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Han S, Basting PJ, Dias GB, Luhur A, Zelhof AC, Bergman CM. Transposable element profiles reveal cell line identity and loss of heterozygosity in Drosophila cell culture. Genetics 2021; 219:6321957. [PMID: 34849875 PMCID: PMC8633141 DOI: 10.1093/genetics/iyab113] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/01/2021] [Indexed: 11/28/2022] Open
Abstract
Cell culture systems allow key insights into biological mechanisms yet suffer from irreproducible outcomes in part because of cross-contamination or mislabeling of cell lines. Cell line misidentification can be mitigated by the use of genotyping protocols, which have been developed for human cell lines but are lacking for many important model species. Here, we leverage the classical observation that transposable elements (TEs) proliferate in cultured Drosophila cells to demonstrate that genome-wide TE insertion profiles can reveal the identity and provenance of Drosophila cell lines. We identify multiple cases where TE profiles clarify the origin of Drosophila cell lines (Sg4, mbn2, and OSS_E) relative to published reports, and also provide evidence that insertions from only a subset of long-terminal repeat retrotransposon families are necessary to mark Drosophila cell line identity. We also develop a new bioinformatics approach to detect TE insertions and estimate intra-sample allele frequencies in legacy whole-genome sequencing data (called ngs_te_mapper2), which revealed loss of heterozygosity as a mechanism shaping the unique TE profiles that identify Drosophila cell lines. Our work contributes to the general understanding of the forces impacting metazoan genomes as they evolve in cell culture and paves the way for high-throughput protocols that use TE insertions to authenticate cell lines in Drosophila and other organisms.
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Affiliation(s)
- Shunhua Han
- Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Preston J Basting
- Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Guilherme B Dias
- Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.,Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Arthur Luhur
- Drosophila Genomics Resource Center, Indiana University, Bloomington, IN 47405, USA.,Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Andrew C Zelhof
- Drosophila Genomics Resource Center, Indiana University, Bloomington, IN 47405, USA.,Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Casey M Bergman
- Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.,Department of Genetics, University of Georgia, Athens, GA 30602, USA
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Mohamed M, Dang NTM, Ogyama Y, Burlet N, Mugat B, Boulesteix M, Mérel V, Veber P, Salces-Ortiz J, Severac D, Pélisson A, Vieira C, Sabot F, Fablet M, Chambeyron S. A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore. Cells 2020; 9:E1776. [PMID: 32722451 PMCID: PMC7465170 DOI: 10.3390/cells9081776] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/17/2020] [Accepted: 07/23/2020] [Indexed: 11/17/2022] Open
Abstract
Transposable elements (TEs) are the main components of genomes. However, due to their repetitive nature, they are very difficult to study using data obtained with short-read sequencing technologies. Here, we describe an efficient pipeline to accurately recover TE insertion (TEI) sites and sequences from long reads obtained by Oxford Nanopore Technology (ONT) sequencing. With this pipeline, we could precisely describe the landscapes of the most recent TEIs in wild-type strains of Drosophila melanogaster and Drosophila simulans. Their comparison suggests that this subset of TE sequences is more similar than previously thought in these two species. The chromosome assemblies obtained using this pipeline also allowed recovering piRNA cluster sequences, which was impossible using short-read sequencing. Finally, we used our pipeline to analyze ONT sequencing data from a D. melanogaster unstable line in which LTR transposition was derepressed for 73 successive generations. We could rely on single reads to identify new insertions with intact target site duplications. Moreover, the detailed analysis of TEIs in the wild-type strains and the unstable line did not support the trap model claiming that piRNA clusters are hotspots of TE insertions.
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Affiliation(s)
- Mourdas Mohamed
- Institute of Human Genetics, UMR9002, CNRS and Montpellier University, 34396 Montpellier, France; (M.M.); (Y.O.); (B.M.); (A.P.)
| | - Nguyet Thi-Minh Dang
- IRD/UM UMR DIADE, 911 avenue Agropolis BP64501, 34394 Montpellier, France; (N.T.-M.D.); (F.S.)
| | - Yuki Ogyama
- Institute of Human Genetics, UMR9002, CNRS and Montpellier University, 34396 Montpellier, France; (M.M.); (Y.O.); (B.M.); (A.P.)
| | - Nelly Burlet
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
| | - Bruno Mugat
- Institute of Human Genetics, UMR9002, CNRS and Montpellier University, 34396 Montpellier, France; (M.M.); (Y.O.); (B.M.); (A.P.)
| | - Matthieu Boulesteix
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
| | - Vincent Mérel
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
| | - Philippe Veber
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
| | - Judit Salces-Ortiz
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Dany Severac
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, 34094 Montpellier, France;
| | - Alain Pélisson
- Institute of Human Genetics, UMR9002, CNRS and Montpellier University, 34396 Montpellier, France; (M.M.); (Y.O.); (B.M.); (A.P.)
| | - Cristina Vieira
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
| | - François Sabot
- IRD/UM UMR DIADE, 911 avenue Agropolis BP64501, 34394 Montpellier, France; (N.T.-M.D.); (F.S.)
| | - Marie Fablet
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
| | - Séverine Chambeyron
- Institute of Human Genetics, UMR9002, CNRS and Montpellier University, 34396 Montpellier, France; (M.M.); (Y.O.); (B.M.); (A.P.)
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Qiu GH. Genome defense against exogenous nucleic acids in eukaryotes by non-coding DNA occurs through CRISPR-like mechanisms in the cytosol and the bodyguard protection in the nucleus. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2016; 767:31-41. [DOI: 10.1016/j.mrrev.2016.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 10/22/2015] [Accepted: 01/03/2016] [Indexed: 02/07/2023]
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Abstract
Retroelements with long-terminal repeats (LTRs) inhabit nearly all eukaryotic genomes. During the time of their rich evolutionary history they have developed highly diverse forms, ranging from ordinary retrotransposons to complex pathogenic retroviruses such as HIV-I. Errantiviruses are a group of insect endogenous LTR elements that share structural and functional features with vertebrate endogenous retroviruses. The errantiviruses illustrate one of the evolutionary strategies of retrotransposons to become infective, which together with their similarities to vertebrate retroviruses make them an attractive object of research promising to shed more light on the evolution of retroviruses.
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Affiliation(s)
- Yury Stefanov
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; Moscow, Russia
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Insulator and Ovo proteins determine the frequency and specificity of insertion of the gypsy retrotransposon in Drosophila melanogaster. Genetics 2008; 180:1367-78. [PMID: 18791225 DOI: 10.1534/genetics.108.094318] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The gypsy retrovirus of Drosophila is quite unique among retroviruses in that it shows a strong preference for integration into specific sites in the genome. In particular, gypsy integrates with a frequency of > 10% into the regulatory region of the ovo gene. We have used in vivo transgenic assays to dissect the role of Ovo proteins and the gypsy insulator during the process of gypsy site-specific integration. Here we show that DNA containing binding sites for the Ovo protein is required to promote site-specific gypsy integration into the regulatory region of the ovo gene. Using a synthetic sequence, we find that Ovo binding sites alone are also sufficient to promote gypsy site-specific integration into transgenes. These results indicate that Ovo proteins can determine the specificity of gypsy insertion. In addition, we find that interactions between a gypsy provirus and the gypsy preintegration complex may also participate in the process leading to the selection of gypsy integration sites. Finally, the results suggest that the relative orientation of two integrated gypsy sequences has an important role in the enhancer-blocking activity of the gypsy insulator.
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Faye B, Arnaud F, Peyretaillade E, Brasset E, Dastugue B, Vaury C. Functional characteristics of a highly specific integrase encoded by an LTR-retrotransposon. PLoS One 2008; 3:e3185. [PMID: 18784842 PMCID: PMC2527525 DOI: 10.1371/journal.pone.0003185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2008] [Accepted: 08/03/2008] [Indexed: 12/18/2022] Open
Abstract
Background The retroviral Integrase protein catalyzes the insertion of linear viral DNA into host cell DNA. Although different retroviruses have been shown to target distinctive chromosomal regions, few of them display a site-specific integration. ZAM, a retroelement from Drosophila melanogaster very similar in structure and replication cycle to mammalian retroviruses is highly site-specific. Indeed, ZAM copies target the genomic 5′-CGCGCg-3′ consensus-sequences. To enlighten the determinants of this high integration specificity, we investigated the functional properties of its integrase protein denoted ZAM-IN. Principal Findings Here we show that ZAM-IN displays the property to nick DNA molecules in vitro. This endonuclease activity targets specific sequences that are present in a 388 bp fragment taken from the white locus and known to be a genomic ZAM integration site in vivo. Furthermore, ZAM-IN displays the unusual property to directly bind specific genomic DNA sequences. Two specific and independent sites are recognized within the 388 bp fragment of the white locus: the CGCGCg sequence and a closely apposed site different in sequence. Conclusion This study strongly argues that the intrinsic properties of ZAM-IN, ie its binding properties and its endonuclease activity, play an important part in ZAM integration specificity. Its ability to select two binding sites and to nick the DNA molecule reminds the strategy used by some site-specific recombination enzymes and forms the basis for site-specific integration strategies potentially useful in a broad range of genetic engineering applications.
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Affiliation(s)
- Babacar Faye
- UMR/CNRS 6247, Clermont Université, INSERM, U931, Faculté de Médecine, Clermont-Ferrand, France
| | - Frederick Arnaud
- UMR/CNRS 6247, Clermont Université, INSERM, U931, Faculté de Médecine, Clermont-Ferrand, France
| | - Eric Peyretaillade
- UMR/CNRS 6247, Clermont Université, INSERM, U931, Faculté de Médecine, Clermont-Ferrand, France
| | - Emilie Brasset
- UMR/CNRS 6247, Clermont Université, INSERM, U931, Faculté de Médecine, Clermont-Ferrand, France
| | - Bernard Dastugue
- UMR/CNRS 6247, Clermont Université, INSERM, U931, Faculté de Médecine, Clermont-Ferrand, France
| | - Chantal Vaury
- UMR/CNRS 6247, Clermont Université, INSERM, U931, Faculté de Médecine, Clermont-Ferrand, France
- * E-mail:
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Conte C, Dastugue B, Vaury C. Promoter competition as a mechanism of transcriptional interference mediated by retrotransposons. EMBO J 2002; 21:3908-16. [PMID: 12110602 PMCID: PMC126113 DOI: 10.1093/emboj/cdf367] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Enhancers can function over great distances and interact with almost any kind of promoter, but insulators or promoter competition generally limit their effect to a single gene. We provide in vivo evidence that retroelements may establish promoter competition with their neighboring genes and restrict the range of action of an enhancer. We report that the retroelement Idefix from Drosophila melanogaster inhibits white gene expression in testes by a promoter competition mechanism that does not occur in the eyes. The sequence specificity of the two TATA-less promoters of white and Idefix is a prime determinant in the competition that takes place in tissues where both are transcriptionally active. This study brings to light a novel mechanism whereby transcriptional interference by an active retrotransposon may perturb expression of neighboring genes. This capacity to interfere with the transcriptional regulation of their host, together with the facts that retroelements preferentially move within the germline and do not excise to replicate, suggest that these elements are cis-regulatory sequences able to imprint specific and heritable controls essential for eukaryotic gene regulation.
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Affiliation(s)
| | | | - Chantal Vaury
- Unité INSERM 384, Faculté de Médecine, 28 place Henri-Dunant, 63000 Clermont-Ferrand, France
Corresponding author e-mail:
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Conte C, Dastugue B, Vaury C. Coupling of enhancer and insulator properties identified in two retrotransposons modulates their mutagenic impact on nearby genes. Mol Cell Biol 2002; 22:1767-77. [PMID: 11865056 PMCID: PMC135603 DOI: 10.1128/mcb.22.6.1767-1777.2002] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We recently reported a novel transposition system in which two retroelements from Drosophila melanogaster, ZAM and Idefix, are highly mobilized and preferentially insert within intergenic regions. Among the loci where new copies are detected, a hot spot for their insertion was identified at the white locus, where up to three elements occurred within a 3-kb fragment upstream of the transcriptional start site of white. We have used these insertions as molecular entry points to throw light on the mutagenic effect exerted by multiple insertions of retrotransposons within intergenic regions of a genome. Analysis of the molecular mechanisms by which ZAM and Idefix elements interfere with the regulation of the white gene has shown that ZAM bears cis-acting regulatory sequences able to enhance transcription of the white gene in the eyes of the flies. This activation may be counteracted by Idefix, which acts as an insulator able to isolate the white gene from the upstream ZAM enhancer. In addition to revealing a novel insulator sequence with its own specific features, our data clearly illustrate how retroelements can act as epigenetic factors able to interfere with the transcriptional regulation of their host.
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Affiliation(s)
- Caroline Conte
- Unité INSERM 384, Faculté de Médecine, 28 place Henri-Dunant, 63000 Clermont-Ferrand, France
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Marsano RM, Moschetti R, Caggese C, Lanave C, Barsanti P, Caizzi R. The complete Tirant transposable element in Drosophila melanogaster shows a structural relationship with retrovirus-like retrotransposons. Gene 2000; 247:87-95. [PMID: 10773447 DOI: 10.1016/s0378-1119(00)00115-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We have determined the structure and organization of Tirant, a retrotransposon of Drosophila melanogaster reported in literature to be responsible for four independent mutations. Tirant is a long terminal repeat (LTR) retrotransposon 8527bp long. It possesses three open reading frames (ORF) encoding Gag, Pol and Env proteins with a strong similarity with ZAM, a recently identified member of the gypsy class of retrovirus-like mobile elements. Molecular analysis of the Tirant genomic copies present in four D. melanogaster strains revealed that most of them are defective, non-autonomous elements that differ in the position and extension of the conserved internal portion. Defective elements lacking the Gag ORF but retaining the Env ORF are abundant in heterochromatin. Four discrete Tirant transcripts are observed during embryogenesis in the strain Oregon-R, the smaller of which, 1.8kb in size, originates from the splicing of a primary transcript and leads to a subgenomic RNA coding for the Env product.
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Affiliation(s)
- R M Marsano
- Istituto di Genetica, Università di Bari, Via Amendola 165/A, 70126, Bari, Italy
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