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Abraham LN, Oggenfuss U, Croll D. Population-level transposable element expression dynamics influence trait evolution in a fungal crop pathogen. mBio 2024; 15:e0284023. [PMID: 38349152 PMCID: PMC10936205 DOI: 10.1128/mbio.02840-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/22/2024] [Indexed: 03/14/2024] Open
Abstract
The rapid adaptive evolution of microbes is driven by strong selection pressure acting on genetic variation. How adaptive genetic variation is generated within species and how such variation influences phenotypic trait expression is often not well understood though. We focused on the recent activity of transposable elements (TEs) using deep population genomics and transcriptomics analyses of a fungal plant pathogen with a highly active content of TEs in the genome. Zymoseptoria tritici causes one of the most damaging diseases on wheat, with recent adaptation to the host and environment being facilitated by TE-associated mutations. We obtained genomic and RNA-sequencing data from 146 isolates collected from a single wheat field. We established a genome-wide map of TE insertion polymorphisms in the population by analyzing recent TE insertions among individuals. We quantified the locus-specific transcription of individual TE copies and found considerable population variation at individual TE loci in the population. About 20% of all TE copies show transcription in the genome suggesting that genomic defenses such as repressive epigenetic marks and repeat-induced polymorphisms are at least partially ineffective at preventing the proliferation of TEs in the genome. A quarter of recent TE insertions are associated with expression variation of neighboring genes providing broad potential to influence trait expression. We indeed found that TE insertions are likely responsible for variation in virulence on the host and potentially diverse components of secondary metabolite production. Our large-scale transcriptomics study emphasizes how TE-derived polymorphisms segregate even in individual microbial populations and can broadly underpin trait variation in pathogens.IMPORTANCEPathogens can rapidly adapt to new hosts, antimicrobials, or changes in the environment. Adaptation arises often from mutations in the genome; however, how such variation is generated remains poorly understood. We investigated the most dynamic regions of the genome of Zymoseptoria tritici, a major fungal pathogen of wheat. We focused on the transcription of transposable elements. A large proportion of the transposable elements not only show signatures of potential activity but are also variable within a single population of the pathogen. We find that this variation in activity is likely influencing many important traits of the pathogen. Hence, our work provides insights into how a microbial species can adapt over the shortest time periods based on the activity of transposable elements.
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Affiliation(s)
- Leen Nanchira Abraham
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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2
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Chen J, Basting PJ, Han S, Garfinkel DJ, Bergman CM. Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast. Mob DNA 2023; 14:8. [PMID: 37452430 PMCID: PMC10347736 DOI: 10.1186/s13100-023-00296-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/09/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Many computational methods have been developed to detect non-reference transposable element (TE) insertions using short-read whole genome sequencing data. The diversity and complexity of such methods often present challenges to new users seeking to reproducibly install, execute, or evaluate multiple TE insertion detectors. RESULTS We previously developed the McClintock meta-pipeline to facilitate the installation, execution, and evaluation of six first-generation short-read TE detectors. Here, we report a completely re-implemented version of McClintock written in Python using Snakemake and Conda that improves its installation, error handling, speed, stability, and extensibility. McClintock 2 now includes 12 short-read TE detectors, auxiliary pre-processing and analysis modules, interactive HTML reports, and a simulation framework to reproducibly evaluate the accuracy of component TE detectors. When applied to the model microbial eukaryote Saccharomyces cerevisiae, we find substantial variation in the ability of McClintock 2 components to identify the precise locations of non-reference TE insertions, with RelocaTE2 showing the highest recall and precision in simulated data. We find that RelocaTE2, TEMP, TEMP2 and TEBreak provide consistent estimates of [Formula: see text]50 non-reference TE insertions per strain and that Ty2 has the highest number of non-reference TE insertions in a species-wide panel of [Formula: see text]1000 yeast genomes. Finally, we show that best-in-class predictors for yeast applied to resequencing data have sufficient resolution to reveal a dyad pattern of integration in nucleosome-bound regions upstream of yeast tRNA genes for Ty1, Ty2, and Ty4, allowing us to extend knowledge about fine-scale target preferences revealed previously for experimentally-induced Ty1 insertions to spontaneous insertions for other copia-superfamily retrotransposons in yeast. CONCLUSION McClintock ( https://github.com/bergmanlab/mcclintock/ ) provides a user-friendly pipeline for the identification of TEs in short-read WGS data using multiple TE detectors, which should benefit researchers studying TE insertion variation in a wide range of different organisms. Application of the improved McClintock system to simulated and empirical yeast genome data reveals best-in-class methods and novel biological insights for one of the most widely-studied model eukaryotes and provides a paradigm for evaluating and selecting non-reference TE detectors in other species.
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Affiliation(s)
- Jingxuan Chen
- Institute of Bioinformatics, University of Georgia, Athens, GA USA
| | | | - Shunhua Han
- Institute of Bioinformatics, University of Georgia, Athens, GA USA
| | - David J. Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA USA
| | - Casey M. Bergman
- Institute of Bioinformatics, University of Georgia, Athens, GA USA
- Department of Genetics, University of Georgia, Athens, GA USA
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3
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Nguyen PQ, Huecas S, Asif-Laidin A, Plaza-Pegueroles A, Capuzzi B, Palmic N, Conesa C, Acker J, Reguera J, Lesage P, Fernández-Tornero C. Structural basis of Ty1 integrase tethering to RNA polymerase III for targeted retrotransposon integration. Nat Commun 2023; 14:1729. [PMID: 36977686 PMCID: PMC10050235 DOI: 10.1038/s41467-023-37109-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
The yeast Ty1 retrotransposon integrates upstream of genes transcribed by RNA polymerase III (Pol III). Specificity of integration is mediated by an interaction between the Ty1 integrase (IN1) and Pol III, currently uncharacterized at the atomic level. We report cryo-EM structures of Pol III in complex with IN1, revealing a 16-residue segment at the IN1 C-terminus that contacts Pol III subunits AC40 and AC19, an interaction that we validate by in vivo mutational analysis. Binding to IN1 associates with allosteric changes in Pol III that may affect its transcriptional activity. The C-terminal domain of subunit C11, involved in RNA cleavage, inserts into the Pol III funnel pore, providing evidence for a two-metal mechanism during RNA cleavage. Additionally, ordering next to C11 of an N-terminal portion from subunit C53 may explain the connection between these subunits during termination and reinitiation. Deletion of the C53 N-terminal region leads to reduced chromatin association of Pol III and IN1, and a major fall in Ty1 integration events. Our data support a model in which IN1 binding induces a Pol III configuration that may favor its retention on chromatin, thereby improving the likelihood of Ty1 integration.
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Affiliation(s)
- Phong Quoc Nguyen
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040, Madrid, Spain
- Aix-Marseille Université, CNRS, AFMB UMR 7257, 13288, Marseille, France
| | - Sonia Huecas
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040, Madrid, Spain
| | - Amna Asif-Laidin
- Université Paris Cité, IRSL, Inserm, U944, CNRS, UMR7212, 75010, Paris, France
| | | | - Beatrice Capuzzi
- Université Paris Cité, IRSL, Inserm, U944, CNRS, UMR7212, 75010, Paris, France
| | - Noé Palmic
- Université Paris Cité, IRSL, Inserm, U944, CNRS, UMR7212, 75010, Paris, France
| | - Christine Conesa
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Joël Acker
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Juan Reguera
- Aix-Marseille Université, CNRS, AFMB UMR 7257, 13288, Marseille, France
- INSERM, AFMB UMR7257, 13288, Marseille, France
| | - Pascale Lesage
- Université Paris Cité, IRSL, Inserm, U944, CNRS, UMR7212, 75010, Paris, France.
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4
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Chen J, Basting PJ, Han S, Garfinkel DJ, Bergman CM. Reproducible evaluation of short-read transposable element detectors and species-wide data mining of insertion patterns in yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.528343. [PMID: 36824955 PMCID: PMC9948991 DOI: 10.1101/2023.02.13.528343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Background Many computational methods have been developed to detect non-reference transposable element (TE) insertions using short-read whole genome sequencing data. The diversity and complexity of such methods often present challenges to new users seeking to reproducibly install, execute or evaluate multiple TE insertion detectors. Results We previously developed the McClintock meta-pipeline to facilitate the installation, execution, and evaluation of six first-generation short-read TE detectors. Here, we report a completely re-implemented version of McClintock written in Python using Snakemake and Conda that improves its installation, error handling, speed, stability, and extensibility. McClintock 2 now includes 12 short-read TE detectors, auxiliary pre-processing and analysis modules, interactive HTML reports, and a simulation framework to reproducibly evaluate the accuracy of component TE detectors. When applied to the model microbial eukaryote Saccharomyces cerevisiae , we find substantial variation in the ability of McClintock 2 components to identify the precise locations of non-reference TE insertions, with RelocaTE2 showing the highest recall and precision in simulated data. We find that RelocaTE2, TEMP, TEMP2 and TEBreak provide a consistent and biologically meaningful view of non-reference TE insertions in a species-wide panel of ∼ 1000 yeast genomes, as evaluated by coverage-based abundance estimates and expected patterns of tRNA promoter targeting. Finally, we show that best-in-class predictors for yeast have sufficient resolution to reveal a dyad pattern of integration in nucleosome-bound regions upstream of yeast tRNA genes for Ty1, Ty2, and Ty4, allowing us to extend knowledge aboutfine-scale target preferences first revealed experimentally for Ty1 to natural insertions and related copia -superfamily retrotransposons in yeast. Conclusion McClintock ( https://github.com/bergmanlab/mcclintock/ ) provides a user-friendly pipeline for the identification of TEs in short-read WGS data using multiple TE detectors, which should benefit researchers studying TE insertion variation in a wide range of different organisms. Application of the improved McClintock system to simulated and empirical yeast genome data reveals best-in-class methods and novel biological insights for one of the most widely-studied model eukaryotes and provides a paradigm for evaluating and selecting non-reference TE detectors for other species.
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5
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Barkova A, Adhya I, Conesa C, Asif-Laidin A, Bonnet A, Rabut E, Chagneau C, Lesage P, Acker J. A proteomic screen of Ty1 integrase partners identifies the protein kinase CK2 as a regulator of Ty1 retrotransposition. Mob DNA 2022; 13:26. [PMCID: PMC9673352 DOI: 10.1186/s13100-022-00284-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/13/2022] [Indexed: 11/19/2022] Open
Abstract
Abstract
Background
Transposable elements are ubiquitous and play a fundamental role in shaping genomes during evolution. Since excessive transposition can be mutagenic, mechanisms exist in the cells to keep these mobile elements under control. Although many cellular factors regulating the mobility of the retrovirus-like transposon Ty1 in Saccharomyces cerevisiae have been identified in genetic screens, only very few of them interact physically with Ty1 integrase (IN).
Results
Here, we perform a proteomic screen to establish Ty1 IN interactome. Among the 265 potential interacting partners, we focus our study on the conserved CK2 kinase. We confirm the interaction between IN and CK2, demonstrate that IN is a substrate of CK2 in vitro and identify the modified residues. We find that Ty1 IN is phosphorylated in vivo and that these modifications are dependent in part on CK2. No significant change in Ty1 retromobility could be observed when we introduce phospho-ablative mutations that prevent IN phosphorylation by CK2 in vitro. However, the absence of CK2 holoenzyme results in a strong stimulation of Ty1 retrotransposition, characterized by an increase in Ty1 mRNA and protein levels and a high accumulation of cDNA.
Conclusion
Our study shows that Ty1 IN is phosphorylated, as observed for retroviral INs and highlights an important role of CK2 in the regulation of Ty1 retrotransposition. In addition, the proteomic approach enabled the identification of many new Ty1 IN interacting partners, whose potential role in the control of Ty1 mobility will be interesting to study.
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6
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Li Y, Molyneaux N, Zhang H, Zhou G, Kerr C, Adams MD, Berkner KL, Runge KW. A multiplexed, three-dimensional pooling and next-generation sequencing strategy for creating barcoded mutant arrays: construction of a Schizosaccharomyces pombe transposon insertion library. Nucleic Acids Res 2022; 50:e102. [PMID: 35766443 PMCID: PMC9508820 DOI: 10.1093/nar/gkac546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/02/2022] [Accepted: 06/12/2022] [Indexed: 11/14/2022] Open
Abstract
Arrayed libraries of defined mutants have been used to elucidate gene function in the post-genomic era. Yeast haploid gene deletion libraries have pioneered this effort, but are costly to construct, do not reveal phenotypes that may occur with partial gene function and lack essential genes required for growth. We therefore devised an efficient method to construct a library of barcoded insertion mutants with a wider range of phenotypes that can be generalized to other organisms or collections of DNA samples. We developed a novel but simple three-dimensional pooling and multiplexed sequencing approach that leveraged sequence information to reduce the number of required sequencing reactions by orders of magnitude, and were able to identify the barcode sequences and DNA insertion sites of 4391 Schizosaccharomyces pombe insertion mutations with only 40 sequencing preparations. The insertion mutations are in the genes and untranslated regions of nonessential, essential and noncoding RNA genes, and produced a wider range of phenotypes compared to the cognate deletion mutants, including novel phenotypes. This mutant library represents both a proof of principle for an efficient method to produce novel mutant libraries and a valuable resource for the S. pombe research community.
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Affiliation(s)
- Yanhui Li
- Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Cleveland, OH 44195, USA
- Department of Genetics and Genomic Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Neil Molyneaux
- Department of Genetics and Genomic Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Haitao Zhang
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Cleveland, OH 44195, USA
| | - Gang Zhou
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Cleveland, OH 44195, USA
| | - Carly Kerr
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Cleveland, OH 44195, USA
| | - Mark D Adams
- Department of Genetics and Genomic Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Kathleen L Berkner
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Cleveland, OH 44195, USA
| | - Kurt W Runge
- Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Cleveland, OH 44195, USA
- Department of Genetics and Genomic Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Cleveland, OH 44195, USA
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7
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Ballandras-Colas A, Chivukula V, Gruszka DT, Shan Z, Singh PK, Pye VE, McLean RK, Bedwell GJ, Li W, Nans A, Cook NJ, Fadel HJ, Poeschla EM, Griffiths DJ, Vargas J, Taylor IA, Lyumkis D, Yardimci H, Engelman AN, Cherepanov P. Multivalent interactions essential for lentiviral integrase function. Nat Commun 2022; 13:2416. [PMID: 35504909 PMCID: PMC9065133 DOI: 10.1038/s41467-022-29928-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/07/2022] [Indexed: 12/24/2022] Open
Abstract
A multimer of retroviral integrase (IN) synapses viral DNA ends within a stable intasome nucleoprotein complex for integration into a host cell genome. Reconstitution of the intasome from the maedi-visna virus (MVV), an ovine lentivirus, revealed a large assembly containing sixteen IN subunits1. Herein, we report cryo-EM structures of the lentiviral intasome prior to engagement of target DNA and following strand transfer, refined at 3.4 and 3.5 Å resolution, respectively. The structures elucidate details of the protein-protein and protein-DNA interfaces involved in lentiviral intasome formation. We show that the homomeric interfaces involved in IN hexadecamer formation and the α-helical configuration of the linker connecting the C-terminal and catalytic core domains are critical for MVV IN strand transfer activity in vitro and for virus infectivity. Single-molecule microscopy in conjunction with photobleaching reveals that the MVV intasome can bind a variable number, up to sixteen molecules, of the lentivirus-specific host factor LEDGF/p75. Concordantly, ablation of endogenous LEDGF/p75 results in gross redistribution of MVV integration sites in human and ovine cells. Our data confirm the importance of the expanded architecture observed in cryo-EM studies of lentiviral intasomes and suggest that this organization underlies multivalent interactions with chromatin for integration targeting to active genes.
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Affiliation(s)
- Allison Ballandras-Colas
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
- Institut de Biologie Structurale (IBS) CNRS, CEA, University Grenoble, Grenoble, France
| | - Vidya Chivukula
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Dominika T Gruszka
- Single Molecule Imaging of Genome Duplication and Maintenance Laboratory, The Francis Crick Institute, London, UK
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics and Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Zelin Shan
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Parmit K Singh
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Valerie E Pye
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Rebecca K McLean
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, UK
- The Pirbright Institute, Ash Road, Pirbright, Woking, GU24 0NF, UK
| | - Gregory J Bedwell
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Wen Li
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | - Nicola J Cook
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Hind J Fadel
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN, USA
| | - Eric M Poeschla
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - David J Griffiths
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, UK
| | - Javier Vargas
- Departmento de Óptica, Universidad Complutense de Madrid, Madrid, Spain
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, UK
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Hasan Yardimci
- Single Molecule Imaging of Genome Duplication and Maintenance Laboratory, The Francis Crick Institute, London, UK.
| | - Alan N Engelman
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK.
- Department of Infectious Disease, St-Mary's Campus, Imperial College London, London, UK.
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Abstract
A hallmark of retroviral replication is establishment of the proviral state, wherein a DNA copy of the viral RNA genome is stably incorporated into a host cell chromosome. Integrase is the viral enzyme responsible for the catalytic steps involved in this process, and integrase strand transfer inhibitors are widely used to treat people living with HIV. Over the past decade, a series of X-ray crystallography and cryogenic electron microscopy studies have revealed the structural basis of retroviral DNA integration. A variable number of integrase molecules congregate on viral DNA ends to assemble a conserved intasome core machine that facilitates integration. The structures additionally informed on the modes of integrase inhibitor action and the means by which HIV acquires drug resistance. Recent years have witnessed the development of allosteric integrase inhibitors, a highly promising class of small molecules that antagonize viral morphogenesis. In this Review, we explore recent insights into the organization and mechanism of the retroviral integration machinery and highlight open questions as well as new directions in the field.
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9
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Miskey C, Kesselring L, Querques I, Abrusán G, Barabas O, Ivics Z. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2807-2825. [PMID: 35188569 PMCID: PMC8934666 DOI: 10.1093/nar/gkac092] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/24/2022] [Accepted: 02/08/2022] [Indexed: 11/14/2022] Open
Abstract
The Sleeping Beauty (SB) transposon system is a popular tool for genome engineering, but random integration into the genome carries a certain genotoxic risk in therapeutic applications. Here we investigate the role of amino acids H187, P247 and K248 in target site selection of the SB transposase. Structural modeling implicates these three amino acids located in positions analogous to amino acids with established functions in target site selection in retroviral integrases and transposases. Saturation mutagenesis of these residues in the SB transposase yielded variants with altered target site selection properties. Transposon integration profiling of several mutants reveals increased specificity of integrations into palindromic AT repeat target sequences in genomic regions characterized by high DNA bendability. The H187V and K248R mutants redirect integrations away from exons, transcriptional regulatory elements and nucleosomal DNA in the human genome, suggesting enhanced safety and thus utility of these SB variants in gene therapy applications.
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Affiliation(s)
| | | | - Irma Querques
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - György Abrusán
- Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged 6726, Hungary
| | - Orsolya Barabas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland
| | - Zoltán Ivics
- To whom correspondence should be addressed. Tel: +49 6103 77 6000; Fax: +49 6103 77 1280;
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10
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Nguyen PQ, Conesa C, Rabut E, Bragagnolo G, Gouzerh C, Fernández-Tornero C, Lesage P, Reguera J, Acker J. Ty1 integrase is composed of an active N-terminal domain and a large disordered C-terminal module dispensable for its activity in vitro. J Biol Chem 2021; 297:101093. [PMID: 34416236 PMCID: PMC8487063 DOI: 10.1016/j.jbc.2021.101093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/05/2021] [Accepted: 08/16/2021] [Indexed: 11/16/2022] Open
Abstract
Long-terminal repeat (LTR) retrotransposons are genetic elements that, like retroviruses, replicate by reverse transcription of an RNA intermediate into a complementary DNA (cDNA) that is next integrated into the host genome by their own integrase. The Ty1 LTR retrotransposon has proven to be a reliable working model to investigate retroelement integration site preference. However, the low yield of recombinant Ty1 integrase production reported so far has been a major obstacle for structural studies. Here we analyze the biophysical and biochemical properties of a stable and functional recombinant Ty1 integrase highly expressed in E.coli. The recombinant protein is monomeric and has an elongated shape harboring the three-domain structure common to all retroviral integrases at the N-terminal half, an extra folded region, and a large intrinsically disordered region at the C-terminal half. Recombinant Ty1 integrase efficiently catalyzes concerted integration in vitro, and the N-terminal domain displays similar activity. These studies that will facilitate structural analyses may allow elucidating the molecular mechanisms governing Ty1 specific integration into safe places in the genome.
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Affiliation(s)
| | - Christine Conesa
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Elise Rabut
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Célia Gouzerh
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Pascale Lesage
- INSERM U944, CNRS UMR 7212, Genomes and Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | - Juan Reguera
- Aix-Marseille Université, CNRS, AFMB UMR 7257, Marseille, France; INSERM, AFMB UMR7257, Marseille, France.
| | - Joël Acker
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France.
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11
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Bonnet A, Lesage P. Light and shadow on the mechanisms of integration site selection in yeast Ty retrotransposon families. Curr Genet 2021; 67:347-357. [PMID: 33590295 DOI: 10.1007/s00294-021-01154-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/04/2021] [Accepted: 01/07/2021] [Indexed: 12/21/2022]
Abstract
Transposable elements are ubiquitous in genomes. Their successful expansion depends in part on their sites of integration in their host genome. In Saccharomyces cerevisiae, evolution has selected various strategies to target the five Ty LTR-retrotransposon families into gene-poor regions in a genome, where coding sequences occupy 70% of the DNA. The integration of Ty1/Ty2/Ty4 and Ty3 occurs upstream and at the transcription start site of the genes transcribed by RNA polymerase III, respectively. Ty5 has completely different integration site preferences, targeting heterochromatin regions. Here, we review the history that led to the identification of the cellular tethering factors that play a major role in anchoring Ty retrotransposons to their preferred sites. We also question the involvement of additional factors in the fine-tuning of the integration site selection, with several studies converging towards an importance of the structure and organization of the chromatin.
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Affiliation(s)
- Amandine Bonnet
- INSERM U944, CNRS UMR 7212, Genomes and Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | - Pascale Lesage
- INSERM U944, CNRS UMR 7212, Genomes and Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France.
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Asif‐Laidin A, Conesa C, Bonnet A, Grison C, Adhya I, Menouni R, Fayol H, Palmic N, Acker J, Lesage P. A small targeting domain in Ty1 integrase is sufficient to direct retrotransposon integration upstream of tRNA genes. EMBO J 2020; 39:e104337. [PMID: 32677087 PMCID: PMC7459421 DOI: 10.15252/embj.2019104337] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 06/09/2020] [Accepted: 06/18/2020] [Indexed: 12/25/2022] Open
Abstract
Integration of transposable elements into the genome is mutagenic. Mechanisms targeting integrations into relatively safe locations, hence minimizing deleterious consequences for cell fitness, have emerged during evolution. In budding yeast, integration of the Ty1 LTR retrotransposon upstream of RNA polymerase III (Pol III)-transcribed genes requires interaction between Ty1 integrase (IN1) and AC40, a subunit common to Pol I and Pol III. Here, we identify the Ty1 targeting domain of IN1 that ensures (i) IN1 binding to Pol I and Pol III through AC40, (ii) IN1 genome-wide recruitment to Pol I- and Pol III-transcribed genes, and (iii) Ty1 integration only at Pol III-transcribed genes, while IN1 recruitment by AC40 is insufficient to target Ty1 integration into Pol I-transcribed genes. Swapping the targeting domains between Ty5 and Ty1 integrases causes Ty5 integration at Pol III-transcribed genes, indicating that the targeting domain of IN1 alone confers Ty1 integration site specificity.
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Affiliation(s)
- Amna Asif‐Laidin
- INSERM U944, CNRS UMR 7212Genomes& Cell Biology of Disease UnitInstitut de Recherche Saint‐LouisHôpital Saint‐LouisUniversité de ParisParisFrance
| | - Christine Conesa
- CEACNRSInstitute for Integrative Biology of the Cell (I2BC)Université Paris‐SaclayGif‐sur‐YvetteFrance
| | - Amandine Bonnet
- INSERM U944, CNRS UMR 7212Genomes& Cell Biology of Disease UnitInstitut de Recherche Saint‐LouisHôpital Saint‐LouisUniversité de ParisParisFrance
| | - Camille Grison
- INSERM U944, CNRS UMR 7212Genomes& Cell Biology of Disease UnitInstitut de Recherche Saint‐LouisHôpital Saint‐LouisUniversité de ParisParisFrance
| | - Indranil Adhya
- CEACNRSInstitute for Integrative Biology of the Cell (I2BC)Université Paris‐SaclayGif‐sur‐YvetteFrance
| | - Rachid Menouni
- INSERM U944, CNRS UMR 7212Genomes& Cell Biology of Disease UnitInstitut de Recherche Saint‐LouisHôpital Saint‐LouisUniversité de ParisParisFrance
| | - Hélène Fayol
- INSERM U944, CNRS UMR 7212Genomes& Cell Biology of Disease UnitInstitut de Recherche Saint‐LouisHôpital Saint‐LouisUniversité de ParisParisFrance
| | - Noé Palmic
- INSERM U944, CNRS UMR 7212Genomes& Cell Biology of Disease UnitInstitut de Recherche Saint‐LouisHôpital Saint‐LouisUniversité de ParisParisFrance
| | - Joël Acker
- CEACNRSInstitute for Integrative Biology of the Cell (I2BC)Université Paris‐SaclayGif‐sur‐YvetteFrance
| | - Pascale Lesage
- INSERM U944, CNRS UMR 7212Genomes& Cell Biology of Disease UnitInstitut de Recherche Saint‐LouisHôpital Saint‐LouisUniversité de ParisParisFrance
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Zhang X, Zhao M, McCarty DR, Lisch D. Transposable elements employ distinct integration strategies with respect to transcriptional landscapes in eukaryotic genomes. Nucleic Acids Res 2020; 48:6685-6698. [PMID: 32442316 PMCID: PMC7337890 DOI: 10.1093/nar/gkaa370] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 12/27/2022] Open
Abstract
Transposable elements (TEs) are ubiquitous DNA segments capable of moving from one site to another within host genomes. The extant distributions of TEs in eukaryotic genomes have been shaped by both bona fide TE integration preferences in eukaryotic genomes and by selection following integration. Here, we compare TE target site distribution in host genomes using multiple de novo transposon insertion datasets in both plants and animals and compare them in the context of genome-wide transcriptional landscapes. We showcase two distinct types of transcription-associated TE targeting strategies that suggest a process of convergent evolution among eukaryotic TE families. The integration of two precision-targeting elements are specifically associated with initiation of RNA Polymerase II transcription of highly expressed genes, suggesting the existence of novel mechanisms of precision TE targeting in addition to passive targeting of open chromatin. We also highlight two features that can facilitate TE survival and rapid proliferation: tissue-specific transposition and minimization of negative impacts on nearby gene function due to precision targeting.
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Affiliation(s)
- Xinyan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Meixia Zhao
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Donald R McCarty
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
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14
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Maxwell PH. Diverse transposable element landscapes in pathogenic and nonpathogenic yeast models: the value of a comparative perspective. Mob DNA 2020; 11:16. [PMID: 32336995 PMCID: PMC7175516 DOI: 10.1186/s13100-020-00215-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/16/2020] [Indexed: 12/14/2022] Open
Abstract
Genomics and other large-scale analyses have drawn increasing attention to the potential impacts of transposable elements (TEs) on their host genomes. However, it remains challenging to transition from identifying potential roles to clearly demonstrating the level of impact TEs have on genome evolution and possible functions that they contribute to their host organisms. I summarize TE content and distribution in four well-characterized yeast model systems in this review: the pathogens Candida albicans and Cryptococcus neoformans, and the nonpathogenic species Saccharomyces cerevisiae and Schizosaccharomyces pombe. I compare and contrast their TE landscapes to their lifecycles, genomic features, as well as the presence and nature of RNA interference pathways in each species to highlight the valuable diversity represented by these models for functional studies of TEs. I then review the regulation and impacts of the Ty1 and Ty3 retrotransposons from Saccharomyces cerevisiae and Tf1 and Tf2 retrotransposons from Schizosaccharomyces pombe to emphasize parallels and distinctions between these well-studied elements. I propose that further characterization of TEs in the pathogenic yeasts would enable this set of four yeast species to become an excellent set of models for comparative functional studies to address outstanding questions about TE-host relationships.
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15
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Jedlicka P, Lexa M, Vanat I, Hobza R, Kejnovsky E. Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study. Mob DNA 2019; 10:50. [PMID: 31871489 PMCID: PMC6911290 DOI: 10.1186/s13100-019-0186-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/31/2019] [Indexed: 01/08/2023] Open
Abstract
Background Nesting is common in LTR retrotransposons, especially in large genomes containing a high number of elements. Results We analyzed 12 plant genomes and obtained 1491 pairs of nested and original (pre-existing) LTR retrotransposons. We systematically analyzed mutual nesting of individual LTR retrotransposons and found that certain families, more often belonging to the Ty3/gypsy than Ty1/copia superfamilies, showed a higher nesting frequency as well as a higher preference for older copies of the same family ("autoinsertions"). Nested LTR retrotransposons were preferentially located in the 3'UTR of other LTR retrotransposons, while coding and regulatory regions (LTRs) are not commonly targeted. Insertions displayed a weak preference for palindromes and were associated with a strong positional pattern of higher predicted nucleosome occupancy. Deviation from randomness in target site choice was also found in 13,983 non-nested plant LTR retrotransposons. Conclusions We reveal that nesting of LTR retrotransposons is not random. Integration is correlated with sequence composition, secondary structure and the chromatin environment. Insertion into retrotransposon positions with a low negative impact on family fitness supports the concept of the genome being viewed as an ecosystem of various elements.
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Affiliation(s)
- Pavel Jedlicka
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200 Brno, Czech Republic
| | - Matej Lexa
- 2Faculty of Informatics, Masaryk University, Botanicka 68a, 60200 Brno, Czech Republic
| | - Ivan Vanat
- 2Faculty of Informatics, Masaryk University, Botanicka 68a, 60200 Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200 Brno, Czech Republic
| | - Eduard Kejnovsky
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200 Brno, Czech Republic
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16
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Patterson K, Shavarebi F, Magnan C, Chang I, Qi X, Baldi P, Bilanchone V, Sandmeyer SB. Local features determine Ty3 targeting frequency at RNA polymerase III transcription start sites. Genome Res 2019; 29:1298-1309. [PMID: 31249062 PMCID: PMC6673722 DOI: 10.1101/gr.240861.118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 06/12/2019] [Indexed: 12/27/2022]
Abstract
Retroelement integration into host genomes affects chromosome structure and function. A goal of a considerable number of investigations is to elucidate features influencing insertion site selection. The Saccharomyces cerevisiae Ty3 retrotransposon inserts proximal to the transcription start sites (TSS) of genes transcribed by RNA polymerase III (RNAP3). In this study, differential patterns of insertion were profiled genome-wide using a random barcode-tagged Ty3. Saturation transposition showed that tRNA genes (tDNAs) are targeted at widely different frequencies even within isoacceptor families. Ectopic expression of Ty3 integrase (IN) showed that it localized to targets independent of other Ty3 proteins and cDNA. IN, RNAP3, and transcription factor Brf1 were enriched at tDNA targets with high frequencies of transposition. To examine potential effects of cis-acting DNA features on transposition, targeting was tested on high-copy plasmids with restricted amounts of 5′ flanking sequence plus tDNA. Relative activity of targets was reconstituted in these constructions. Weighting of genomic insertions according to frequency identified an A/T-rich sequence followed by C as the dominant site of strand transfer. This site lies immediately adjacent to the adenines previously implicated in the RNAP3 TSS motif (CAA). In silico DNA structural analysis upstream of this motif showed that targets with elevated DNA curvature coincide with reduced integration. We propose that integration mediated by the Ty3 intasome complex (IN and cDNA) is subject to inputs from a combination of host factor occupancy and insertion site architecture, and that this results in the wide range of Ty3 targeting frequencies.
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Affiliation(s)
- Kurt Patterson
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
| | - Farbod Shavarebi
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
| | - Christophe Magnan
- School of Information and Computer Sciences, University of California, Irvine, Irvine, California 92697, USA
| | - Ivan Chang
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
| | - Xiaojie Qi
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
| | - Pierre Baldi
- School of Information and Computer Sciences, University of California, Irvine, Irvine, California 92697, USA
| | - Virginia Bilanchone
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
| | - Suzanne B Sandmeyer
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
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17
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Barkova A, Asif-Laidin A, Lesage P. Genome-Wide Mapping of Yeast Retrotransposon Integration Target Sites. Methods Enzymol 2018; 612:197-223. [PMID: 30502942 DOI: 10.1016/bs.mie.2018.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Transposable elements (TEs) are present in virtually all organisms. TE integration into genomes contributes to their structure and evolution, but can also be harmful in some cases. Deciphering where and how TE integration is targeted is fundamental to understand their intricate relationship with their host and explore the outcome of TE mobility on genome evolution and cell fitness. In general, TEs display integration site preference, which differs between elements. High-throughput mapping of de novo insertions by deep sequencing has recently allowed identifying genome-wide integration preferences of several TEs. These studies have provided invaluable clues to address the molecular determinants of integration site preference. Here, we provide a step-by-step methodology to generate massive de novo insertion events and prepare a library of genomic DNA for next-generation sequencing. We also describe a primary bioinformatic procedure to map these insertions in the genome. The whole procedure comes from our recent work on the integration of Ty1 in Saccharomyces cerevisiae, but could be easily adapted to the study of other TEs.
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Affiliation(s)
- Anastasia Barkova
- INSERM U944, CNRS UMR 7212, Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Hôpital St. Louis, Paris Cedex 10, France
| | - Amna Asif-Laidin
- INSERM U944, CNRS UMR 7212, Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Hôpital St. Louis, Paris Cedex 10, France
| | - Pascale Lesage
- INSERM U944, CNRS UMR 7212, Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Hôpital St. Louis, Paris Cedex 10, France.
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18
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Border collies of the genome: domestication of an autonomous retrovirus-like transposon. Curr Genet 2018; 65:71-78. [PMID: 29931377 DOI: 10.1007/s00294-018-0857-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 06/07/2018] [Accepted: 06/08/2018] [Indexed: 12/23/2022]
Abstract
Retrotransposons often spread rapidly through eukaryotic genomes until they are neutralized by host-mediated silencing mechanisms, reduced by recombination and mutation, and lost or transformed into benevolent entities. But the Ty1 retrotransposon appears to have been domesticated to guard the genome of Saccharomyces cerevisiae.
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19
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Cheung S, Manhas S, Measday V. Retrotransposon targeting to RNA polymerase III-transcribed genes. Mob DNA 2018; 9:14. [PMID: 29713390 PMCID: PMC5911963 DOI: 10.1186/s13100-018-0119-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 04/16/2018] [Indexed: 12/20/2022] Open
Abstract
Retrotransposons are genetic elements that are similar in structure and life cycle to retroviruses by replicating via an RNA intermediate and inserting into a host genome. The Saccharomyces cerevisiae (S. cerevisiae) Ty1-5 elements are long terminal repeat (LTR) retrotransposons that are members of the Ty1-copia (Pseudoviridae) or Ty3-gypsy (Metaviridae) families. Four of the five S. cerevisiae Ty elements are inserted into the genome upstream of RNA Polymerase (Pol) III-transcribed genes such as transfer RNA (tRNA) genes. This particular genomic locus provides a safe environment for Ty element insertion without disruption of the host genome and is a targeting strategy used by retrotransposons that insert into compact genomes of hosts such as S. cerevisiae and the social amoeba Dictyostelium. The mechanism by which Ty1 targeting is achieved has been recently solved due to the discovery of an interaction between Ty1 Integrase (IN) and RNA Pol III subunits. We describe the methods used to identify the Ty1-IN interaction with Pol III and the Ty1 targeting consequences if the interaction is perturbed. The details of Ty1 targeting are just beginning to emerge and many unexplored areas remain including consideration of the 3-dimensional shape of genome. We present a variety of other retrotransposon families that insert adjacent to Pol III-transcribed genes and the mechanism by which the host machinery has been hijacked to accomplish this targeting strategy. Finally, we discuss why retrotransposons selected Pol III-transcribed genes as a target during evolution and how retrotransposons have shaped genome architecture.
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Affiliation(s)
- Stephanie Cheung
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Savrina Manhas
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Vivien Measday
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Food Science, Wine Research Centre, Faculty of Land and Food Systems, University of British Columbia, Room 325-2205 East Mall, Vancouver, British Columbia V6T 1Z4 Canada
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20
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Manhas S, Ma L, Measday V. The yeast Ty1 retrotransposon requires components of the nuclear pore complex for transcription and genomic integration. Nucleic Acids Res 2018; 46:3552-3578. [PMID: 29514267 PMCID: PMC5909446 DOI: 10.1093/nar/gky109] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 02/01/2018] [Accepted: 02/26/2018] [Indexed: 01/06/2023] Open
Abstract
Nuclear pore complexes (NPCs) orchestrate cargo between the cytoplasm and nucleus and regulate chromatin organization. NPC proteins, or nucleoporins (Nups), are required for human immunodeficiency virus type 1 (HIV-1) gene expression and genomic integration of viral DNA. We utilize the Ty1 retrotransposon of Saccharomyces cerevisiae (S. cerevisiae) to study retroviral integration because retrotransposons are the progenitors of retroviruses and have conserved integrase (IN) enzymes. Ty1-IN targets Ty1 elements into the genome upstream of RNA polymerase (Pol) III transcribed genes such as transfer RNA (tRNA) genes. Evidence that S. cerevisiae tRNA genes are recruited to NPCs prompted our investigation of a functional role for the NPC in Ty1 targeting into the genome. We find that Ty1 mobility is reduced in multiple Nup mutants that cannot be accounted for by defects in Ty1 gene expression, cDNA production or Ty1-IN nuclear entry. Instead, we find that Ty1 insertion upstream of tRNA genes is impaired. We also identify Nup mutants with wild type Ty1 mobility but impaired Ty1 targeting. The NPC nuclear basket, which interacts with chromatin, is required for both Ty1 expression and nucleosome targeting. Deletion of components of the NPC nuclear basket causes mis-targeting of Ty1 elements to the ends of chromosomes.
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Affiliation(s)
- Savrina Manhas
- Department of Biochemistry and Molecular Biology, 2350 Health Sciences Mall, Life Sciences Centre, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Lina Ma
- Wine Research Centre, 2205 East Mall, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Vivien Measday
- Department of Biochemistry and Molecular Biology, 2350 Health Sciences Mall, Life Sciences Centre, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Wine Research Centre, 2205 East Mall, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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21
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Hosaka A, Kakutani T. Transposable elements, genome evolution and transgenerational epigenetic variation. Curr Opin Genet Dev 2018. [DOI: 10.1016/j.gde.2018.02.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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22
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Rai SK, Sangesland M, Lee M, Esnault C, Cui Y, Chatterjee AG, Levin HL. Host factors that promote retrotransposon integration are similar in distantly related eukaryotes. PLoS Genet 2017; 13:e1006775. [PMID: 29232693 PMCID: PMC5741268 DOI: 10.1371/journal.pgen.1006775] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 12/22/2017] [Accepted: 11/07/2017] [Indexed: 12/14/2022] Open
Abstract
Retroviruses and Long Terminal Repeat (LTR)-retrotransposons have distinct patterns of integration sites. The oncogenic potential of retrovirus-based vectors used in gene therapy is dependent on the selection of integration sites associated with promoters. The LTR-retrotransposon Tf1 of Schizosaccharomyces pombe is studied as a model for oncogenic retroviruses because it integrates into the promoters of stress response genes. Although integrases (INs) encoded by retroviruses and LTR-retrotransposons are responsible for catalyzing the insertion of cDNA into the host genome, it is thought that distinct host factors are required for the efficiency and specificity of integration. We tested this hypothesis with a genome-wide screen of host factors that promote Tf1 integration. By combining an assay for transposition with a genetic assay that measures cDNA recombination we could identify factors that contribute differentially to integration. We utilized this assay to test a collection of 3,004 S. pombe strains with single gene deletions. Using these screens and immunoblot measures of Tf1 proteins, we identified a total of 61 genes that promote integration. The candidate integration factors participate in a range of processes including nuclear transport, transcription, mRNA processing, vesicle transport, chromatin structure and DNA repair. Two candidates, Rhp18 and the NineTeen complex were tested in two-hybrid assays and were found to interact with Tf1 IN. Surprisingly, a number of pathways we identified were found previously to promote integration of the LTR-retrotransposons Ty1 and Ty3 in Saccharomyces cerevisiae, indicating the contribution of host factors to integration are common in distantly related organisms. The DNA repair factors are of particular interest because they may identify the pathways that repair the single stranded gaps flanking the sites of strand transfer following integration of LTR retroelements. Retroviruses and retrotransposons are genetic elements that propagate by integrating into chromosomes of eukaryotic cells. Genetic disorders are being treated with retrovirus-based vectors that integrate corrective genes into the chromosomes of patients. Unfortunately, the vectors can alter expression of adjacent genes and depending on the position of integration, cancer genes can be induced. It is therefore essential that we understand how integration sites are selected. Interestingly, different retroviruses and retrotransposons have different profiles of integration sites. While specific proteins have been identified that select target sites, it’s not known what other cellular factors promote integration. In this paper, we report a comprehensive screen of host factors that promote LTR-retrotransposon integration in the widely-studied yeast, Schizosaccharomyces pombe. Unexpectedly, we found a wide range of pathways and host factors participate in integration. And importantly, we found the cellular processes that promote integration relative to recombination in S. pombe are the same that drive integration of LTR-retrotransposons in the distantly related yeast Saccharomyces cerevisiae. This suggests a specific set of cellular pathways are responsible for integration in a wide range of eukaryotic hosts.
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Affiliation(s)
- Sudhir Kumar Rai
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Maya Sangesland
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Michael Lee
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Caroline Esnault
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Yujin Cui
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Atreyi Ghatak Chatterjee
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Henry L. Levin
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
- * E-mail:
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23
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Shapiro JA. Living Organisms Author Their Read-Write Genomes in Evolution. BIOLOGY 2017; 6:E42. [PMID: 29211049 PMCID: PMC5745447 DOI: 10.3390/biology6040042] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/17/2017] [Accepted: 11/28/2017] [Indexed: 12/18/2022]
Abstract
Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with "non-coding" DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called "non-coding" RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
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24
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Ribosome Biogenesis Modulates Ty1 Copy Number Control in Saccharomyces cerevisiae. Genetics 2017; 207:1441-1456. [PMID: 29046400 PMCID: PMC5714458 DOI: 10.1534/genetics.117.300388] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/12/2017] [Indexed: 11/26/2022] Open
Abstract
Transposons can impact the host genome by altering gene expression and participating in chromosome rearrangements. Therefore, organisms evolved different ways to minimize the level of transposition. In Saccharomyces cerevisiae and its close relative S. paradoxus, Ty1 copy number control (CNC) is mediated by the self-encoded restriction factor p22, which is derived from the GAG capsid gene and inhibits virus-like particle (VLP) assembly and function. Based on secondary screens of Ty1 cofactors, we identified LOC1, a RNA localization/ribosome biogenesis gene that affects Ty1 mobility predominantly in strains harboring Ty1 elements. Ribosomal protein mutants rps0bΔ and rpl7aΔ displayed similar CNC-specific phenotypes as loc1Δ, suggesting that ribosome biogenesis is critical for CNC. The level of Ty1 mRNA and Ty1 internal (Ty1i) transcripts encoding p22 was altered in these mutants, and displayed a trend where the level of Ty1i RNA increased relative to full-length Ty1 mRNA. The level of p22 increased in these mutants, and the half-life of p22 also increased in a loc1Δ mutant. Transcriptomic analyses revealed small changes in the level of Ty1 transcripts or efficiency of translation initiation in a loc1Δ mutant. Importantly, a loc1Δ mutant had defects in assembly of Gag complexes and packaging Ty1 RNA. Our results indicate that defective ribosome biogenesis enhances CNC by increasing the level of p22, and raise the possibility for versatile links between VLP assembly, its cytoplasmic environment, and a novel stress response.
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McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data. G3-GENES GENOMES GENETICS 2017. [PMID: 28637810 PMCID: PMC5555480 DOI: 10.1534/g3.117.043893] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Transposable element (TE) insertions are among the most challenging types of variants to detect in genomic data because of their repetitive nature and complex mechanisms of replication . Nevertheless, the recent availability of large resequencing data sets has spurred the development of many new methods to detect TE insertions in whole-genome shotgun sequences. Here we report an integrated bioinformatics pipeline for the detection of TE insertions in whole-genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods. We demonstrate the utility of McClintock by evaluating six TE detection methods using simulated and real genome data from the model microbial eukaryote, Saccharomyces cerevisiae We find substantial variation among McClintock component methods in their ability to detect nonreference TEs in the yeast genome, but show that nonreference TEs at nearly all biologically realistic locations can be detected in simulated data by combining multiple methods that use split-read and read-pair evidence. In general, our results reveal that split-read methods detect fewer nonreference TE insertions than read-pair methods, but generally have much higher positional accuracy. Analysis of a large sample of real yeast genomes reveals that most McClintock component methods can recover known aspects of TE biology in yeast such as the transpositional activity status of families, target preferences, and target site duplication structure, albeit with varying levels of accuracy. Our work provides a general framework for integrating and analyzing results from multiple TE detection methods, as well as useful guidance for researchers studying TEs in yeast resequencing data.
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Zhang Y, Li S, Abyzov A, Gerstein MB. Landscape and variation of novel retroduplications in 26 human populations. PLoS Comput Biol 2017; 13:e1005567. [PMID: 28662076 PMCID: PMC5510864 DOI: 10.1371/journal.pcbi.1005567] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 07/14/2017] [Accepted: 05/12/2017] [Indexed: 01/10/2023] Open
Abstract
Retroduplications come from reverse transcription of mRNAs and their insertion back into the genome. Here, we performed comprehensive discovery and analysis of retroduplications in a large cohort of 2,535 individuals from 26 human populations, as part of 1000 Genomes Phase 3. We developed an integrated approach to discover novel retroduplications combining high-coverage exome and low-coverage whole-genome sequencing data, utilizing information from both exon-exon junctions and discordant paired-end reads. We found 503 parent genes having novel retroduplications absent from the reference genome. Based solely on retroduplication variation, we built phylogenetic trees of human populations; these represent superpopulation structure well and indicate that variable retroduplications are effective population markers. We further identified 43 retroduplication parent genes differentiating superpopulations. This group contains several interesting insertion events, including a SLMO2 retroduplication and insertion into CAV3, which has a potential disease association. We also found retroduplications to be associated with a variety of genomic features: (1) Insertion sites were correlated with regular nucleosome positioning. (2) They, predictably, tend to avoid conserved functional regions, such as exons, but, somewhat surprisingly, also avoid introns. (3) Retroduplications tend to be co-inserted with young L1 elements, indicating recent retrotranspositional activity, and (4) they have a weak tendency to originate from highly expressed parent genes. Our investigation provides insight into the functional impact and association with genomic elements of retroduplications. We anticipate our approach and analytical methodology to have application in a more clinical context, where exome sequencing data is abundant and the discovery of retroduplications can potentially improve the accuracy of SNP calling.
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Affiliation(s)
- Yan Zhang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Shantao Li
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
| | - Alexej Abyzov
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Mark B. Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Computer Science, Yale University, New Haven, Connecticut, United States of America
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Integration site selection by retroviruses and transposable elements in eukaryotes. Nat Rev Genet 2017; 18:292-308. [PMID: 28286338 DOI: 10.1038/nrg.2017.7] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transposable elements and retroviruses are found in most genomes, can be pathogenic and are widely used as gene-delivery and functional genomics tools. Exploring whether these genetic elements target specific genomic sites for integration and how this preference is achieved is crucial to our understanding of genome evolution, somatic genome plasticity in cancer and ageing, host-parasite interactions and genome engineering applications. High-throughput profiling of integration sites by next-generation sequencing, combined with large-scale genomic data mining and cellular or biochemical approaches, has revealed that the insertions are usually non-random. The DNA sequence, chromatin and nuclear context, and cellular proteins cooperate in guiding integration in eukaryotic genomes, leading to a remarkable diversity of insertion site distribution and evolutionary strategies.
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Gadaleta MC, Noguchi E. Regulation of DNA Replication through Natural Impediments in the Eukaryotic Genome. Genes (Basel) 2017; 8:genes8030098. [PMID: 28272375 PMCID: PMC5368702 DOI: 10.3390/genes8030098] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 03/03/2017] [Indexed: 02/07/2023] Open
Abstract
All living organisms need to duplicate their genetic information while protecting it from unwanted mutations, which can lead to genetic disorders and cancer development. Inaccuracies during DNA replication are the major cause of genomic instability, as replication forks are prone to stalling and collapse, resulting in DNA damage. The presence of exogenous DNA damaging agents as well as endogenous difficult-to-replicate DNA regions containing DNA–protein complexes, repetitive DNA, secondary DNA structures, or transcribing RNA polymerases, increases the risk of genomic instability and thus threatens cell survival. Therefore, understanding the cellular mechanisms required to preserve the genetic information during S phase is of paramount importance. In this review, we will discuss our current understanding of how cells cope with these natural impediments in order to prevent DNA damage and genomic instability during DNA replication.
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Affiliation(s)
- Mariana C Gadaleta
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA.
| | - Eishi Noguchi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA.
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Paralog-Specific Functions of RPL7A and RPL7B Mediated by Ribosomal Protein or snoRNA Dosage in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2017; 7:591-606. [PMID: 28007835 PMCID: PMC5295604 DOI: 10.1534/g3.116.035931] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Most ribosomal proteins in Saccharomyces cerevisiae are encoded by two paralogs that additively produce the optimal protein level for cell growth. Nonetheless, deleting one paralog of most ribosomal protein gene pairs results in a variety of phenotypes not observed when the other paralog is deleted. To determine whether paralog-specific phenotypes associated with deleting RPL7A or RPL7B stem from distinct functions or different levels of the encoded isoforms, the coding region and introns of one paralog, including an intron-embedded snoRNA (small nucleolar RNA) gene, were exchanged with that of the other paralog. Among mutants harboring a single native or chimeric RPL7 allele, expression from the RPL7A locus exceeded that from the RPL7B locus, and more Rpl7a was expressed from either locus than Rpl7b. Phenotypic differences in tunicamycin sensitivity, ASH1 mRNA localization, and mobility of the Ty1 retrotransposon were strongly correlated with Rpl7 and ribosome levels, but not with the Rpl7 or snoRNA isoform expressed. Although Ty1 RNA is cotranslationally localized, depletion of Rpl7 minimally affected synthesis of Ty1 Gag protein, but strongly influenced Ty1 RNA localization. Unlike the other processes studied, Ty1 cDNA accumulation was influenced by both the level and isoform of Rpl7 or snoRNA expressed. These cellular processes had different minimal threshold values for Rpl7 and ribosome levels, but all were functional when isoforms of either paralog were expressed from the RPL7A locus or both RPL7 loci. This study illustrates the broad range of phenotypes that can result from depleting ribosomes to different levels.
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Małolepszy A, Mun T, Sandal N, Gupta V, Dubin M, Urbański D, Shah N, Bachmann A, Fukai E, Hirakawa H, Tabata S, Nadzieja M, Markmann K, Su J, Umehara Y, Soyano T, Miyahara A, Sato S, Hayashi M, Stougaard J, Andersen SU. The LORE1 insertion mutant resource. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:306-317. [PMID: 27322352 DOI: 10.1111/tpj.13243] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 06/07/2016] [Accepted: 06/10/2016] [Indexed: 05/08/2023]
Abstract
Long terminal repeat (LTR) retrotransposons are closely related to retroviruses, and their activities shape eukaryotic genomes. Here, we present a complete Lotus japonicus insertion mutant collection generated by identification of 640 653 new insertion events following de novo activation of the LTR element Lotus retrotransposon 1 (LORE1) (http://lotus.au.dk). Insertion preferences are critical for effective gene targeting, and we exploit our large dataset to analyse LTR element characteristics in this context. We infer the mechanism that generates the consensus palindromes typical of retroviral and LTR retrotransposon insertion sites, identify a short relaxed insertion site motif, and demonstrate selective integration into CHG-hypomethylated genes. These characteristics result in a steep increase in deleterious mutation rate following activation, and allow LORE1 active gene targeting to approach saturation within a population of 134 682 L. japonicus lines. We suggest that saturation mutagenesis using endogenous LTR retrotransposons with germinal activity can be used as a general and cost-efficient strategy for generation of non-transgenic mutant collections for unrestricted use in plant research.
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Affiliation(s)
- Anna Małolepszy
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Terry Mun
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Niels Sandal
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Vikas Gupta
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Manu Dubin
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Dorian Urbański
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Niraj Shah
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Asger Bachmann
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Eigo Fukai
- Division of Plant Sciences, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannon-dai, Tsukuba, 305-8602, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Marcin Nadzieja
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Katharina Markmann
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Junyi Su
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Yosuke Umehara
- Division of Plant Sciences, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannon-dai, Tsukuba, 305-8602, Japan
| | - Takashi Soyano
- Division of Plant Sciences, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannon-dai, Tsukuba, 305-8602, Japan
| | - Akira Miyahara
- Division of Plant Sciences, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannon-dai, Tsukuba, 305-8602, Japan
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Makoto Hayashi
- Division of Plant Sciences, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannon-dai, Tsukuba, 305-8602, Japan
| | - Jens Stougaard
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Stig U Andersen
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
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Spaller T, Kling E, Glöckner G, Hillmann F, Winckler T. Convergent evolution of tRNA gene targeting preferences in compact genomes. Mob DNA 2016; 7:17. [PMID: 27583033 PMCID: PMC5006619 DOI: 10.1186/s13100-016-0073-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/20/2016] [Indexed: 11/30/2022] Open
Abstract
Background In gene-dense genomes, mobile elements are confronted with highly selective pressure to amplify without causing excessive damage to the host. The targeting of tRNA genes as potentially safe integration sites has been developed by retrotransposons in various organisms such as the social amoeba Dictyostelium discoideum and the yeast Saccharomyces cerevisiae. In D. discoideum, tRNA gene-targeting retrotransposons have expanded to approximately 3 % of the genome. Recently obtained genome sequences of species representing the evolutionary history of social amoebae enabled us to determine whether the targeting of tRNA genes is a generally successful strategy for mobile elements to colonize compact genomes. Results During the evolution of dictyostelids, different retrotransposon types independently developed the targeting of tRNA genes at least six times. DGLT-A elements are long terminal repeat (LTR) retrotransposons that display integration preferences ~15 bp upstream of tRNA gene-coding regions reminiscent of the yeast Ty3 element. Skipper elements are chromoviruses that have developed two subgroups: one has canonical chromo domains that may favor integration in centromeric regions, whereas the other has diverged chromo domains and is found ~100 bp downstream of tRNA genes. The integration of D. discoideum non-LTR retrotransposons ~50 bp upstream (TRE5 elements) and ~100 bp downstream (TRE3 elements) of tRNA genes, respectively, likely emerged at the root of dictyostelid evolution. We identified two novel non-LTR retrotransposons unrelated to TREs: one with a TRE5-like integration behavior and the other with preference ~4 bp upstream of tRNA genes. Conclusions Dictyostelid retrotransposons demonstrate convergent evolution of tRNA gene targeting as a probable means to colonize the compact genomes of their hosts without being excessively mutagenic. However, high copy numbers of tRNA gene-associated retrotransposons, such as those observed in D. discoideum, are an exception, suggesting that the targeting of tRNA genes does not necessarily favor the amplification of position-specific integrating elements to high copy numbers under the repressive conditions that prevail in most host cells. Electronic supplementary material The online version of this article (doi:10.1186/s13100-016-0073-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas Spaller
- Institute of Pharmacy, Department of Pharmaceutical Biology, Friedrich Schiller University Jena, Semmelweisstraße 10, Jena, 07743 Germany
| | - Eva Kling
- Institute of Pharmacy, Department of Pharmaceutical Biology, Friedrich Schiller University Jena, Semmelweisstraße 10, Jena, 07743 Germany
| | - Gernot Glöckner
- Institute for Biochemistry I, Medical Faculty, University of Cologne, Berlin, Germany ; Institute for Freshwater Ecology and Inland Fisheries, IGB, Berlin, Germany
| | - Falk Hillmann
- Junior Research Group Evolution of Microbial Interaction, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - Thomas Winckler
- Institute of Pharmacy, Department of Pharmaceutical Biology, Friedrich Schiller University Jena, Semmelweisstraße 10, Jena, 07743 Germany
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32
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Gilbert C, Peccoud J, Chateigner A, Moumen B, Cordaux R, Herniou EA. Continuous Influx of Genetic Material from Host to Virus Populations. PLoS Genet 2016; 12:e1005838. [PMID: 26829124 PMCID: PMC4735498 DOI: 10.1371/journal.pgen.1005838] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 01/11/2016] [Indexed: 11/18/2022] Open
Abstract
Many genes of large double-stranded DNA viruses have a cellular origin, suggesting that host-to-virus horizontal transfer (HT) of DNA is recurrent. Yet, the frequency of these transfers has never been assessed in viral populations. Here we used ultra-deep DNA sequencing of 21 baculovirus populations extracted from two moth species to show that a large diversity of moth DNA sequences (n = 86) can integrate into viral genomes during the course of a viral infection. The majority of the 86 different moth DNA sequences are transposable elements (TEs, n = 69) belonging to 10 superfamilies of DNA transposons and three superfamilies of retrotransposons. The remaining 17 sequences are moth sequences of unknown nature. In addition to bona fide DNA transposition, we uncover microhomology-mediated recombination as a mechanism explaining integration of moth sequences into viral genomes. Many sequences integrated multiple times at multiple positions along the viral genome. We detected a total of 27,504 insertions of moth sequences in the 21 viral populations and we calculate that on average, 4.8% of viruses harbor at least one moth sequence in these populations. Despite this substantial proportion, no insertion of moth DNA was maintained in any viral population after 10 successive infection cycles. Hence, there is a constant turnover of host DNA inserted into viral genomes each time the virus infects a moth. Finally, we found that at least 21 of the moth TEs integrated into viral genomes underwent repeated horizontal transfers between various insect species, including some lepidopterans susceptible to baculoviruses. Our results identify host DNA influx as a potent source of genetic diversity in viral populations. They also support a role for baculoviruses as vectors of DNA HT between insects, and call for an evaluation of possible gene or TE spread when using viruses as biopesticides or gene delivery vectors. While gene exchange is known to occur between viruses and their hosts, this phenomenon has never been studied at the level of the viral population. Here we report that each time a virus from the Baculoviridae family infects a moth, a large number (dozens to hundreds) and high diversity of moth DNA sequences (86 different sequences) can integrate into replicating viral genomes. These findings show that viral populations carry a measurable load of host DNA sequences, further supporting the role of viruses as vectors of horizontal transfer of DNA between insect species. The potential uncontrolled gene spread associated with the use of viruses produced in insect cells as gene delivery vectors and/or biopesticides should therefore be evaluated.
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Affiliation(s)
- Clément Gilbert
- UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, Poitiers, France
- * E-mail:
| | - Jean Peccoud
- UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, Poitiers, France
| | - Aurélien Chateigner
- Institut de Recherche sur la Biologie de l’Insecte, UMR CNRS 7261, UFR des Sciences et Techniques, Université François-Rabelais, Tours, France
| | - Bouziane Moumen
- UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, Poitiers, France
| | - Richard Cordaux
- UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, Poitiers, France
| | - Elisabeth A. Herniou
- Institut de Recherche sur la Biologie de l’Insecte, UMR CNRS 7261, UFR des Sciences et Techniques, Université François-Rabelais, Tours, France
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Cheung S, Ma L, Chan PHW, Hu HL, Mayor T, Chen HT, Measday V. Ty1 Integrase Interacts with RNA Polymerase III-specific Subcomplexes to Promote Insertion of Ty1 Elements Upstream of Polymerase (Pol) III-transcribed Genes. J Biol Chem 2016; 291:6396-411. [PMID: 26797132 DOI: 10.1074/jbc.m115.686840] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Indexed: 01/01/2023] Open
Abstract
Retrotransposons are eukaryotic mobile genetic elements that transpose by reverse transcription of an RNA intermediate and are derived from retroviruses. The Ty1 retrotransposon of Saccharomyces cerevisiae belongs to the Ty1/Copia superfamily, which is present in every eukaryotic genome. Insertion of Ty1 elements into the S. cerevisiae genome, which occurs upstream of genes transcribed by RNA Pol III, requires the Ty1 element-encoded integrase (IN) protein. Here, we report that Ty1-IN interacts in vivo and in vitro with RNA Pol III-specific subunits to mediate insertion of Ty1 elements upstream of Pol III-transcribed genes. Purification of Ty1-IN from yeast cells followed by mass spectrometry (MS) analysis identified an enrichment of peptides corresponding to the Rpc82/34/31 and Rpc53/37 Pol III-specific subcomplexes. GFP-Trap purification of multiple GFP-tagged RNA Pol III subunits from yeast extracts revealed that the majority of Pol III subunits co-purify with Ty1-IN but not two other complexes required for Pol III transcription, transcription initiation factors (TF) IIIB and IIIC. In vitro binding studies with bacterially purified RNA Pol III proteins demonstrate that Rpc31, Rpc34, and Rpc53 interact directly with Ty1-IN. Deletion of the N-terminal 280 amino acids of Rpc53 abrogates insertion of Ty1 elements upstream of the hot spot SUF16 tRNA locus and abolishes the interaction of Ty1-IN with Rpc37. The Rpc53/37 complex therefore has an important role in targeting Ty1-IN to insert Ty1 elements upstream of Pol III-transcribed genes.
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Affiliation(s)
- Stephanie Cheung
- From the Department of Biochemistry and Molecular Biology, Wine Research Centre, and
| | | | - Patrick H W Chan
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada and
| | - Hui-Lan Hu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115
| | - Thibault Mayor
- From the Department of Biochemistry and Molecular Biology, Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada and
| | - Hung-Ta Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115
| | - Vivien Measday
- From the Department of Biochemistry and Molecular Biology, Wine Research Centre, and
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Servant G, Deininger PL. Insertion of Retrotransposons at Chromosome Ends: Adaptive Response to Chromosome Maintenance. Front Genet 2016; 6:358. [PMID: 26779254 PMCID: PMC4700185 DOI: 10.3389/fgene.2015.00358] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/10/2015] [Indexed: 01/30/2023] Open
Abstract
The telomerase complex is a specialized reverse transcriptase (RT) that inserts tandem DNA arrays at the linear chromosome ends and contributes to the protection of the genetic information in eukaryotic genomes. Telomerases are phylogenetically related to retrotransposons, encoding also the RT activity required for the amplification of their sequences throughout the genome. Intriguingly the telomerase gene is lost from the Drosophila genome and tandem retrotransposons replace telomeric sequences at the chromosome extremities. This observation suggests the versatility of RT activity in counteracting the chromosome shortening associated with genome replication and that retrotransposons can provide this activity in case of a dysfunctional telomerase. In this review paper, we describe the major classes of retroelements present in eukaryotic genomes in order to point out the differences and similarities with the telomerase complex. In a second part, we discuss the insertion of retroelements at the ends of chromosomes as an adaptive response for dysfunctional telomeres.
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Affiliation(s)
| | - Prescott L. Deininger
- Tulane Cancer Center, Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LAUSA
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35
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Garfinkel DJ, Tucker JM, Saha A, Nishida Y, Pachulska-Wieczorek K, Błaszczyk L, Purzycka KJ. A self-encoded capsid derivative restricts Ty1 retrotransposition in Saccharomyces. Curr Genet 2015; 62:321-9. [PMID: 26650614 DOI: 10.1007/s00294-015-0550-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 11/24/2015] [Indexed: 11/27/2022]
Abstract
Retrotransposons and retroviral insertions have molded the genomes of many eukaryotes. Since retroelements transpose via an RNA intermediate, the additive nature of the replication cycle can result in massive increases in copy number if left unchecked. Host organisms have countered with several defense systems, including domestication of retroelement genes that now act as restriction factors to minimize propagation. We discovered a novel truncated form of the Saccharomyces Ty1 retrotransposon capsid protein, dubbed p22 that inhibits virus-like particle (VLP) assembly and function. The p22 restriction factor expands the repertoire of defense proteins targeting the capsid and highlights a novel host-parasite strategy. Instead of inhibiting all transposition by domesticating the restriction gene as a distinct locus, Ty1 and budding yeast may have coevolved a relationship that allows high levels of transposition when Ty1 copy numbers are low and progressively less transposition as copy numbers rise. Here, we offer a perspective on p22 restriction, including its mode of expression, effect on VLP functions, interactions with its target, properties as a nucleic acid chaperone, similarities to other restriction factors, and future directions.
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Affiliation(s)
- David J Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, 30602, USA.
| | - Jessica M Tucker
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, 30602, USA
| | - Agniva Saha
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, 30602, USA
| | - Yuri Nishida
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, 30602, USA
| | - Katarzyna Pachulska-Wieczorek
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Leszek Błaszczyk
- Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - Katarzyna J Purzycka
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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36
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Jacobs JZ, Rosado-Lugo JD, Cranz-Mileva S, Ciccaglione KM, Tournier V, Zaratiegui M. Arrested replication forks guide retrotransposon integration. Science 2015; 349:1549-53. [PMID: 26404838 DOI: 10.1126/science.aaa3810] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Long terminal repeat (LTR) retrotransposons are an abundant class of genomic parasites that replicate by insertion of new copies into the host genome. Fungal LTR retrotransposons prevent mutagenic insertions through diverse targeting mechanisms that avoid coding sequences, but conserved principles guiding their target site selection have not been established. Here, we show that insertion of the fission yeast LTR retrotransposon Tf1 is guided by the DNA binding protein Sap1 and that the efficiency and location of the targeting depend on the activity of Sap1 as a replication fork barrier. We propose that Sap1 and the fork arrest it causes guide insertion of Tf1 by tethering the integration complex to target sites.
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Affiliation(s)
- Jake Z Jacobs
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Nelson A133, 604 Allison Road, Piscataway, NJ 08854, USA
| | - Jesus D Rosado-Lugo
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Nelson A133, 604 Allison Road, Piscataway, NJ 08854, USA
| | - Susanne Cranz-Mileva
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Nelson A133, 604 Allison Road, Piscataway, NJ 08854, USA
| | - Keith M Ciccaglione
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Nelson A133, 604 Allison Road, Piscataway, NJ 08854, USA
| | - Vincent Tournier
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Nelson A133, 604 Allison Road, Piscataway, NJ 08854, USA
| | - Mikel Zaratiegui
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Nelson A133, 604 Allison Road, Piscataway, NJ 08854, USA.
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Preferential retrotransposition in aging yeast mother cells is correlated with increased genome instability. DNA Repair (Amst) 2015; 34:18-27. [PMID: 26298836 DOI: 10.1016/j.dnarep.2015.07.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 07/05/2015] [Accepted: 07/19/2015] [Indexed: 01/02/2023]
Abstract
Retrotransposon expression or mobility is increased with age in multiple species and could promote genome instability or altered gene expression during aging. However, it is unclear whether activation of retrotransposons during aging is an indirect result of global changes in chromatin and gene regulation or a result of retrotransposon-specific mechanisms. Retromobility of a marked chromosomal Ty1 retrotransposon in Saccharomyces cerevisiae was elevated in mother cells relative to their daughter cells, as determined by magnetic cell sorting of mothers and daughters. Retromobility frequencies in aging mother cells were significantly higher than those predicted by cell age and the rate of mobility in young populations, beginning when mother cells were only several generations old. New Ty1 insertions in aging mothers were more strongly correlated with gross chromosome rearrangements than in young cells and were more often at non-preferred target sites. Mother cells were more likely to have high concentrations and bright foci of Ty1 Gag-GFP than their daughter cells. Levels of extrachromosomal Ty1 cDNA were also significantly higher in aged mother cell populations than their daughter cell populations. These observations are consistent with a retrotransposon-specific mechanism that causes retrotransposition to occur preferentially in yeast mother cells as they begin to age, as opposed to activation by phenotypic changes associated with very old age. These findings will likely be relevant for understanding retrotransposons and aging in many organisms, based on similarities in regulation and consequences of retrotransposition in diverse species.
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Maskell DP, Renault L, Serrao E, Lesbats P, Matadeen R, Hare S, Lindemann D, Engelman AN, Costa A, Cherepanov P. Structural basis for retroviral integration into nucleosomes. Nature 2015; 523:366-9. [PMID: 26061770 PMCID: PMC4530500 DOI: 10.1038/nature14495] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 04/15/2015] [Indexed: 01/01/2023]
Abstract
Retroviral integration is catalysed by a tetramer of integrase (IN) assembled on viral DNA ends in a stable complex, known as the intasome. How the intasome interfaces with chromosomal DNA, which exists in the form of nucleosomal arrays, is currently unknown. Here we show that the prototype foamy virus (PFV) intasome is proficient at stable capture of nucleosomes as targets for integration. Single-particle cryo-electron microscopy reveals a multivalent intasome-nucleosome interface involving both gyres of nucleosomal DNA and one H2A-H2B heterodimer. While the histone octamer remains intact, the DNA is lifted from the surface of the H2A-H2B heterodimer to allow integration at strongly preferred superhelix location ±3.5 positions. Amino acid substitutions disrupting these contacts impinge on the ability of the intasome to engage nucleosomes in vitro and redistribute viral integration sites on the genomic scale. Our findings elucidate the molecular basis for nucleosome capture by the viral DNA recombination machinery and the underlying nucleosome plasticity that allows integration.
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Affiliation(s)
- Daniel P. Maskell
- Chromatin Structure and Mobile DNA, Clare Hall Laboratories, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, UK
| | - Ludovic Renault
- Architecture and Dynamics of Macromolecular Machines, Clare Hall Laboratories, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, UK
- National Institute for Biological Standards and Control, Microscopy and Imaging, Blanche Lane, South Mimms, EN6 3QG, UK
| | - Erik Serrao
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Paul Lesbats
- Chromatin Structure and Mobile DNA, Clare Hall Laboratories, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, UK
| | - Rishi Matadeen
- NeCEN, Gorlaeus Laboratory, Einsteinweg 55, Leiden, 2333, The Netherlands
| | - Stephen Hare
- Division of Medicine, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Dirk Lindemann
- Institute of Virology, Technische Universität Dresden, Fetscherstr.74, Dresden, 01307, Germany
| | - Alan N. Engelman
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Alessandro Costa
- Architecture and Dynamics of Macromolecular Machines, Clare Hall Laboratories, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, UK
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA, Clare Hall Laboratories, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, UK
- Division of Medicine, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
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Bridier-Nahmias A, Tchalikian-Cosson A, Baller JA, Menouni R, Fayol H, Flores A, Saïb A, Werner M, Voytas DF, Lesage P. Retrotransposons. An RNA polymerase III subunit determines sites of retrotransposon integration. Science 2015; 348:585-8. [PMID: 25931562 DOI: 10.1126/science.1259114] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Mobile genetic elements are ubiquitous. Their integration site influences genome stability and gene expression. The Ty1 retrotransposon of the yeast Saccharomyces cerevisiae integrates upstream of RNA polymerase III (Pol III)-transcribed genes, yet the primary determinant of target specificity has remained elusive. Here we describe an interaction between Ty1 integrase and the AC40 subunit of Pol III and demonstrate that AC40 is the predominant determinant targeting Ty1 integration upstream of Pol III-transcribed genes. Lack of an integrase-AC40 interaction dramatically alters target site choice, leading to a redistribution of Ty1 insertions in the genome, mainly to chromosome ends. The mechanism of target specificity allows Ty1 to proliferate and yet minimizes genetic damage to its host.
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Affiliation(s)
- Antoine Bridier-Nahmias
- Université Paris Diderot, Sorbonne Paris Cité, INSERM U944, CNRS UMR 7212, Institut Universitaire d'Hématologie, Hôpital St. Louis, 75010 Paris, France. Department CASER Conservatoire National des Arts et Métiers (Cnam), 75003 Paris, France
| | - Aurélie Tchalikian-Cosson
- Université Paris Diderot, Sorbonne Paris Cité, INSERM U944, CNRS UMR 7212, Institut Universitaire d'Hématologie, Hôpital St. Louis, 75010 Paris, France
| | - Joshua A Baller
- Department of Genetics, Cell Biology and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA. Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rachid Menouni
- Université Paris Diderot, Sorbonne Paris Cité, INSERM U944, CNRS UMR 7212, Institut Universitaire d'Hématologie, Hôpital St. Louis, 75010 Paris, France
| | - Hélène Fayol
- Université Paris Diderot, Sorbonne Paris Cité, INSERM U944, CNRS UMR 7212, Institut Universitaire d'Hématologie, Hôpital St. Louis, 75010 Paris, France
| | - Amando Flores
- IBiTec-S, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), CNRS, Université Paris-Sud, CP 22, CEA-Saclay, 91191 Gif-sur-Yvette, France
| | - Ali Saïb
- Université Paris Diderot, Sorbonne Paris Cité, INSERM U944, CNRS UMR 7212, Institut Universitaire d'Hématologie, Hôpital St. Louis, 75010 Paris, France. Department CASER Conservatoire National des Arts et Métiers (Cnam), 75003 Paris, France
| | - Michel Werner
- IBiTec-S, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), CNRS, Université Paris-Sud, CP 22, CEA-Saclay, 91191 Gif-sur-Yvette, France
| | - Daniel F Voytas
- Department of Genetics, Cell Biology and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Pascale Lesage
- Université Paris Diderot, Sorbonne Paris Cité, INSERM U944, CNRS UMR 7212, Institut Universitaire d'Hématologie, Hôpital St. Louis, 75010 Paris, France.
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Abstract
Long-terminal repeat (LTR)-retrotransposons generate a copy of their DNA (cDNA) by reverse transcription of their RNA genome in cytoplasmic nucleocapsids. They are widespread in the eukaryotic kingdom and are the evolutionary progenitors of retroviruses [1]. The Ty1 element of the budding yeast Saccharomyces cerevisiae was the first LTR-retrotransposon demonstrated to mobilize through an RNA intermediate, and not surprisingly, is the best studied. The depth of our knowledge of Ty1 biology stems not only from the predominance of active Ty1 elements in the S. cerevisiae genome but also the ease and breadth of genomic, biochemical and cell biology approaches available to study cellular processes in yeast. This review describes the basic structure of Ty1 and its gene products, the replication cycle, the rapidly expanding compendium of host co-factors known to influence retrotransposition and the nature of Ty1's elaborate symbiosis with its host. Our goal is to illuminate the value of Ty1 as a paradigm to explore the biology of LTR-retrotransposons in multicellular organisms, where the low frequency of retrotransposition events presents a formidable barrier to investigations of retrotransposon biology.
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41
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Ho KL, Ma L, Cheung S, Manhas S, Fang N, Wang K, Young B, Loewen C, Mayor T, Measday V. A role for the budding yeast separase, Esp1, in Ty1 element retrotransposition. PLoS Genet 2015; 11:e1005109. [PMID: 25822502 PMCID: PMC4378997 DOI: 10.1371/journal.pgen.1005109] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 02/27/2015] [Indexed: 12/18/2022] Open
Abstract
Separase/Esp1 is a protease required at the onset of anaphase to cleave cohesin and thereby enable sister chromatid separation. Esp1 also promotes release of the Cdc14 phosphatase from the nucleolus to enable mitotic exit. To uncover other potential roles for separase, we performed two complementary genome-wide genetic interaction screens with a strain carrying the budding yeast esp1-1 separase mutation. We identified 161 genes that when mutated aggravate esp1-1 growth and 44 genes that upon increased dosage are detrimental to esp1-1 viability. In addition to the expected cell cycle and sister chromatid segregation genes that were identified, 24% of the genes identified in the esp1-1 genetic screens have a role in Ty1 element retrotransposition. Retrotransposons, like retroviruses, replicate through reverse transcription of an mRNA intermediate and the resultant cDNA product is integrated into the genome by a conserved transposon or retrovirus encoded integrase protein. We purified Esp1 from yeast and identified an interaction between Esp1 and Ty1 integrase using mass spectrometry that was subsequently confirmed by co-immunoprecipitation analysis. Ty1 transposon mobility and insertion upstream of the SUF16 tRNA gene are both reduced in an esp1-1 strain but increased in cohesin mutant strains. Securin/Pds1, which is required for efficient localization of Esp1 to the nucleus, is also required for efficient Ty1 transposition. We propose that Esp1 serves two roles to mediate Ty1 transposition - one to remove cohesin and the second to target Ty1-IN to chromatin.
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Affiliation(s)
- Krystina L. Ho
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Wine Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lina Ma
- Wine Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephanie Cheung
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Wine Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Savrina Manhas
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Wine Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nancy Fang
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kaiqian Wang
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Wine Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Barry Young
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher Loewen
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Thibault Mayor
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Vivien Measday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Wine Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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42
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El Hage A, Webb S, Kerr A, Tollervey D. Genome-wide distribution of RNA-DNA hybrids identifies RNase H targets in tRNA genes, retrotransposons and mitochondria. PLoS Genet 2014; 10:e1004716. [PMID: 25357144 PMCID: PMC4214602 DOI: 10.1371/journal.pgen.1004716] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Accepted: 08/27/2014] [Indexed: 01/08/2023] Open
Abstract
During transcription, the nascent RNA can invade the DNA template, forming extended RNA-DNA duplexes (R-loops). Here we employ ChIP-seq in strains expressing or lacking RNase H to map targets of RNase H activity throughout the budding yeast genome. In wild-type strains, R-loops were readily detected over the 35S rDNA region, transcribed by Pol I, and over the 5S rDNA, transcribed by Pol III. In strains lacking RNase H activity, R-loops were elevated over other Pol III genes, notably tRNAs, SCR1 and U6 snRNA, and were also associated with the cDNAs of endogenous TY1 retrotransposons, which showed increased rates of mobility to the 5′-flanking regions of tRNA genes. Unexpectedly, R-loops were also associated with mitochondrial genes in the absence of RNase H1, but not of RNase H2. Finally, R-loops were detected on actively transcribed protein-coding genes in the wild-type, particularly over the second exon of spliced ribosomal protein genes. R-loops (RNA-DNA hybrids) are potentially deleterious for gene expression and genome stability, but can be beneficial, for example, during immunoglobulin gene class-switch recombination. Here we made use of antibody S9.6, with specificity for RNA-DNA duplexes independently of their sequence. The genome-wide distribution of R-loops in wild-type yeast showed association with the highly transcribed ribosomal DNA, and protein-coding genes, particularly the second exon of spliced genes. On RNA polymerase III loci such as the highly transcribed transfer RNA genes (tRNAs), R-loop accumulation was strongly detected in the absence of both ribonucleases H1 and H2 (RNase H1 and H2), indicating that R-loops are inherently formed but rapidly cleared by RNase H. Importantly, stable R-loops lead to reduced synthesis of tRNA precursors in mutants lacking RNase H and DNA topoisomerase activities. RNA-DNA hybrids associated with TY1 cDNA retrotransposition intermediates were elevated in the absence of RNase H, and this was accompanied by increased retrotransposition, in particular to 5′-flanking regions of tRNAs. Our findings show that RNase H participates in silencing of TY1 life cycle. Surprisingly, R-loops associated with mitochondrial transcription units were suppressed specifically by RNase H1. These findings have potentially important implications for understanding human diseases caused by mutations in RNase H.
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Affiliation(s)
- Aziz El Hage
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (AEH); (DT)
| | - Shaun Webb
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Alastair Kerr
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - David Tollervey
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (AEH); (DT)
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Zhou K, Kuo A, Grigoriev IV. Reverse transcriptase and intron number evolution. Stem Cell Investig 2014; 1:17. [PMID: 27358863 DOI: 10.3978/j.issn.2306-9759.2014.08.01] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 08/04/2014] [Indexed: 11/14/2022]
Abstract
BACKGROUND Introns are universal in eukaryotic genomes and play important roles in transcriptional regulation, mRNA export to the cytoplasm, nonsense-mediated decay as both a regulatory and a splicing quality control mechanism, R-loop avoidance, alternative splicing, chromatin structure, and evolution by exon-shuffling. METHODS Sixteen complete fungal genomes were used 13 of which were sequenced and annotated by JGI. Ustilago maydis, Cryptococcus neoformans, and Coprinus cinereus (also named Coprinopsis cinerea) were from the Broad Institute. Gene models from JGI-annotated genomes were taken from the GeneCatalog track that contained the best representative gene models. Varying fractions of the GeneCatalog were manually curated by external users. For clarity, we used the JGI unique database identifier. RESULTS The last common ancestor of eukaryotes (LECA) has an estimated 6.4 coding exons per gene (EPG) and evolved into the diverse eukaryotic life forms, which is recapitulated by the development of a stem cell. We found a parallel between the simulated reverse transcriptase (RT)-mediated intron loss and the comparative analysis of 16 fungal genomes that spanned a wide range of intron density. Although footprints of RT (RTF) were dynamic, relative intron location (RIL) to the 5'-end of mRNA faithfully traced RT-mediated intron loss and revealed 7.7 EPG for LECA. The mode of exon length distribution was conserved in simulated intron loss, which was exemplified by the shared mode of 75 nt between fungal and Chlamydomonas genomes. The dominant ancient exon length was corroborated by the average exon length of the most intron-rich genes in fungal genomes and consistent with ancient protein modules being ~25 aa. Combined with the conservation of a protein length of 400 aa, the earliest ancestor of eukaryotes could have 16 EPG. During earlier evolution, Ascomycota's ancestor had significantly more 3'-biased RT-mediated intron loss that was followed by dramatic RTF loss. There was a down trend of EPG from more conserved to less conserved genes. Moreover, species-specific genes have higher exon-densities, shorter exons, and longer introns when compared to genes conserved at the phylum level. However, intron length in species-specific genes became shorter than that of genes conserved in all species after genomes experiencing drastic intron loss. The estimated EPG from the most frequent exon length is more than double that from the RIL method. CONCLUSIONS This implies significant intron loss during the very early period of eukaryotic evolution. De novo gene-birth contributes to shorter exons, longer introns, and higher exon-density in species-specific genes relative to conserved genes.
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Affiliation(s)
- Kemin Zhou
- 1 Computational Genomics, Bristol-Myers Squibb, 311 Pennington Rocky Hill Road, Pennington, NJ 08534, USA ; 2 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Alan Kuo
- 1 Computational Genomics, Bristol-Myers Squibb, 311 Pennington Rocky Hill Road, Pennington, NJ 08534, USA ; 2 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Igor V Grigoriev
- 1 Computational Genomics, Bristol-Myers Squibb, 311 Pennington Rocky Hill Road, Pennington, NJ 08534, USA ; 2 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
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Aiyer S, Swapna GVT, Malani N, Aramini JM, Schneider WM, Plumb MR, Ghanem M, Larue RC, Sharma A, Studamire B, Kvaratskhelia M, Bushman FD, Montelione GT, Roth MJ. Altering murine leukemia virus integration through disruption of the integrase and BET protein family interaction. Nucleic Acids Res 2014; 42:5917-28. [PMID: 24623816 PMCID: PMC4027182 DOI: 10.1093/nar/gku175] [Citation(s) in RCA: 53] [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: 11/12/2013] [Revised: 02/12/2014] [Accepted: 02/12/2014] [Indexed: 12/17/2022] Open
Abstract
We report alterations to the murine leukemia virus (MLV) integrase (IN) protein that successfully result in decreasing its integration frequency at transcription start sites and CpG islands, thereby reducing the potential for insertional activation. The host bromo and extraterminal (BET) proteins Brd2, 3 and 4 interact with the MLV IN protein primarily through the BET protein ET domain. Using solution NMR, protein interaction studies, and next generation sequencing, we show that the C-terminal tail peptide region of MLV IN is important for the interaction with BET proteins and that disruption of this interaction through truncation mutations affects the global targeting profile of MLV vectors. The use of the unstructured tails of gammaretroviral INs to direct association with complexes at active promoters parallels that used by histones and RNA polymerase II. Viruses bearing MLV IN C-terminal truncations can provide new avenues to improve the safety profile of gammaretroviral vectors for human gene therapy.
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Affiliation(s)
- Sriram Aiyer
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, 675 Hoes Lane, Piscataway, NJ 08854, USA
| | - G V T Swapna
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, 679 Hoes Lane West Piscataway, NJ 08854, USA
| | - Nirav Malani
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA 19104, USA
| | - James M Aramini
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, 679 Hoes Lane West Piscataway, NJ 08854, USA
| | - William M Schneider
- Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, 675 Hoes Lane, Piscataway, NJ 08854, USA
| | - Matthew R Plumb
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, 484 W. 12th Ave., 508 Riffe Building, Columbus, OH 43210, USA
| | - Mustafa Ghanem
- Department of Biology, Brooklyn College, 417 Ingersoll Extension and the Graduate Center of the City University of New York, Brooklyn, NY 11210, USA
| | - Ross C Larue
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, 484 W. 12th Ave., 508 Riffe Building, Columbus, OH 43210, USA
| | - Amit Sharma
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, 484 W. 12th Ave., 508 Riffe Building, Columbus, OH 43210, USA
| | - Barbara Studamire
- Department of Biology, Brooklyn College, 417 Ingersoll Extension and the Graduate Center of the City University of New York, Brooklyn, NY 11210, USA
| | - Mamuka Kvaratskhelia
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, 484 W. 12th Ave., 508 Riffe Building, Columbus, OH 43210, USA
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA 19104, USA
| | - Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, 679 Hoes Lane West Piscataway, NJ 08854, USA Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, 675 Hoes Lane, Piscataway, NJ 08854, USA
| | - Monica J Roth
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, 675 Hoes Lane, Piscataway, NJ 08854, USA Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, 675 Hoes Lane, Piscataway, NJ 08854, USA
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Shapiro JA. Epigenetic control of mobile DNA as an interface between experience and genome change. Front Genet 2014; 5:87. [PMID: 24795749 PMCID: PMC4007016 DOI: 10.3389/fgene.2014.00087] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/01/2014] [Indexed: 12/29/2022] Open
Abstract
Mobile DNA in the genome is subject to RNA-targeted epigenetic control. This control regulates the activity of transposons, retrotransposons and genomic proviruses. Many different life history experiences alter the activities of mobile DNA and the expression of genetic loci regulated by nearby insertions. The same experiences induce alterations in epigenetic formatting and lead to trans-generational modifications of genome expression and stability. These observations lead to the hypothesis that epigenetic formatting directed by non-coding RNA provides a molecular interface between life history events and genome alteration.
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Affiliation(s)
- James A. Shapiro
- Department of Biochemistry and Molecular Biology, University of ChicagoChicago, IL, USA
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46
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Bridier-Nahmias A, Lesage P. Two large-scale analyses of Ty1 LTR-retrotransposon de novo insertion events indicate that Ty1 targets nucleosomal DNA near the H2A/H2B interface. Mob DNA 2012; 3:22. [PMID: 23244340 PMCID: PMC3545840 DOI: 10.1186/1759-8753-3-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 08/29/2012] [Indexed: 11/10/2022] Open
Abstract
UNLABELLED BACKGROUND Over the years, a number of reports have revealed that Ty1 integration occurs in a 1-kb window upstream of Pol III-transcribed genes with an approximate 80-bp periodicity between each integration hotspot and that this targeting requires active Pol III transcription at the site of integration. However, the molecular bases of Ty1 targeting are still not understood. FINDINGS The publications by Baller et al. and Mularoni et al. in the April issue of Genome Res. report the first high-throughput sequencing analysis of Ty1 de novo insertion events. Their observations converge to the same conclusion, that Ty1 targets a specific surface of the nucleosome at he H2A/H2B interface. CONCLUSION This discovery is important, and should help identifying factor(s) involved in Ty1 targeting. Recent data on transposable elements and retroviruses integration site choice obtained by large-scale analyses indicate that transcription and chromatin structure play an important role in this process. The studies reported in this commentary add a new evidence of the importance of chromatin in integration selectivity that should be of interest for everyone interested in transposable elements integration.
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Affiliation(s)
- Antoine Bridier-Nahmias
- CNRS/P7 UMR7212, INSERMU 944, Laboratoire Pathologie et Virologie Moléculaire Institut Universitaire d'Hématologie, 1 avenue Claude Vellefaux, F75010, Paris, France.
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Carr M, Bensasson D, Bergman CM. Evolutionary genomics of transposable elements in Saccharomyces cerevisiae. PLoS One 2012; 7:e50978. [PMID: 23226439 PMCID: PMC3511429 DOI: 10.1371/journal.pone.0050978] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 10/31/2012] [Indexed: 11/18/2022] Open
Abstract
Saccharomyces cerevisiae is one of the premier model systems for studying the genomics and evolution of transposable elements. The availability of the S. cerevisiae genome led to unprecedented insights into its five known transposable element families (the LTR retrotransposons Ty1-Ty5) in the years shortly after its completion. However, subsequent advances in bioinformatics tools for analysing transposable elements and the recent availability of genome sequences for multiple strains and species of yeast motivates new investigations into Ty evolution in S. cerevisiae. Here we provide a comprehensive phylogenetic and population genetic analysis of all Ty families in S. cerevisiae based on a systematic re-annotation of Ty elements in the S288c reference genome. We show that previous annotation efforts have underestimated the total copy number of Ty elements for all known families. In addition, we identify a new family of Ty3-like elements related to the S. paradoxus Ty3p which is composed entirely of degenerate solo LTRs. Phylogenetic analyses of LTR sequences identified three families with short-branch, recently active clades nested among long branch, inactive insertions (Ty1, Ty3, Ty4), one family with essentially all recently active elements (Ty2) and two families with only inactive elements (Ty3p and Ty5). Population genomic data from 38 additional strains of S. cerevisiae show that the majority of Ty insertions in the S288c reference genome are fixed in the species, with insertions in active clades being predominantly polymorphic and insertions in inactive clades being predominantly fixed. Finally, we use comparative genomic data to provide evidence that the Ty2 and Ty3p families have arisen in the S. cerevisiae genome by horizontal transfer. Our results demonstrate that the genome of a single individual contains important information about the state of TE population dynamics within a species and suggest that horizontal transfer may play an important role in shaping the genomic diversity of transposable elements in unicellular eukaryotes.
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Affiliation(s)
- Martin Carr
- School of Applied Sciences, University of Huddersfield, West Yorkshire, UK.
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Abstract
Transposable elements possess specific patterns of integration. The biological impact of these integration profiles is not well understood. Tf1, a long-terminal repeat retrotransposon in Schizosaccharomyces pombe, integrates into promoters with a preference for the promoters of stress response genes. To determine the biological significance of Tf1 integration, we took advantage of saturated maps of insertion activity and studied how integration at hot spots affected the expression of the adjacent genes. Our study revealed that Tf1 integration did not reduce gene expression. Importantly, the insertions activated the expression of 6 of 32 genes tested. We found that Tf1 increased gene expression by inserting enhancer activity. Interestingly, the enhancer activity of Tf1 could be limited by Abp1, a host surveillance factor that sequesters transposon sequences into structures containing histone deacetylases. We found the Tf1 promoter was activated by heat treatment and, remarkably, only genes that themselves were induced by heat could be activated by Tf1 integration, suggesting a synergy of Tf1 enhancer sequence with the stress response elements of target promoters. We propose that the integration preference of Tf1 for the promoters of stress response genes and the ability of Tf1 to enhance the expression of these genes co-evolved to promote the survival of cells under stress.
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Affiliation(s)
- Gang Feng
- Section on Eukaryotic Transposable Elements, Program in Cellular Regulation and Metabolism, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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Aslankoohi E, Voordeckers K, Sun H, Sanchez-Rodriguez A, van der Zande E, Marchal K, Verstrepen KJ. Nucleosomes affect local transformation efficiency. Nucleic Acids Res 2012; 40:9506-12. [PMID: 22904077 PMCID: PMC3479212 DOI: 10.1093/nar/gks777] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Genetic transformation is a natural process during which foreign DNA enters a cell and integrates into the genome. Apart from its relevance for horizontal gene transfer in nature, transformation is also the cornerstone of today's recombinant gene technology. Despite its importance, relatively little is known about the factors that determine transformation efficiency. We hypothesize that differences in DNA accessibility associated with nucleosome positioning may affect local transformation efficiency. We investigated the landscape of transformation efficiency at various positions in the Saccharomyces cerevisiae genome and correlated these measurements with nucleosome positioning. We find that transformation efficiency shows a highly significant inverse correlation with relative nucleosome density. This correlation was lost when the nucleosome pattern, but not the underlying sequence was changed. Together, our results demonstrate a novel role for nucleosomes and also allow researchers to predict transformation efficiency of a target region and select spots in the genome that are likely to yield higher transformation efficiency.
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Affiliation(s)
- Elham Aslankoohi
- Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, B-3001 Leuven, Belgium
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Risler JK, Kenny AE, Palumbo RJ, Gamache ER, Curcio MJ. Host co-factors of the retrovirus-like transposon Ty1. Mob DNA 2012; 3:12. [PMID: 22856544 PMCID: PMC3522557 DOI: 10.1186/1759-8753-3-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 06/18/2012] [Indexed: 11/10/2022] Open
Abstract
UNLABELLED BACKGROUND Long-terminal repeat (LTR) retrotransposons have complex modes of mobility involving reverse transcription of their RNA genomes in cytoplasmic virus-like particles (VLPs) and integration of the cDNA copies into the host genome. The limited coding capacity of retrotransposons necessitates an extensive reliance on host co-factors; however, it has been challenging to identify co-factors that are required for endogenous retrotransposon mobility because retrotransposition is such a rare event. RESULTS To circumvent the low frequency of Ty1 LTR-retrotransposon mobility in Saccharomyces cerevisiae, we used iterative synthetic genetic array (SGA) analysis to isolate host mutations that reduce retrotransposition. Query strains that harbor a chromosomal Ty1his3AI reporter element and either the rtt101Δ or med1Δ mutation, both of which confer a hypertransposition phenotype, were mated to 4,847 haploid ORF deletion strains. Retrotransposition was measured in the double mutant progeny, and a set of 275 ORF deletions that suppress the hypertransposition phenotypes of both rtt101Δ and med1Δ were identified. The corresponding set of 275 retrotransposition host factors (RHFs) includes 45 previously identified Ty1 or Ty3 co-factors. More than half of the RHF genes have statistically robust human homologs (E < 1 x 10-10). The level of unintegrated Ty1 cDNA in 181 rhfΔ single mutants was altered <2-fold, suggesting that the corresponding co-factors stimulate retrotransposition at a step after cDNA synthesis. However, deletion of 43 RHF genes, including specific ribosomal protein and ribosome biogenesis genes and RNA degradation, modification and transport genes resulted in low Ty1 cDNA levels. The level of Ty1 Gag but not RNA was reduced in ribosome biogenesis mutants bud21Δ, hcr1Δ, loc1Δ, and puf6Δ. CONCLUSION Ty1 retrotransposition is dependent on multiple co-factors acting at different steps in the replication cycle. Human orthologs of these RHFs are potential, or in a few cases, presumptive HIV-1 co-factors in human cells. RHF genes whose absence results in decreased Ty1 cDNA include characterized RNA metabolism and modification genes, consistent with their having roles in early steps in retrotransposition such as expression, nuclear export, translation, localization, or packaging of Ty1 RNA. Our results suggest that Bud21, Hcr1, Loc1, and Puf6 promote efficient synthesis or stability of Ty1 Gag.
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Affiliation(s)
- Jenni K Risler
- Laboratory of Molecular Genetics, Wadsworth Center, Albany, NY, 12201, USA.
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