1
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Zhang S, Wang R, Zhu X, Zhang L, Liu X, Sun L. Characteristics and expression of lncRNA and transposable elements in Drosophila aneuploidy. iScience 2023; 26:108494. [PMID: 38125016 PMCID: PMC10730892 DOI: 10.1016/j.isci.2023.108494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/28/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Aneuploidy can globally affect the expression of the whole genome, which is detrimental to organisms. Dosage-sensitive regulators usually have multiple intermolecular interactions, and changes in their stoichiometry are responsible for the dysregulation of the regulatory network. Currently, studies on noncoding genes in aneuploidy are relatively rare. We studied the characteristics and expression profiles of long noncoding RNAs (lncRNAs) and transposable elements (TEs) in aneuploid Drosophila. It is found that lncRNAs and TEs are affected by genomic imbalance and appear to be more sensitive to an inverse dosage effect than mRNAs. Several dosage-sensitive lncRNAs and TEs were detected for their expression patterns during embryogenesis, and their biological functions in the ovary and testes were investigated using tissue-specific RNAi. This study advances our understanding of the noncoding sequences in imbalanced genomes and provides a novel perspective for the study of aneuploidy-related human diseases such as cancer.
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Affiliation(s)
- Shuai Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ruixue Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xilin Zhu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ludan Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xinyu Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Lin Sun
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, Beijing 100875, China
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2
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Coronado-Zamora M, González J. Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes across Drosophila natural strains. Genome Res 2023; 33:1541-1553. [PMID: 37793782 PMCID: PMC10620055 DOI: 10.1101/gr.277565.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 08/08/2023] [Indexed: 10/06/2023]
Abstract
Transcriptomes are dynamic, with cells, tissues, and body parts expressing particular sets of transcripts. Transposable elements (TEs) are a known source of transcriptome diversity; however, studies often focus on a particular type of chimeric transcript, analyze single body parts or cell types, or are based on incomplete TE annotations from a single reference genome. In this work, we have implemented a method based on de novo transcriptome assembly that minimizes the potential sources of errors while identifying a comprehensive set of gene-TE chimeras. We applied this method to the head, gut, and ovary dissected from five Drosophila melanogaster natural strains, with individual reference genomes available. We found that ∼19% of body part-specific transcripts are gene-TE chimeras. Overall, chimeric transcripts contribute a mean of 43% to the total gene expression, and they provide protein domains for DNA binding, catalytic activity, and DNA polymerase activity. Our comprehensive data set is a rich resource for follow-up analysis. Moreover, because TEs are present in virtually all species sequenced to date, their role in spatially restricted transcript expression is likely not exclusive to the species analyzed in this work.
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Affiliation(s)
| | - Josefa González
- Institute of Evolutionary Biology, CSIC, UPF, Barcelona 08003, Spain
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3
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Gebrie A. Transposable elements as essential elements in the control of gene expression. Mob DNA 2023; 14:9. [PMID: 37596675 PMCID: PMC10439571 DOI: 10.1186/s13100-023-00297-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/08/2023] [Indexed: 08/20/2023] Open
Abstract
Interspersed repetitions called transposable elements (TEs), commonly referred to as mobile elements, make up a significant portion of the genomes of higher animals. TEs contribute in controlling the expression of genes locally and even far away at the transcriptional and post-transcriptional levels, which is one of their significant functional effects on gene function and genome evolution. There are different mechanisms through which TEs control the expression of genes. First, TEs offer cis-regulatory regions in the genome with their inherent regulatory features for their own expression, making them potential factors for controlling the expression of the host genes. Promoter and enhancer elements contain cis-regulatory sites generated from TE, which function as binding sites for a variety of trans-acting factors. Second, a significant portion of miRNAs and long non-coding RNAs (lncRNAs) have been shown to have TEs that encode for regulatory RNAs, revealing the TE origin of these RNAs. Furthermore, it was shown that TE sequences are essential for these RNAs' regulatory actions, which include binding to the target mRNA. By being a member of cis-regulatory and regulatory RNA sequences, TEs therefore play essential regulatory roles. Additionally, it has been suggested that TE-derived regulatory RNAs and cis-regulatory regions both contribute to the evolutionary novelty of gene regulation. Additionally, these regulatory systems arising from TE frequently have tissue-specific functions. The objective of this review is to discuss TE-mediated gene regulation, with a particular emphasis on the processes, contributions of various TE types, differential roles of various tissue types, based mostly on recent studies on humans.
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Affiliation(s)
- Alemu Gebrie
- Department of Biomedical Sciences, School of Medicine, Debre Markos University, Debre Markos, Ethiopia.
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4
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Lerat E. Recent Bioinformatic Progress to Identify Epigenetic Changes Associated to Transposable Elements. Front Genet 2022; 13:891194. [PMID: 35646069 PMCID: PMC9140218 DOI: 10.3389/fgene.2022.891194] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Transposable elements (TEs) are recognized for their great impact on the functioning and evolution of their host genomes. They are associated to various deleterious effects, which has led to the evolution of regulatory epigenetic mechanisms to control their activity. Despite these negative effects, TEs are also important actors in the evolution of genomes by promoting genetic diversity and new regulatory elements. Consequently, it is important to study the epigenetic modifications associated to TEs especially at a locus-specific level to determine their individual influence on gene functioning. To this aim, this short review presents the current bioinformatic tools to achieve this task.
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Colonna Romano N, Fanti L. Transposable Elements: Major Players in Shaping Genomic and Evolutionary Patterns. Cells 2022; 11:cells11061048. [PMID: 35326499 PMCID: PMC8947103 DOI: 10.3390/cells11061048] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/04/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
Transposable elements (TEs) are ubiquitous genetic elements, able to jump from one location of the genome to another, in all organisms. For this reason, on the one hand, TEs can induce deleterious mutations, causing dysfunction, disease and even lethality in individuals. On the other hand, TEs can increase genetic variability, making populations better equipped to respond adaptively to environmental change. To counteract the deleterious effects of TEs, organisms have evolved strategies to avoid their activation. However, their mobilization does occur. Usually, TEs are maintained silent through several mechanisms, but they can be reactivated during certain developmental windows. Moreover, TEs can become de-repressed because of drastic changes in the external environment. Here, we describe the ‘double life’ of TEs, being both ‘parasites’ and ‘symbionts’ of the genome. We also argue that the transposition of TEs contributes to two important evolutionary processes: the temporal dynamic of evolution and the induction of genetic variability. Finally, we discuss how the interplay between two TE-dependent phenomena, insertional mutagenesis and epigenetic plasticity, plays a role in the process of evolution.
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6
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What Have We Learned in 30 Years of Investigations on Bari Transposons? Cells 2022; 11:cells11030583. [PMID: 35159391 PMCID: PMC8834629 DOI: 10.3390/cells11030583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 12/17/2022] Open
Abstract
Transposable elements (TEs) have been historically depicted as detrimental genetic entities that selfishly aim at perpetuating themselves, invading genomes, and destroying genes. Scientists often co-opt "special" TEs to develop new and powerful genetic tools, that will hopefully aid in changing the future of the human being. However, many TEs are gentle, rarely unleash themselves to harm the genome, and bashfully contribute to generating diversity and novelty in the genomes they have colonized, yet they offer the opportunity to develop new molecular tools. In this review we summarize 30 years of research focused on the Bari transposons. Bari is a "normal" transposon family that has colonized the genomes of several Drosophila species and introduced genomic novelties in the melanogaster species. We discuss how these results have contributed to advance the field of TE research and what future studies can still add to the current knowledge.
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Bodelón A, Fablet M, Veber P, Vieira C, García Guerreiro MP. OUP accepted manuscript. Genome Biol Evol 2022; 14:6526395. [PMID: 35143649 PMCID: PMC8872975 DOI: 10.1093/gbe/evac024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2022] [Indexed: 11/21/2022] Open
Abstract
Interspecific hybridization is often seen as a genomic stress that may lead to new gene expression patterns and deregulation of transposable elements (TEs). The understanding of expression changes in hybrids compared with parental species is essential to disentangle their putative role in speciation processes. However, to date we ignore the detailed mechanisms involved in genomic deregulation in hybrids. We studied the ovarian transcriptome and epigenome of the Drosophila buzzatii and Drosophila koepferae species together with their F1 hybrid females. We found a trend toward underexpression of genes and TE families in hybrids. The epigenome in hybrids was highly similar to the parental epigenomes and showed intermediate histone enrichments between parental species in most cases. Differential gene expression in hybrids was often associated only with changes in H3K4me3 enrichments, whereas differential TE family expression in hybrids may be associated with changes in H3K4me3, H3K9me3, or H3K27me3 enrichments. We identified specific genes and TE families, which their differential expression in comparison with the parental species was explained by their differential chromatin mark combination enrichment. Finally, cis–trans compensatory regulation could also contribute in some way to the hybrid deregulation. This work provides the first study of histone content in Drosophila interspecific hybrids and their effect on gene and TE expression deregulation.
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Affiliation(s)
- Alejandra Bodelón
- Grup de Genòmica, Bioinformática i Biologia Evolutiva, Departament de Genètica i Microbiologia (Edifici C), Universitat Autònoma de Barcelona, Spain
| | - Marie Fablet
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Claude Bernard Lyon 1, Villeurbanne, France
- Institut universitaire de France, France
| | - Philippe Veber
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Maria Pilar García Guerreiro
- Grup de Genòmica, Bioinformática i Biologia Evolutiva, Departament de Genètica i Microbiologia (Edifici C), Universitat Autònoma de Barcelona, Spain
- Corresponding author: E-mail:
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8
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Ullastres A, Merenciano M, González J. Regulatory regions in natural transposable element insertions drive interindividual differences in response to immune challenges in Drosophila. Genome Biol 2021; 22:265. [PMID: 34521452 PMCID: PMC8439047 DOI: 10.1186/s13059-021-02471-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 08/19/2021] [Indexed: 02/08/2023] Open
Abstract
Background Variation in gene expression underlies interindividual variability in relevant traits including immune response. However, the genetic variation responsible for these gene expression changes remains largely unknown. Among the non-coding variants that could be relevant, transposable element insertions are promising candidates as they have been shown to be a rich and diverse source of cis-regulatory elements. Results In this work, we use a population genetics approach to identify transposable element insertions likely to increase the tolerance of Drosophila melanogaster to bacterial infection by affecting the expression of immune-related genes. We identify 12 insertions associated with allele-specific expression changes in immune-related genes. We experimentally validate three of these insertions including one likely to be acting as a silencer, one as an enhancer, and one with a dual role as enhancer and promoter. The direction in the change of gene expression associated with the presence of several of these insertions is consistent with an increased survival to infection. Indeed, for one of the insertions, we show that this is the case by analyzing both natural populations and CRISPR/Cas9 mutants in which the insertion is deleted from its native genomic context. Conclusions We show that transposable elements contribute to gene expression variation in response to infection in D. melanogaster and that this variation is likely to affect their survival capacity. Because the role of transposable elements as regulatory elements is not restricted to Drosophila, transposable elements are likely to play a role in immune response in other organisms as well. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02471-3.
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Affiliation(s)
- Anna Ullastres
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Miriam Merenciano
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Josefa González
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain.
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Marin P, Jaquet A, Picarle J, Fablet M, Merel V, Delignette-Muller ML, Ferrarini MG, Gibert P, Vieira C. Phenotypic and Transcriptomic Responses to Stress Differ According to Population Geography in an Invasive Species. Genome Biol Evol 2021; 13:evab208. [PMID: 34505904 PMCID: PMC8483892 DOI: 10.1093/gbe/evab208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2021] [Indexed: 11/14/2022] Open
Abstract
Adaptation to rapid environmental changes must occur within a short-time scale. In this context, studies of invasive species may provide insights into the underlying mechanisms of rapid adaptation as these species have repeatedly encountered and adapted to novel environmental conditions. We investigated how invasive and noninvasive genotypes of Drosophila suzukii deal with oxidative stress at the phenotypic and molecular levels. We also studied the impact of transposable element (TE) insertions on the gene expression in response to stress. Our results show that flies from invasive areas (France and the United States) live longer in natural conditions than the ones from native Japanese areas. As expected, lifespan for all genotypes was significantly reduced following exposure to paraquat, but this reduction varied among genotypes (genotype-by-environment interaction) with invasive genotypes appearing more affected by exposure than noninvasive ones. A transcriptomic analysis of genotypes upon paraquat treatment detected many genes differentially expressed (DE). Although a small core set of genes were DE in all genotypes following paraquat exposure, much of the response of each genotype was unique. Moreover, we showed that TEs were not activated after oxidative stress and DE genes were significantly depleted of TEs. In conclusion, it is likely that transcriptomic changes are involved in the rapid adaptation to local environments. We provide new evidence that in the decade since the invasion from Asia, the sampled genotypes in Europe and the United States of D. suzukii diverged from the ones from the native area regarding their phenotypic and genomic response to oxidative stress.
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Affiliation(s)
- Pierre Marin
- Université de Lyon, Université Lyon 1, CNRS, VetAgro Sup, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| | - Angelo Jaquet
- Université de Lyon, Université Lyon 1, CNRS, VetAgro Sup, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| | - Justine Picarle
- Université de Lyon, Université Lyon 1, CNRS, VetAgro Sup, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| | - Marie Fablet
- Université de Lyon, Université Lyon 1, CNRS, VetAgro Sup, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| | - Vincent Merel
- Université de Lyon, Université Lyon 1, CNRS, VetAgro Sup, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| | - Marie-Laure Delignette-Muller
- Université de Lyon, Université Lyon 1, CNRS, VetAgro Sup, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| | - Mariana Galvão Ferrarini
- Université de Lyon, Université Lyon 1, CNRS, VetAgro Sup, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
- Université de Lyon, INSA-Lyon, INRAE, BF2I, UMR0203, Villeurbanne, France
| | - Patricia Gibert
- Université de Lyon, Université Lyon 1, CNRS, VetAgro Sup, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| | - Cristina Vieira
- Université de Lyon, Université Lyon 1, CNRS, VetAgro Sup, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
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10
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de Oliveira DS, Rosa MT, Vieira C, Loreto ELS. Oxidative and radiation stress induces transposable element transcription in Drosophila melanogaster. J Evol Biol 2021; 34:628-638. [PMID: 33484011 DOI: 10.1111/jeb.13762] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/27/2020] [Accepted: 12/06/2020] [Indexed: 12/20/2022]
Abstract
It has been shown that stressors are capable of activating transposable elements (TEs). Currently, there is a hypothesis that stress activation of TEs may be involved in adaptive evolution, favouring the increase in genetic variability when the population is under adverse conditions. However, TE activation under stress is still poorly understood. In the present study, we estimated the fraction of differentially expressed TEs (DETEs) under ionizing radiation (144, 360 and 864 Gy) and oxidative stress (dioxin, formaldehyde and toluene) treatments. The stress intensity of each treatment was estimated by measuring the number of differentially expressed genes, and we show that several TEs families are activated by stress whereas others are repressed. The proportion of DETEs was positively related to stress intensity. However, even under the strongest stress, only a small fraction of TE families were activated (9.28%) and 17.72% were repressed. Considering all treatments together, the activated proportion was 19.83%. Nevertheless, as several TEs are incomplete or degenerated, only 10.55% of D. melanogaster mobilome is, at same time, activated by the stressors and able to transpose or at least code a protein. Thus, our study points out that although stress activates TEs, it is not a generalized activation process, and for some families, the stress induces repression.
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Affiliation(s)
- Daniel Siqueira de Oliveira
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, 1- Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France
| | - Marcos Trindade Rosa
- PPG Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, 1- Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France
| | - Elgion L S Loreto
- Dep de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
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11
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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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12
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Stoffel TJR, Segatto AL, Silva MM, Prestes A, Barbosa NBV, Rocha JBT, Loreto ELS. Cyclophosphamide in Drosophila promotes genes and transposable elements differential expression and mitochondrial dysfunction. Comp Biochem Physiol C Toxicol Pharmacol 2020; 230:108718. [PMID: 31982542 DOI: 10.1016/j.cbpc.2020.108718] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/17/2020] [Accepted: 01/21/2020] [Indexed: 01/01/2023]
Abstract
Cyclophosphamide (CPA) is an alkylating agent used for cancer chemotherapy, organ transplantation, and autoimmune disease treatment. Here, mRNA sequencing and high-resolution respirometry were performed to evaluate the alterations of Drosophila melanogaster gene expression fed with CPA under acute (0.1 mg/mL, for 24 h) and chronic (0.05 mg/mL, for 35 days) treatments. Differential expression analysis was performed using Cufflinks-Cuffdiff, DESeq2, and edgeR software. CPA affected genes are involved in several biological functions, including stress response and immune-related pathways, oxi-reduction and apoptotic processes, and cuticle and vitelline membrane formation. In particular, this is the first report of CPA-induced mitochondrial dysfunction caused by the downregulation of genes involved with mitochondria constituents. CPA treatment also changed the transcription pattern of transposable elements (TEs) from the gypsy and copia superfamilies. The results presented here provided evidence of CPA mitochondrial toxicity mechanisms and that CPA can modify TEs transcription in Drosophila flies.
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Affiliation(s)
- Tailini J R Stoffel
- PPG Genética e Biologia Molecular, Univ. Fed. do Rio Grande do Sul, Porto Alegre, Brazil
| | - Ana L Segatto
- Dep de Bioquímica e Biologia Molecular, Univ. Fed. de Santa Maria, Santa Maria, Brazil
| | - Monica M Silva
- Dep de Bioquímica e Biologia Molecular, Univ. Fed. de Santa Maria, Santa Maria, Brazil
| | - Alessandro Prestes
- Dep de Bioquímica e Biologia Molecular, Univ. Fed. de Santa Maria, Santa Maria, Brazil; Department of Civil and Environmental, Universidad de la Costa, Calle 58 #55-66, 080002, Barranquilla, Atlántico, Colombia
| | - Nilda B V Barbosa
- Dep de Bioquímica e Biologia Molecular, Univ. Fed. de Santa Maria, Santa Maria, Brazil
| | - João B T Rocha
- Dep de Bioquímica e Biologia Molecular, Univ. Fed. de Santa Maria, Santa Maria, Brazil
| | - Elgion L S Loreto
- PPG Genética e Biologia Molecular, Univ. Fed. do Rio Grande do Sul, Porto Alegre, Brazil; Dep de Bioquímica e Biologia Molecular, Univ. Fed. de Santa Maria, Santa Maria, Brazil.
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13
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Moschetti R, Palazzo A, Lorusso P, Viggiano L, Massimiliano Marsano R. "What You Need, Baby, I Got It": Transposable Elements as Suppliers of Cis-Operating Sequences in Drosophila. BIOLOGY 2020; 9:E25. [PMID: 32028630 PMCID: PMC7168160 DOI: 10.3390/biology9020025] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 01/27/2020] [Accepted: 01/30/2020] [Indexed: 12/18/2022]
Abstract
Transposable elements (TEs) are constitutive components of both eukaryotic and prokaryotic genomes. The role of TEs in the evolution of genes and genomes has been widely assessed over the past years in a variety of model and non-model organisms. Drosophila is undoubtedly among the most powerful model organisms used for the purpose of studying the role of transposons and their effects on the stability and evolution of genes and genomes. Besides their most intuitive role as insertional mutagens, TEs can modify the transcriptional pattern of host genes by juxtaposing new cis-regulatory sequences. A key element of TE biology is that they carry transcriptional control elements that fine-tune the transcription of their own genes, but that can also perturb the transcriptional activity of neighboring host genes. From this perspective, the transposition-mediated modulation of gene expression is an important issue for the short-term adaptation of physiological functions to the environmental changes, and for long-term evolutionary changes. Here, we review the current literature concerning the regulatory and structural elements operating in cis provided by TEs in Drosophila. Furthermore, we highlight that, besides their influence on both TEs and host genes expression, they can affect the chromatin structure and epigenetic status as well as both the chromosome's structure and stability. It emerges that Drosophila is a good model organism to study the effect of TE-linked regulatory sequences, and it could help future studies on TE-host interactions in any complex eukaryotic genome.
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Affiliation(s)
- Roberta Moschetti
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Via Orabona 4, 70125 Bari, Italy; (R.M.); (P.L.); (L.V.)
| | - Antonio Palazzo
- Laboratory of Translational Nanotechnology, “Istituto Tumori Giovanni Paolo II” I.R.C.C.S, Viale Orazio Flacco 65, 70125 Bari, Italy;
| | - Patrizio Lorusso
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Via Orabona 4, 70125 Bari, Italy; (R.M.); (P.L.); (L.V.)
| | - Luigi Viggiano
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Via Orabona 4, 70125 Bari, Italy; (R.M.); (P.L.); (L.V.)
| | - René Massimiliano Marsano
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Via Orabona 4, 70125 Bari, Italy; (R.M.); (P.L.); (L.V.)
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Drongitis D, Aniello F, Fucci L, Donizetti A. Roles of Transposable Elements in the Different Layers of Gene Expression Regulation. Int J Mol Sci 2019; 20:ijms20225755. [PMID: 31731828 PMCID: PMC6888579 DOI: 10.3390/ijms20225755] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/12/2019] [Accepted: 11/14/2019] [Indexed: 02/03/2023] Open
Abstract
The biology of transposable elements (TEs) is a fascinating and complex field of investigation. TEs represent a substantial fraction of many eukaryotic genomes and can influence many aspects of DNA function that range from the evolution of genetic information to duplication, stability, and gene expression. Their ability to move inside the genome has been largely recognized as a double-edged sword, as both useful and deleterious effects can result. A fundamental role has been played by the evolution of the molecular processes needed to properly control the expression of TEs. Today, we are far removed from the original reductive vision of TEs as “junk DNA”, and are more convinced that TEs represent an essential element in the regulation of gene expression. In this review, we summarize some of the more recent findings, mainly in the animal kingdom, concerning the active roles that TEs play at every level of gene expression regulation, including chromatin modification, splicing, and protein translation.
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Affiliation(s)
- Denise Drongitis
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, Consiglio Nazionale delle Ricerche, 80131 Naples, Italy;
| | - Francesco Aniello
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (F.A.); (L.F.)
| | - Laura Fucci
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (F.A.); (L.F.)
| | - Aldo Donizetti
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (F.A.); (L.F.)
- Correspondence:
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Lerat E, Casacuberta J, Chaparro C, Vieira C. On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses. Genes (Basel) 2019; 10:genes10040258. [PMID: 30935103 PMCID: PMC6523952 DOI: 10.3390/genes10040258] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/27/2019] [Accepted: 03/27/2019] [Indexed: 12/21/2022] Open
Abstract
Eukaryotic genomes comprise a large proportion of repeated sequences, an important fraction of which are transposable elements (TEs). TEs are mobile elements that have a significant impact on genome evolution and on gene functioning. Although some TE insertions could provide adaptive advantages to species, transposition is a highly mutagenic event that has to be tightly controlled to ensure its viability. Genomes have evolved sophisticated mechanisms to control TE activity, the most important being epigenetic silencing. However, the epigenetic control of TEs can also affect genes located nearby that can become epigenetically regulated. It has been proposed that the combination of TE mobilization and the induced changes in the epigenetic landscape could allow a rapid phenotypic adaptation to global environmental changes. In this review, we argue the crucial need to take into account the repeated part of genomes when studying the global impact of epigenetic modifications on an organism. We emphasize more particularly why it is important to carefully consider TEs and what bioinformatic tools can be used to do so.
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Affiliation(s)
- Emmanuelle Lerat
- CNRS, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, UMR 5558, F-69622 Villeurbanne, France.
| | - Josep Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain.
| | - Cristian Chaparro
- CNRS, IHPE UMR 5244, University of Perpignan Via Domitia, IFREMER, University Montpellier, F-66860 Perpignan, France.
| | - Cristina Vieira
- CNRS, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, UMR 5558, F-69622 Villeurbanne, France.
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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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