Transposable Elements: The Impact on the Structural and Functional Organization of the Genome

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Cell Nuclei: Function, Transport and Receptors".

Deadline for manuscript submissions: closed (15 May 2022) | Viewed by 33404

Special Issue Editor

Department of Biology and Biotechnology “Charles Darwin”, Laboratory of Epigenetics, “Sapienza” University of Rome, Rome, Italy
Interests: transposable elements; epigenetics; chromosome organization; genome evolution
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Transposable elements are a relevant and fascinating part of the genome of all living organisms, from bacteria to humans, which simultaneously show both their bad and their good sides. On the one hand, these elements are, in fact, capable of producing harmful effects due to their ability to jump from one part of the genome to the other. On the other hand, it is clear that these elements have, nevertheless, played an important role from an evolutionary point of view.

Since their discovery about 70 years ago by Barbara McClintock, the transposons have aroused great fervour in various fields of research, ranging from genetics, to cell biology, evolutionary biology, and biomedicine. Recent results have highlighted that transposable elements are not only implicated in the genesis of various complex diseases, but also in normal brain development. Despite the risks of their coexistence with host genomes, transposons have been recognized as important evolutionary tools for their capacity to reshape genomes by creating new regulatory elements, gene mutations and chromosome rearrangements—all of which are factors involved in adaptation processes.

We encourage contributions to the transposon field in this Special Issue, the purpose of which is to offer a panoramic view about the advances in recent research on such a versatile part of the genome.

We are looking forward to your contributions to this Special Issue.

Prof. Laura Fanti
Guest Editor

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Keywords

  • transposable elements
  • human diseases
  • gene regulation
  • chromosome organization
  • genome evolution

Published Papers (9 papers)

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Research

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9 pages, 1603 KiB  
Communication
Retrotransposons Down- and Up-Regulation in Aging Somatic Tissues
by Giorgia Giordani, Valeria Cavaliere, Giuseppe Gargiulo, Giovanna Lattanzi and Davide Andrenacci
Cells 2022, 11(1), 79; https://doi.org/10.3390/cells11010079 - 28 Dec 2021
Cited by 3 | Viewed by 2180
Abstract
The transposon theory of aging hypothesizes the activation of transposable elements (TEs) in somatic tissues with age, leading to a shortening of the lifespan. It is thought that TE activation in aging produces an increase in DNA double-strand breaks, contributing to genome instability [...] Read more.
The transposon theory of aging hypothesizes the activation of transposable elements (TEs) in somatic tissues with age, leading to a shortening of the lifespan. It is thought that TE activation in aging produces an increase in DNA double-strand breaks, contributing to genome instability and promoting the activation of inflammatory responses. To investigate how TE regulation changes in somatic tissues during aging, we analyzed the expression of some TEs, as well as a source of small RNAs that specifically silence the analyzed TEs; the Drosophila cluster named flamenco. We found significant variations in the expression levels of all the analyzed TEs during aging, with a trend toward reduction in middle-aged adults and reactivation in older individuals that suggests dynamic regulation during the lifespan. Full article
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20 pages, 4585 KiB  
Article
Transposable Element Expression and Regulation Profile in Gonads of Interspecific Hybrids of Drosophila arizonae and Drosophila mojavensis wrigleyi
by Cecília Artico Banho, Daniel Siqueira Oliveira, Annabelle Haudry, Marie Fablet, Cristina Vieira and Claudia Marcia Aparecida Carareto
Cells 2021, 10(12), 3574; https://doi.org/10.3390/cells10123574 - 18 Dec 2021
Cited by 1 | Viewed by 2184
Abstract
Interspecific hybridization may lead to sterility and/or inviability through differential expression of genes and transposable elements (TEs). In Drosophila, studies have reported massive TE mobilization in hybrids from interspecific crosses of species presenting high divergence times. However, few studies have examined the [...] Read more.
Interspecific hybridization may lead to sterility and/or inviability through differential expression of genes and transposable elements (TEs). In Drosophila, studies have reported massive TE mobilization in hybrids from interspecific crosses of species presenting high divergence times. However, few studies have examined the consequences of TE mobilization upon hybridization in recently diverged species, such as Drosophila arizonae and D. mojavensis. We have sequenced transcriptomes of D. arizonae and the subspecies D. m. wrigleyi and their reciprocal hybrids, as well as piRNAs, to analyze the impact of genomic stress on TE regulation. Our results revealed that the differential expression in both gonadal tissues of parental species was similar. Globally, ovaries and testes showed few deregulated TEs compared with both parental lines. Analyses of small RNA data showed that in ovaries, the TE upregulation is likely due to divergence of copies inherited from parental genomes and lack of piRNAs mapping to them. Nevertheless, in testes, the divergent expression of genes associated with chromatin state and piRNA pathway potentially indicates that TE differential expression is related to the divergence of regulatory genes that play a role in modulating transcriptional and post-transcriptional mechanisms. Full article
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14 pages, 2491 KiB  
Article
THAP9 Transposase Cleaves DNA via Conserved Acidic Residues in an RNaseH-Like Domain
by Vasudha Sharma, Prachi Thakore and Sharmistha Majumdar
Cells 2021, 10(6), 1351; https://doi.org/10.3390/cells10061351 - 29 May 2021
Cited by 1 | Viewed by 2759
Abstract
The catalytic domain of most ‘cut and paste’ DNA transposases have the canonical RNase-H fold, which is also shared by other polynucleotidyl transferases such as the retroviral integrases and the RAG1 subunit of V(D)J recombinase. The RNase-H fold is a mixture of beta [...] Read more.
The catalytic domain of most ‘cut and paste’ DNA transposases have the canonical RNase-H fold, which is also shared by other polynucleotidyl transferases such as the retroviral integrases and the RAG1 subunit of V(D)J recombinase. The RNase-H fold is a mixture of beta sheets and alpha helices with three acidic residues (Asp, Asp, Glu/Asp—DDE/D) that are involved in the metal-mediated cleavage and subsequent integration of DNA. Human THAP9 (hTHAP9), homologous to the well-studied Drosophila P-element transposase (DmTNP), is an active DNA transposase that, although domesticated, still retains the catalytic activity to mobilize transposons. In this study we have modeled the structure of hTHAP9 using the recently available cryo-EM structure of DmTNP as a template to identify an RNase-H like fold along with important acidic residues in its catalytic domain. Site-directed mutagenesis of the predicted catalytic residues followed by screening for DNA excision and integration activity has led to the identification of candidate Ds and Es in the RNaseH fold that may be a part of the catalytic triad in hTHAP9. This study has helped widen our knowledge about the catalytic activity of a functionally uncharacterized transposon-derived gene in the human genome. Full article
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Review

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28 pages, 3001 KiB  
Review
All Quiet on the TE Front? The Role of Chromatin in Transposable Element Silencing
by Luisa Di Stefano
Cells 2022, 11(16), 2501; https://doi.org/10.3390/cells11162501 - 11 Aug 2022
Cited by 1 | Viewed by 3768
Abstract
Transposable elements (TEs) are mobile genetic elements that constitute a sizeable portion of many eukaryotic genomes. Through their mobility, they represent a major source of genetic variation, and their activation can cause genetic instability and has been linked to aging, cancer and neurodegenerative [...] Read more.
Transposable elements (TEs) are mobile genetic elements that constitute a sizeable portion of many eukaryotic genomes. Through their mobility, they represent a major source of genetic variation, and their activation can cause genetic instability and has been linked to aging, cancer and neurodegenerative diseases. Accordingly, tight regulation of TE transcription is necessary for normal development. Chromatin is at the heart of TE regulation; however, we still lack a comprehensive understanding of the precise role of chromatin marks in TE silencing and how chromatin marks are established and maintained at TE loci. In this review, I discuss evidence documenting the contribution of chromatin-associated proteins and histone marks in TE regulation across different species with an emphasis on Drosophila and mammalian systems. Full article
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21 pages, 1733 KiB  
Review
Transposable Elements: Major Players in Shaping Genomic and Evolutionary Patterns
by Nunzia Colonna Romano and Laura Fanti
Cells 2022, 11(6), 1048; https://doi.org/10.3390/cells11061048 - 19 Mar 2022
Cited by 14 | Viewed by 6303
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 [...] Read more.
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. Full article
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14 pages, 672 KiB  
Review
Constitutive Heterochromatin in Eukaryotic Genomes: A Mine of Transposable Elements
by René Massimiliano Marsano and Patrizio Dimitri
Cells 2022, 11(5), 761; https://doi.org/10.3390/cells11050761 - 22 Feb 2022
Cited by 15 | Viewed by 3058
Abstract
Transposable elements (TEs) are abundant components of constitutive heterochromatin of the most diverse evolutionarily distant organisms. TEs enrichment in constitutive heterochromatin was originally described in the model organism Drosophila melanogaster, but it is now considered as a general feature of this peculiar [...] Read more.
Transposable elements (TEs) are abundant components of constitutive heterochromatin of the most diverse evolutionarily distant organisms. TEs enrichment in constitutive heterochromatin was originally described in the model organism Drosophila melanogaster, but it is now considered as a general feature of this peculiar portion of the genomes. The phenomenon of TE enrichment in constitutive heterochromatin has been proposed to be the consequence of a progressive accumulation of transposable elements caused by both reduced recombination and lack of functional genes in constitutive heterochromatin. However, this view does not take into account classical genetics studies and most recent evidence derived by genomic analyses of heterochromatin in Drosophila and other species. In particular, the lack of functional genes does not seem to be any more a general feature of heterochromatin. Sequencing and annotation of Drosophila melanogaster constitutive heterochromatin have shown that this peculiar genomic compartment contains hundreds of transcriptionally active genes, generally larger in size than that of euchromatic ones. Together, these genes occupy a significant fraction of the genomic territory of heterochromatin. Moreover, transposable elements have been suggested to drive the formation of heterochromatin by recruiting HP1 and repressive chromatin marks. In addition, there are several pieces of evidence that transposable elements accumulation in the heterochromatin might be important for centromere and telomere structure. Thus, there may be more complexity to the relationship between transposable elements and constitutive heterochromatin, in that different forces could drive the dynamic of this phenomenon. Among those forces, preferential transposition may be an important factor. In this article, we present an overview of experimental findings showing cases of transposon enrichment into the heterochromatin and their positive evolutionary interactions with an impact to host genomes. Full article
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19 pages, 13462 KiB  
Review
Taming, Domestication and Exaptation: Trajectories of Transposable Elements in Genomes
by Pierre Capy
Cells 2021, 10(12), 3590; https://doi.org/10.3390/cells10123590 - 20 Dec 2021
Cited by 10 | Viewed by 4103
Abstract
During evolution, several types of sequences pass through genomes. Along with mutations and internal genetic tinkering, they are a useful source of genetic variability for adaptation and evolution. Most of these sequences are acquired by horizontal transfers (HT), but some of them may [...] Read more.
During evolution, several types of sequences pass through genomes. Along with mutations and internal genetic tinkering, they are a useful source of genetic variability for adaptation and evolution. Most of these sequences are acquired by horizontal transfers (HT), but some of them may come from the genomes themselves. If they are not lost or eliminated quickly, they can be tamed, domesticated, or even exapted. Each of these processes results from a series of events, depending on the interactions between these sequences and the host genomes, but also on environmental constraints, through their impact on individuals or population fitness. After a brief reminder of the characteristics of each of these states (taming, domestication, exaptation), the evolutionary trajectories of these new or acquired sequences will be presented and discussed, emphasizing that they are not totally independent insofar as the first can constitute a step towards the second, and the second is another step towards the third. Full article
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35 pages, 3024 KiB  
Review
The Evolutionary Volte-Face of Transposable Elements: From Harmful Jumping Genes to Major Drivers of Genetic Innovation
by Melody Nicolau, Nathalie Picault and Guillaume Moissiard
Cells 2021, 10(11), 2952; https://doi.org/10.3390/cells10112952 - 29 Oct 2021
Cited by 15 | Viewed by 4511
Abstract
Transposable elements (TEs) are self-replicating DNA elements that constitute major fractions of eukaryote genomes. Their ability to transpose can modify the genome structure with potentially deleterious effects. To repress TE activity, host cells have developed numerous strategies, including epigenetic pathways, such as DNA [...] Read more.
Transposable elements (TEs) are self-replicating DNA elements that constitute major fractions of eukaryote genomes. Their ability to transpose can modify the genome structure with potentially deleterious effects. To repress TE activity, host cells have developed numerous strategies, including epigenetic pathways, such as DNA methylation or histone modifications. Although TE neo-insertions are mostly deleterious or neutral, they can become advantageous for the host under specific circumstances. The phenomenon leading to the appropriation of TE-derived sequences by the host is known as TE exaptation or co-option. TE exaptation can be of different natures, through the production of coding or non-coding DNA sequences with ultimately an adaptive benefit for the host. In this review, we first give new insights into the silencing pathways controlling TE activity. We then discuss a model to explain how, under specific environmental conditions, TEs are unleashed, leading to a TE burst and neo-insertions, with potential benefits for the host. Finally, we review our current knowledge of coding and non-coding TE exaptation by providing several examples in various organisms and describing a method to identify TE co-option events. Full article
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11 pages, 740 KiB  
Review
The Role of HSP90 in Preserving the Integrity of Genomes Against Transposons Is Evolutionarily Conserved
by Valeria Specchia and Maria Pia Bozzetti
Cells 2021, 10(5), 1096; https://doi.org/10.3390/cells10051096 - 04 May 2021
Cited by 8 | Viewed by 2541
Abstract
The HSP90 protein is a molecular chaperone intensively studied for its role in numerous cellular processes both under physiological and stress conditions. This protein acts on a wide range of substrates with a well-established role in cancer and neurological disorders. In this review, [...] Read more.
The HSP90 protein is a molecular chaperone intensively studied for its role in numerous cellular processes both under physiological and stress conditions. This protein acts on a wide range of substrates with a well-established role in cancer and neurological disorders. In this review, we focused on the involvement of HSP90 in the silencing of transposable elements and in the genomic integrity maintenance. The common feature of transposable elements is the potential jumping in new genomic positions, causing chromosome structure rearrangements, gene mutations, and influencing gene expression levels. The role of HSP90 in the control of these elements is evolutionarily conserved and opens new perspectives in the HSP90-related mechanisms underlying human disorders. Here, we discuss the hypothesis that its role in the piRNA pathway regulating transposons may be implicated in the onset of neurological diseases. Full article
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