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Functional & Integrative Genomics Aug 2023Transposable elements, often referred to as "jumping genes," have long been recognized as genomic parasites due to their ability to integrate and disrupt normal gene... (Review)
Review
Transposable elements, often referred to as "jumping genes," have long been recognized as genomic parasites due to their ability to integrate and disrupt normal gene function and induce extensive genomic alterations, thereby compromising the host's fitness. To counteract this, the host has evolved a plethora of mechanisms to suppress the activity of the transposons. Recent research has unveiled the host-transposon relationships to be nuanced and complex phenomena, resulting in the coevolution of both entities. Transposition increases the mutational rate in the host genome, often triggering physiological pathways such as immune and stress responses. Current gene transfer technologies utilizing transposable elements have potential drawbacks, including off-target integration, induction of mutations, and modifications of cellular machinery, which makes an in-depth understanding of the host-transposon relationship imperative. This review highlights the dynamic interplay between the host and transposable elements, encompassing various factors and components of the cellular machinery. We provide a comprehensive discussion of the strategies employed by transposable elements for their propagation, as well as the mechanisms utilized by the host to mitigate their parasitic effects. Additionally, we present an overview of recent research identifying host proteins that act as facilitators or inhibitors of transposition. We further discuss the evolutionary outcomes resulting from the genetic interactions between the host and the transposable elements. Finally, we pose open questions in this field and suggest potential avenues for future research.
Topics: Animals; Parasites; DNA Transposable Elements; Genomics; Mutation
PubMed: 37610667
DOI: 10.1007/s10142-023-01206-w -
Genes & Genetic Systems Jan 2020The majority of eukaryotic genomes contain a large fraction of repetitive sequences that primarily originate from transpositional bursts of transposable elements (TEs).... (Review)
Review
The majority of eukaryotic genomes contain a large fraction of repetitive sequences that primarily originate from transpositional bursts of transposable elements (TEs). Repbase serves as a database for eukaryotic repetitive sequences and has now become the largest collection of eukaryotic TEs. During the development of Repbase, many new superfamilies/lineages of TEs, which include Helitron, Polinton, Ginger and SINEU, were reported. The unique composition of protein domains and DNA motifs in TEs sometimes indicates novel mechanisms of transposition, replication, anti-suppression or proliferation. In this review, our current understanding regarding the diversity of eukaryotic TEs in sequence, protein domain composition and structural hallmarks is introduced and summarized, based on the classification system implemented in Repbase. Autonomous eukaryotic TEs can be divided into two groups: Class I TEs, also called retrotransposons, and Class II TEs, or DNA transposons. Long terminal repeat (LTR) retrotransposons, including endogenous retroviruses, non-LTR retrotransposons, tyrosine recombinase retrotransposons and Penelope-like elements, are well accepted groups of autonomous retrotransposons. They share reverse transcriptase for replication but are distinct in the catalytic components responsible for integration into the host genome. Similarly, at least three transposition machineries have been reported in eukaryotic DNA transposons: DDD/E transposase, tyrosine recombinase and HUH endonuclease combined with helicase. Among these, TEs with DDD/E transposase are dominant and are classified into 21 superfamilies in Repbase. Non-autonomous TEs are either simple derivatives generated by internal deletion, or are composed of several units that originated independently.
Topics: Computational Biology; DNA Transposable Elements; Eukaryota; Genetic Variation; Protein Domains; Retroelements
PubMed: 30416149
DOI: 10.1266/ggs.18-00024 -
Trends in Microbiology Jun 2020Staphylococcus aureus is an important human bacterial pathogen that has a cosmopolitan host range, including livestock, companion and wild animal species. Genomic and... (Review)
Review
Staphylococcus aureus is an important human bacterial pathogen that has a cosmopolitan host range, including livestock, companion and wild animal species. Genomic and epidemiological studies show that S. aureus has jumped between host species many times over its evolutionary history. These jumps have involved the dynamic gain and loss of host-specific adaptive genes, usually located on mobile genetic elements. The same functional elements are often consistently gained in jumps into a particular species. Further sampling of diverse animal species is likely to uncover an even broader host range and greater genetic diversity of S. aureus than is already known, and understanding S. aureus host specificity in these hosts will mitigate the risks of emergent human and livestock strains.
Topics: Animals; Bacteria; Evolution, Molecular; Genomics; Host Adaptation; Host Specificity; Humans; Interspersed Repetitive Sequences; Livestock; Staphylococcal Infections; Staphylococcus aureus; Whole Genome Sequencing
PubMed: 31948727
DOI: 10.1016/j.tim.2019.12.007 -
Cell Host & Microbe Jan 2023Phage-inducible chromosomal islands (PICIs) steal structural proteins from helper phages. In two related studies, Penadés and coworkers reveal that PICIs are not...
Phage-inducible chromosomal islands (PICIs) steal structural proteins from helper phages. In two related studies, Penadés and coworkers reveal that PICIs are not parasites but mutualists. Some PICIs mobilize defense systems that restrict niche competitors, while other PICIs encode their own capsids and steal helper phage tails without affecting their fitness.
Topics: Genomic Islands; Bacteriophages; Capsid
PubMed: 36634621
DOI: 10.1016/j.chom.2022.12.008 -
Environmental Pollution (Barking, Essex... Oct 2022Many contaminants were carried by dust, a common environment media that is easy to contact with human beings, and antibiotic resistance genes (ARGs) as an emergency...
Many contaminants were carried by dust, a common environment media that is easy to contact with human beings, and antibiotic resistance genes (ARGs) as an emergency pollutant also harbor in dust and pose serious threats to human health especially those carried by opportunistic pathogens because inactivation of antibiotics caused by ARGs may enhance pathogenicity. Considering there is a gap of investigation of dust ARGs, 16 S rRNA gene sequences and high-throughput quantitative PCR were employed to obtain information of microbial communities and accumulated ARGs in dust from different urban places, including the malls, hospitals, schools and parks, to investigate the distribution and influencing factors of ARGs and discover the potential hosts of ARGs in dust. Here, 9 types of ARGs such as sulfonamide, tetracycline, and beta-lactamase and 71 subtypes of ARGs like sul1, tetM-01, and drfA1 were detected in dust. ARGs had varying distribution in different public places and seasons in dust. The abundances of total ARGs, MLSB and tetracycline genes were higher in spring than summer. The diversity of ARGs was highest in malls, follow by hospitals, schools, and parks. Additionally, multi-drug resistance genes in dust were more abundant in hospitals than in schools and parks. The microbes were distinguished as the most important driving factors for ARGs in dust, followed by the mobile genetic elements (MGEs) and different places, while dust physicochemical parameters only exert a negligible impact. Notably, several opportunistic pathogens like the Streptococcus, Vibrio, and Pseudomonas were inferred as potential hosts of high-risk ARGs such as mecA, tetM-02, and tetO-01 in dust because of strongly positive co-occurrence. These results imply that dust is likely an important reservoir of ARGs. We should realize that ARGs may be harbored in some opportunistic pathogens occur in dust and endanger human health because of dust contacting to human easily.
Topics: Anti-Bacterial Agents; Drug Resistance, Microbial; Dust; Genes, Bacterial; Humans; Interspersed Repetitive Sequences; Microbiota; Tetracycline
PubMed: 35987288
DOI: 10.1016/j.envpol.2022.119991 -
Biomolecules Apr 2023Neurofibromatosis type 1 is an autosomal-dominant condition caused by gene inactivation. Clinical diagnosis is corroborated by genetic tests on gDNA and cDNA, which are...
Neurofibromatosis type 1 is an autosomal-dominant condition caused by gene inactivation. Clinical diagnosis is corroborated by genetic tests on gDNA and cDNA, which are inconclusive in approximately 3-5% of cases. Genomic DNA approaches may overlook splicing-affecting intronic variants and structural rearrangements, especially in regions enriched in repetitive sequences. On the other hand, while cDNA-based methods provide direct information about the effect of a variant on gene transcription, they are hampered by non-sense-mediated mRNA decay and skewed or monoallelic expression. Moreover, analyses on gene transcripts in some patients do not allow tracing back to the causative event, which is crucial for addressing genetic counselling, prenatal monitoring, and developing targeted therapies. We report on a familial NF1, caused by an insertion of a partial LINE-1 element inside intron 15, leading to exon 15 skipping. Only a few cases of LINE-1 insertion have been reported so far, hampering gDNA studies because of their size. Often, they result in exon skipping, and their recognition of cDNA may be difficult. A combined approach, based on Optical Genome Mapping, WGS, and cDNA studies, enabled us to detect the LINE-1 insertion and test its effects. Our results improve knowledge of the NF1 mutational spectrum and highlight the importance of custom-built approaches in undiagnosed patients.
Topics: Pregnancy; Female; Humans; Neurofibromatosis 1; Introns; DNA, Complementary; Long Interspersed Nucleotide Elements; Mutation
PubMed: 37238595
DOI: 10.3390/biom13050725 -
Journal of Bioinformatics and... Dec 2021In this paper, we investigate througth a premilinary study the influence of repeat elements during the assembly process. We analyze the link between the presence and the...
In this paper, we investigate througth a premilinary study the influence of repeat elements during the assembly process. We analyze the link between the presence and the nature of one type of repeat element, called transposable element (TE) and misassembly events in genome assemblies. We propose to improve assemblies by taking into account the presence of repeat elements, including TEs, during the scaffolding step. We analyze the results and relate the misassemblies to TEs before and after correction.
Topics: DNA Transposable Elements
PubMed: 34923926
DOI: 10.1142/S0219720021400163 -
Methods in Molecular Biology (Clifton,... 2023During their proliferation and the host's concomitant attempts to suppress it, LINE-1 (L1) retrotransposons give rise to a collection of heterogeneous ribonucleoproteins...
During their proliferation and the host's concomitant attempts to suppress it, LINE-1 (L1) retrotransposons give rise to a collection of heterogeneous ribonucleoproteins (RNPs); their protein and RNA compositions remain poorly defined. The constituents of L1-associated macromolecules can differ depending on numerous factors, including, for example, position within the L1 life cycle, whether the macromolecule is productive or under suppression, and the cell type within which the proliferation is occurring. This chapter describes techniques that aid the capture and characterization of protein and RNA components of L1 macromolecules from tissues that natively express them. The protocols described have been applied to embryonal carcinoma cell lines that are popular model systems for L1 molecular biology (e.g., N2102Ep, NTERA-2, and PA-1 cells), as well as colorectal cancer tissues. N2102Ep cells are given as the use case for this chapter; the protocols should be applicable to essentially any tissue exhibiting endogenous L1 expression with minor modifications.
Topics: Long Interspersed Nucleotide Elements; Macromolecular Substances; Retroelements; Embryonal Carcinoma Stem Cells; RNA
PubMed: 36449166
DOI: 10.1007/978-1-0716-2883-6_12 -
Nature Genetics Jun 2023
Topics: Animals; DNA Transposable Elements; Mammals
PubMed: 37308671
DOI: 10.1038/s41588-023-01430-x -
Current Genetics Aug 2021Transposable elements (TEs) are ubiquitous mobile genetic elements that hold both disruptive and adaptive potential for species. It has long been postulated that their... (Review)
Review
Transposable elements (TEs) are ubiquitous mobile genetic elements that hold both disruptive and adaptive potential for species. It has long been postulated that their activity may be triggered by hybridization, a hypothesis that received mixed support from studies in various species. While host defense mechanisms against TEs are being elucidated, the increasing volume of genomic data and bioinformatic tools specialized in TE detection enable in-depth characterization of TEs at the levels of species and populations. Here, I borrow elements from the genome ecology theory to illustrate how knowledge of the diversity of TEs and host defense mechanisms may help predict the activity of TEs in the face of hybridization, and how current limitations make this task especially challenging.
Topics: DNA Transposable Elements; Evolution, Molecular; Genome; Genomics; Hybridization, Genetic; Interspersed Repetitive Sequences
PubMed: 33738571
DOI: 10.1007/s00294-021-01169-0