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Orthoptera-TElib: a library of Orthoptera transposable elements for TE annotation Mobile DNA (IF 4.9) Pub Date : 2024-03-15 Xuanzeng Liu, Lina Zhao, Muhammad Majid, Yuan Huang
Transposable elements (TEs) are a major component of eukaryotic genomes and are present in almost all eukaryotic organisms. TEs are highly dynamic between and within species, which significantly affects the general applicability of the TE databases. Orthoptera is the only known group in the class Insecta with a significantly enlarged genome (0.93-21.48 Gb). When analyzing the large genome using the
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The role of Smarcad1 in retroviral repression in mouse embryonic stem cells Mobile DNA (IF 4.9) Pub Date : 2024-03-11 Igor Bren, Ayellet Tal, Carmit Strauss, Sharon Schlesinger
Moloney murine leukemia virus (MLV) replication is suppressed in mouse embryonic stem cells (ESCs) by the Trim28-SETDB1 complex. The chromatin remodeler Smarcad1 interacts with Trim28 and was suggested to allow the deposition of the histone variant H3.3. However, the role of Trim28, H3.3, and Smarcad1 in MLV repression in ESCs still needs to be fully understood. In this study, we used MLV to explore
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CRISPR-TE: a web-based tool to generate single guide RNAs targeting transposable elements Mobile DNA (IF 4.9) Pub Date : 2024-02-01 Yixin Guo, Ziwei Xue, Meiting Gong, Siqian Jin, Xindi Wu, Wanlu Liu
The CRISPR/Cas systems have emerged as powerful tools in genome engineering. Recent studies highlighting the crucial role of transposable elements (TEs) have stimulated research interest in manipulating these elements to understand their functions. However, designing single guide RNAs (sgRNAs) that are specific and efficient for TE manipulation is a significant challenge, given their sequence repetitiveness
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A systematic screen for co-option of transposable elements across the fungal kingdom Mobile DNA (IF 4.9) Pub Date : 2024-01-20 Ursula Oggenfuss, Thomas Badet, Daniel Croll
How novel protein functions are acquired is a central question in molecular biology. Key paths to novelty include gene duplications, recombination or horizontal acquisition. Transposable elements (TEs) are increasingly recognized as a major source of novel domain-encoding sequences. However, the impact of TE coding sequences on the evolution of the proteome remains understudied. Here, we analyzed 1237
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Evolutionary dynamics of the LTR-retrotransposon crapaud in the Podospora anserina species complex and the interaction with repeat-induced point mutations Mobile DNA (IF 4.9) Pub Date : 2024-01-13 Ivar Westerberg, S. Lorena Ament-Velásquez, Aaron A. Vogan, Hanna Johannesson
The genome of the filamentous ascomycete Podospora anserina shows a relatively high abundance of retrotransposons compared to other interspersed repeats. The LTR-retrotransposon family crapaud is particularly abundant in the genome, and consists of multiple diverged sequence variations specifically localized in the 5’ half of both long terminal repeats (LTRs). P. anserina is part of a recently diverged
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The sixth Japanese meeting on biological function and evolution through interactions between hosts and transposable elements Mobile DNA (IF 4.9) Pub Date : 2023-12-12 Kenji Ichiyanagi, Yoko Ikeda, Kuniaki Saito
The sixth Japanese meeting on host–transposon interactions, titled “Biological Function and Evolution through Interactions between Hosts and Transposable Elements,” was held on August 24th and 25th, 2023, at the National Institute of Genetics as well as online. This meeting was supported by the National Institute of Genetics and aimed to bring together researchers studying the diverse roles of TEs
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SINE-derived satellites in scaled reptiles Mobile DNA (IF 4.9) Pub Date : 2023-12-07 Nikita S. Vassetzky, Sergei A. Kosushkin, Alexey P. Ryskov
The genomes of many eukaryotes contain DNA repeats in the form of both tandem and interspersed elements with distinct structure, evolutionary histories, and mechanisms of emergence and amplification. Although there is considerable knowledge regarding their diversity, there is little evidence directly linking these two types. Different tandem repeats derived from portions of short interspersed elements
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An intronic LINE-1 regulates IFNAR1 expression in human immune cells Mobile DNA (IF 4.9) Pub Date : 2023-11-30 Carmen A. Buttler, Daniel Ramirez, Robin D. Dowell, Edward B. Chuong
Despite their origins as selfish parasitic sequences, some transposons in the human genome have been co-opted to serve as regulatory elements, contributing to the evolution of transcriptional networks. Most well-characterized examples of transposon-derived regulatory elements derive from endogenous retroviruses (ERVs), due to the intrinsic regulatory activity of proviral long terminal repeat regions
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Meeting report: transposable elements at the crossroads of evolution, health and disease 2023 Mobile DNA (IF 4.9) Pub Date : 2023-11-27 Irina R. Arkhipova, Kathleen H. Burns, Katherine B. Chiappinelli, Edward B. Chuong, Clement Goubert, Alba Guarné, Amanda M. Larracuente, E. Alice Lee, Henry L. Levin
The conference “Transposable Elements at the Crossroads of Evolution, Health and Disease” was hosted by Keystone Symposia in Whistler, British Columbia, Canada, on September 3–6, 2023, and was organized by Kathleen Burns, Harmit Malik and Irina Arkhipova. The central theme of the meeting was the incredible diversity of ways in which transposable elements (TEs) interact with the host, from disrupting
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Proceedings of the inaugural Dark Genome Symposium: November 2022 Mobile DNA (IF 4.9) Pub Date : 2023-11-21 Jef D. Boeke, Kathleen H. Burns, Katherine B. Chiappinelli, Marie Classon, John M. Coffin, Daniel D. DeCarvalho, Joseph D. Dukes, Benjamin Greenbaum, George Kassiotis, Sarah K. Knutson, Arnold J. Levine, Avindra Nath, Sophie Papa, Daniel Rios, John Sedivy, David T. Ting
In November 2022 the first Dark Genome Symposium was held in Boston, USA. The meeting was hosted by Rome Therapeutics and Enara Bio, two biotechnology companies working on translating our growing understanding of this vast genetic landscape into therapies for human disease. The spirit and ambition of the meeting was one of shared knowledge, looking to strengthen the network of researchers engaged in
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Long noncoding RNAs emerge from transposon-derived antisense sequences and may contribute to infection stage-specific transposon regulation in a fungal phytopathogen Mobile DNA (IF 4.9) Pub Date : 2023-11-15 Jiangzhao Qian, Heba M. M. Ibrahim, Myriam Erz, Florian Kümmel, Ralph Panstruga, Stefan Kusch
The genome of the obligate biotrophic phytopathogenic barley powdery mildew fungus Blumeria hordei is inflated due to highly abundant and possibly active transposable elements (TEs). In the absence of the otherwise common repeat-induced point mutation transposon defense mechanism, noncoding RNAs could be key for regulating the activity of TEs and coding genes during the pathogenic life cycle. We performed
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Co-expression of distinct L1 retrotransposon coiled coils can lead to their entanglement Mobile DNA (IF 4.9) Pub Date : 2023-10-20 Nikola A. Mizgier, Charlie E. Jones, Anthony V. Furano
L1 (LINE1) non-LTR retrotransposons are ubiquitous genomic parasites and the dominant transposable element in humans having generated about 40% of their genomic DNA during their ~ 100 million years (Myr) of activity in primates. L1 replicates in germ line cells and early embryos, causing genetic diversity and defects, but can be active in some somatic stem cells, tumors and during aging. L1 encodes
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Plants acquired mitochondrial linear plasmids horizontally from fungi likely during the conquest of land Mobile DNA (IF 4.9) Pub Date : 2023-10-17 Yutong Wei, Zhen Gong, Guan-Zhu Han
Mitochondrial linear plasmids have been sporadically reported in fungi and plants. Yet, much remains obscure about the diversity, distribution, and evolution of mitochondrial linear plasmids. Here, through phylogenomic analyses across 7,163 cellular organisms (including 991 plants), we find that mitochondrial linear plasmids are widely present in land plants and fungi. Phylogenetic analyses indicate
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Teleost genomic repeat landscapes in light of diversification rates and ecology Mobile DNA (IF 4.9) Pub Date : 2023-10-03 William B. Reinar, Ole K. Tørresen, Alexander J. Nederbragt, Michael Matschiner, Sissel Jentoft, Kjetill S. Jakobsen
Repetitive DNA make up a considerable fraction of most eukaryotic genomes. In fish, transposable element (TE) activity has coincided with rapid species diversification. Here, we annotated the repetitive content in 100 genome assemblies, covering the major branches of the diverse lineage of teleost fish. We investigated if TE content correlates with family level net diversification rates and found support
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Pan cancer characterization of genes whose expression has been associated with LINE-1 antisense promoter activity Mobile DNA (IF 4.9) Pub Date : 2023-09-18 Baohong Xu, Xueer Li, Shaoqi Zhang, Meina Lian, Wenbin Huang, Yin Zhang, Yudong Wang, Zhiquan Huang
Long interspersed nuclear element-1 (LINE-1 or L1) comprises 17% of the human genome. As the only autonomous and active retrotransposons, L1 may take part in cancer initiation and progression in some ways. The studies of L1 in cancer mainly focus on the impact of L1 insertion into the new genome locus. The L1 5´ untranslated region (UTR) also contains antisense promoter (ASP) activity, generating L1-gene
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Retro-miRs: novel and functional miRNAs originating from mRNA retrotransposition Mobile DNA (IF 4.9) Pub Date : 2023-09-08 Rafael L. V. Mercuri, Helena B. Conceição, Gabriela D. A. Guardia, Gabriel Goldstein, Maria D. Vibranovski, Ludwig C. Hinske, Pedro A. F. Galante
Reverse-transcribed gene copies (retrocopies) have emerged as major sources of evolutionary novelty. MicroRNAs (miRNAs) are small and highly conserved RNA molecules that serve as key post-transcriptional regulators of gene expression. The origin and subsequent evolution of miRNAs have been addressed but not fully elucidated. In this study, we performed a comprehensive investigation of miRNA origination
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SARS-CoV-2 infection induces epigenetic changes in the LTR69 subfamily of endogenous retroviruses Mobile DNA (IF 4.9) Pub Date : 2023-09-04 Ankit Arora, Jan Eric Kolberg, Smitha Srinivasachar Badarinarayan, Natalia Savytska, Daksha Munot, Martin Müller, Veronika Krchlíková, Daniel Sauter, Vikas Bansal
Accumulating evidence suggests that endogenous retroviruses (ERVs) play an important role in the host response to infection and the development of disease. By analyzing ChIP-sequencing data sets, we show that SARS-CoV-2 infection induces H3K27 acetylation of several loci within the LTR69 subfamily of ERVs. Using functional assays, we identified one SARS-CoV-2-activated LTR69 locus, termed Dup69, which
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Themes and variations on piRNA-guided transposon control Mobile DNA (IF 4.9) Pub Date : 2023-09-02 Zuzana Loubalova, Parthena Konstantinidou, Astrid D. Haase
PIWI-interacting RNAs (piRNAs) are responsible for preventing the movement of transposable elements in germ cells and protect the integrity of germline genomes. In this review, we examine the common elements of piRNA-guided silencing as well as the differences observed between species. We have categorized the mechanisms of piRNA biogenesis and function into modules. Individual PIWI proteins combine
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Transposable elements as essential elements in the control of gene expression Mobile DNA (IF 4.9) Pub Date : 2023-08-18 Alemu Gebrie
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
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Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast Mobile DNA (IF 4.9) Pub Date : 2023-07-14 Jingxuan Chen, Preston J. Basting, Shunhua Han, David J. Garfinkel, Casey M. Bergman
Many computational methods have been developed to detect non-reference transposable element (TE) insertions using short-read whole genome sequencing data. The diversity and complexity of such methods often present challenges to new users seeking to reproducibly install, execute, or evaluate multiple TE insertion detectors. We previously developed the McClintock meta-pipeline to facilitate the installation
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Host range of strand-biased circularizing integrative elements: a new class of mobile DNA elements nesting in Gammaproteobacteria Mobile DNA (IF 4.9) Pub Date : 2023-05-26 Desmila Idola, Hiroshi Mori, Yuji Nagata, Lisa Nonaka, Hirokazu Yano
The strand-biased circularizing integrative elements (SEs) are putatively non-mobilizable integrative elements for transmitting antimicrobial resistance genes. The transposition mode and the prevalence of SEs in prokaryotes remain vague. To corroborate the transposition mode and the prevalence of SEs, hypothetical transposition intermediates of an SE were searched for in genomic DNA fractions of an
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THE1B may have no role in human pregnancy due to ZNF430-mediated silencing Mobile DNA (IF 4.9) Pub Date : 2023-05-22 Zheng Zuo
THE1-family retrovirus invaded the primate genome more than 40 million years ago. Dunn-Fletcher et al. reported one THE1B element upstream of CRH gene alters gestation length by upregulating corticotropin-releasing hormone expression in transgenic mice and concluded it has the same role in human as well. However, no promoter or enhancer mark has been detected around this CRH-proximal element in any
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Expression of L1 retrotransposons in granulocytes from patients with active systemic lupus erythematosus Mobile DNA (IF 4.9) Pub Date : 2023-05-10 Kennedy C. Ukadike, Rayan Najjar, Kathryn Ni, Amanda Laine, Xiaoxing Wang, Alison Bays, Martin S. Taylor, John LaCava, Tomas Mustelin
Patients with systemic lupus erythematosus (SLE) have autoantibodies against the L1-encoded open-reading frame 1 protein (ORF1p). Here, we report (i) which immune cells ORF1p emanates from, (ii) which L1 loci are transcriptionally active, (iii) whether the cells express L1-dependent interferon and interferon-stimulated genes, and (iv) the effect of inhibition of L1 ORF2p by reverse transcriptase inhibitors
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Analysis of antibiotic resistance gene cassettes in a newly identified Salmonella enterica serovar Gallinarum strain in Korea Mobile DNA (IF 4.9) Pub Date : 2023-04-24 Thanh Quang Tran, Minyoung Park, Jong Eun Lee, Soo Hyun Kim, Jae-Ho Jeong, Hyon E. Choy
Antimicrobial resistant pathogens are a global health threat driven by the indiscriminate use of antimicrobials. Antimicrobial resistance can be acquired by resistance genes encoded by mobile genetic elements. In this study, we identified a strain of Salmonella enterica serovar Gallinarum (SG4021) from an infected chicken in Korea and characterized the presence of resistance genes in its plasmid by
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Telomeric retrotransposons show propensity to form G-quadruplexes in various eukaryotic species Mobile DNA (IF 4.9) Pub Date : 2023-04-10 Pavel Jedlička, Viktor Tokan, Iva Kejnovská, Roman Hobza, Eduard Kejnovský
Canonical telomeres (telomerase-synthetised) are readily forming G-quadruplexes (G4) on the G-rich strand. However, there are examples of non-canonical telomeres among eukaryotes where telomeric tandem repeats are invaded by specific retrotransposons. Drosophila melanogaster represents an extreme example with telomeres composed solely by three retrotransposons—Het-A, TAHRE and TART (HTT). Even though
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Expression of down-regulated ERV LTR elements associates with immune activation in human small-cell lung cancers Mobile DNA (IF 4.9) Pub Date : 2023-03-14 Marco Russo, Sara Morelli, Giovanni Capranico
Small-cell lung cancer (SCLC) is an aggressive cancer characterized by immunosuppressive features leading to poor responses to current immunotherapies. Activation of transposable elements (TE) can trigger an innate immune response, which can synergize with immunotherapeutic protocols in patients. However, TE activity in relation to immune gene response is not fully known in human SCLC. Here, we compared
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Mobility of mPing and its associated elements is regulated by both internal and terminal sequences Mobile DNA (IF 4.9) Pub Date : 2023-02-11 Priscilla S. Redd, Stephanie Diaz, David Weidner, Jazmine Benjamin, C. Nathan Hancock
DNA transposable elements are mobilized by a “cut and paste” mechanism catalyzed by the binding of one or more transposase proteins to terminal inverted repeats (TIRs) to form a transpositional complex. Study of the rice genome indicates that the mPing element has experienced a recent burst in transposition compared to the closely related Ping and Pong elements. A previously developed yeast transposition
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Obituary: Haig Kazazian and Horizontal Transfer (1937 – 2022) Mobile DNA (IF 4.9) Pub Date : 2022-12-28 Editorial Board, Mobile DNA
Haig Kazazian (1937 – 2022) In January the Mobile DNA field lost one of its most influential investigators, Dr. Haig Kazazian, the physician-scientist who first demonstrated the activity of transposable elements in humans and whose laboratories at Johns Hopkins University School of Medicine and the University of Pennsylvania made outsized contributions to our understandings of long interspersed element-1
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CAULIFINDER: a pipeline for the automated detection and annotation of caulimovirid endogenous viral elements in plant genomes Mobile DNA (IF 4.9) Pub Date : 2022-12-03 Vassilieff, Héléna, Haddad, Sana, Jamilloux, Véronique, Choisne, Nathalie, Sharma, Vikas, Giraud, Delphine, Wan, Mariène, Serfraz, Saad, Geering, Andrew D. W., Teycheney, Pierre-Yves, Maumus, Florian
Plant, animal and protist genomes often contain endogenous viral elements (EVEs), which correspond to partial and sometimes entire viral genomes that have been captured in the genome of their host organism through a variety of integration mechanisms. While the number of sequenced eukaryotic genomes is rapidly increasing, the annotation and characterization of EVEs remains largely overlooked. EVEs that
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Generalized nuclear localization of retroelement transcripts Mobile DNA (IF 4.9) Pub Date : 2022-12-02 Das, Simanti, Jones, Amanda E., Abrams, John M.
LINE-1s, Alus and SVAs are the only retrotransposition competent elements in humans. Their mobilization followed by insertional mutagenesis is often linked to disease. Apart from these rare integration events, accumulation of retrotransposition intermediates in the cytoplasm is potentially pathogenic due to induction of inflammatory response pathways. Although the retrotransposition of LINE-1 and Alu
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T3E: a tool for characterising the epigenetic profile of transposable elements using ChIP-seq data Mobile DNA (IF 4.9) Pub Date : 2022-11-30 Almeida da Paz, Michelle, Taher, Leila
Despite the advent of Chromatin Immunoprecipitation Sequencing (ChIP-seq) having revolutionised our understanding of the mammalian genome’s regulatory landscape, many challenges remain. In particular, because of their repetitive nature, the sequencing reads derived from transposable elements (TEs) pose a real bioinformatics challenge, to the point that standard analysis pipelines typically ignore reads
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Recurrent co-domestication of PIF/Harbinger transposable element proteins in insects Mobile DNA (IF 4.9) Pub Date : 2022-11-30 Markova, Dragomira N., Ruma, Fatema B., Casola, Claudio, Mirsalehi, Ayda, Betrán, Esther
Transposable elements (TEs) are selfish DNA sequences capable of moving and amplifying at the expense of host cells. Despite this, an increasing number of studies have revealed that TE proteins are important contributors to the emergence of novel host proteins through molecular domestication. We previously described seven transposase-derived domesticated genes from the PIF/Harbinger DNA family of TEs
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The coevolution between APOBEC3 and retrotransposons in primates Mobile DNA (IF 4.9) Pub Date : 2022-11-29 Modenini, Giorgia, Abondio, Paolo, Boattini, Alessio
Retrotransposons are genetic elements with the ability to replicate in the genome using reverse transcriptase: they have been associated with the development of different biological structures, such as the Central Nervous System (CNS), and their high mutagenic potential has been linked to various diseases, including cancer and neurological disorders. Throughout evolution and over time, Primates and
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A proteomic screen of Ty1 integrase partners identifies the protein kinase CK2 as a regulator of Ty1 retrotransposition Mobile DNA (IF 4.9) Pub Date : 2022-11-18 Barkova, Anastasia, Adhya, Indranil, Conesa, Christine, Asif-Laidin, Amna, Bonnet, Amandine, Rabut, Elise, Chagneau, Carine, Lesage, Pascale, Acker, Joël
Transposable elements are ubiquitous and play a fundamental role in shaping genomes during evolution. Since excessive transposition can be mutagenic, mechanisms exist in the cells to keep these mobile elements under control. Although many cellular factors regulating the mobility of the retrovirus-like transposon Ty1 in Saccharomyces cerevisiae have been identified in genetic screens, only very few
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Exploration of the regulatory relationship between KRAB-Zfp clusters and their target transposable elements via a gene editing strategy at the cluster specific linker-associated sequences by CRISPR-Cas9 Mobile DNA (IF 4.9) Pub Date : 2022-11-10 Zhang, Yang, He, Fei, Zhang, Yanning, Dai, Qian, Li, Qintong, Nan, Jing, Miao, Ruidong, Cheng, Bo
Krüppel Associated Box-containing Zinc Finger Proteins (KRAB-ZFPs), representing the largest superfamily of transcription factors in mammals, are predicted to primarily target and repress transposable elements (TEs). It is challenging to dissect the distinct functions of these transcription regulators due to their sequence similarity and diversity, and also the complicated repetitiveness of their targeting
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A unique eukaryotic lineage of composite-like DNA transposons encoding a DDD/E transposase and a His-Me finger homing endonuclease Mobile DNA (IF 4.9) Pub Date : 2022-10-22 Kojima, Kenji K., Bao, Weidong
DNA transposons are ubiquitous components of eukaryotic genomes. A major group of them encode a DDD/E transposase and contain terminal inverted repeats (TIRs) of varying lengths. The Kolobok superfamily of DNA transposons has been found in a wide spectrum of organisms. Here we report a new Kolobok lineage, designated KolobokP. They were identified in 7 animal phyla (Mollusca, Phoronida, Annelida, Nemertea
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Mobile group I introns at nuclear rDNA position L2066 harbor sense and antisense homing endonuclease genes intervened by spliceosomal introns Mobile DNA (IF 4.9) Pub Date : 2022-10-08 Lian, Kjersti, Furulund, Betty M. N., Tveita, Anders A., Haugen, Peik, Johansen, Steinar D.
Mobile group I introns encode homing endonucleases that confer intron mobility initiated by a double-strand break in the intron-lacking allele at the site of insertion. Nuclear ribosomal DNA of some fungi and protists contain mobile group I introns harboring His-Cys homing endonuclease genes (HEGs). An intriguing question is how protein-coding genes embedded in nuclear ribosomal DNA become expressed
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Transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells Mobile DNA (IF 4.9) Pub Date : 2022-09-06 Pasquesi, Giulia Irene Maria, Kelly, Conor J., Ordonez, Andrea D., Chuong, Edward B.
Bats are a major reservoir of zoonotic viruses, and there has been growing interest in characterizing bat-specific features of innate immunity and inflammation. Recent studies have revealed bat-specific adaptations affecting interferon (IFN) signaling and IFN-stimulated genes (ISGs), but we still have a limited understanding of the genetic mechanisms that have shaped the evolution of bat immunity.
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SCIFER: approach for analysis of LINE-1 mRNA expression in single cells at a single locus resolution Mobile DNA (IF 4.9) Pub Date : 2022-08-26 Stow, Emily C., Baddoo, Melody, LaRosa, Alexis J., LaCoste, Dawn, Deininger, Prescott, Belancio, Victoria
Endogenous expression of L1 mRNA is the first step in an L1-initiated mutagenesis event. However, the contribution of individual cell types to patterns of organ-specific L1 mRNA expression remains poorly understood, especially at single-locus resolution. We introduce a method to quantify expression of mobile elements at the single-locus resolution in scRNA-Seq datasets called Single Cell Implementation
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Multiple horizontal transfers of a Helitron transposon associated with a parasitoid wasp Mobile DNA (IF 4.9) Pub Date : 2022-08-19 Heringer, Pedro, Kuhn, Gustavo C. S.
In a previous study we described a Helitron transposon that apparently became one of the segments in the symbiotic Cotesia vestalis bracovirus (CvBV) from the parasitoid wasp C. vestalis. We presented evidence that this Helitron, named Hel_c35, invaded the C. vestalis genome through a horizontal transfer (HT) event from a dipteran and was later transferred horizontally from C. vestalis to a lepidopteran
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Genomic analysis reveals the role of integrative and conjugative elements in plant pathogenic bacteria Mobile DNA (IF 4.9) Pub Date : 2022-08-12 de Assis, Jéssica Catarine Silva, Gonçalves, Osiel Silva, Fernandes, Alexia Suellen, de Queiroz, Marisa Vieira, Bazzolli, Denise Mara Soares, Santana, Mateus Ferreira
ICEs are mobile genetic elements found integrated into bacterial chromosomes that can excise and be transferred to a new cell. They play an important role in horizontal gene transmission and carry accessory genes that may provide interesting phenotypes for the bacteria. Here, we seek to research the presence and the role of ICEs in 300 genomes of phytopathogenic bacteria with the greatest scientific
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Amplification of LTRs of extrachromosomal linear DNAs (ALE-seq) identifies two active Oryco LTR retrotransposons in the rice cultivar Dongjin Mobile DNA (IF 4.9) Pub Date : 2022-06-13 Koo, Hyunjin, Kim, Soomin, Park, Hyun-Seung, Lee, Sang-Ji, Paek, Nam-Chon, Cho, Jungnam, Yang, Tae-Jin
Long terminal repeat retrotransposons (LTR-RTs) make up a considerable portion of plant genomes. New insertions of these active LTR-RTs modify gene structures and functions and play an important role in genome evolution. Therefore, identifying active forms of LTR-RTs could uncover the effects of these elements in plants. Extrachromosomal linear DNA (eclDNA) forms during LTR-RT replication; therefore
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Correction: Characterization of transposable elements within the Bemisia tabaci species complex Mobile DNA (IF 4.9) Pub Date : 2022-06-08 Sicat, Juan Paolo A., Visendi, Paul, Sewe, Steven O., Bouvaine, Sophie, Seal, Susan E.
Correction: Mobile DNA 13, 12 (2022) https://doi.org/10.1186/s13100-022-00270-6 Following the publication of the original article [1] the authors requested to change the wording in Acknowledgements and Funding sections. The original article [1] has been updated. The revised wording should be: Sicat JPA, Visendi P, Sewe SO, et al. Characterization of transposable elements within the Bemisia tabaci species
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Comprehensive analysis of both long and short read transcriptomes of a clonal and a seed-propagated model species reveal the prerequisites for transcriptional activation of autonomous and non-autonomous transposons in plants Mobile DNA (IF 4.9) Pub Date : 2022-05-12 Chen, Ting-Hsuan, Winefield, Christopher
Transposable element (TE) transcription is a precursor to its mobilisation in host genomes. However, the characteristics of expressed TE loci, the identification of self-competent transposon loci contributing to new insertions, and the genomic conditions permitting their mobilisation remain largely unknown. Using Vitis vinifera embryogenic callus, we explored the impact of biotic stressors on transposon
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Correction: A beginner’s guide to manual curation of transposable elements Mobile DNA (IF 4.9) Pub Date : 2022-05-04 Goubert, Clement, Craig, Rory J., Bilat, Agustin F., Peona, Valentina, Vogan, Aaron A., Protasio, Anna V.
Correction to: Mobile DNA 13, 7 (2022) https://doi.org/10.1186/s13100-021-00259-7 Following the publication of the original article [1] the author reported that Additional files 3, 4 and 5 in the published article are corrupted. The original article [1] has been updated. Goubert C, Craig RJ, Bilat AF, et al. A beginner’s guide to manual curation of transposable elements. Mobile DNA. 2022;13:7. https://doi
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Software evaluation for de novo detection of transposons Mobile DNA (IF 4.9) Pub Date : 2022-04-27 Rodriguez, Matias, Makałowski, Wojciech
Transposable elements (TEs) are major genomic components in most eukaryotic genomes and play an important role in genome evolution. However, despite their relevance the identification of TEs is not an easy task and a number of tools were developed to tackle this problem. To better understand how they perform, we tested several widely used tools for de novo TE detection and compared their performance
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Subfamily-specific differential contribution of individual monomers and the tether sequence to mouse L1 promoter activity Mobile DNA (IF 4.9) Pub Date : 2022-04-20 Kong, Lingqi, Saha, Karabi, Hu, Yuchi, Tschetter, Jada N., Habben, Chase E., Whitmore, Leanne S., Yao, Changfeng, Ge, Xijin, Ye, Ping, Newkirk, Simon J., An, Wenfeng
The internal promoter in L1 5’UTR is critical for autonomous L1 transcription and initiating retrotransposition. Unlike the human genome, which features one contemporarily active subfamily, four subfamilies (A_I, Gf_I and Tf_I/II) have been amplifying in the mouse genome in the last one million years. Moreover, mouse L1 5’UTRs are organized into tandem repeats called monomers, which are separated from
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Characterization of transposable elements within the Bemisia tabaci species complex Mobile DNA (IF 4.9) Pub Date : 2022-04-19 Sicat, Juan Paolo A., Visendi, Paul, Sewe, Steven O., Bouvaine, Sophie, Seal, Susan E.
Whiteflies are agricultural pests that cause negative impacts globally to crop yields resulting at times in severe economic losses and food insecurity. The Bemisia tabaci whitefly species complex is the most damaging in terms of its broad crop host range and its ability to serve as vector for over 400 plant viruses. Genomes of whiteflies belonging to this species complex have provided valuable genomic
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TE Density: a tool to investigate the biology of transposable elements Mobile DNA (IF 4.9) Pub Date : 2022-04-12 Teresi, Scott J., Teresi, Michael B., Edger, Patrick P.
Transposable elements (TEs) are powerful creators of genotypic and phenotypic diversity due to their inherent mutagenic capabilities and in this way they serve as a deep reservoir of sequences for genomic variation. As agents of genetic disruption, a TE’s potential to impact phenotype is partially a factor of its location in the genome. Previous research has shown TEs’ ability to impact the expression
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RNA sensor MDA5 suppresses LINE-1 retrotransposition by regulating the promoter activity of LINE-1 5′-UTR Mobile DNA (IF 4.9) Pub Date : 2022-04-12 Yan, Jiaxiu, Zhao, Yifei, Du, Juan, Wang, Yu, Wang, Shaohua, Wang, Qing, Zhao, Xu, Xu, Wei, Zhao, Ke
Type 1 long interspersed elements, or LINE-1, are the only retroelements that replicate autonomously in human cells. The retrotransposition process of LINE-1 can trigger the activation of the innate immune system and has been proposed to play a role in the development of several autoimmune diseases, including Aicardi-Goutières syndrome (AGS). In contrast, all known AGS-associated proteins, except MDA5
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SETMAR, a case of primate co-opted genes: towards new perspectives Mobile DNA (IF 4.9) Pub Date : 2022-04-08 Lié, Oriane, Renault, Sylvaine, Augé-Gouillou, Corinne
We carry out a review of the history and biological activities of one domesticated gene in higher primates, SETMAR, by discussing current controversies. Our purpose is to open a new outlook that will serve as a framework for future work about SETMAR, possibly in the field of cognition development. What is newly important about SETMAR can be summarized as follows: (1) the whole protein sequence is under
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The structural diversity of CACTA transposons in genomes of Chenopodium (Amaranthaceae, Caryophyllales) species: specific traits and comparison with the similar elements of angiosperms Mobile DNA (IF 4.9) Pub Date : 2022-04-04 Belyayev, Alexander, Josefiová, Jiřina, Jandová, Michaela, Kalendar, Ruslan, Mahelka, Václav, Mandák, Bohumil, Krak, Karol
CACTA transposable elements (TEs) comprise one of the most abundant superfamilies of Class 2 (cut-and-paste) transposons. Over recent decades, CACTA elements were widely identified in species from the plant, fungi, and animal kingdoms, but sufficiently studied in the genomes of only a few model species although non-model genomes can bring additional and valuable information. It primarily concerned
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A beginner’s guide to manual curation of transposable elements Mobile DNA (IF 4.9) Pub Date : 2022-03-30 Goubert, Clement, Craig, Rory J., Bilat, Agustin F., Peona, Valentina, Vogan, Aaron A., Protasio, Anna V.
In the study of transposable elements (TEs), the generation of a high confidence set of consensus sequences that represent the diversity of TEs found in a given genome is a key step in the path to investigate these fascinating genomic elements. Many algorithms and pipelines are available to automatically identify putative TE families present in a genome. Despite the availability of these valuable resources
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Eco-evolutionary significance of domesticated retroelements in microbial genomes Mobile DNA (IF 4.9) Pub Date : 2022-02-23 Paul, Blair G., Eren, A. Murat
Since the first discovery of reverse transcriptase in bacteria, and later in archaea, bacterial and archaeal retroelements have been defined by their common enzyme that coordinates diverse functions. Yet, evolutionary refinement has produced distinct retroelements across the tree of microbial life that are perhaps best described in terms of their programmed RNA—a compact sequence that preserves core
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Migrators within migrators: exploring transposable element dynamics in the monarch butterfly, Danaus plexippus Mobile DNA (IF 4.9) Pub Date : 2022-02-16 Baril, Tobias, Hayward, Alexander
Lepidoptera (butterflies and moths) are an important model system in ecology and evolution. A high-quality chromosomal genome assembly is available for the monarch butterfly (Danaus plexippus), but it lacks an in-depth transposable element (TE) annotation, presenting an opportunity to explore monarch TE dynamics and the impact of TEs on shaping the monarch genome. We find 6.21% of the monarch genome
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KRAB zinc finger protein ZNF676 controls the transcriptional influence of LTR12-related endogenous retrovirus sequences Mobile DNA (IF 4.9) Pub Date : 2022-01-18 Iouranova, Alexandra, Grun, Delphine, Rossy, Tamara, Duc, Julien, Coudray, Alexandre, Imbeault, Michael, de Tribolet-Hardy, Jonas, Turelli, Priscilla, Persat, Alexandre, Trono, Didier
Transposable element-embedded regulatory sequences (TEeRS) and their KRAB-containing zinc finger protein (KZFP) controllers are increasingly recognized as modulators of gene expression. We aim to characterize the contribution of this system to gene regulation in early human development and germ cells. Here, after studying genes driven by the long terminal repeat (LTR) of endogenous retroviruses, we
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The fifth Japanese meeting on biological function and evolution through interactions between hosts and transposable elements Mobile DNA (IF 4.9) Pub Date : 2022-01-13 Ichiyanagi, Kenji, Saito, Kuniaki
The fifth Japanese meeting on host–transposon interactions, titled “Biological Function and Evolution through Interactions between Hosts and Transposable Elements (TEs),” was held online on August 26–27, 2021. The meeting was supported by National Institute of Genetics and aimed to bring together researchers studying the diverse roles of TEs in genome function and evolution, as well as host defense
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Response from Varani et al. to “Comment on ‘the IS6 family, a clinically important group of insertion sequences including IS26’ by Ruth M. Hall” Mobile DNA (IF 4.9) Pub Date : 2022-01-03 Varani, Alessandro, He, Susu, Siguier, Patricia, Ross, Karen, Chandler, Michael
The IS6 family of insertion sequences is a large but coherent group which was originally named to avoid confusion between a number of identical or nearly identical IS that were identified at about the same time and given different names (IS15D, IS26, IS46, IS140, IS160, IS176). The underlying common mechanistic feature of all IS6 family members which have been investigated is that they appear to transpose
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Comment on “the IS6 family, a clinically important group of insertion sequences including IS26” by Varani and co-authors Mobile DNA (IF 4.9) Pub Date : 2022-01-03 Hall, Ruth M.
The insertion sequence IS26 has long been known to play a major role in the recruitment of antibiotic resistance genes into the mobile resistance gene pool of Gram-negative bacteria and IS26 also plays a major role in their subsequent broad dissemination. Related IS, IS431/257 and IS1216 are important in the same roles in Gram positive bacteria. However, until recently the properties of IS26 movement
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Whole-genome analysis reveals the contribution of non-coding de novo transposon insertions to autism spectrum disorder Mobile DNA (IF 4.9) Pub Date : 2021-11-27 Borges-Monroy, Rebeca, Chu, Chong, Dias, Caroline, Choi, Jaejoon, Lee, Soohyun, Gao, Yue, Shin, Taehwan, Park, Peter J., Walsh, Christopher A., Lee, Eunjung Alice
Retrotransposons have been implicated as causes of Mendelian disease, but their role in autism spectrum disorder (ASD) has not been systematically defined, because they are only called with adequate sensitivity from whole genome sequencing (WGS) data and a large enough cohort for this analysis has only recently become available. We analyzed WGS data from a cohort of 2288 ASD families from the Simons