombopoietin, a critical HSC maintenance factor, through its ability to promote a potent interferon-like, antiviral gene response in HSCs. This uncovers a novel mechanism allowing HSCs to minimize irradiation-induced injury and reinforces the links between DNA damage, REs, and antiviral immunity.
Collapse
Affiliation(s)
- Daniela Barbieri
- INSERM UMR1170, Villejuif, France.,Université Paris-Saclay, Paris, France.,Gustave Roussy Cancer Campus, Paris, France
| | - Emilie Elvira-Matelot
- INSERM UMR1170, Villejuif, France.,Université Paris-Saclay, Paris, France.,Gustave Roussy Cancer Campus, Paris, France
| | - Yanis Pelinski
- INSERM UMR1170, Villejuif, France.,Université Paris-Saclay, Paris, France.,Gustave Roussy Cancer Campus, Paris, France
| | - Laetitia Genève
- INSERM UMR1170, Villejuif, France.,Université Paris-Saclay, Paris, France.,Gustave Roussy Cancer Campus, Paris, France
| | - Bérengère de Laval
- Centre d'Immunologie Marseille-Luminy, Université Aix-Marseille, Institut National de la Santé et de la Recherche Médicale, U1104, Centre National de la Recherche Scientifique, UMR 7280
| | - Gayathri Yogarajah
- INSERM UMR1170, Villejuif, France.,Université Paris-Saclay, Paris, France.,Gustave Roussy Cancer Campus, Paris, France
| | - Christian Pecquet
- Ludwig Institute for Cancer Research, Brussels, Belgium.,SIGN Pole, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Stefan N Constantinescu
- Ludwig Institute for Cancer Research, Brussels, Belgium.,SIGN Pole, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Françoise Porteu
- INSERM UMR1170, Villejuif, France .,Université Paris-Saclay, Paris, France.,Gustave Roussy Cancer Campus, Paris, France
| |
Collapse
|
6
|
Khazina E, Weichenrieder O. Human LINE-1 retrotransposition requires a metastable coiled coil and a positively charged N-terminus in L1ORF1p. eLife 2018; 7:34960. [PMID: 29565245 PMCID: PMC5940361 DOI: 10.7554/elife.34960] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/21/2018] [Indexed: 12/22/2022] Open
Abstract
LINE-1 (L1) is an autonomous retrotransposon, which acted throughout mammalian evolution and keeps contributing to human genotypic diversity, genetic disease and cancer. L1 encodes two essential proteins: L1ORF1p, a unique RNA-binding protein, and L1ORF2p, an endonuclease and reverse transcriptase. L1ORF1p contains an essential, but rapidly evolving N-terminal portion, homo-trimerizes via a coiled coil and packages L1RNA into large assemblies. Here, we determined crystal structures of the entire coiled coil domain of human L1ORF1p. We show that retrotransposition requires a non-ideal and metastable coiled coil structure, and a strongly basic L1ORF1p amino terminus. Human L1ORF1p therefore emerges as a highly calibrated molecular machine, sensitive to mutation but functional in different hosts. Our analysis rationalizes the locally rapid L1ORF1p sequence evolution and reveals striking mechanistic parallels to coiled coil-containing membrane fusion proteins. It also suggests how trimeric L1ORF1p could form larger meshworks and indicates critical novel steps in L1 retrotransposition. Almost half of the human genome consists of DNA strings that have been copied and pasted from one part of the genome to another many thousands of times. These strings of DNA are called mobile genetic elements. Mobile elements can disrupt important genes, causing disease and cancer, but they can also drive evolution. Presently, only one type of mobile element, called LINE-1, is active in the human genome and able to multiply without help from other mobile elements. LINE-1 DNA is ‘transcribed’ to form molecules of LINE-1 RNA, which can then be ‘translated’ into two distinct proteins. These bind to LINE-1 RNA, which then gets back-transcribed into DNA and inserted as a new LINE-1 element in a new region of the genome. One of the two proteins, called L1ORF1p, forms complexes where three copies of the protein come together. These ‘trimers’ cover and protect LINE-1 RNA and are required for LINE-1 mobility. Different versions of L1ORF1p are found in different animals. Part of the protein is the same across all mammals, and this ‘conserved’ part controls the ability of L1ORF1p to bind to RNA. The non-conserved part of L1ORF1p differs even between humans and their closest animal relatives and little was known about its structure or role. However, this rapidly evolving part of L1ORF1p is essential for LINE-1 mobility. Using X-ray crystallography, Khazina and Weichenrieder obtained a molecular snapshot of the part of L1ORF1p that interacts with other copies of the protein to form trimers. Combined with earlier snapshots of L1ORF1p’s conserved part, this generated a complete structural model of the L1ORF1p trimer. Additional biophysical characterizations suggest that L1ORF1p trimers form a semi-stable structure that can partially open up, indicating how trimers could form larger assemblies of L1ORF1p on LINE-1 RNA. Indeed, the need to maintain a semi-stable structure could explain why L1ORF1p is evolving so rapidly. A second important finding is that the beginning of L1ORF1p needs to be positively charged – a requirement that warrants further exploration. The structural and mechanistic insight into L1ORF1p points to critical new steps in LINE-1 mobilization. It will help to design inhibitor molecules with the goal to halt the mobilization process at various points and to dissect such steps in great detail. Understanding how to control LINE-1 mobility could help to improve stem cell therapies and reproduction assistance techniques, due to the fact that LINE-1 mobility is a potential source of mutation in stem cells, egg and sperm cells, and newly formed embryos.
Collapse
Affiliation(s)
- Elena Khazina
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Oliver Weichenrieder
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| |
Collapse
|
7
|
Spliced integrated retrotransposed element (SpIRE) formation in the human genome. PLoS Biol 2018; 16:e2003067. [PMID: 29505568 PMCID: PMC5860796 DOI: 10.1371/journal.pbio.2003067] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 03/20/2018] [Accepted: 02/14/2018] [Indexed: 12/20/2022] Open
Abstract
Human Long interspersed element-1 (L1) retrotransposons contain an internal RNA polymerase II promoter within their 5′ untranslated region (UTR) and encode two proteins, (ORF1p and ORF2p) required for their mobilization (i.e., retrotransposition). The evolutionary success of L1 relies on the continuous retrotransposition of full-length L1 mRNAs. Previous studies identified functional splice donor (SD), splice acceptor (SA), and polyadenylation sequences in L1 mRNA and provided evidence that a small number of spliced L1 mRNAs retrotransposed in the human genome. Here, we demonstrate that the retrotransposition of intra-5′UTR or 5′UTR/ORF1 spliced L1 mRNAs leads to the generation of spliced integrated retrotransposed elements (SpIREs). We identified a new intra-5′UTR SpIRE that is ten times more abundant than previously identified SpIREs. Functional analyses demonstrated that both intra-5′UTR and 5′UTR/ORF1 SpIREs lack Cis-acting transcription factor binding sites and exhibit reduced promoter activity. The 5′UTR/ORF1 SpIREs also produce nonfunctional ORF1p variants. Finally, we demonstrate that sequence changes within the L1 5′UTR over evolutionary time, which permitted L1 to evade the repressive effects of a host protein, can lead to the generation of new L1 splicing events, which, upon retrotransposition, generates a new SpIRE subfamily. We conclude that splicing inhibits L1 retrotransposition, SpIREs generally represent evolutionary “dead-ends” in the L1 retrotransposition process, mutations within the L1 5′UTR alter L1 splicing dynamics, and that retrotransposition of the resultant spliced transcripts can generate interindividual genomic variation. Long interspersed element-1 (L1) sequences comprise about 17% of the human genome reference sequence. The average human genome contains about 100 active L1s that mobilize throughout the genome by a “copy and paste” process termed retrotransposition. Active L1s encode two proteins (ORF1p and ORF2p). ORF1p and ORF2p preferentially bind to their encoding RNA, forming a ribonucleoprotein particle (RNP). During retrotransposition, the L1 RNP translocates to the nucleus, where the ORF2p endonuclease makes a single-strand nick in target site DNA that exposes a 3′ hydroxyl group in genomic DNA. The 3′ hydroxyl group then is used as a primer by the ORF2p reverse transcriptase to copy the L1 RNA into cDNA, leading to the integration of an L1 copy at a new genomic location. The evolutionary success of L1 requires the faithful retrotransposition of full-length L1 mRNAs; thus, it was surprising to find that a small number of L1 retrotransposition events are derived from spliced L1 mRNAs. By using genetic, biochemical, and computational approaches, we demonstrate that spliced L1 mRNAs can undergo an initial round of retrotransposition, leading to the generation of spliced integrated retrotransposed elements (SpIREs). SpIREs represent about 2% of previously annotated full-length primate-specific L1s in the human genome reference sequence. However, because splicing leads to intra-L1 deletions that remove critical sequences required for L1 expression, SpIREs generally cannot undergo subsequent rounds of retrotransposition and can be considered “dead on arrival” insertions. Our data further highlight how genetic conflict between L1 and its host has influenced L1 expression, L1 retrotransposition, and L1 splicing dynamics over evolutionary time.
Collapse
|
8
|
Mita P, Wudzinska A, Sun X, Andrade J, Nayak S, Kahler DJ, Badri S, LaCava J, Ueberheide B, Yun CY, Fenyö D, Boeke JD. LINE-1 protein localization and functional dynamics during the cell cycle. eLife 2018; 7:30058. [PMID: 29309036 PMCID: PMC5821460 DOI: 10.7554/elife.30058] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 01/04/2018] [Indexed: 01/12/2023] Open
Abstract
LINE-1/L1 retrotransposon sequences comprise 17% of the human genome. Among the many classes of mobile genetic elements, L1 is the only autonomous retrotransposon that still drives human genomic plasticity today. Through its co-evolution with the human genome, L1 has intertwined itself with host cell biology. However, a clear understanding of L1’s lifecycle and the processes involved in restricting its insertion and intragenomic spread remains elusive. Here we identify modes of L1 proteins’ entrance into the nucleus, a necessary step for L1 proliferation. Using functional, biochemical, and imaging approaches, we also show a clear cell cycle bias for L1 retrotransposition that peaks during the S phase. Our observations provide a basis for novel interpretations about the nature of nuclear and cytoplasmic L1 ribonucleoproteins (RNPs) and the potential role of DNA replication in L1 retrotransposition. Only two percent of our genetic material or genome are occupied by genes, while between 60-70 percent are made up of hundreds of thousands of copies of very similar DNA sequences. These repetitive sequences evolved from genetic elements called transposons. Transposons are often referred to as ‘jumping genes’, as they can randomly move within the genome and thereby create dangerous mutations that may lead to cancer or other genetic diseases. LINE-1 is the only remaining active transposon in humans, and it expands by copying and pasting itself to new locations via a process called 'retrotransposition'. To do so, it is first transcribed into RNA – the molecules that help to make proteins – and then converted back into identical DNA sequences. Previous research has shown that LINE-1 can form complexes with a series of proteins, including the two encoded by LINE-1 RNA itself: ORF1p and ORF2p. The LINE-1 complexes can enter the nucleus of the cell and insert a new copy of LINE-1 into the genome. However, until now it was not known how they do this. To investigate this further, Mita et al. used human cancer cells grown in the lab and tracked LINE-1 during the different stages of the cell cycle. The results showed that LINE-1 enters the nucleus as the cell starts to divide and the membrane of the nucleus breaks down. The LINE-1 complexes are then retained in the nucleus while the membrane of the nucleus reforms. Later, as the cell duplicates its genetic material, LINE-1 starts to copy and paste itself. Mita et al., together with another group of researchers, also found that during this process, only LINE-1 RNA and ORF2p were found in the nucleus. This shows that the cell cycle dictates both where the LINE-1 complexes gather and when LINE-1 is active. A next step will be to further investigate how the ‘copy and paste’ mechanisms of LINE-1 and the two LINE-1 proteins are regulated during the cell cycle. In future, this may help to identify LINE-1’s role in processes like aging or in diseases such as cancer.
Collapse
Affiliation(s)
- Paolo Mita
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States
| | - Aleksandra Wudzinska
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States
| | - Xiaoji Sun
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States
| | - Joshua Andrade
- Proteomics laboratory, NYU Langone Health, New York, United States
| | - Shruti Nayak
- Proteomics laboratory, NYU Langone Health, New York, United States
| | - David J Kahler
- High Throughput Biology (HTB) Laboratory, NYU Langone Health, New York, United States
| | - Sana Badri
- Department of Pathology, NYU Langone Health, New York, United States
| | - John LaCava
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States.,Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
| | - Beatrix Ueberheide
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States.,Proteomics laboratory, NYU Langone Health, New York, United States
| | - Chi Y Yun
- High Throughput Biology (HTB) Laboratory, NYU Langone Health, New York, United States
| | - David Fenyö
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States
| | - Jef D Boeke
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States
| |
Collapse
|
9
|
MacLennan M, García-Cañadas M, Reichmann J, Khazina E, Wagner G, Playfoot CJ, Salvador-Palomeque C, Mann AR, Peressini P, Sanchez L, Dobie K, Read D, Hung CC, Eskeland R, Meehan RR, Weichenrieder O, García-Pérez JL, Adams IR. Mobilization of LINE-1 retrotransposons is restricted by Tex19.1 in mouse embryonic stem cells. eLife 2017; 6:e26152. [PMID: 28806172 PMCID: PMC5570191 DOI: 10.7554/elife.26152] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 07/11/2017] [Indexed: 12/21/2022] Open
Abstract
Mobilization of retrotransposons to new genomic locations is a significant driver of mammalian genome evolution, but these mutagenic events can also cause genetic disorders. In humans, retrotransposon mobilization is mediated primarily by proteins encoded by LINE-1 (L1) retrotransposons, which mobilize in pluripotent cells early in development. Here we show that TEX19.1, which is induced by developmentally programmed DNA hypomethylation, can directly interact with the L1-encoded protein L1-ORF1p, stimulate its polyubiquitylation and degradation, and restrict L1 mobilization. We also show that TEX19.1 likely acts, at least in part, through promoting the activity of the E3 ubiquitin ligase UBR2 towards L1-ORF1p. Moreover, loss of Tex19.1 increases L1-ORF1p levels and L1 mobilization in pluripotent mouse embryonic stem cells, implying that Tex19.1 prevents de novo retrotransposition in the pluripotent phase of the germline cycle. These data show that post-translational regulation of L1 retrotransposons plays a key role in maintaining trans-generational genome stability in mammals.
Collapse
Affiliation(s)
- Marie MacLennan
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
| | - Marta García-Cañadas
- Centro de Genómica e
Investigación Oncológica (GENYO), Pfizer-Universidad de
Granada-Junta de Andalucía, PTS Granada, Granada,
Spain
| | - Judith Reichmann
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
| | - Elena Khazina
- Department of
Biochemistry, Max Planck Institute for Developmental
Biology, Tübingen, Germany
| | - Gabriele Wagner
- Department of
Biochemistry, Max Planck Institute for Developmental
Biology, Tübingen, Germany
| | - Christopher J Playfoot
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
| | - Carmen Salvador-Palomeque
- Centro de Genómica e
Investigación Oncológica (GENYO), Pfizer-Universidad de
Granada-Junta de Andalucía, PTS Granada, Granada,
Spain
| | - Abigail R Mann
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
| | - Paula Peressini
- Centro de Genómica e
Investigación Oncológica (GENYO), Pfizer-Universidad de
Granada-Junta de Andalucía, PTS Granada, Granada,
Spain
| | - Laura Sanchez
- Centro de Genómica e
Investigación Oncológica (GENYO), Pfizer-Universidad de
Granada-Junta de Andalucía, PTS Granada, Granada,
Spain
| | - Karen Dobie
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
| | - David Read
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
| | - Chao-Chun Hung
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
| | - Ragnhild Eskeland
- Department of
Biosciences, University of Oslo,
Oslo,
Norway
- Norwegian Center for
Stem Cell Research, Department of Immunology, Oslo
University Hospital, Oslo, Norway
| | - Richard R Meehan
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
| | - Oliver Weichenrieder
- Department of
Biochemistry, Max Planck Institute for Developmental
Biology, Tübingen, Germany
| | - Jose Luis García-Pérez
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
- Centro de Genómica e
Investigación Oncológica (GENYO), Pfizer-Universidad de
Granada-Junta de Andalucía, PTS Granada, Granada,
Spain
| | - Ian R Adams
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
| |
Collapse
|
10
|
Kannan M, Li J, Fritz SE, Husarek KE, Sanford JC, Sullivan TL, Tiwary PK, An W, Boeke JD, Symer DE. Dynamic silencing of somatic L1 retrotransposon insertions reflects the developmental and cellular contexts of their genomic integration. Mob DNA 2017; 8:8. [PMID: 28491150 PMCID: PMC5424313 DOI: 10.1186/s13100-017-0091-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 05/03/2017] [Indexed: 02/15/2023] Open
Abstract
Background The ongoing mobilization of mammalian transposable elements (TEs) contributes to natural genetic variation. To survey the epigenetic control and expression of reporter genes inserted by L1 retrotransposition in diverse cellular and genomic contexts, we engineered highly sensitive, real-time L1 retrotransposon reporter constructs. Results Here we describe different patterns of expression and epigenetic controls of newly inserted sequences retrotransposed by L1 in various somatic cells and tissues including cultured human cancer cells, mouse embryonic stem cells, and tissues of pseudofounder transgenic mice and their progeny. In cancer cell lines, the newly inserted sequences typically underwent rapid transcriptional gene silencing, but they lacked cytosine methylation even after many cell divisions. L1 reporter expression was reversible and oscillated frequently. Silenced or variegated reporter expression was strongly and uniformly reactivated by treatment with inhibitors of histone deacetylation, revealing the mechanism for their silencing. By contrast, de novo integrants retrotransposed by L1 in pluripotent mouse embryonic stem (ES) cells underwent rapid silencing by dense cytosine methylation. Similarly, de novo cytosine methylation also was identified at new integrants when studied in several distinct somatic tissues of adult founder mice. Pre-existing L1 elements in cultured human cancer cells were stably silenced by dense cytosine methylation, whereas their transcription modestly increased when cytosine methylation was experimentally reduced in cells lacking DNA methyltransferases DNMT1 and DNMT3b. As a control, reporter genes mobilized by piggyBac (PB), a DNA transposon, revealed relatively stable and robust expression without apparent silencing in both cultured cancer cells and ES cells. Conclusions We hypothesize that the de novo methylation marks at newly inserted sequences retrotransposed by L1 in early pre-implantation development are maintained or re-established in adult somatic tissues. By contrast, histone deacetylation reversibly silences L1 reporter insertions that had mobilized at later timepoints in somatic development and differentiation, e.g., in cancer cell lines. We conclude that the cellular contexts of L1 retrotransposition can determine expression or silencing of newly integrated sequences. We propose a model whereby reporter expression from somatic TE insertions reflects the timing, molecular mechanism, epigenetic controls and the genomic, cellular and developmental contexts of their integration. Electronic supplementary material The online version of this article (doi:10.1186/s13100-017-0091-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Manoj Kannan
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Pilani, 333031 Rajasthan India.,Laboratory of Immunobiology, Mouse Cancer Genetics Program and Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA.,Present Address: Birla Institute of Technology and Science, Pilani, Dubai campus, Dubai, United Arab Emirates
| | - Jingfeng Li
- Laboratory of Immunobiology, Mouse Cancer Genetics Program and Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA.,Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH USA.,Department of Internal Medicine, The Ohio State University, Columbus, OH USA
| | - Sarah E Fritz
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH USA.,Present Address: National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Kathryn E Husarek
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH USA.,Present Address: Aventiv Research, Inc., Columbus, OH USA
| | - Jonathan C Sanford
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH USA.,Present Address: Drug Safety Research and Development, Pfizer, Inc., Groton, CT USA
| | - Teresa L Sullivan
- Laboratory of Immunobiology, Mouse Cancer Genetics Program and Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA
| | - Pawan Kumar Tiwary
- Laboratory of Immunobiology, Mouse Cancer Genetics Program and Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA.,Present Address: Biocon, Bangalore, India
| | - Wenfeng An
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD USA.,Present Address: Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD USA
| | - Jef D Boeke
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD USA.,Present Address: Institute for Systems Genetics, New York University Langone Medical Center, New York, NY USA
| | - David E Symer
- Laboratory of Immunobiology, Mouse Cancer Genetics Program and Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA.,Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH USA.,Human Cancer Genetics Program, and Department of Biomedical Informatics, The Ohio State University, Columbus, OH USA.,Human Cancer Genetics Program, Department of Cancer Biology and Genetics, and Department of Biomedical Informatics, The Ohio State University, Tzagournis Research Facility, Room 440, 420 West 12th Ave, Columbus, OH 43210 USA
| |
Collapse
|
11
|
Richardson SR, Gerdes P, Gerhardt DJ, Sanchez-Luque FJ, Bodea GO, Muñoz-Lopez M, Jesuadian JS, Kempen MJHC, Carreira PE, Jeddeloh JA, Garcia-Perez JL, Kazazian HH, Ewing AD, Faulkner GJ. Heritable L1 retrotransposition in the mouse primordial germline and early embryo. Genome Res 2017; 27:1395-1405. [PMID: 28483779 PMCID: PMC5538555 DOI: 10.1101/gr.219022.116] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 05/02/2017] [Indexed: 12/31/2022]
Abstract
LINE-1 (L1) retrotransposons are a noted source of genetic diversity and disease in mammals. To expand its genomic footprint, L1 must mobilize in cells that will contribute their genetic material to subsequent generations. Heritable L1 insertions may therefore arise in germ cells and in pluripotent embryonic cells, prior to germline specification, yet the frequency and predominant developmental timing of such events remain unclear. Here, we applied mouse retrotransposon capture sequencing (mRC-seq) and whole-genome sequencing (WGS) to pedigrees of C57BL/6J animals, and uncovered an L1 insertion rate of ≥1 event per eight births. We traced heritable L1 insertions to pluripotent embryonic cells and, strikingly, to early primordial germ cells (PGCs). New L1 insertions bore structural hallmarks of target-site primed reverse transcription (TPRT) and mobilized efficiently in a cultured cell retrotransposition assay. Together, our results highlight the rate and evolutionary impact of heritable L1 retrotransposition and reveal retrotransposition-mediated genomic diversification as a fundamental property of pluripotent embryonic cells in vivo.
Collapse
Affiliation(s)
- Sandra R Richardson
- Mater Research Institute-University of Queensland, Woolloongabba QLD 4102, Australia
| | - Patricia Gerdes
- Mater Research Institute-University of Queensland, Woolloongabba QLD 4102, Australia
| | - Daniel J Gerhardt
- Mater Research Institute-University of Queensland, Woolloongabba QLD 4102, Australia.,Invenra, Incorporated, Madison, Wisconsin 53719, USA
| | - Francisco J Sanchez-Luque
- Mater Research Institute-University of Queensland, Woolloongabba QLD 4102, Australia.,Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - Gabriela-Oana Bodea
- Mater Research Institute-University of Queensland, Woolloongabba QLD 4102, Australia
| | - Martin Muñoz-Lopez
- Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - J Samuel Jesuadian
- Mater Research Institute-University of Queensland, Woolloongabba QLD 4102, Australia
| | | | - Patricia E Carreira
- Mater Research Institute-University of Queensland, Woolloongabba QLD 4102, Australia
| | | | - Jose L Garcia-Perez
- Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain.,Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Haig H Kazazian
- Institute of Genetic Medicine and Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Adam D Ewing
- Mater Research Institute-University of Queensland, Woolloongabba QLD 4102, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute-University of Queensland, Woolloongabba QLD 4102, Australia.,School of Biomedical Sciences.,Queensland Brain Institute, University of Queensland, Brisbane QLD 4072, Australia
| |
Collapse
|
12
|
Opossum APOBEC1 is a DNA mutator with retrovirus and retroelement restriction activity. Sci Rep 2017; 7:46719. [PMID: 28429755 PMCID: PMC5399452 DOI: 10.1038/srep46719] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/23/2017] [Indexed: 01/12/2023] Open
Abstract
APOBEC3s (A3s) are single-stranded DNA cytosine deaminases that provide innate immune defences against retroviruses and mobile elements. A3s are specific to eutherian mammals because no direct homologs exist at the syntenic genomic locus in metatherian (marsupial) or prototherian (monotreme) mammals. However, the A3s in these species have the likely evolutionary precursors, the antibody gene deaminase AID and the RNA/DNA editing enzyme APOBEC1 (A1). Here, we used cell culture-based assays to determine whether opossum A1 restricts the infectivity of retroviruses including human immunodeficiency virus type 1 (HIV-1) and the mobility of LTR/non-LTR retrotransposons. Opossum A1 partially inhibited HIV-1, as well as simian immunodeficiency virus (SIV), murine leukemia virus (MLV), and the retrotransposon MusD. The mechanism of inhibition required catalytic activity, except for human LINE1 (L1) restriction, which was deamination-independent. These results indicate that opossum A1 functions as an innate barrier to infection by retroviruses such as HIV-1, and controls LTR/non-LTR retrotransposition in marsupials.
Collapse
|
13
|
Fu Q, Pandey RR, Leu NA, Pillai RS, Wang PJ. Mutations in the MOV10L1 ATP Hydrolysis Motif Cause piRNA Biogenesis Failure and Male Sterility in Mice. Biol Reprod 2016; 95:103. [PMID: 27655786 PMCID: PMC5178147 DOI: 10.1095/biolreprod.116.142430] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/19/2016] [Indexed: 11/17/2022] Open
Abstract
Piwi-interacting RNAs (piRNAs) are a class of small noncoding RNAs. piRNAs protect the genome integrity of the germline by silencing active transposable elements and are essential for germ cell development. Most piRNA pathway proteins are evolutionarily conserved. MOV10L1, a testis-specific RNA helicase, binds to piRNA precursors and is a master regulator of piRNA biogenesis in mouse. Here we report that mutation of the MOV10L1 ATP hydrolysis site leads to depletion of piRNAs on Piwi proteins, de-repression of transposable elements, and conglomeration of piRNA pathway proteins into polar granules. The Mov10l1 mutant mice exhibit meiotic arrest and male sterility. Our results show that mutation of the MOV10L1 ATP hydrolysis site perturbs piRNA biogenesis.
Collapse
Affiliation(s)
- Qi Fu
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania
| | - Radha Raman Pandey
- Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - N. Adrian Leu
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania
| | - Ramesh S. Pillai
- Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - P. Jeremy Wang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania
- Correspondence: P. Jeremy Wang, Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104. E-mail:
| |
Collapse
|
14
|
SAMHD1 Inhibits LINE-1 Retrotransposition by Promoting Stress Granule Formation. PLoS Genet 2015; 11:e1005367. [PMID: 26134849 PMCID: PMC4489885 DOI: 10.1371/journal.pgen.1005367] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 06/17/2015] [Indexed: 01/17/2023] Open
Abstract
The SAM domain and HD domain containing protein 1 (SAMHD1) inhibits retroviruses, DNA viruses and long interspersed element 1 (LINE-1). Given that in dividing cells, SAMHD1 loses its antiviral function yet still potently restricts LINE-1, we propose that, instead of blocking viral DNA synthesis by virtue of its dNTP triphosphohydrolase activity, SAMHD1 may exploit a different mechanism to control LINE-1. Here, we report a new activity of SAMHD1 in promoting cellular stress granule assembly, which correlates with increased phosphorylation of eIF2α and diminished eIF4A/eIF4G interaction. This function of SAMHD1 enhances sequestration of LINE-1 RNP in stress granules and consequent blockade to LINE-1 retrotransposition. In support of this new mechanism of action, depletion of stress granule marker proteins G3BP1 or TIA1 abrogates stress granule formation and overcomes SAMHD1 inhibition of LINE-1. Together, these data reveal a new mechanism for SAMHD1 to control LINE-1 by activating cellular stress granule pathway. Long interspersed element 1 (LINE-1 or L1) comprises 17% of human genome, and has played a major role in shaping the evolution of human genome. Approximately 100 copies of LINE-1 are still active in an average individual genome. Movement of these LINE-1 sequences to new loci in the genome has the potential of causing sporadic cases of disease. Among the multi-layered mechanisms by which the host controls LINE-1 activity is a group of host restriction factors including APOBEC3 proteins. SAMHD1 was known for the association of its mutations with the Aicardi-Goutieres syndrome (AGS), a congenital autoimmune disease. SAMHD1 was recently reported as a host restriction factor that inhibits a number of retroviruses and DNA viruses including human immunodeficiency virus type 1 (HIV-1) and herpes simplex virus 1 (HSV-1). Here, we demonstrate that SAMHD1 inhibits LINE-1 retrotransposition through promoting the sequestration of LINE-1 RNP within the cytoplasmic stress granules. SAMHD1 promotes the formation of large stress granules by inducing phosphorylation of eIF2α and disrupting eIF4A/eIF4G interaction. This is the first report describing the role of SAMHD1 in modulating the formation of stress granules. We envision that this function of SAMHD1 not only contributes to the inhibition of LINE-1, but also the restriction of various viruses.
Collapse
|
15
|
Ichiyanagi T, Ichiyanagi K, Ogawa A, Kuramochi-Miyagawa S, Nakano T, Chuma S, Sasaki H, Udono H. HSP90α plays an important role in piRNA biogenesis and retrotransposon repression in mouse. Nucleic Acids Res 2014; 42:11903-11. [PMID: 25262350 PMCID: PMC4231750 DOI: 10.1093/nar/gku881] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
HSP90, found in all kingdoms of life, is a major chaperone protein regulating many client proteins. We demonstrated that HSP90α, one of two paralogs duplicated in vertebrates, plays an important role in the biogenesis of fetal PIWI-interacting RNAs (piRNA), which act against the transposon activities, in mouse male germ cells. The knockout mutation of Hsp90α resulted in a large reduction in the expression of primary and secondary piRNAs and mislocalization of MIWI2, a PIWI homolog. Whereas the mutation in Fkbp6 encoding a co-chaperone reduced piRNAs of 28–32 nucleotides in length, the Hsp90α mutation reduced piRNAs of 24–32 nucleotides, suggesting the presence of both FKBP6-dependent and -independent actions of HSP90α. Although DNA methylation and mRNA levels of L1 retrotransposon were largely unchanged in the Hsp90α mutant testes, the L1-encoded protein was increased, suggesting the presence of post-transcriptional regulation. This study revealed the specialized function of the HSP90α isofom in the piRNA biogenesis and repression of retrotransposons during the development of male germ cells in mammals.
Collapse
Affiliation(s)
- Tomoko Ichiyanagi
- Department of Immunology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Kita-ku, Okayama 700-8558, Japan Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kenji Ichiyanagi
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Ayako Ogawa
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Satomi Kuramochi-Miyagawa
- Department of Pathology, Medical School and Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan CREST, Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
| | - Toru Nakano
- Department of Pathology, Medical School and Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan CREST, Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
| | - Shinichiro Chuma
- Department of Development and Differentiation, Institute for Frontier Medical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Heiichiro Udono
- Department of Immunology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Kita-ku, Okayama 700-8558, Japan
| |
Collapse
|
16
|
Knittel G, Metzner M, Beck-Engeser G, Kan A, Ahrends T, Eilat D, Huppi K, Wabl M. Insertional hypermutation in mineral oil-induced plasmacytomas. Eur J Immunol 2014; 44:2785-801. [PMID: 24975032 PMCID: PMC4165787 DOI: 10.1002/eji.201344322] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 05/22/2014] [Accepted: 06/24/2014] [Indexed: 01/07/2023]
Abstract
Unless stimulated by a chronic inflammatory agent, such as mineral oil, plasma cell tumors are rare in young BALB/c mice. This raises the questions: What do inflammatory tissues provide to promote mutagenesis? And what is the nature of mutagenesis? We determined that mineral oil-induced plasmacytomas produce large amounts of endogenous retroelements--ecotropic and polytropic murine leukemia virus and intracisternal A particles. Therefore, plasmacytoma formation might occur, in part, by de novo insertion of these retroelements, induced or helped by the inflammation. We recovered up to ten de novo insertions in a single plasmacytoma, mostly in genes with common retroviral integration sites. Additional integrations accompany tumor evolution from a solid tumor through several generations in cell culture. The high frequency of de novo integrations into cancer genes suggests that endogenous retroelements are coresponsible for plasmacytoma formation and progression in BALB/c mice.
Collapse
Affiliation(s)
- Gero Knittel
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143-0414
| | - Mirjam Metzner
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143-0414
| | - Gabriele Beck-Engeser
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143-0414
| | - Ada Kan
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143-0414
| | - Tomasz Ahrends
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143-0414
| | - Dan Eilat
- Department of Medicine, Hadassah University Hospital and The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel
| | - Konrad Huppi
- National Cancer Institute, Genetics Branch, Gene Silencing Section, Bethesda, MD 20892
| | - Matthias Wabl
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143-0414
| |
Collapse
|
17
|
Castañeda J, Genzor P, van der Heijden GW, Sarkeshik A, Yates JR, Ingolia NT, Bortvin A. Reduced pachytene piRNAs and translation underlie spermiogenic arrest in Maelstrom mutant mice. EMBO J 2014; 33:1999-2019. [PMID: 25063675 DOI: 10.15252/embj.201386855] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Pachytene piRNAs are a class of Piwi-interacting small RNAs abundant in spermatids of the adult mouse testis. They are processed from piRNA primary transcripts by a poorly understood mechanism and, unlike fetal transposon-derived piRNAs, lack complementary targets in the spermatid transcriptome. We report that immunopurified complexes of a conserved piRNA pathway protein Maelstrom (MAEL) are enriched in MIWI (Piwi partner of pachytene piRNAs), Tudor-domain proteins and processing intermediates of pachytene piRNA primary transcripts. We provide evidence of functional significance of these complexes in Mael129 knockout mice that exhibit spermiogenic arrest with acrosome and flagellum malformation. Mael129-null mutant testes possess low levels of piRNAs derived from MAEL-associated piRNA precursors and exhibit reduced translation of numerous spermiogenic mRNAs including those encoding acrosome and flagellum proteins. These translation defects in haploid round spermatids are likely indirect, as neither MAEL nor piRNA precursors associate with polyribosomes, and they may arise from an imbalance between pachytene piRNAs and MIWI.
Collapse
Affiliation(s)
- Julio Castañeda
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| | - Pavol Genzor
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| | | | - Ali Sarkeshik
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nicholas T Ingolia
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| | - Alex Bortvin
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| |
Collapse
|
18
|
Yang L, Brunsfeld J, Scott L, Wichman H. Reviving the dead: history and reactivation of an extinct l1. PLoS Genet 2014; 10:e1004395. [PMID: 24968166 PMCID: PMC4072516 DOI: 10.1371/journal.pgen.1004395] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 04/07/2014] [Indexed: 11/18/2022] Open
Abstract
Although L1 sequences are present in the genomes of all placental mammals and marsupials examined to date, their activity was lost in the megabat family, Pteropodidae, ∼24 million years ago. To examine the characteristics of L1s prior to their extinction, we analyzed the evolutionary history of L1s in the genome of a megabat, Pteropus vampyrus, and found a pattern of periodic L1 expansion and quiescence. In contrast to the well-characterized L1s in human and mouse, megabat genomes have accommodated two or more simultaneously active L1 families throughout their evolutionary history, and major peaks of L1 deposition into the genome always involved multiple families. We compared the consensus sequences of the two major megabat L1 families at the time of their extinction to consensus L1s of a variety of mammalian species. Megabat L1s are comparable to the other mammalian L1s in terms of adenosine content and conserved amino acids in the open reading frames (ORFs). However, the intergenic region (IGR) of the reconstructed element from the more active family is dramatically longer than the IGR of well-characterized human and mouse L1s. We synthesized the reconstructed element from this L1 family and tested the ability of its components to support retrotransposition in a tissue culture assay. Both ORFs are capable of supporting retrotransposition, while the IGR is inhibitory to retrotransposition, especially when combined with either of the reconstructed ORFs. We dissected the inhibitory effect of the IGR by testing truncated and shuffled versions and found that length is a key factor, but not the only one affecting inhibition of retrotransposition. Although the IGR is inhibitory to retrotransposition, this inhibition does not account for the extinction of L1s in megabats. Overall, the evolution of the L1 sequence or the quiescence of L1 is unlikely the reason of L1 extinction.
Collapse
Affiliation(s)
- Lei Yang
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
| | - John Brunsfeld
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - LuAnn Scott
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Holly Wichman
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- * E-mail:
| |
Collapse
|
19
|
Dai L, LaCava J, Taylor MS, Boeke JD. Expression and detection of LINE-1 ORF-encoded proteins. Mob Genet Elements 2014; 4:e29319. [PMID: 25054082 PMCID: PMC4091050 DOI: 10.4161/mge.29319] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 05/19/2014] [Accepted: 05/22/2014] [Indexed: 11/30/2022] Open
Abstract
LINE-1 (L1) elements are endogenous retrotransposons active in mammalian genomes. The L1 RNA is bicistronic, encoding two non-overlapping open reading frames, ORF1 and ORF2, whose protein products (ORF1p and ORF2p) bind the L1 RNA to form a ribonucleoprotein (RNP) complex that is presumed to be a critical retrotransposition intermediate. However, ORF2p is expressed at a significantly lower level than ORF1p; these differences are thought to be controlled at the level of translation, due to a low frequency ribosome reinitiation mechanism controlling ORF2 expression. As a result, while ORF1p is readily detectable, ORF2p has previously been very challenging to detect in vitro and in vivo. To address this, we recently tested several epitope tags fused to the N- or C-termini of the ORF proteins in an effort to enable robust detection and affinity purification from native (L1RP) and synthetic (ORFeus-Hs) L1 constructs. An analysis of tagged RNPs from both L1RP and ORFeus-Hs showed similar host-cell-derived protein interactors. Our observations also revealed that the tag sequences affected the retrotransposition competency of native and synthetic L1s differently although they encode identical ORF proteins. Unexpectedly, we observed apparently stochastic expression of ORF2p within seemingly homogenous L1-expressing cell populations.
Collapse
Affiliation(s)
- Lixin Dai
- High Throughput Biology Center and Department of Molecular Biology and Genetics; Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - John LaCava
- Laboratory of Cellular and Structural Biology; The Rockefeller University; New York, NY USA
| | - Martin S Taylor
- High Throughput Biology Center and Department of Pharmacology and Molecular Sciences; Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Jef D Boeke
- Institute for Systems Genetics; New York University School of Medicine; New York, NY USA
| |
Collapse
|
20
|
Crichton JH, Dunican DS, MacLennan M, Meehan RR, Adams IR. Defending the genome from the enemy within: mechanisms of retrotransposon suppression in the mouse germline. Cell Mol Life Sci 2014; 71:1581-605. [PMID: 24045705 PMCID: PMC3983883 DOI: 10.1007/s00018-013-1468-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 08/27/2013] [Accepted: 08/29/2013] [Indexed: 12/15/2022]
Abstract
The viability of any species requires that the genome is kept stable as it is transmitted from generation to generation by the germ cells. One of the challenges to transgenerational genome stability is the potential mutagenic activity of transposable genetic elements, particularly retrotransposons. There are many different types of retrotransposon in mammalian genomes, and these target different points in germline development to amplify and integrate into new genomic locations. Germ cells, and their pluripotent developmental precursors, have evolved a variety of genome defence mechanisms that suppress retrotransposon activity and maintain genome stability across the generations. Here, we review recent advances in understanding how retrotransposon activity is suppressed in the mammalian germline, how genes involved in germline genome defence mechanisms are regulated, and the consequences of mutating these genome defence genes for the developing germline.
Collapse
Affiliation(s)
- James H. Crichton
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
| | - Donncha S. Dunican
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
| | - Marie MacLennan
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
| | - Richard R. Meehan
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
| | - Ian R. Adams
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
| |
Collapse
|
21
|
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.
Collapse
Affiliation(s)
- Ekaterina Belan
- Genetics Laboratory, Royal University Hospital, Saskatoon, SK S7N 0W8, Canada.
| |
Collapse
|
22
|
Reichmann J, Reddington JP, Best D, Read D, Öllinger R, Meehan RR, Adams IR. The genome-defence gene Tex19.1 suppresses LINE-1 retrotransposons in the placenta and prevents intra-uterine growth retardation in mice. Hum Mol Genet 2013; 22:1791-806. [PMID: 23364048 PMCID: PMC3613164 DOI: 10.1093/hmg/ddt029] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 12/19/2012] [Accepted: 01/24/2013] [Indexed: 12/11/2022] Open
Abstract
DNA methylation plays an important role in suppressing retrotransposon activity in mammalian genomes, yet there are stages of mammalian development where global hypomethylation puts the genome at risk of retrotransposition-mediated genetic instability. Hypomethylated primordial germ cells appear to limit this risk by expressing a cohort of retrotransposon-suppressing genome-defence genes whose silencing depends on promoter DNA methylation. Here, we investigate whether similar mechanisms operate in hypomethylated trophectoderm-derived components of the mammalian placenta to couple expression of genome-defence genes to the potential for retrotransposon activity. We show that the hypomethylated state of the mouse placenta results in activation of only one of the hypomethylation-sensitive germline genome-defence genes: Tex19.1. Tex19.1 appears to play an important role in placenta function as Tex19.1(-/-) mouse embryos exhibit intra-uterine growth retardation and have small placentas due to a reduction in the number of spongiotrophoblast, glycogen trophoblast and sinusoidal trophoblast giant cells. Furthermore, we show that retrotransposon mRNAs are derepressed in Tex19.1(-/-) placentas and that protein encoded by the LINE-1 retrotransposon is upregulated in hypomethylated trophectoderm-derived cells that normally express Tex19.1. This study suggests that post-transcriptional genome-defence mechanisms are operating in the placenta to protect the hypomethylated cells in this tissue from retrotransposons and suggests that imbalances between retrotransposon activity and genome-defence mechanisms could contribute to placenta dysfunction and disease.
Collapse
Affiliation(s)
| | | | | | | | | | - Richard R. Meehan
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Ian R. Adams
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| |
Collapse
|
23
|
Peddigari S, Li PWL, Rabe JL, Martin SL. hnRNPL and nucleolin bind LINE-1 RNA and function as host factors to modulate retrotransposition. Nucleic Acids Res 2013; 41:575-85. [PMID: 23161687 PMCID: PMC3592465 DOI: 10.1093/nar/gks1075] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 10/09/2012] [Accepted: 10/13/2012] [Indexed: 12/18/2022] Open
Abstract
Long INterspersed Element one (LINE-1, or L1), is a widely distributed, autonomous retrotransposon in mammalian genomes. During retrotransposition, L1 RNA functions first as a dicistronic mRNA and then as a template for cDNA synthesis. Previously, we defined internal ribosome entry sequences (IRESs) upstream of both ORFs (ORF1 and ORF2) in the dicistronic mRNA encoded by mouse L1. Here, RNA affinity chromatography was used to isolate cellular proteins that bind these regions of L1 RNA. Four proteins, the heterogeneous nuclear ribonucleoproteins (hnRNPs) R, Q and L, and nucleolin (NCL), appeared to interact specifically with the ORF2 IRES. These were depleted from HeLa cells to examine their effects on L1 IRES-mediated translation and L1 retrotransposition. NCL knockdown specifically reduced the ORF2 IRES activity, L1 and L1-assisted Alu retrotransposition without altering L1 RNA or protein abundance. These findings are consistent with NCL acting as an IRES trans-acting factor (ITAF) for ORF2 translation and hence a positive host factor for L1 retrotransposition. In contrast, hnRNPL knockdown dramatically increased L1 retrotransposition as well as L1 RNA and ORF1 protein, indicating that this cellular protein normally interferes with retrotransposition. Thus, hnRNPL joins a small, but growing list of cellular proteins that are potent negative regulators of L1 retrotransposition.
Collapse
Affiliation(s)
- Suresh Peddigari
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, PO Box 6511, MS 8108, Aurora, CO 80045, USA.
| | | | | | | |
Collapse
|
24
|
Metzner M, Jäck HM, Wabl M. LINE-1 retroelements complexed and inhibited by activation induced cytidine deaminase. PLoS One 2012; 7:e49358. [PMID: 23133680 PMCID: PMC3487726 DOI: 10.1371/journal.pone.0049358] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 10/08/2012] [Indexed: 12/31/2022] Open
Abstract
LINE-1 (abbreviated L1) is a major class of retroelements in humans and mice. If unrestricted, retroelements accumulate in the cytoplasm and insert their DNA into the host genome, with the potential to cause autoimmune disease and cancer. Retroviruses and other retroelements are inhibited by proteins of the APOBEC family, of which activation-induced cytidine deaminase (AID) is a member. Although AID is mainly known for being a DNA mutator shaping the antibody repertoire in B lymphocytes, we found that AID also restricts de novo L1 integrations in B- and non-B-cell lines. It does so by decreasing the protein level of open reading frame 1 (ORF1) of both exogenous and endogenous L1. In activated B lymphocytes, AID deficiency increased L1 mRNA 1.6-fold and murine leukemia virus (MLV) mRNA 2.7-fold. In cell lines and activated B lymphocytes, AID forms cytoplasmic high-molecular-mass complexes with L1 mRNA, which may contribute to L1 restriction. Because AID-deficient activated B lymphocytes do not express ORF1 protein, we suggest that ORF1 protein expression is inhibited by additional restriction factors in these cells. The greater increase in MLV compared to L1 mRNA in AID-deficient activated B lymphocytes may indicate less strict surveillance of retrovirus.
Collapse
Affiliation(s)
- Mirjam Metzner
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America.
| | | | | |
Collapse
|
25
|
Rosser JM, An W. L1 expression and regulation in humans and rodents. Front Biosci (Elite Ed) 2012; 4:2203-25. [PMID: 22202032 DOI: 10.2741/537] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Long interspersed elements type 1 (LINE-1s, or L1s) have impacted mammalian genomes at multiple levels. L1 transcription is mainly controlled by its 5' untranslated region (5'UTR), which differs significantly among active human and rodent L1 families. In this review, L1 expression and its regulation are examined in the context of human and rodent development. First, endogenous L1 expression patterns in three different species-human, rat, and mouse-are compared and contrasted. A detailed account of relevant experimental evidence is presented according to the source material, such as cell lines, tumors, and normal somatic and germline tissues from different developmental stages. Second, factors involved in the regulation of L1 expression at both transcriptional and posttranscriptional levels are discussed. These include transcription factors, DNA methylation, PIWI-interacting RNAs (piRNAs), RNA interference (RNAi), and posttranscriptional host factors. Similarities and differences between human and rodent L1s are highlighted. Third, recent findings from transgenic mouse models of L1 are summarized and contrasted with those from endogenous L1 studies. Finally, the challenges and opportunities for L1 mouse models are discussed.
Collapse
Affiliation(s)
- James M Rosser
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA
| | | |
Collapse
|
26
|
Harris CR, Normart R, Yang Q, Stevenson E, Haffty BG, Ganesan S, Cordon-Cardo C, Levine AJ, Tang LH. Association of nuclear localization of a long interspersed nuclear element-1 protein in breast tumors with poor prognostic outcomes. Genes Cancer 2011; 1:115-24. [PMID: 20948976 DOI: 10.1177/1947601909360812] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Within healthy human somatic cells, retrotransposition by long interspersed nuclear element-1 (also known as LINE-1 or L1) is thought to be held in check by a variety of mechanisms, including DNA methylation and RNAi. The expression of L1-ORF1 protein, which is rarely found in normal tissue, was assayed using antibodies with a variety of clinical cancer specimens and cancer cell lines. L1-ORF1p expression was detected in nearly all breast tumors that the authors examined, and the protein was also present in a high percentage of ileal carcinoids, bladder, and pancreatic neuroendocrine tumors, as well as in a smaller percentage of prostate and colorectal tumors. Tumors generally demonstrated cytoplasmic L1-ORF1p; however, in several breast cancers, L1-ORF1p was nuclear. Patients with breast tumors displaying nuclear L1-ORF1p had a greater incidence of both local recurrence and distal metastases and also showed poorer overall survival when compared with patients with tumors displaying cytoplasmic L1-ORF1p. These data suggest that expression of L1-ORF1p is widespread in many cancers and that redistribution from cytoplasm to nucleus could be a poor prognostic indicator during breast cancer. High expression and nuclear localization of L1-ORF1p may result in a higher rate of L1 retrotransposition, which could increase genomic instability.
Collapse
|
27
|
Wissing S, Muñoz-Lopez M, Macia A, Yang Z, Montano M, Collins W, Garcia-Perez JL, Moran JV, Greene WC. Reprogramming somatic cells into iPS cells activates LINE-1 retroelement mobility. Hum Mol Genet 2011; 21:208-18. [PMID: 21989055 DOI: 10.1093/hmg/ddr455] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Long interspersed element-1 (LINE-1 or L1) retrotransposons account for nearly 17% of human genomic DNA and represent a major evolutionary force that has reshaped the structure and function of the human genome. However, questions remain concerning both the frequency and the developmental timing of L1 retrotransposition in vivo and whether the mobility of these retroelements commonly results in insertional and post-insertional mechanisms of genomic injury. Cells exhibiting high rates of L1 retrotransposition might be especially at risk for such injury. We assessed L1 mRNA expression and L1 retrotransposition in two biologically relevant cell types, human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs), as well as in control parental human dermal fibroblasts (HDFs). Full-length L1 mRNA and the L1 open reading frame 1-encoded protein (ORF1p) were readily detected in hESCs and iPSCs, but not in HDFs. Sequencing analysis proved the expression of human-specific L1 element mRNAs in iPSCs. Bisulfite sequencing revealed that the increased L1 expression observed in iPSCs correlates with an overall decrease in CpG methylation in the L1 promoter region. Finally, retrotransposition of an engineered human L1 element was ~10-fold more efficient in iPSCs than in parental HDFs. These findings indicate that somatic cell reprogramming is associated with marked increases in L1 expression and perhaps increases in endogenous L1 retrotransposition, which could potentially impact the genomic integrity of the resultant iPSCs.
Collapse
Affiliation(s)
- Silke Wissing
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Wissing S, Montano M, Garcia-Perez JL, Moran JV, Greene WC. Endogenous APOBEC3B restricts LINE-1 retrotransposition in transformed cells and human embryonic stem cells. J Biol Chem 2011; 286:36427-37. [PMID: 21878639 DOI: 10.1074/jbc.m111.251058] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Members of the APOBEC3 (A3) family of cytidine deaminase enzymes act as host defense mechanisms limiting both infections by exogenous retroviruses and mobilization of endogenous retrotransposons. Previous studies revealed that the overexpression of some A3 proteins could restrict engineered human Long INterspersed Element-1 (LINE-1 or L1) retrotransposition in HeLa cells. However, whether endogenous A3 proteins play a role in restricting L1 retrotransposition remains largely unexplored. Here, we show that HeLa cells express endogenous A3B and A3C, whereas human embryonic stem cells (hESCs) express A3B, A3C, A3DE, A3F, and A3G. To study the relative contribution of endogenous A3 proteins in restricting L1 retrotransposition, we first generated small hairpin RNAs (shRNAs) to suppress endogenous A3 mRNA expression, and then assessed L1 mobility using a cell-based L1 retrotransposition assay. We demonstrate that in both HeLa and hESCs, shRNA-based knockdown of A3B promotes a ∼2-3.7-fold increase in the retrotransposition efficiency of an engineered human L1. Knockdown of the other A3s produced no significant increase in L1 activity. Thus, A3B appears to restrict engineered L1 retrotransposition in a broad range of cell types, including pluripotent cells.
Collapse
Affiliation(s)
- Silke Wissing
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, California 94158, USA
| | | | | | | | | |
Collapse
|
29
|
Yabuta Y, Ohta H, Abe T, Kurimoto K, Chuma S, Saitou M. TDRD5 is required for retrotransposon silencing, chromatoid body assembly, and spermiogenesis in mice. ACTA ACUST UNITED AC 2011; 192:781-95. [PMID: 21383078 PMCID: PMC3051809 DOI: 10.1083/jcb.201009043] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Tdrd5-deficient mice develop a functional haploid genome despite spermiogenesis arrest at the round spermatid stage. The Tudor domain–containing proteins (TDRDs) are an evolutionarily conserved family of proteins involved in germ cell development. We show here that in mice, TDRD5 is a novel component of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. Tdrd5-deficient males are sterile because of spermiogenic arrest at the round spermatid stage, with occasional failure in meiotic prophase. Without TDRD5, IMCs and CBs are disorganized, with mislocalization of their key components, including TDRD1/6/7/9 and MIWI/MILI/MIWI2. In addition, Tdrd5-deficient germ cells fail to repress LINE-1 retrotransposons with DNA-demethylated promoters. Cyclic adenosine monophosphate response element modulator (CREM) and TRF2, key transcription factors for spermiogenesis, are expressed in Tdrd5-deficient round spermatids, but their targets, including Prm1/Prm2/Tnp1, are severely down-regulated, which indicates the importance of IMC/CB-mediated regulation for postmeiotic gene expression. Strikingly, Tdrd5-deficient round spermatids injected into oocytes contribute to fertile offspring, demonstrating that acquisition of a functional haploid genome may be uncoupled from TDRD5 function.
Collapse
Affiliation(s)
- Yukihiro Yabuta
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | | | | | | | | | | |
Collapse
|
30
|
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.
Collapse
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
| | | |
Collapse
|
31
|
Wang XF, Jin X, Wang X, Liu J, Feng J, Yang Q, Mu W, Shi X, Lu Z. Effects of L1-ORF2 fragments on green fluorescent protein gene expression. Genet Mol Biol 2009; 32:688-96. [PMID: 21637438 PMCID: PMC3036906 DOI: 10.1590/s1415-47572009005000068] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Accepted: 05/15/2009] [Indexed: 11/22/2022] Open
Abstract
The retrotransposon known as long interspersed nuclear element-1 (L1) is 6 kb long, although most L1s in mammalian and other eukaryotic cells are truncated. L1 contains two open reading frames, ORF1 and ORF2, that code for an RNA-binding protein and a protein with endonuclease and reverse transcriptase activities, respectively. In this work, we examined the effects of full length L1-ORF2 and ORF2 fragments on green fluorescent protein gene (GFP) expression when inserted into the pEGFP-C1 vector downstream of GFP. All of the ORF2 fragments in sense orientation inhibited GFP expression more than when in antisense orientation, which suggests that small ORF2 fragments contribute to the distinct inhibitory effects of this ORF on gene expression. These results provide the first evidence that different 280-bp fragments have distinct effects on the termination of gene transcription, and that when inserted in the antisense direction, fragment 280-9 (the 3' end fragment of ORF2) induces premature termination of transcription that is consistent with the effect of ORF2.
Collapse
Affiliation(s)
- Xiu-Fang Wang
- Hebei Key Lab of Laboratory Animal, Department of Genetics, Hebei Medical University, Shijiazhuang, Hebei Province China
| | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Belancio VP, Deininger PL, Roy-Engel AM. LINE dancing in the human genome: transposable elements and disease. Genome Med 2009; 1:97. [PMID: 19863772 PMCID: PMC2784310 DOI: 10.1186/gm97] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Transposable elements (TEs) have been consistently underestimated in their contribution to genetic instability and human disease. TEs can cause human disease by creating insertional mutations in genes, and also contributing to genetic instability through non-allelic homologous recombination and introduction of sequences that evolve into various cis-acting signals that alter gene expression. Other outcomes of TE activity, such as their potential to cause DNA double-strand breaks or to modulate the epigenetic state of chromosomes, are less fully characterized. The currently active human transposable elements are members of the non-LTR retroelement families, LINE-1, Alu (SINE), and SVA. The impact of germline insertional mutagenesis by TEs is well established, whereas the rate of post-insertional TE-mediated germline mutations and all forms of somatic mutations remain less well quantified. The number of human diseases discovered to be associated with non-allelic homologous recombination between TEs, and particularly between Alu elements, is growing at an unprecedented rate. Improvement in the technology for detection of such events, as well as the mounting interest in the research and medical communities in resolving the underlying causes of the human diseases with unknown etiology, explain this increase. Here, we focus on the most recent advances in understanding of the impact of the active human TEs on the stability of the human genome and its relevance to human disease.
Collapse
Affiliation(s)
- Victoria P Belancio
- Department of Structural and Cellular Biology, School of Medicine, Tulane Cancer Center and Tulane Center for Aging, Tulane University, SL-49 1430 Tulane Ave, New Orleans, LA 70112, USA.
| | | | | |
Collapse
|
33
|
Reuter M, Chuma S, Tanaka T, Franz T, Stark A, Pillai RS. Loss of the Mili-interacting Tudor domain-containing protein-1 activates transposons and alters the Mili-associated small RNA profile. Nat Struct Mol Biol 2009; 16:639-46. [PMID: 19465913 DOI: 10.1038/nsmb.1615] [Citation(s) in RCA: 210] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Accepted: 05/06/2009] [Indexed: 12/18/2022]
Abstract
Piwi proteins and their associated Piwi-interacting RNAs (piRNAs) are implicated in transposon silencing in the mouse germ line. There is currently little information on additional proteins in the murine Piwi complex and how they might regulate the entry of transcripts that accumulate as piRNAs in the Piwi ribonucleoprotein (piRNP). We isolated Mili-containing complexes from adult mouse testes and identified Tudor domain-containing protein-1 (Tdrd1) as a factor specifically associated with the Mili piRNP throughout spermatogenesis. Complex formation is promoted by the recognition of symmetrically dimethylated arginines at the N terminus of Mili by the tudor domains of Tdrd1. Similar to a Mili mutant, mice lacking Tdrd1 show derepression of L1 transposons accompanied by a loss of DNA methylation at their regulatory elements and delocalization of Miwi2 from the nucleus to the cytoplasm. Finally, we show that Mili piRNPs devoid of Tdrd1 accept the entry of abundant cellular transcripts into the piRNA pathway and accumulate piRNAs with a profile that is drastically different from that of the wild type. Our data suggest that Tdrd1 ensures the entry of correct transcripts into the normal piRNA pool.
Collapse
Affiliation(s)
- Michael Reuter
- European Molecular Biology Laboratory, Grenoble Outstation, France
| | | | | | | | | | | |
Collapse
|
34
|
Soper SF, van der Heijden GW, Hardiman TC, Goodheart M, Martin SL, de Boer P, Bortvin A. Mouse maelstrom, a component of nuage, is essential for spermatogenesis and transposon repression in meiosis. Dev Cell 2008; 15:285-97. [PMID: 18694567 PMCID: PMC2546488 DOI: 10.1016/j.devcel.2008.05.015] [Citation(s) in RCA: 257] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2008] [Revised: 05/19/2008] [Accepted: 05/30/2008] [Indexed: 11/20/2022]
Abstract
Tight control of transposon activity is essential for the integrity of the germline. Recently, a germ-cell-specific organelle, nuage, was proposed to play a role in transposon repression. To test this hypothesis, we disrupted a murine homolog of a Drosophila nuage protein Maelstrom. Effects on male meiotic chromosome synapsis and derepression of transposable elements (TEs) were observed. In the adult Mael(-/-) testes, LINE-1 (L1) derepression occurred at the onset of meiosis. As a result, Mael(-/-) spermatocytes were flooded with L1 ribonucleoproteins (RNPs) that accumulated in large cytoplasmic enclaves and nuclei. Mael(-/-) spermatocytes with nuclear L1 RNPs exhibited massive DNA damage and severe chromosome asynapsis even in the absence of SPO11-generated meiotic double-strand breaks. This study demonstrates that MAEL, a nuage component, is indispensable for the silencing of TEs and identifies the initiation of meiosis as an important step in TE control in the male germline.
Collapse
Affiliation(s)
- Sarah F.C. Soper
- Biology Department, Johns Hopkins University, Baltimore, MD 21218, USA
| | | | - Tara C. Hardiman
- Department of Embryology, Carnegie Institution of Washington, Baltimore, MD 21218, USA
| | - Mary Goodheart
- Howard Hughes Medical Institute, Whitehead Institute, and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Sandra L. Martin
- Department of Cell and Developmental Biology and Molecular Biology Program, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Peter de Boer
- Department of Obstetrics and Gynaecology, Radboud University Nijmegen Medical Centre, 6500 HB Nijmegen, The Netherlands
| | - Alex Bortvin
- Department of Embryology, Carnegie Institution of Washington, Baltimore, MD 21218, USA
| |
Collapse
|
35
|
Niewiadomska AM, Tian C, Tan L, Wang T, Sarkis PTN, Yu XF. Differential inhibition of long interspersed element 1 by APOBEC3 does not correlate with high-molecular-mass-complex formation or P-body association. J Virol 2007; 81:9577-83. [PMID: 17582006 PMCID: PMC1951403 DOI: 10.1128/jvi.02800-06] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Accepted: 06/08/2007] [Indexed: 02/06/2023] Open
Abstract
The human cytidine deaminase APOBEC3G (A3G) and other APOBEC3 proteins exhibit differential inhibitory activities against diverse endogenous retroelements and retroviruses, including Vif-deficient human immunodeficiency virus type 1. The potential inhibitory activity of human APOBEC proteins against long interspersed element 1 (LINE-1) has not been fully evaluated. Here, we demonstrate inhibition of LINE-1 by multiple human APOBEC3 cytidine deaminases, including previously unreported activity for A3DE and A3G. More ancient members of APOBEC, cytidine deaminases AID and APOBEC2, had no detectable activity against LINE-1. A3A, which did not form high-molecular-mass (HMM) complexes and interacted poorly with P bodies, was the most potent inhibitor of LINE-1. A3A specifically recognizes LINE-1 RNA but not the other cellular RNAs tested. However, in the presence of LINE-1, A3A became associated with HMM complexes containing LINE-1 RNA. The ability of A3A to recognize LINE-1 RNA required its catalytic domain and was important for its LINE-1 suppression. Although the mechanism of LINE-1 restriction did not seem to involve DNA editing, A3A inhibited the accumulation of nascent LINE-1 DNA, suggesting interference with LINE-1 reverse transcription and/or integration or intracellular movement of LINE-1 ribonucleoprotein. Thus, association with P bodies or cellular HMM complexes could not predict the potency of APOBEC3 anti-LINE-1 activities. The catalytic domain of APOBEC3 proteins may be important for proper folding and target factors such as RNA or protein interaction in addition to cytidine deamination.
Collapse
Affiliation(s)
- Anna Maria Niewiadomska
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | | | | | | | | | | |
Collapse
|
36
|
Goodier JL, Zhang L, Vetter MR, Kazazian HH. LINE-1 ORF1 protein localizes in stress granules with other RNA-binding proteins, including components of RNA interference RNA-induced silencing complex. Mol Cell Biol 2007; 27:6469-83. [PMID: 17562864 PMCID: PMC2099616 DOI: 10.1128/mcb.00332-07] [Citation(s) in RCA: 210] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
LINE-1 retrotransposons constitute one-fifth of human DNA and have helped shape our genome. A full-length L1 encodes a 40-kDa RNA-binding protein (ORF1p) and a 150-kDa protein (ORF2p) with endonuclease and reverse transcriptase activities. ORF1p is distinctive in forming large cytoplasmic foci, which we identified as cytoplasmic stress granules. A phylogenetically conserved central region of the protein is critical for wild-type localization and retrotransposition. Yeast two-hybrid screens revealed several RNA-binding proteins that coimmunoprecipitate with ORF1p and colocalize with ORF1p in foci. Two of these proteins, YB-1 and hnRNPA1, were previously reported in stress granules. We identified additional proteins associated with stress granules, including DNA-binding protein A, 9G8, and plasminogen activator inhibitor RNA-binding protein 1 (PAI-RBP1). PAI-RBP1 is a homolog of VIG, a part of the Drosophila melanogaster RNA-induced silencing complex (RISC). Other RISC components, including Ago2 and FMRP, also colocalize with PAI-RBP1 and ORF1p. We suggest that targeting ORF1p, and possibly the L1 RNP, to stress granules is a mechanism for controlling retrotransposition and its associated genetic and cellular damage.
Collapse
Affiliation(s)
- John L Goodier
- Dept. of Genetics, University of Pennsylvania School of Medicine, Rm. 515 CRB, 415 Curie Blvd., Philadelphia, PA 19104, USA.
| | | | | | | |
Collapse
|
37
|
Li PWL, Li J, Timmerman SL, Krushel LA, Martin SL. The dicistronic RNA from the mouse LINE-1 retrotransposon contains an internal ribosome entry site upstream of each ORF: implications for retrotransposition. Nucleic Acids Res 2006; 34:853-64. [PMID: 16464823 PMCID: PMC1361618 DOI: 10.1093/nar/gkj490] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Most eukaryotic mRNAs are monocistronic and translated by cap-dependent initiation. LINE-1 RNA is exceptional because it is naturally dicistronic, encoding two proteins essential for retrotransposition, ORF1p and ORF2p. Here, we show that sequences upstream of ORF1 and ORF2 in mouse L1 function as internal ribosome entry sites (IRESes). Deletion analysis of the ORF1 IRES indicates that RNA structure is critical for its function. Conversely, the ORF2 IRES localizes to 53 nt near the 3′ end of ORF1, and appears to depend upon sequence rather than structure. The 40 nt intergenic region (IGR) is not essential for ORF2 IRES function or retrotransposition. Because of strong cis-preference for both proteins during L1 retrotransposition, correct stoichiometry of the two proteins can only be achieved post-transcriptionally. Although the precise stoichiometry is unknown, the retrotransposition intermediate likely contains hundreds of ORF1ps for every ORF2p, together with one L1 RNA. IRES-mediated translation initiation is a well-established mechanism of message-specific regulation, hence, unique mechanisms for the recognition and control of these two IRESes in the L1 RNA could explain differences in translational efficiency of ORF1 and ORF2. In addition, translational regulation may provide an additional layer of control on L1 retrotransposition efficiency, thereby protecting the integrity of the genome.
Collapse
Affiliation(s)
- Patrick Wai-Lun Li
- Cell and Developmental Biology, University of Colorado School of Medicine12801 E. 17th Avenue, Aurora, CO 80010, USA
- Human Medical Genetics Program, University of Colorado School of Medicine12801 E. 17th Avenue, Aurora, CO 80010, USA
| | - Jinfang Li
- Cell and Developmental Biology, University of Colorado School of Medicine12801 E. 17th Avenue, Aurora, CO 80010, USA
| | - Stephanie L. Timmerman
- Biochemistry and Molecular Genetics, University of Colorado School of Medicine12801 E. 17th Avenue, Aurora, CO 80010, USA
| | - Les A. Krushel
- Program in Molecular Biology, University of Colorado School of Medicine12801 E. 17th Avenue, Aurora, CO 80010, USA
- Department of Pharmacology, University of Colorado School of Medicine12801 E. 17th Avenue, Aurora, CO 80010, USA
| | - Sandra L. Martin
- Cell and Developmental Biology, University of Colorado School of Medicine12801 E. 17th Avenue, Aurora, CO 80010, USA
- Program in Molecular Biology, University of Colorado School of Medicine12801 E. 17th Avenue, Aurora, CO 80010, USA
- To whom correspondence should be addressed. Tel: +1 303 724 3467; Fax: +1 303 724 3420;
| |
Collapse
|
38
|
Sciamanna I, Landriscina M, Pittoggi C, Quirino M, Mearelli C, Beraldi R, Mattei E, Serafino A, Cassano A, Sinibaldi-Vallebona P, Garaci E, Barone C, Spadafora C. Inhibition of endogenous reverse transcriptase antagonizes human tumor growth. Oncogene 2005; 24:3923-31. [PMID: 15806170 DOI: 10.1038/sj.onc.1208562] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Undifferentiated cells and embryos express high levels of endogenous non-telomerase reverse transcriptase (RT) of retroposon/retroviral origin. We previously found that RT inhibitors modulate cell growth and differentiation in several cell lines. We have now sought to establish whether high levels of RT activity are directly linked to cell transformation. To address this possibility, we have employed two different approaches to inhibit RT activity in melanoma and prostate carcinoma cell lines: pharmacological inhibition by two characterized RT inhibitors, nevirapine and efavirenz, and downregulation of expression of RT-encoding LINE-1 elements by RNA interference (RNAi). Both treatments reduced proliferation, induced morphological differentiation and reprogrammed gene expression. These features are reversible upon discontinuation of the anti-RT treatment, suggesting that RT contributes to an epigenetic level of control. Most importantly, inhibition of RT activity in vivo antagonized tumor growth in animal experiments. Moreover, pretreatment with RT inhibitors attenuated the tumorigenic phenotype of prostate carcinoma cells inoculated in nude mice. Based on these data, the endogenous RT can be regarded as an epigenetic regulator of cell differentiation and proliferation and may represent a novel target in cancer therapy.
Collapse
Affiliation(s)
- Ilaria Sciamanna
- Istituto Superiore di Sanità, Viale Regina Elena 299, Via del Castro Laurenziano 25, 00161 Rome, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Wang Q, Carmichael GG. Effects of length and location on the cellular response to double-stranded RNA. Microbiol Mol Biol Rev 2004; 68:432-52, table of contents. [PMID: 15353564 PMCID: PMC515255 DOI: 10.1128/mmbr.68.3.432-452.2004] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Since double-stranded RNA (dsRNA) has not until recently generally been thought to be deliberately expressed in cells, it has commonly been assumed that the major source of cellular dsRNA is viral infections. In this view, the cellular responses to dsRNA would be natural and perhaps ancient antiviral responses. While the cell may certainly react to some dsRNAs as an antiviral response, this does not represent the only response or even, perhaps, the major one. A number of recent observations have pointed to the possibility that dsRNA molecules are not seen only as evidence of viral infection or recognized for degradation because they cannot be translated. In some instances they may also play important roles in normal cell growth and function. The purpose of this review is to outline our current understanding of the fate of dsRNA in cells, with a focus on the apparent fact that their fates and functions appear to depend critically not only on where in the cell dsRNA molecules are found, but also on how long they are and perhaps on how abundant they are.
Collapse
Affiliation(s)
- Qiaoqiao Wang
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, CT 06030-3301, USA
| | | |
Collapse
|
40
|
Matsumoto T, Takahashi H, Fujiwara H. Targeted nuclear import of open reading frame 1 protein is required for in vivo retrotransposition of a telomere-specific non-long terminal repeat retrotransposon, SART1. Mol Cell Biol 2004; 24:105-22. [PMID: 14673147 PMCID: PMC303349 DOI: 10.1128/mcb.24.1.105-122.2004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Non-long terminal repeat (non-LTR) retrotransposons, most of which carry two open reading frames (ORFs), are abundant mobile elements that are distributed widely among eukaryotes. ORF2 encodes enzymatic domains, such as reverse transcriptase, that are conserved in all retroelements, but the functional roles of ORF1 in vivo are little understood. We show with green fluorescent protein-ORF1 fusion proteins that the ORF1 proteins of SART1, a telomeric repeat-specific non-LTR retrotransposon in Bombyx mori, are transported into the nucleus to produce a dotted localization pattern. Nuclear localization signals N1 (RRKR) and N2 (PSKRGRG) at the N terminus and a highly basic region in the center of SART1 ORF1 are involved in nuclear import and the dotted localization pattern in the nucleus, respectively. An in vivo retrotransposition assay clarified that at least three ORF1 domains, N1/N2, the central basic domain, and CCHC zinc fingers are required for SART1 retrotransposition. The nuclear import activity of SART1 ORF1 makes it clear that the ORF1 proteins of non-LTR retrotransposons work mainly in the nucleus, in contrast to the cytoplasmic action of Gag proteins of LTR elements. The functional domains found here in SART1 ORF1 will be useful for developing a more efficient and target-specific LINE-based gene delivery vector.
Collapse
Affiliation(s)
- Takumi Matsumoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | | | | |
Collapse
|
41
|
Martin SL, Branciforte D, Keller D, Bain DL. Trimeric structure for an essential protein in L1 retrotransposition. Proc Natl Acad Sci U S A 2003; 100:13815-20. [PMID: 14615577 PMCID: PMC283504 DOI: 10.1073/pnas.2336221100] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2003] [Indexed: 02/01/2023] Open
Abstract
Two proteins are encoded by the mammalian retrotransposon long interspersed nuclear element 1 (LINE-1 or L1); both are essential for retrotransposition. The function of the protein encoded by the 5'-most ORF, ORF1p, is incompletely understood, although the ORF1p from mouse L1 is known to bind single-stranded nucleic acids and function as a nucleic acid chaperone. ORF1p self-associates by means of a long coiled-coil domain in the N-terminal region of the protein, and the basic, C-terminal region (C-1/3 domain) contains the nucleic acid binding activity. The full-length and C-1/3 domains of ORF1p were purified to near homogeneity then analyzed by gel filtration chromatography and analytical ultracentrifugation. Both proteins were structurally homogeneous and asymmetric in solution, with the full-length version forming a stable trimer and the C-1/3 domain remaining a monomer. Examination of the full-length protein by atomic force microscopy revealed an asymmetric dumbbell shape, congruent with the chromatography and ultracentrifugation results. These structural features are compatible with the nucleic acid binding and chaperone activities of L1 ORF1p and offer further insight into the functions of this unique protein during LINE-1 retrotransposition.
Collapse
Affiliation(s)
- Sandra L Martin
- Department of Cell and Developmental Biology and Program in Molecular Biology, University of Colorado School of Medicine, 4200 East Ninth Avenue, Denver, CO 80262, USA.
| | | | | | | |
Collapse
|
42
|
Mangiacasale R, Pittoggi C, Sciamanna I, Careddu A, Mattei E, Lorenzini R, Travaglini L, Landriscina M, Barone C, Nervi C, Lavia P, Spadafora C. Exposure of normal and transformed cells to nevirapine, a reverse transcriptase inhibitor, reduces cell growth and promotes differentiation. Oncogene 2003; 22:2750-61. [PMID: 12747369 DOI: 10.1038/sj.onc.1206354] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Endogenous, nontelomeric reverse transcriptase (RT) is encoded by two classes of repeated elements: retrotransposons and endogenous retroviruses. Expression of RT-coding genes is generally repressed in differentiated nonpathological tissues, yet is active in the mammalian germ line, embryonic tissues and tumor cells. Nevirapine is a non-nucleoside RT inhibitor with a well-characterized inhibitory activity on RT enzymes of retroviral origin. Here, we show that nevirapine is also an effective inhibitor of the endogenous RT in murine and human cell lines. In addition, progenitor and transformed cells undergo a significant reduction in the rate of cell growth upon exposure to nevirapine. This is accompanied by the onset of differentiation, as depicted in F9 and C2C7 progenitor cells cultures in which nevirapine triggers the expression of differentiation-specific markers. Consistent with this, an extensive reprogramming of cell cycle gene expression was depicted in nevirapine-treated F9 cultures. Furthermore, nevirapine exposure rescued the differentiation block present in acute myeloid leukemia (AML) cell lines and primary blasts from two AML patients, as indicated by morphological, functional and immunophenotypic assays. The finding that an RT inhibitor can modulate cell proliferation and differentiation suggests that RT may represent a novel target in the development of therapeutical approaches to neoplasia.
Collapse
|
43
|
Martin SL, Bushman FD. Nucleic acid chaperone activity of the ORF1 protein from the mouse LINE-1 retrotransposon. Mol Cell Biol 2001; 21:467-75. [PMID: 11134335 PMCID: PMC86601 DOI: 10.1128/mcb.21.2.467-475.2001] [Citation(s) in RCA: 262] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Non-LTR retrotransposons such as L1 elements are major components of the mammalian genome, but their mechanism of replication is incompletely understood. Like retroviruses and LTR-containing retrotransposons, non-LTR retrotransposons replicate by reverse transcription of an RNA intermediate. The details of cDNA priming and integration, however, differ between these two classes. In retroviruses, the nucleocapsid (NC) protein has been shown to assist reverse transcription by acting as a "nucleic acid chaperone," promoting the formation of the most stable duplexes between nucleic acid molecules. A protein-coding region with an NC-like sequence is present in most non-LTR retrotransposons, but no such sequence is evident in mammalian L1 elements or other members of its class. Here we investigated the ORF1 protein from mouse L1 and found that it does in fact display nucleic acid chaperone activities in vitro. L1 ORF1p (i) promoted annealing of complementary DNA strands, (ii) facilitated strand exchange to form the most stable hybrids in competitive displacement assays, and (iii) facilitated melting of an imperfect duplex but stabilized perfect duplexes. These findings suggest a role for L1 ORF1p in mediating nucleic acid strand transfer steps during L1 reverse transcription.
Collapse
Affiliation(s)
- S L Martin
- Department of Cellular and Structural Biology, University of Colorado School of Medicine, Denver, Colorado 80262, USA.
| | | |
Collapse
|
44
|
Fitzsimmons SP, Rotz BT, Shapiro MA. Asymmetric Contribution to Ig Repertoire Diversity by Vκ Exons: Differences in the Utilization of Vκ10 Exons. THE JOURNAL OF IMMUNOLOGY 1998. [DOI: 10.4049/jimmunol.161.5.2290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract
The mouse has approximately 140 germline Vκ genes, and functional Vκ exons are expressed at roughly equivalent levels in the preimmune repertoire. We have examined the expression of individual members of the Vκ10 family. Vκ10A and Vκ10B genes have been utilized in numerous hybridomas and myelomas, while Vκ10C has not. In this study, we have cloned the Vκ10C gene and shown that it is structurally functional, has the expected promoter elements and recombination signal sequences, and that it is capable of recombination. Vκ10C mRNA, however, is present at levels at least 1000-fold lower than Vκ10A and Vκ10B in adult spleens. While there are no sequence differences in the octamer or TATA box between Vκ10C and Vκ10A, there are three nucleotide changes in the promoter region. These promoters equally drive the expression of a reporter gene in B cells or plasma cells, but the Vκ10A promoter is able to drive expression in pre-B cell lines significantly better than the Vκ10C promoter (p < 0.05). Vκ10C rearrangements can be detected in bone marrow and splenic DNA. Therefore, the lack of Vκ10C expression may reflect the inability of Vκ10C-rearranged cells to undergo positive or negative selection. Our results suggest that the available Ab repertoire is shaped not only by the number of structurally functional genes, but also by the ability of assembled genes to be expressed at critical points during B cell maturation.
Collapse
Affiliation(s)
- Sean P. Fitzsimmons
- Center for Biologics Evaluation and Research, Food and Drug Administration, Rockville, MD 20892
| | - Benjamin T. Rotz
- Center for Biologics Evaluation and Research, Food and Drug Administration, Rockville, MD 20892
| | - Marjorie A. Shapiro
- Center for Biologics Evaluation and Research, Food and Drug Administration, Rockville, MD 20892
| |
Collapse
|
45
|
Clements AP, Singer MF. The human LINE-1 reverse transcriptase:effect of deletions outside the common reverse transcriptase domain. Nucleic Acids Res 1998; 26:3528-35. [PMID: 9671814 PMCID: PMC147723 DOI: 10.1093/nar/26.15.3528] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Heterologous expression of human LINE-1 ORF2 in yeast yielded a single polypeptide (Mr145 000) which reacted with specific antibodies and co-purified with a reverse transcriptase activity not present in the host cells. Various deletion derivatives of the ORF2 polypeptide were also synthesized. Reverse transcriptase assays using synthetic polynucleotides as template and primer revealed that ORF2 protein missing a significant portion of the N-terminal endonuclease domain still retains some activity. Deletion of the C-terminal cysteine-rich motif reduces activity only a small amount. Three non-overlapping deletions spanning 144 amino acids just N-terminal to the common polymerase domain of the ORF2 protein were analyzed for their effect on reverse transcriptase activity; this region contains the previously-noted conserved Z motif. The two deletions most proximal to the polymerase domain eliminate activity while the third, most-distal deletion had no effect. An inactive enzyme was also produced by substitution of two different amino acids in a highly-conserved octapeptide sequence, Z8, located within the region removed to make the deletion most proximal to the polymerase domain; substitution of a third had no effect. We conclude that the octapeptide sequence and neighboring amino acids in the Z region are essential for reverse transcriptase activity, while the endonuclease and cysteine-rich domains are not absolutely required.
Collapse
Affiliation(s)
- A P Clements
- Laboratory of Biochemistry, National Cancer Institute, Building 37, Room 4A-01, Bethesda, MD 20892, USA
| | | |
Collapse
|
46
|
Hohjoh H, Singer MF. Sequence-specific single-strand RNA binding protein encoded by the human LINE-1 retrotransposon. EMBO J 1997; 16:6034-43. [PMID: 9312060 PMCID: PMC1170233 DOI: 10.1093/emboj/16.19.6034] [Citation(s) in RCA: 160] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Previous experiments using human teratocarcinoma cells indicated that p40, the protein encoded by the first open reading frame (ORF) of the human LINE-1 (L1Hs) retrotransposon, occurs in a large cytoplasmic ribonucleoprotein complex in direct association with L1Hs RNA(s), the p40 RNP complex. We have now investigated the interaction between partially purified p40 and L1Hs RNA in vitro using an RNA binding assay dependent on co-immunoprecipitation of p40 and bound RNA. These experiments identified two p40 binding sites on the full-length sense strand L1Hs RNA. Both sites are in the second ORF of the 6000 nt RNA: site A between residues 1999 and 2039 and site B between residues 4839 and 4875. The two RNA segments share homologous regions. Experiments involving UV cross-linking followed by immunoprecipitation indicate that p40 in the in vitro complex is directly associated with L1Hs RNA, as it is in the p40 RNP complex found in teratocarcinoma cells. Binding and competition experiments demonstrate that p40 binds to single-stranded RNA containing a p40 binding site, but not to single-stranded or double-stranded DNA, double-stranded RNA or a DNA-RNA hybrid containing a binding site sequence. Thus, p40 appears to be a sequence-specific, single-strand RNA binding protein.
Collapse
Affiliation(s)
- H Hohjoh
- Laboratory of Biochemistry, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | |
Collapse
|
47
|
Kolosha VO, Martin SL. In vitro properties of the first ORF protein from mouse LINE-1 support its role in ribonucleoprotein particle formation during retrotransposition. Proc Natl Acad Sci U S A 1997; 94:10155-60. [PMID: 9294179 PMCID: PMC23331 DOI: 10.1073/pnas.94.19.10155] [Citation(s) in RCA: 118] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
LINEs are transposable elements, widely distributed among eukaryotes, that move via reverse transcription of an RNA intermediate. Mammalian LINEs have two ORFs (ORF1 and ORF2). The proteins encoded by these ORFs play important roles in the retrotransposition process. Although the predicted amino acid sequence of ORF1 is not closely related to any known proteins, it is highly basic; thus, it has long been hypothesized that ORF1 protein functions to bind LINE-1 (L1) RNA during retrotransposition. Cofractionation of ORF1 protein and L1 RNA in extracts from both mouse and human embryonal carcinoma cells indicated that ORF1 protein binds L1 RNA, forming a ribonucleoprotein particle. Based on UV crosslinking and electrophoretic mobility-shift assays using purified components, we demonstrate here that the ORF1 protein encoded by mouse L1 binds nucleic acids with a strong preference for RNA and other single-stranded nucleic acids. Furthermore, multiple copies of ORF1 protein appear to bind single-stranded nucleic acid in a manner suggesting positive cooperativity; such binding characteristics are likely to be facilitated by the protein-protein interactions detected among molecules of ORF1 polypeptide by coimmunoprecipitation. These observations are consistent with the formation of ribonucleoprotein particles containing L1 RNA and ORF1 protein and provide additional evidence for the role of ORF1 protein during retrotransposition of L1.
Collapse
Affiliation(s)
- V O Kolosha
- Department of Cellular and Structural Biology, Box B-111, University of Colorado School of Medicine, 4200 East Ninth Avenue, Denver, CO 80262, USA
| | | |
Collapse
|
48
|
Pont-Kingdon G, Chi E, Christensen S, Carroll D. Ribonucleoprotein formation by the ORF1 protein of the non-LTR retrotransposon Tx1L in Xenopus oocytes. Nucleic Acids Res 1997; 25:3088-94. [PMID: 9224609 PMCID: PMC146839 DOI: 10.1093/nar/25.15.3088] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The Tx1L elements constitute a family of site-specific non-LTR retrotransposons found in the genome of the frog Xenopus laevis . The elements have two open reading frames (ORFs) with homology to proteins of retroviruses and other retroelements. This study demonstrates an expected activity of one of the element-encoded proteins. The RNA binding properties of ORF1p, the product of the first ORF of Tx1L, were examined after expression from RNA injected into Xenopus oocytes. Using sucrose gradient sedimentation and non-denaturing gel electrophoresis, we show that ORF1p associates with RNA in cytoplasmic ribonucleoprotein (RNP) particles. Discrete RNPs are formed with well-defined mobilities. The ORF1p RNPs are distinct from endogenous RNPs that contain stored oocyte mRNAs and two specific endogenous mRNAs do not become associated with ORF1p. ORF1p appears to be capable of associating with its own mRNA and with other injected RNAs, independent of specific recognition sequences. Although nuclear localization of ORF1p was anticipated, based both on the supposed mechanism of transposition and on the presence of a potential nuclear localization signal, no significant fraction of the protein was found in the oocyte nucleus. Nonetheless, the RNA binding capability of ORF1p is consistent with the proposed model for transposition of non-LTR retrotransposons.
Collapse
Affiliation(s)
- G Pont-Kingdon
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84132, USA.
| | | | | | | |
Collapse
|
49
|
Trelogan SA, Martin SL. Tightly regulated, developmentally specific expression of the first open reading frame from LINE-1 during mouse embryogenesis. Proc Natl Acad Sci U S A 1995; 92:1520-4. [PMID: 7878012 PMCID: PMC42551 DOI: 10.1073/pnas.92.5.1520] [Citation(s) in RCA: 133] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
LINE-1 (L1) has achieved its status as a middle repetitive DNA family in mammalian genomes by duplicative transposition. Although transposition may occur in any cell type, expression and transposition of a full-length functional element in the germ line are necessary for evolutionarily significant propagation of L1. An immunohistochemical analysis of adult mouse ovaries and mouse postimplantation embryos revealed expression of L1 open reading frame 1 in the germ line as well as in steroidogenic tissues. These results demonstrate that L1 expression is controlled by a tightly regulated temporal and spatial program of events during development and imply that multiple loci of L1 in the mouse genome are active for expression.
Collapse
Affiliation(s)
- S A Trelogan
- University of Colorado Health Sciences Center, Department of Cellular and Structural Biology, Denver 80262
| | | |
Collapse
|
50
|
Developmental and cell type specificity of LINE-1 expression in mouse testis: implications for transposition. Mol Cell Biol 1994. [PMID: 8139560 DOI: 10.1128/mcb.14.4.2584] [Citation(s) in RCA: 147] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The LINE-1, or L1, family of interspersed repeated DNA constitutes roughly 10% of the mammalian genome. Its abundance is due to duplicative transposition via an RNA intermediate, L1-encoded proteins, and reverse transcription. Although, in principle, transposition may occur in any cell type, expression and transposition of a full-length functional element in the germ line are necessary to explain the evolutionary genetics of L1. We have found differential expression of L1 protein and RNA in germ and somatic cells of the mouse testis during development. Of particular interest is the coexpression of full-length, sense-strand L1 RNA and L1-encoded protein in leptotene and zygotene spermatocytes at postnatal day 14 of development. Expression in meiotic prophase precedes the strand breakage that occurs during chromosomal recombination; this offers an avenue for L1 insertion into new locations in chromosomal DNA in a cell type that ensures L1 propagation in future generations.
Collapse
|