Special Issue "Genomic Impact of Transposable Elements"

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Genetics and Genomics".

Deadline for manuscript submissions: 31 December 2022 | Viewed by 6533

Special Issue Editor

Dr. Kyudong Han
E-Mail Website
Guest Editor
Department of Nanobiomedical Science , BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, 119, Dandae-ro, Dongnam-gu, Cheonan-si, Chungnam 31116, Korea
Interests: comparative genomics; transposable element; genomic instability; genomic rearrangement; species-specific transposable element; molecular marker; phylogenetic analysis

Special Issue Information

Dear Colleagues,

Transposable elements (TEs) have been found in a variety of genomes. TEs are a major source of genetic diversity in eukaryotes. TEs have played an important role in the diversification and enrichment of mammalian transcriptomes. These elements are associated with genomic instability, cancer, epigenetics, gene expression, biomarkers, and DNA repair. We invite investigators to contribute original research articles as well as review articles that will stimulate the continuing efforts to understand TEs’ significance in the host genome. We are interested in articles that explore aspects of genomic/genetic diversity mediated by TEs in all mammals. Potential topics include but are not limited to:

  • Genomic rearrangement by transposable elements;
  • Phylogenetic relationship based on transposable elements;
  • Genetic conflict between host and transposable elements;
  • Role of transposable elements in host factors and epigenetics;
  • Population genetics study by transposable elements;
  • Transposable element research by next-generation sequencing;
  • Transposable elements as a molecular biomarker.

Dr. Kyudong Han
Guest Editor

Manuscript Submission Information

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Published Papers (5 papers)

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Research

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Article
Transposable Elements in Bats Show Differential Accumulation Patterns Determined by Class and Functionality
Life 2022, 12(8), 1190; https://doi.org/10.3390/life12081190 - 04 Aug 2022
Viewed by 262
Abstract
Bat genomes are characterized by a diverse transposable element (TE) repertoire. In particular, the genomes of members of the family Vespertilionidae contain both active retrotransposons and active DNA transposons. Each TE type is characterized by a distinct pattern of accumulation over the past [...] Read more.
Bat genomes are characterized by a diverse transposable element (TE) repertoire. In particular, the genomes of members of the family Vespertilionidae contain both active retrotransposons and active DNA transposons. Each TE type is characterized by a distinct pattern of accumulation over the past ~40 million years. Each also exhibits its own target site preferences (sometimes shared with other TEs) that impact where they are likely to insert when mobilizing. Therefore, bats provide a great resource for understanding the diversity of TE insertion patterns. To gain insight into how these diverse TEs impact genome structure, we performed comparative spatial analyses between different TE classes and genomic features, including genic regions and CpG islands. Our results showed a depletion of all TEs in the coding sequence and revealed patterns of species- and element-specific attraction in the transcript. Trends of attraction in the distance tests also suggested significant TE activity in regions adjacent to genes. In particular, the enrichment of small, non-autonomous TE insertions in introns and near coding regions supports the hypothesis that the genomic distribution of TEs is the product of a balance of the TE insertion preference in open chromatin regions and the purifying selection against TEs within genes. Full article
(This article belongs to the Special Issue Genomic Impact of Transposable Elements)
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Review

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Review
Do Ty3/Gypsy Transposable Elements Play Preferential Roles in Sex Chromosome Differentiation?
Life 2022, 12(4), 522; https://doi.org/10.3390/life12040522 - 01 Apr 2022
Cited by 2 | Viewed by 724
Abstract
Transposable elements (TEs) comprise a substantial portion of eukaryotic genomes. They have the unique ability to integrate into new locations and serve as the main source of genomic novelties by mediating chromosomal rearrangements and regulating portions of functional genes. Recent studies have revealed [...] Read more.
Transposable elements (TEs) comprise a substantial portion of eukaryotic genomes. They have the unique ability to integrate into new locations and serve as the main source of genomic novelties by mediating chromosomal rearrangements and regulating portions of functional genes. Recent studies have revealed that TEs are abundant in sex chromosomes. In this review, we propose evolutionary relationships between specific TEs, such as Ty3/Gypsy, and sex chromosomes in different lineages based on the hypothesis that these elements contributed to sex chromosome differentiation processes. We highlight how TEs can drive the dynamics of sex-determining regions via suppression recombination under a selective force to affect the organization and structural evolution of sex chromosomes. The abundance of TEs in the sex-determining regions originates from TE-poor genomic regions, suggesting a link between TE accumulation and the emergence of the sex-determining regions. TEs are generally considered to be a hallmark of chromosome degeneration. Finally, we outline recent approaches to identify TEs and study their sex-related roles and effects in the differentiation and evolution of sex chromosomes. Full article
(This article belongs to the Special Issue Genomic Impact of Transposable Elements)
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Review
Domesticated LTR-Retrotransposon gag-Related Gene (Gagr) as a Member of the Stress Response Network in Drosophila
Life 2022, 12(3), 364; https://doi.org/10.3390/life12030364 - 03 Mar 2022
Viewed by 533
Abstract
The most important sources of new components of genomes are transposable elements, which can occupy more than half of the nucleotide sequence of the genome in higher eukaryotes. Among the mobile components of a genome, a special place is occupied by retroelements, which [...] Read more.
The most important sources of new components of genomes are transposable elements, which can occupy more than half of the nucleotide sequence of the genome in higher eukaryotes. Among the mobile components of a genome, a special place is occupied by retroelements, which are similar to retroviruses in terms of their mechanisms of integration into a host genome. The process of positive selection of certain sequences of transposable elements and retroviruses in a host genome is commonly called molecular domestication. There are many examples of evolutionary adaptations of gag (retroviral capsid) sequences as new regulatory sequences of different genes in mammals, where domesticated gag genes take part in placenta functioning and embryogenesis, regulation of apoptosis, hematopoiesis, and metabolism. The only gag-related gene has been found in the Drosophila genome—Gagr. According to the large-scale transcriptomic and proteomic analysis data, the Gagr gene in D. melanogaster is a component of the protein complex involved in the stress response. In this work, we consider the evolutionary processes that led to the formation of a new function of the domesticated gag gene and its adaptation to participation in the stress response. We discuss the possible functional role of the Gagr as part of the complex with its partners in Drosophila, and the pathway of evolution of proteins of the complex in eukaryotes to determine the benefit of the domesticated retroelement gag gene. Full article
(This article belongs to the Special Issue Genomic Impact of Transposable Elements)
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Review
Role of Transposable Elements in Gene Regulation in the Human Genome
Life 2021, 11(2), 118; https://doi.org/10.3390/life11020118 - 04 Feb 2021
Cited by 16 | Viewed by 2350
Abstract
Transposable elements (TEs), also known as mobile elements (MEs), are interspersed repeats that constitute a major fraction of the genomes of higher organisms. As one of their important functional impacts on gene function and genome evolution, TEs participate in regulating the expression of [...] Read more.
Transposable elements (TEs), also known as mobile elements (MEs), are interspersed repeats that constitute a major fraction of the genomes of higher organisms. As one of their important functional impacts on gene function and genome evolution, TEs participate in regulating the expression of genes nearby and even far away at transcriptional and post-transcriptional levels. There are two known principal ways by which TEs regulate the expression of genes. First, TEs provide cis-regulatory sequences in the genome with their intrinsic regulatory properties for their own expression, making them potential factors for regulating the expression of the host genes. TE-derived cis-regulatory sites are found in promoter and enhancer elements, providing binding sites for a wide range of trans-acting factors. Second, TEs encode for regulatory RNAs with their sequences showed to be present in a substantial fraction of miRNAs and long non-coding RNAs (lncRNAs), indicating the TE origin of these RNAs. Furthermore, TEs sequences were found to be critical for regulatory functions of these RNAs, including binding to the target mRNA. TEs thus provide crucial regulatory roles by being part of cis-regulatory and regulatory RNA sequences. Moreover, both TE-derived cis-regulatory sequences and TE-derived regulatory RNAs have been implicated in providing evolutionary novelty to gene regulation. These TE-derived regulatory mechanisms also tend to function in a tissue-specific fashion. In this review, we aim to comprehensively cover the studies regarding these two aspects of TE-mediated gene regulation, mainly focusing on the mechanisms, contribution of different types of TEs, differential roles among tissue types, and lineage-specificity, based on data mostly in humans. Full article
(This article belongs to the Special Issue Genomic Impact of Transposable Elements)
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Review
Bioinformatics Analysis of Evolution and Human Disease Related Transposable Element-Derived microRNAs
Life 2020, 10(6), 95; https://doi.org/10.3390/life10060095 - 25 Jun 2020
Cited by 7 | Viewed by 1569
Abstract
Transposable element (TE) has the ability to insert into certain parts of the genome, and due to this event, it is possible for TEs to generate new factors and one of these factors are microRNAs (miRNA). miRNAs are non-coding RNAs made up of [...] Read more.
Transposable element (TE) has the ability to insert into certain parts of the genome, and due to this event, it is possible for TEs to generate new factors and one of these factors are microRNAs (miRNA). miRNAs are non-coding RNAs made up of 19 to 24 nucleotides and numerous miRNAs are derived from TE. In this study, to support general knowledge on TE and miRNAs derived from TE, several bioinformatics tools and databases were used to analyze miRNAs derived from TE in two aspects: evolution and human disease. The distribution of TEs in diverse species presents that almost half of the genome is covered with TE in mammalians and less than a half in other vertebrates and invertebrates. Based on selected evolution-related miRNAs studies, a total of 51 miRNAs derived from TE were found and analyzed. For the human disease-related miRNAs, total of 34 miRNAs derived from TE were organized from the previous studies. In summary, abundant miRNAs derived from TE are found, however, the function of miRNAs derived from TE is not informed either. Therefore, this study provides theoretical understanding of miRNAs derived from TE by using various bioinformatics tools. Full article
(This article belongs to the Special Issue Genomic Impact of Transposable Elements)
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