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Fablet M, Salces-Ortiz J, Jacquet A, Menezes BF, Dechaud C, Veber P, Rebollo R, Vieira C. A Quantitative, Genome-Wide Analysis in Drosophila Reveals Transposable Elements' Influence on Gene Expression Is Species-Specific. Genome Biol Evol 2023; 15:evad160. [PMID: 37652057 PMCID: PMC10492446 DOI: 10.1093/gbe/evad160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/02/2023] Open
Abstract
Transposable elements (TEs) are parasite DNA sequences that are able to move and multiply along the chromosomes of all genomes. They can be controlled by the host through the targeting of silencing epigenetic marks, which may affect the chromatin structure of neighboring sequences, including genes. In this study, we used transcriptomic and epigenomic high-throughput data produced from ovarian samples of several Drosophila melanogaster and Drosophila simulans wild-type strains, in order to finely quantify the influence of TE insertions on gene RNA levels and histone marks (H3K9me3 and H3K4me3). Our results reveal a stronger epigenetic effect of TEs on ortholog genes in D. simulans compared with D. melanogaster. At the same time, we uncover a larger contribution of TEs to gene H3K9me3 variance within genomes in D. melanogaster, which is evidenced by a stronger correlation of TE numbers around genes with the levels of this chromatin mark in D. melanogaster. Overall, this work contributes to the understanding of species-specific influence of TEs within genomes. It provides a new light on the considerable natural variability provided by TEs, which may be associated with contrasted adaptive and evolutionary potentials.
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Affiliation(s)
- Marie Fablet
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon; Université Lyon 1; CNRS; UMR 5558, Villeurbanne, France
- Institut Universitaire de France (IUF), Paris, France
| | - Judit Salces-Ortiz
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon; Université Lyon 1; CNRS; UMR 5558, Villeurbanne, France
| | - Angelo Jacquet
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon; Université Lyon 1; CNRS; UMR 5558, Villeurbanne, France
| | - Bianca F Menezes
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon; Université Lyon 1; CNRS; UMR 5558, Villeurbanne, France
| | - Corentin Dechaud
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Philippe Veber
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon; Université Lyon 1; CNRS; UMR 5558, Villeurbanne, France
| | - Rita Rebollo
- Univ Lyon, INRAE, INSA-Lyon, BF2I, UMR 203, Villeurbanne, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon; Université Lyon 1; CNRS; UMR 5558, Villeurbanne, France
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2
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Tiedeman Z, Signor S. The transposable elements of the Drosophila serrata reference panel. Genome Biol Evol 2021; 13:6265467. [PMID: 33950180 PMCID: PMC8434751 DOI: 10.1093/gbe/evab100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2021] [Indexed: 11/13/2022] Open
Abstract
Transposable elements (TEs) are an important component of the complex genomic ecosystem. Understanding the tempo and mode of TE proliferation, that is whether it is in maintained in transposition selection balance, or is induced periodically by environmental stress or other factors, is important for understanding the evolution of organismal genomes through time. Although TEs have been characterized in individuals or limited samples, a true understanding of the population genetics of TEs, and therefore the tempo and mode of transposition, is still lacking. Here, we characterize the TE landscape in an important model Drosophila, Drosophila serrata using the D. serrata reference panel, which is comprised of 102 sequenced inbred genotypes. We annotate the families of TEs in the D. serrata genome and investigate variation in TE copy number between genotypes. We find that many TEs have low copy number in the population, but this varies by family and includes a single TE making up to 50% of the genome content of TEs. We find that some TEs proliferate in particular genotypes compared with population levels. In addition, we characterize variation in each TE family allowing copy number to vary in each genotype and find that some TEs have diversified very little between individuals suggesting recent spread. TEs are important sources of spontaneous mutations in Drosophila, making up a large fraction of the total number of mutations in particular genotypes. Understanding the dynamics of TEs within populations will be an important step toward characterizing the origin of variation within and between species.
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Affiliation(s)
- Zachery Tiedeman
- Department of Biological Sciences, North Dakota State University, Fargo, North Dakota, U.S.A
| | - Sarah Signor
- Department of Biological Sciences, North Dakota State University, Fargo, North Dakota, U.S.A
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3
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Mérel V, Boulesteix M, Fablet M, Vieira C. Transposable elements in Drosophila. Mob DNA 2020; 11:23. [PMID: 32636946 PMCID: PMC7334843 DOI: 10.1186/s13100-020-00213-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 04/14/2020] [Indexed: 12/25/2022] Open
Abstract
Drosophila has been studied as a biological model for many years and many discoveries in biology rely on this species. Research on transposable elements (TEs) is not an exception. Drosophila has contributed significantly to our knowledge on the mechanisms of transposition and their regulation, but above all, it was one of the first organisms on which genetic and genomic studies of populations were done. In this review article, in a very broad way, we will approach the TEs of Drosophila with a historical hindsight as well as recent discoveries in the field.
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Affiliation(s)
- Vincent Mérel
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Matthieu Boulesteix
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Marie Fablet
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Cristina Vieira
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
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4
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Drosophila Interspecific Hybridization Causes A Deregulation of the piRNA Pathway Genes. Genes (Basel) 2020; 11:genes11020215. [PMID: 32092860 PMCID: PMC7073935 DOI: 10.3390/genes11020215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/11/2020] [Accepted: 02/14/2020] [Indexed: 12/17/2022] Open
Abstract
Almost all eukaryotes have transposable elements (TEs) against which they have developed defense mechanisms. In the Drosophila germline, the main transposable element (TE) regulation pathway is mediated by specific Piwi-interacting small RNAs (piRNAs). Nonetheless, for unknown reasons, TEs sometimes escape cellular control during interspecific hybridization processes. Because the piRNA pathway genes are involved in piRNA biogenesis and TE control, we sequenced and characterized nine key genes from this pathway in Drosophila buzzatii and Drosophila koepferae species and studied their expression pattern in ovaries of both species and their F1 hybrids. We found that gene structure is, in general, maintained between both species and that two genes—armitage and aubergine—are under positive selection. Three genes—krimper, methyltransferase 2, and zucchini—displayed higher expression values in hybrids than both parental species, while others had RNA levels similar to the parental species with the highest expression. This suggests that the overexpression of some piRNA pathway genes can be a primary response to hybrid stress. Therefore, these results reinforce the hypothesis that TE deregulation may be due to the protein incompatibility caused by the rapid evolution of these genes, leading to a TE silencing failure, rather than to an underexpression of piRNA pathway genes.
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Abstract
Transposable elements (TEs) are mobile DNA sequences that colonize genomes and threaten genome integrity. As a result, several mechanisms appear to have emerged during eukaryotic evolution to suppress TE activity. However, TEs are ubiquitous and account for a prominent fraction of most eukaryotic genomes. We argue that the evolutionary success of TEs cannot be explained solely by evasion from host control mechanisms. Rather, some TEs have evolved commensal and even mutualistic strategies that mitigate the cost of their propagation. These coevolutionary processes promote the emergence of complex cellular activities, which in turn pave the way for cooption of TE sequences for organismal function.
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Affiliation(s)
- Rachel L Cosby
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Ni-Chen Chang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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6
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Erwin AA, Blumenstiel JP. Aging in the Drosophila ovary: contrasting changes in the expression of the piRNA machinery and mitochondria but no global release of transposable elements. BMC Genomics 2019; 20:305. [PMID: 31014230 PMCID: PMC6480902 DOI: 10.1186/s12864-019-5668-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 04/08/2019] [Indexed: 01/06/2023] Open
Abstract
Background Evolutionary theory indicates that the dynamics of aging in the soma and reproductive tissues may be distinct. This difference arises from the fact that only the germline lineage establishes future generations. In the soma, changes in the landscape of heterochromatin have been proposed to have an important role in aging. This is because redistribution of heterochromatin during aging has been linked to the derepression of transposable elements and an overall loss of somatic gene regulation. A role for changes in the chromatin landscape in the aging of reproductive tissues is less well established. Whether or not epigenetic factors, such as heterochromatin marks, are perturbed in aging reproductive tissues is of interest because, in special cases, epigenetic variation may be heritable. Using mRNA sequencing data from late-stage egg chambers in Drosophila melanogaster, we characterized the landscape of altered gene and transposable element expression in aged reproductive tissues. This allowed us to test the hypothesis that reproductive tissues may differ from somatic tissues in their response to aging. Results We show that age-related expression changes in late-stage egg chambers tend to occur in genes residing in heterochromatin, particularly on the largely heterochromatic 4th chromosome. However, these expression differences are seen as both decreases and increases during aging, inconsistent with a general loss of heterochromatic silencing. We also identify an increase in expression of the piRNA machinery, suggesting an age-related increased investment in the maintenance of genome stability. We further identify a strong age-related reduction in the expression of mitochondrial transcripts. However, we find no evidence for global TE derepression in reproductive tissues. Rather, the observed effects of aging on TEs are primarily strain and family specific. Conclusions These results identify unique responses in somatic versus reproductive tissue with regards to aging. As in somatic tissues, female reproductive tissues show reduced expression of mitochondrial genes. In contrast, the piRNA machinery shows increased expression during aging. Overall, these results also indicate that global loss of TE control observed in other studies may be unique to the soma and sensitive to genetic background and TE family. Electronic supplementary material The online version of this article (10.1186/s12864-019-5668-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexandra A Erwin
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA.
| | - Justin P Blumenstiel
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA.
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Marin P, Genitoni J, Barloy D, Maury S, Gibert P, Ghalambor CK, Vieira C. Biological invasion: The influence of the hidden side of the (epi)genome. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13317] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Pierre Marin
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1 Université de Lyon Villeurbanne France
| | - Julien Genitoni
- ESE, Ecology and Ecosystem Health, Agrocampus Ouest INRA Rennes France
- LBLGC EA 1207 INRA, Université d'Orléans, USC 1328 Orléans France
| | - Dominique Barloy
- ESE, Ecology and Ecosystem Health, Agrocampus Ouest INRA Rennes France
| | - Stéphane Maury
- LBLGC EA 1207 INRA, Université d'Orléans, USC 1328 Orléans France
| | - Patricia Gibert
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1 Université de Lyon Villeurbanne France
| | - Cameron K. Ghalambor
- Department of Biology and Graduate Degree Program in Ecology Colorado State University Fort Collins Colorado
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1 Université de Lyon Villeurbanne France
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Lerat E, Fablet M, Modolo L, Lopez-Maestre H, Vieira C. TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes. Nucleic Acids Res 2018; 45:e17. [PMID: 28204592 PMCID: PMC5389681 DOI: 10.1093/nar/gkw953] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 09/29/2016] [Accepted: 10/11/2016] [Indexed: 11/24/2022] Open
Abstract
Over recent decades, substantial efforts have been made to understand the interactions between host genomes and transposable elements (TEs). The impact of TEs on the regulation of host genes is well known, with TEs acting as platforms of regulatory sequences. Nevertheless, due to their repetitive nature it is considerably hard to integrate TE analysis into genome-wide studies. Here, we developed a specific tool for the analysis of TE expression: TEtools. This tool takes into account the TE sequence diversity of the genome, it can be applied to unannotated or unassembled genomes and is freely available under the GPL3 (https://github.com/l-modolo/TEtools). TEtools performs the mapping of RNA-seq data obtained from classical mRNAs or small RNAs onto a list of TE sequences and performs differential expression analyses with statistical relevance. Using this tool, we analyzed TE expression from five Drosophila wild-type strains. Our data show for the first time that the activity of TEs is strictly linked to the activity of the genes implicated in the piwi-interacting RNA biogenesis and therefore fits an arms race scenario between TE sequences and host control genes.
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Affiliation(s)
- Emmanuelle Lerat
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France
| | - Marie Fablet
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France
| | - Laurent Modolo
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France
| | - Hélène Lopez-Maestre
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France
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9
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Romero-Soriano V, Modolo L, Lopez-Maestre H, Mugat B, Pessia E, Chambeyron S, Vieira C, Garcia Guerreiro MP. Transposable Element Misregulation Is Linked to the Divergence between Parental piRNA Pathways in Drosophila Hybrids. Genome Biol Evol 2018; 9:1450-1470. [PMID: 28854624 PMCID: PMC5499732 DOI: 10.1093/gbe/evx091] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2017] [Indexed: 12/30/2022] Open
Abstract
Interspecific hybridization is a genomic stress condition that leads to the activation of transposable elements (TEs) in both animals and plants. In hybrids between Drosophila buzzatii and Drosophila koepferae, mobilization of at least 28 TEs has been described. However, the molecular mechanisms underlying this TE release remain poorly understood. To give insight on the causes of this TE activation, we performed a TE transcriptomic analysis in ovaries (notorious for playing a major role in TE silencing) of parental species and their F1 and backcrossed (BC) hybrids. We find that 15.2% and 10.6% of the expressed TEs are deregulated in F1 and BC1 ovaries, respectively, with a bias toward overexpression in both cases. Although differences between parental piRNA (Piwi-interacting RNA) populations explain only partially these results, we demonstrate that piRNA pathway proteins have divergent sequences and are differentially expressed between parental species. Thus, a functional divergence of the piRNA pathway between parental species, together with some differences between their piRNA pools, might be at the origin of hybrid instabilities and ultimately cause TE misregulation in ovaries. These analyses were complemented with the study of F1 testes, where TEs tend to be less expressed than in D. buzzatii. This can be explained by an increase in piRNA production, which probably acts as a defence mechanism against TE instability in the male germline. Hence, we describe a differential impact of interspecific hybridization in testes and ovaries, which reveals that TE expression and regulation are sex-biased.
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Affiliation(s)
- Valèria Romero-Soriano
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Spain
| | - Laurent Modolo
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Hélène Lopez-Maestre
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Bruno Mugat
- Institut de Génétique Humaine, UMR9002, CNRS-Université de Montpellier, France
| | - Eugénie Pessia
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Séverine Chambeyron
- Institut de Génétique Humaine, UMR9002, CNRS-Université de Montpellier, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Maria Pilar Garcia Guerreiro
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Spain
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10
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Saint-Leandre B, Clavereau I, Hua-Van A, Capy P. Transcriptional polymorphism ofpiRNA regulatory genes underlies themarineractivity inDrosophila simulanstestes. Mol Ecol 2017; 26:3715-3731. [DOI: 10.1111/mec.14145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 12/28/2016] [Indexed: 02/03/2023]
Affiliation(s)
- Bastien Saint-Leandre
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS; Univ. Paris-Sud, IRD; Université Paris-Saclay; Gif-sur-Yvette Cedex France
| | - Isabelle Clavereau
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS; Univ. Paris-Sud, IRD; Université Paris-Saclay; Gif-sur-Yvette Cedex France
| | - Aurelie Hua-Van
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS; Univ. Paris-Sud, IRD; Université Paris-Saclay; Gif-sur-Yvette Cedex France
| | - Pierre Capy
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS; Univ. Paris-Sud, IRD; Université Paris-Saclay; Gif-sur-Yvette Cedex France
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Silencing of Transposable Elements by piRNAs in Drosophila: An Evolutionary Perspective. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:164-176. [PMID: 28602845 PMCID: PMC5487533 DOI: 10.1016/j.gpb.2017.01.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/02/2017] [Accepted: 01/12/2017] [Indexed: 11/28/2022]
Abstract
Transposable elements (TEs) are DNA sequences that can move within the genome. TEs have greatly shaped the genomes, transcriptomes, and proteomes of the host organisms through a variety of mechanisms. However, TEs generally disrupt genes and destabilize the host genomes, which substantially reduce fitness of the host organisms. Understanding the genomic distribution and evolutionary dynamics of TEs will greatly deepen our understanding of the TE-mediated biological processes. Most TE insertions are highly polymorphic in Drosophila melanogaster, providing us a good system to investigate the evolution of TEs at the population level. Decades of theoretical and experimental studies have well established “transposition-selection” population genetics model, which assumes that the equilibrium between TE replication and purifying selection determines the copy number of TEs in the genome. In the last decade, P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) were demonstrated to be master repressors of TE activities in Drosophila. The discovery of piRNAs revolutionized our understanding of TE repression, because it reveals that the host organisms have evolved an adaptive mechanism to defend against TE invasion. Tremendous progress has been made to understand the molecular mechanisms by which piRNAs repress active TEs, although many details in this process remain to be further explored. The interaction between piRNAs and TEs well explains the molecular mechanisms underlying hybrid dysgenesis for the I-R and P-M systems in Drosophila, which have puzzled evolutionary biologists for decades. The piRNA repression pathway provides us an unparalleled system to study the co-evolutionary process between parasites and host organisms.
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Ryazansky S, Radion E, Mironova A, Akulenko N, Abramov Y, Morgunova V, Kordyukova MY, Olovnikov I, Kalmykova A. Natural variation of piRNA expression affects immunity to transposable elements. PLoS Genet 2017; 13:e1006731. [PMID: 28448516 PMCID: PMC5407775 DOI: 10.1371/journal.pgen.1006731] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/31/2017] [Indexed: 11/25/2022] Open
Abstract
In the Drosophila germline, transposable elements (TEs) are silenced by PIWI-interacting RNA (piRNA) that originate from distinct genomic regions termed piRNA clusters and are processed by PIWI-subfamily Argonaute proteins. Here, we explore the variation in the ability to restrain an alien TE in different Drosophila strains. The I-element is a retrotransposon involved in the phenomenon of I-R hybrid dysgenesis in Drosophila melanogaster. Genomes of R strains do not contain active I-elements, but harbour remnants of ancestral I-related elements. The permissivity to I-element activity of R females, called reactivity, varies considerably in natural R populations, indicating the existence of a strong natural polymorphism in defense systems targeting transposons. To reveal the nature of such polymorphisms, we compared ovarian small RNAs between R strains with low and high reactivity and show that reactivity negatively correlates with the ancestral I-element-specific piRNA content. Analysis of piRNA clusters containing remnants of I-elements shows increased expression of the piRNA precursors and enrichment by the Heterochromatin Protein 1 homolog, Rhino, in weak R strains, which is in accordance with stronger piRNA expression by these regions. To explore the nature of the differences in piRNA production, we focused on two R strains, weak and strong, and showed that the efficiency of maternal inheritance of piRNAs as well as the I-element copy number are very similar in both strains. At the same time, germline and somatic uni-strand piRNA clusters generate more piRNAs in strains with low reactivity, suggesting the relationship between the efficiency of primary piRNA production and variable response to TE invasions. The strength of adaptive genome defense is likely driven by naturally occurring polymorphisms in the rapidly evolving piRNA pathway proteins. We hypothesize that hyper-efficient piRNA production is contributing to elimination of a telomeric retrotransposon HeT-A, which we have observed in one particular transposon-resistant R strain. Transposon activity in the germline is suppressed by the PIWI-interacting RNA (piRNA) pathway. The resistance of natural Drosophila strains to transposon invasion varies considerably, but the nature of this variability is unknown. We discovered that natural variation in the efficiency of primary piRNA production in the germline causes dramatic differences in the susceptibility to expansion of a newly invaded transposon. A high level of piRNA production in the germline is achieved by increased expression of piRNA precursors. In one of the most transposon-resistant strains, increased content of primary piRNA is observed in both the germline and ovarian somatic cells. We suggest that polymorphisms in piRNA pathway factors are responsible for increased piRNA production. piRNA pathway proteins have been shown to be evolving rapidly under selective pressure. Our data are the first to describe a phenotype that might be caused by this kind of polymorphism. We also demonstrate a likely explanation as to why an overly active piRNA pathway can cause more harm than good in Drosophila: Highly efficient piRNA processing leads to elimination of domesticated telomeric retrotransposons essential for telomere elongation, an effect which has been observed in a natural strain that is extremely resistant to transposon invasion.
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Affiliation(s)
- Sergei Ryazansky
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Elizaveta Radion
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Anastasia Mironova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Natalia Akulenko
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Yuri Abramov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Valeriya Morgunova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Maria Y. Kordyukova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Ivan Olovnikov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Alla Kalmykova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
- * E-mail:
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13
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Tao W, Sun L, Chen J, Shi H, Wang D. Genomic identification, rapid evolution, and expression of Argonaute genes in the tilapia, Oreochromis niloticus. Dev Genes Evol 2016; 226:339-48. [PMID: 27491892 DOI: 10.1007/s00427-016-0554-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/28/2016] [Indexed: 12/21/2022]
Abstract
Argonaute proteins are key components of the small RNA-induced silencing complex and have multiple roles in RNA-directed regulatory pathways. Argonaute genes can be divided into two subfamilies: the Ago (interacting with microRNA/small interfering RNA) and Piwi subfamilies (interacting with piwi-interacting RNAs (piRNAs)). In the present study, genome-wide analyses firstly yielded the identification of different members of Agos and Piwis in the tilapia, coelacanth, spotted gar, and elephant shark. The additional teleost Ago3b was generated following the fish-specific genome duplication event. Selective pressure analysis on Agos and Piwis between cichlids and other teleosts showed an accelerated evolution of Piwil1 in the cichlid lineages, and the positive selected sites were located in the region of PIWI domain, suggesting that these amino acid substitutions are adapt to targeted cleavage of messenger RNA (mRNA) in cichlids. Ago1 and Ago4 were detected at higher levels at 5 days after hatching (dah) in both ovaries and testes compared with other stages, supporting the previously reported requirement of Ago-mediated pathways to clear the maternal mRNAs during the early embryogenesis. The Piwis were abundantly expressed in tilapia testes, indicating their essential roles in male germline, especially in spermatogenesis. Notable expression of Piwis was also detected in skeletal muscle, indicating that piRNA pathway may not only be confined to development and maintenance of the germline but may also play important roles in somatic tissues. The expression of Piwil1 and Piwil2 was examined by quantitative PCR (qPCR) and in situ hybridization (ISH) to validate the spatial and temporal expression profiles. Taken together, these results present a thorough overview of tilapia Argonaute family and provide a new perspective on the evolution and function of this family in teleosts.
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Affiliation(s)
- Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, 400715, Chongqing, People's Republic of China
| | - Lina Sun
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, 400715, Chongqing, People's Republic of China
| | - Jinlin Chen
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, 400715, Chongqing, People's Republic of China
| | - Hongjuan Shi
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, 400715, Chongqing, People's Republic of China
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, 400715, Chongqing, People's Republic of China.
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14
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Romero-Soriano V, Garcia Guerreiro MP. Expression of the Retrotransposon Helena Reveals a Complex Pattern of TE Deregulation in Drosophila Hybrids. PLoS One 2016; 11:e0147903. [PMID: 26812285 PMCID: PMC4728067 DOI: 10.1371/journal.pone.0147903] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 01/11/2016] [Indexed: 11/18/2022] Open
Abstract
Transposable elements (TEs), repeated mobile sequences, are ubiquitous in the eukaryotic kingdom. Their mobilizing capacity confers on them a high mutagenic potential, which must be strongly regulated to guarantee genome stability. In the Drosophila germline, a small RNA-mediated silencing system, the piRNA (Piwi-interacting RNA) pathway, is the main responsible TE regulating mechanism, but some stressful conditions can destabilize it. For instance, during interspecific hybridization, genomic stress caused by the shock of two different genomes can lead, in both animals and plants, to higher transposition rates. A recent study in D. buzatii-D. koepferae hybrids detected mobilization of 28 TEs, yet little is known about the molecular mechanisms explaining this transposition release. We have characterized one of the mobilized TEs, the retrotransposon Helena, and used quantitative expression to assess whether its high transposition rates in hybrids are preceded by increased expression. We have also localized Helena expression in the gonads to see if cellular expression patterns have changed in the hybrids. To give more insight into changes in TE regulation in hybrids, we analysed Helena-specific piRNA populations of hybrids and parental species. Helena expression is not globally altered in somatic tissues, but male and female gonads have different patterns of deregulation. In testes, Helena is repressed in F1, increasing then its expression up to parental values. This is linked with a mislocation of Helena transcripts along with an increase of their specific piRNA levels. Ovaries have additive levels of Helena expression, but the ping-pong cycle efficiency seems to be reduced in F1 hybrids. This could be at the origin of new Helena insertions in hybrids, which would be transmitted to F1 hybrid female progeny.
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Affiliation(s)
- Valèria Romero-Soriano
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva, Departament de Genètica i Microbiologia (Edifici C), Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Maria Pilar Garcia Guerreiro
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva, Departament de Genètica i Microbiologia (Edifici C), Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
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15
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Host control of insect endogenous retroviruses: small RNA silencing and immune response. Viruses 2014; 6:4447-64. [PMID: 25412365 PMCID: PMC4246233 DOI: 10.3390/v6114447] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 11/04/2014] [Accepted: 11/11/2014] [Indexed: 12/02/2022] Open
Abstract
Endogenous retroviruses are relics of ancient infections from retroviruses that managed to integrate into the genome of germline cells and remained vertically transmitted from parent to progeny. Subsequent to the endogenization process, these sequences can move and multiply in the host genome, which can have deleterious consequences and disturb genomic stability. Natural selection favored the establishment of silencing pathways that protect host genomes from the activity of endogenous retroviruses. RNA silencing mechanisms are involved, which utilize piRNAs. The response to exogenous viral infections uses siRNAs, a class of small RNAs that are generated via a distinct biogenesis pathway from piRNAs. However, interplay between both pathways has been identified, and interactions with anti-bacterial and anti-fungal immune responses are also suspected. This review focuses on Diptera (Arthropods) and intends to compile pieces of evidence showing that the RNA silencing pathway of endogenous retrovirus regulation is not independent from immunity and the response to infections. This review will consider the mechanisms that allow the lasting coexistence of viral sequences and host genomes from an evolutionary perspective.
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16
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Yi M, Chen F, Luo M, Cheng Y, Zhao H, Cheng H, Zhou R. Rapid evolution of piRNA pathway in the teleost fish: implication for an adaptation to transposon diversity. Genome Biol Evol 2014; 6:1393-407. [PMID: 24846630 PMCID: PMC4079211 DOI: 10.1093/gbe/evu105] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The Piwi-interacting RNA (piRNA) pathway is responsible for germline specification, gametogenesis, transposon silencing, and genome integrity. Transposable elements can disrupt genome and its functions. However, piRNA pathway evolution and its adaptation to transposon diversity in the teleost fish remain unknown. This article unveils evolutionary scene of piRNA pathway and its association with diverse transposons by systematically comparative analysis on diverse teleost fish genomes. Selective pressure analysis on piRNA pathway and miRNA/siRNA (microRNA/small interfering RNA) pathway genes between teleosts and mammals showed an accelerated evolution of piRNA pathway genes in the teleost lineages, and positive selection on functional PAZ (Piwi/Ago/Zwille) and Tudor domains involved in the Piwi-piRNA/Tudor interaction, suggesting that the amino acid substitutions are adaptive to their functions in piRNA pathway in the teleost fish species. Notably five piRNA pathway genes evolved faster in the swamp eel, a kind of protogynous hermaphrodite fish, than the other teleosts, indicating a differential evolution of piRNA pathway between the swamp eel and other gonochoristic fishes. In addition, genome-wide analysis showed higher diversity of transposons in the teleost fish species compared with mammals. Our results suggest that rapidly evolved piRNA pathway in the teleost fish is likely to be involved in the adaption to transposon diversity.
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Affiliation(s)
- Minhan Yi
- Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Feng Chen
- Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Majing Luo
- Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Yibin Cheng
- Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Huabin Zhao
- Department of Zoology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Hanhua Cheng
- Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Rongjia Zhou
- Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
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