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Special Issue "Transposable Elements"

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: 31 January 2020.

Special Issue Editors

Guest Editor
Prof. Dr. Teresa Capriglione Website E-Mail
Dipartimento di Biologia, Università di Napoli "Federico II", Complesso Universitario di Monte S. Angelo, Via Cinthia, 80126, Napoli, Italia
Interests: PCR; DNA; cloning; molecular biology; RNA; DNA sequencing; molecular genetics; genomics sequencing; molecular cloning; bioinformatics; phylogenetic analysis; chromosomes; gene expression and chromatin biology; microsatellites; cytogenetics; in situ hybridization; developmental neuroscience; hybridization; developmental genetics; vertebrates; southern blot; Y chromosome; centromere; polyploidy; transposable elements; transposons; MirBase
Guest Editor
Dr. Andrea Luchetti Website E-Mail
Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, via Selmi 3, 40126, Bologna, Italy
Interests: DNA; DNA sequencing; genomics; genetics; phylogenetic analysis; population genetics; genetic diversity; phylogenetics; molecular ecology; phylogeny; insect; molecular phylogenetics; phylogeography and phylogenetic biogeography; microsatellites; evolutionary genetics; DNA barcoding; hybridization; molecular taxonomy; nucleic acids; transposable elements; retrotransposons; gynogenesis

Special Issue Information

Dear Colleagues,

Transposable elements are discrete DNA sequences ubiquitous among prokaryotic and eukaryotic genomes. The ability to self-replicate and move within and among chromosomes, inserting in both coding and non-coding regions, makes transposable elements particularly important for genome functionality and evolution. After their first discovery nearly 70 years ago, transposable elements were considered mostly deleterious for host genomes: a kind of genomic parasite. Despite their selfish nature, later studies indicated their high natural abundance within genomes (up to 50% in some instances) and their implications for genome evolution.

Nowadays, the implication of transposable elements in many biological processes is well known, including speciation, adaptation, horizontal transfer, and pathological conditions in humans. At the genome level, transposable elements are currently recognized as a powerful source of genetic variation, genomic restructuring, and gene expression modulation . Moreover, a growing body of evidence highlights events of exaptation, in which transposable element sequences have been “recruited” by host genomes and integrated in gene structures and/or gene regulatory networks. Transposable elements have even been found to play a role in development, neurogenesis, and ageing.

In recent years, the use of transposable elements as a means of genomic modification and transgenesis has been envisaged and, effectively, put into practice. Today, some engineered transposable elements are used for gene transfer therapy.

In the current “genomic era”, in which NGS technologies allow the sequencing and assembly of many genomes and transcriptomes, studies of transposable elements have been boosted by the huge quantity of sequence information available. Therefore, we are now in an exciting moment for transposable element studies! The present Special Issue aims to gather current knowledge from past studies, and from cutting-edge transposable element research, by selecting papers on hot topics of transposable element biology. Therefore, studies based on experimental evidence, suggesting or updating evolutionary models, and dealing with applications are well suited for this Special Issue.

Prof. Dr. Teresa Capriglione
Dr. Andrea Luchetti
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • transposon
  • jumping gene
  • retrotransposon
  • DNA transposon
  • endogenous retrovirus
  • reverse transcription
  • integration
  • host
  • genome evolution
  • genomic modification
  • gene structure
  • disease

Published Papers (8 papers)

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Research

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Open AccessArticle
Alu RNA Modulates the Expression of Cell Cycle Genes in Human Fibroblasts
Int. J. Mol. Sci. 2019, 20(13), 3315; https://doi.org/10.3390/ijms20133315 - 05 Jul 2019
Cited by 1
Abstract
Alu retroelements, whose retrotransposition requires prior transcription by RNA polymerase III to generate Alu RNAs, represent the most numerous non-coding RNA (ncRNA) gene family in the human genome. Alu transcription is generally kept to extremely low levels by tight epigenetic silencing, but it [...] Read more.
Alu retroelements, whose retrotransposition requires prior transcription by RNA polymerase III to generate Alu RNAs, represent the most numerous non-coding RNA (ncRNA) gene family in the human genome. Alu transcription is generally kept to extremely low levels by tight epigenetic silencing, but it has been reported to increase under different types of cell perturbation, such as viral infection and cancer. Alu RNAs, being able to act as gene expression modulators, may be directly involved in the mechanisms determining cellular behavior in such perturbed states. To directly address the regulatory potential of Alu RNAs, we generated IMR90 fibroblasts and HeLa cell lines stably overexpressing two slightly different Alu RNAs, and analyzed genome-wide the expression changes of protein-coding genes through RNA-sequencing. Among the genes that were upregulated or downregulated in response to Alu overexpression in IMR90, but not in HeLa cells, we found a highly significant enrichment of pathways involved in cell cycle progression and mitotic entry. Accordingly, Alu overexpression was found to promote transition from G1 to S phase, as revealed by flow cytometry. Therefore, increased Alu RNA may contribute to sustained cell proliferation, which is an important factor of cancer development and progression. Full article
(This article belongs to the Special Issue Transposable Elements)
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Open AccessCommunication
Identification of a Retroelement-Containing Human Transcript Induced in the Nucleus by Vaccination
Int. J. Mol. Sci. 2019, 20(12), 2875; https://doi.org/10.3390/ijms20122875 - 13 Jun 2019
Abstract
Endogenous retroelements constitute almost half of the mammalian genome. Given that more than 60% of human genomic bases are transcribed, transcripts containing these retroelements may impact various biological processes. However, the physiological roles of most retroelement-containing transcripts are yet to be revealed. Here, [...] Read more.
Endogenous retroelements constitute almost half of the mammalian genome. Given that more than 60% of human genomic bases are transcribed, transcripts containing these retroelements may impact various biological processes. However, the physiological roles of most retroelement-containing transcripts are yet to be revealed. Here, we profiled the expression of retroelement-containing human transcripts during vaccination and found that vaccination upregulated transcripts containing only particular retroelements, such as the MLT-int element of endogenous retroviruses. MLT-int-containing transcripts were distributed mainly in the nucleus, suggesting their unique roles in the nucleus. Furthermore, we demonstrated that MLT-int RNA suppressed interferon promoter activity in the absence of immune stimuli. Based on these lines of evidence, we speculate a model of a role of the previously unnoticed MLT-int element in preventing excess innate immune activation after elimination of immune stimuli. Our results may emphasize the importance of retroelement-containing transcripts in maintaining host immune homeostasis. Full article
(This article belongs to the Special Issue Transposable Elements)
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Open AccessArticle
miR-128 Restriction of LINE-1 (L1) Retrotransposition Is Dependent on Targeting hnRNPA1 mRNA
Int. J. Mol. Sci. 2019, 20(8), 1955; https://doi.org/10.3390/ijms20081955 - 21 Apr 2019
Cited by 1
Abstract
The majority of the human genome is made of transposable elements, giving rise to interspaced repeats, including Long INterspersed Element-1s (LINE-1s or L1s). L1s are active human transposable elements involved in genomic diversity and evolution; however, they can also contribute to genomic instability [...] Read more.
The majority of the human genome is made of transposable elements, giving rise to interspaced repeats, including Long INterspersed Element-1s (LINE-1s or L1s). L1s are active human transposable elements involved in genomic diversity and evolution; however, they can also contribute to genomic instability and diseases. L1s require host factors to complete their life cycles, whereas the host has evolved numerous mechanisms to restrict L1-induced mutagenesis. Restriction mechanisms in somatic cells include methylation of the L1 promoter, anti-viral factors and RNA-mediated processes such as small RNAs. microRNAs (miRNAs or miRs) are small non-coding RNAs that post-transcriptionally repress multiple target genes often found in the same cellular pathways. We have recently established that miR-128 functions as a novel restriction factor inhibiting L1 mobilization in somatic cells. We have further demonstrated that miR-128 functions through a dual mechanism; by directly targeting L1 RNA for degradation and indirectly by inhibiting a cellular co-factor which L1 is dependent on to transpose to new genomic locations (TNPO1). Here, we add another piece to the puzzle of the enigmatic L1 lifecycle. We show that miR-128 also inhibits another key cellular factor, hnRNPA1 (heterogeneous nuclear ribonucleoprotein A1), by significantly reducing mRNA and protein levels through direct interaction with the coding sequence (CDS) of hnRNPA1 mRNA. In addition, we demonstrate that repression of hnRNPA1 using hnRNPA1-shRNA significantly decreases de novo L1 retro-transposition and that induced hnRNPA1 expression enhances L1 mobilization. Furthermore, we establish that hnRNPA1 is a functional target of miR-128. Finally, we determine that induced hnRNPA1 expression in miR-128-overexpressing cells can partly rescue the miR-128-induced repression of L1′s ability to transpose to different genomic locations. Thus, we have identified an additional mechanism by which miR-128 represses L1 retro-transposition and mediates genomic stability. Full article
(This article belongs to the Special Issue Transposable Elements)
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Open AccessArticle
Insertion Hot Spots of DIRS1 Retrotransposon and Chromosomal Diversifications among the Antarctic Teleosts Nototheniidae
Int. J. Mol. Sci. 2019, 20(3), 701; https://doi.org/10.3390/ijms20030701 - 06 Feb 2019
Abstract
By their faculty to transpose, transposable elements are known to play a key role in eukaryote genomes, impacting both their structuration and remodeling. Their integration in targeted sites may lead to recombination mechanisms involved in chromosomal rearrangements. The Antarctic fish family Nototheniidae went [...] Read more.
By their faculty to transpose, transposable elements are known to play a key role in eukaryote genomes, impacting both their structuration and remodeling. Their integration in targeted sites may lead to recombination mechanisms involved in chromosomal rearrangements. The Antarctic fish family Nototheniidae went through several waves of species radiations. It is a suitable model to study transposable element (TE)-mediated mechanisms associated to genome and chromosomal diversifications. After the characterization of Gypsy (GyNoto), Copia (CoNoto), and DIRS1 (YNoto) retrotransposons in the genomes of Nototheniidae (diversity, distribution, conservation), we focused on their chromosome location with an emphasis on the three identified nototheniid radiations (the Trematomus, the plunderfishes, and the icefishes). The strong intrafamily TE conservation and wide distribution across species of the whole family suggest an ancestral acquisition with potential secondary losses in some lineages. GyNoto and CoNoto (including Hydra and GalEa clades) mostly produced interspersed signals along chromosomal arms. On the contrary, insertion hot spots accumulating in localized regions (mainly next to centromeric and pericentromeric regions) highlighted the potential role of YNoto in chromosomal diversifications as facilitator of the fusions which occurred in many nototheniid lineages, but not of the fissions. Full article
(This article belongs to the Special Issue Transposable Elements)
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Open AccessArticle
Inhibition of LINE-1 Retrotransposition by Capsaicin
Int. J. Mol. Sci. 2018, 19(10), 3243; https://doi.org/10.3390/ijms19103243 - 19 Oct 2018
Cited by 4
Abstract
Long interspersed nuclear element 1 (LINE-1 or L1) is a non-long terminal repeat (LTR) retrotransposon that constitutes approximately 17% of the human genome. Since approximately 100 copies are still competent for retrotransposition to other genomic loci, dysregulated retrotransposition of L1 is considered to [...] Read more.
Long interspersed nuclear element 1 (LINE-1 or L1) is a non-long terminal repeat (LTR) retrotransposon that constitutes approximately 17% of the human genome. Since approximately 100 copies are still competent for retrotransposition to other genomic loci, dysregulated retrotransposition of L1 is considered to be a major risk factor of endogenous mutagenesis in humans. Thus, it is important to find drugs to regulate this process. Although various chemicals are reportedly capable of affecting L1 retrotransposition, it is poorly understood whether phytochemicals modulate L1 retrotransposition. Here, we screened a library of compounds that were derived from phytochemicals for reverse transcriptase (RT) inhibition with an in vitro RT assay. We identified capsaicin as a novel RT inhibitor that also suppressed L1 retrotransposition. The inhibitory effect of capsaicin on L1 retrotransposition was mediated neither through its receptor, nor through its modulation of the L1 promoter and/or antisense promoter activity, excluding the possibility that capsaicin indirectly affected L1 retrotransposition. Collectively, capsaicin suppressed L1 retrotransposition most likely by inhibiting the RT activity of L1 ORF2p, which is the L1-encoded RT responsible for L1 retrotransposition. Given that L1-mediated mutagenesis can cause tumorigenesis, our findings suggest the potential of capsaicin for suppressing cancer development. Full article
(This article belongs to the Special Issue Transposable Elements)
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Open AccessArticle
Exploring the Remote Ties between Helitron Transposases and Other Rolling-Circle Replication Proteins
Int. J. Mol. Sci. 2018, 19(10), 3079; https://doi.org/10.3390/ijms19103079 - 09 Oct 2018
Cited by 1
Abstract
Rolling-circle replication (RCR) elements constitute a diverse group that includes viruses, plasmids, and transposons, present in hosts from all domains of life. Eukaryotic RCR transposons, also known as Helitrons, are found in species from all eukaryotic kingdoms, sometimes representing a large portion of [...] Read more.
Rolling-circle replication (RCR) elements constitute a diverse group that includes viruses, plasmids, and transposons, present in hosts from all domains of life. Eukaryotic RCR transposons, also known as Helitrons, are found in species from all eukaryotic kingdoms, sometimes representing a large portion of their genomes. Despite the impact of Helitrons on their hosts, knowledge about their relationship with other RCR elements is still elusive. Here, we compared the endonuclease domain sequence of Helitron transposases with the corresponding region from RCR proteins found in a wide variety of mobile genetic elements. To do that, we used a stepwise alignment approach followed by phylogenetic and multidimensional scaling analyses. Although it has been suggested that Helitrons might have originated from prokaryotic transposons or eukaryotic viruses, our results indicate that Helitron transposases share more similarities with proteins from prokaryotic viruses and plasmids instead. We also provide evidence for the division of RCR endonucleases into three groups (Y1, Y2, and Yx), covering the whole diversity of this protein family. Together, these results point to prokaryotic elements as the likely closest ancestors of eukaryotic RCR transposons, and further demonstrate the fluidity that characterizes the boundaries separating viruses, plasmids, and transposons. Full article
(This article belongs to the Special Issue Transposable Elements)
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Review

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Open AccessReview
Transposable Elements Adaptive Role in Genome Plasticity, Pathogenicity and Evolution in Fungal Phytopathogens
Int. J. Mol. Sci. 2019, 20(14), 3597; https://doi.org/10.3390/ijms20143597 - 23 Jul 2019
Abstract
Transposable elements (TEs) are agents of genetic variability in phytopathogens as they are a source of adaptive evolution through genome diversification. Although many studies have uncovered information on TEs, the exact mechanism behind TE-induced changes within the genome remains poorly understood. Furthermore, convergent [...] Read more.
Transposable elements (TEs) are agents of genetic variability in phytopathogens as they are a source of adaptive evolution through genome diversification. Although many studies have uncovered information on TEs, the exact mechanism behind TE-induced changes within the genome remains poorly understood. Furthermore, convergent trends towards bigger genomes, emergence of novel genes and gain or loss of genes implicate a TE-regulated genome plasticity of fungal phytopathogens. TEs are able to alter gene expression by revamping the cis-regulatory elements or recruiting epigenetic control. Recent findings show that TEs recruit epigenetic control on the expression of effector genes as part of the coordinated infection strategy. In addition to genome plasticity and diversity, fungal pathogenicity is an area of economic concern. A survey of TE distribution suggests that their proximity to pathogenicity genes TEs may act as sites for emergence of novel pathogenicity factors via nucleotide changes and expansion or reduction of the gene family. Through a systematic survey of literature, we were able to conclude that the role of TEs in fungi is wide: ranging from genome plasticity, pathogenicity to adaptive behavior in evolution. This review also identifies the gaps in knowledge that requires further elucidation for a better understanding of TEs’ contribution to genome architecture and versatility. Full article
(This article belongs to the Special Issue Transposable Elements)
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Open AccessReview
Rex Retroelements and Teleost Genomes: An Overview
Int. J. Mol. Sci. 2018, 19(11), 3653; https://doi.org/10.3390/ijms19113653 - 20 Nov 2018
Cited by 2
Abstract
Repetitive DNA is an intriguing portion of the genome still not completely discovered and shows a high variability in terms of sequence, genomic organization, and evolutionary mode. On the basis of the genomic organization, it includes satellite DNAs, which are organized as long [...] Read more.
Repetitive DNA is an intriguing portion of the genome still not completely discovered and shows a high variability in terms of sequence, genomic organization, and evolutionary mode. On the basis of the genomic organization, it includes satellite DNAs, which are organized as long arrays of head-to-tail linked repeats, and transposable elements, which are dispersed throughout the genome. These repeated elements represent a considerable fraction of vertebrate genomes contributing significantly in species evolution. In this review, we focus our attention on Rex1, Rex3 and Rex6, three elements specific of teleost genomes. We report an overview of data available on these retroelements highlighting their significative impact in chromatin and heterochromatin organization, in the differentiation of sex chromosomes, in the formation of supernumerary chromosomes, and in karyotype evolution in teleosts. Full article
(This article belongs to the Special Issue Transposable Elements)
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