Articles

Differential regulation of transposable elements (TEs) during the murine submandibular gland development

The submandibular gland (SG) is a relatively simple organ formed by three cell types: acinar, myoepithelial, and an intricate network of duct-forming epithelial cells, that together fulfills several physiologi...

Authors: Braulio Valdebenito-Maturana, Francisca Torres, Mónica Carrasco and Juan Carlos Tapia

Genomic approaches to trace the history of human brain evolution with an emerging opportunity for transposon profiling of ancient humans

Transposable elements (TEs) significantly contribute to shaping the diversity of the human genome, and lines of evidence suggest TEs as one of driving forces of human brain evolution. Existing computational ap...

Authors: Yilan Wang, Boxun Zhao, Jaejoon Choi and Eunjung Alice Lee

Unbiased proteomic mapping of the LINE-1 promoter using CRISPR Cas9

The autonomous retroelement Long Interspersed Element-1 (LINE-1) mobilizes though a copy and paste mechanism using an RNA intermediate (retrotransposition). Throughout human evolution, around 500,000 LINE-1 se...

Authors: Erica M. Briggs, Paolo Mita, Xiaoji Sun, Susan Ha, Nikita Vasilyev, Zev R. Leopold, Evgeny Nudler, Jef D. Boeke and Susan K. Logan

A 192 bp ERV fragment insertion in the first intron of porcine TLR6 may act as an enhancer associated with the increased expressions of TLR6 and TLR1

Toll-like receptors (TLRs) play important roles in building innate immune and inducing adaptive immune responses. Associations of the TLR genes polymorphisms with disease susceptibility, which are the basis of mo...

Authors: XiaoYan Wang, Zixuan Chen, Eduard Murani, Enrico D’Alessandro, Yalong An, Cai Chen, Kui Li, Grazia Galeano, Klaus Wimmers and Chengyi Song

Correction to: Upregulation of selected HERVW loci in multiple sclerosis

Authors: Sofía Macías-Redondo, Mark Strunk, Alberto Cebollada-Solanas, José-Ramón Ara, Jesús Martín and Jon Schoorlemmer

Upregulation of selected HERVW loci in multiple sclerosis

Authors: Sofía Macías-Redondo, Mark Strunk, Alberto Cebollada-Solanas, José-Ramón Ara, Jesús Martín and Jon Schoorlemmer

SINE jumping contributes to large-scale polymorphisms in the pig genomes

Molecular markers based on retrotransposon insertion polymorphisms (RIPs) have been developed and are widely used in plants and animals. Short interspersed nuclear elements (SINEs) exert wide impacts on gene a...

Authors: Cai Chen, Enrico D’Alessandro, Eduard Murani, Yao Zheng, Domenico Giosa, Naisu Yang, Xiaoyan Wang, Bo Gao, Kui Li, Klaus Wimmers and Chengyi Song

TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation

Transposable elements (TEs) play powerful and varied evolutionary and functional roles, and are widespread in most eukaryotic genomes. Research into their unique biology has driven the creation of a large coll...

Authors: Tyler A. Elliott, Tony Heitkam, Robert Hubley, Hadi Quesneville, Alexander Suh and Travis J. Wheeler

melRNA-seq for Expression Analysis of SINE RNAs and Other Medium-Length Non-Coding RNAs

Small interspersed elements (SINEs) are transcribed by RNA polymerase III (Pol III) to produce RNAs typically 100–500 nucleotides in length. Although their RNA abundance can be evaluated by Northern blotting a...

Authors: Yoshinobu Mori and Kenji Ichiyanagi

The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis

Transposable elements (TEs) are repetitive sequences of viral origin that compose almost half of the human genome. These elements are tightly controlled within cells, and if activated, they can cause changes i...

Authors: Mahboubeh R. Rostami and Martina Bradic

Unbiased profiling of CRISPR RNA-guided transposition products by long-read sequencing

Bacterial transposons propagate through either non-replicative (cut-and-paste) or replicative (copy-and-paste) pathways, depending on how the mobile element is excised from its donor source. In the well-charac...

Authors: Phuc Leo H. Vo, Christopher Acree, Melissa L. Smith and Samuel H. Sternberg

The unusual structure of the PiggyMac cysteine-rich domain reveals zinc finger diversity in PiggyBac-related transposases

Transposons are mobile genetic elements that colonize genomes and drive their plasticity in all organisms. DNA transposon-encoded transposases bind to the ends of their cognate transposons and catalyze their m...

Authors: Marc Guérineau, Luiza Bessa, Séverine Moriau, Ewen Lescop, François Bontems, Nathalie Mathy, Eric Guittet, Julien Bischerour, Mireille Bétermier and Nelly Morellet

The IS6 family, a clinically important group of insertion sequences including IS26

The IS6 family of bacterial and archaeal insertion sequences, first identified in the early 1980s, has proved to be instrumental in the rearrangement and spread of multiple antibiotic resistance. Two IS, IS26 (fo...

Authors: Alessandro Varani, Susu He, Patricia Siguier, Karen Ross and Michael Chandler

New Ther1-derived SINE Squam3 in scaled reptiles

SINEs comprise a significant part of animal genomes and are used to study the evolution of diverse taxa. Despite significant advances in SINE studies in vertebrates and higher eukaryotes in general, their own ...

Authors: Nikita S. Vassetzky, Sergei A. Kosushkin, Vitaly I. Korchagin and Alexey P. Ryskov

Methylation of rRNA as a host defense against rampant group II intron retrotransposition

Group II introns are mobile retroelements, capable of invading new sites in DNA. They are self-splicing ribozymes that complex with an intron-encoded protein to form a ribonucleoprotein that targets DNA after ...

Authors: Justin M. Waldern, Dorie Smith, Carol Lyn Piazza, E. Jake Bailey, Nicholas J. Schiraldi, Reza Nemati, Dan Fabris, Marlene Belfort and Olga Novikova

The association of group IIB intron with integrons in hypersaline environments

Group II introns are mobile genetic elements used as efficient gene targeting tools. They function as both ribozymes and retroelements. Group IIC introns are the only class reported so far to be associated wit...

Authors: Sarah Sonbol and Rania Siam

Transcriptional activity of transposable elements along an elevational gradient in Arabidopsis arenosa

Plant genomes can respond rapidly to environmental changes and transposable elements (TEs) arise as important drivers contributing to genome dynamics. Although some elements were reported to be induced by vari...

Authors: Guillaume Wos, Rimjhim Roy Choudhury, Filip Kolář and Christian Parisod

Genomic properties of variably methylated retrotransposons in mouse

Transposable elements (TEs) are enriched in cytosine methylation, preventing their mobility within the genome. We previously identified a genome-wide repertoire of candidate intracisternal A particle (IAP) TEs...

Authors: Jessica L. Elmer, Amir D. Hay, Noah J. Kessler, Tessa M. Bertozzi, Eve A. C. Ainscough and Anne C. Ferguson-Smith

RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs

Long INterspersed Element-1 (LINE-1) is an autonomous retroelement able to “copy-and-paste” itself into new loci of the host genome through a process called retrotransposition. The LINE-1 bicistronic mRNA code...

Authors: Erica M. Briggs, Wilson McKerrow, Paolo Mita, Jef D. Boeke, Susan K. Logan and David Fenyö

Transposable element subfamily annotation has a reproducibility problem

Transposable element (TE) sequences are classified into families based on the reconstructed history of replication, and into subfamilies based on more fine-grained features that are often intended to capture f...

Authors: Kaitlin M. Carey, Gilia Patterson and Travis J. Wheeler

Association analysis of repetitive elements and R-loop formation across species

Although recent studies have revealed the genome-wide distribution of R-loops, our understanding of R-loop formation is still limited. Genomes are known to have a large number of repetitive elements. Emerging ...

Authors: Chao Zeng, Masahiro Onoguchi and Michiaki Hamada

The Dfam community resource of transposable element families, sequence models, and genome annotations

Dfam is an open access database of repetitive DNA families, sequence models, and genome annotations. The 3.0–3.3 releases of Dfam (https://​dfam.​org) represent an e...

Authors: Jessica Storer, Robert Hubley, Jeb Rosen, Travis J. Wheeler and Arian F. Smit

Transposable element-derived sequences in vertebrate development

Transposable elements (TEs) are major components of all vertebrate genomes that can cause deleterious insertions and genomic instability. However, depending on the specific genomic context of their insertion s...

Authors: Ema Etchegaray, Magali Naville, Jean-Nicolas Volff and Zofia Haftek-Terreau

SeqURE – a new copy-capture based method for sequencing of unknown Retroposition events

Retroelements (REs) occupy a significant part of all eukaryotic genomes including humans. The majority of retroelements in the human genome are inactive and unable to retrotranspose. Dozens of active copies ar...

Authors: Alexander Y. Komkov, Shamil Z. Urazbakhtin, Maria V. Saliutina, Ekaterina A. Komech, Yuri A. Shelygin, Gaiaz A. Nugmanov, Vitaliy P. Shubin, Anastasia O. Smirnova, Mikhail Y. Bobrov, Alexey S. Tsukanov, Anastasia V. Snezhkina, Anna V. Kudryavtseva, Yuri B. Lebedev and Ilgar Z. Mamedov

Intruder (DD38E), a recently evolved sibling family of DD34E/Tc1 transposons in animals

A family of Tc1/mariner transposons with a characteristic DD38E triad of catalytic amino acid residues, named Intruder (IT), was previously discovered in sturgeon genomes, but their evolutionary landscapes remain...

Authors: Bo Gao, Wencheng Zong, Csaba Miskey, Numan Ullah, Mohamed Diaby, Cai Chen, Xiaoyan Wang, Zoltán Ivics and Chengyi Song

Correction to: Characterising a human endogenous retrovirus(HERV)-derived tumour-associated antigen: enriched RNA-Seq analysis of HERV-K(HML-2) in mantle cell lymphoma cell lines

An amendment to this paper has been published and can be accessed via the original article.

Authors: Witold Tatkiewicz, James Dickie, Franchesca Bedford, Alexander Jones, Mark Atkin, Michele Kiernan, Emmanuel Atangana Maze, Bora Agit, Garry Farnham, Alexander Kanapin and Robert Belshaw

Characterisation of mobile genetic elements in Mycoplasma hominis with the description of ICEHo-II, a variant mycoplasma integrative and conjugative element

Mobile genetic elements are found in genomes throughout the microbial world, mediating genome plasticity and important prokaryotic phenotypes. Even the cell wall-less mycoplasmas, which are known to harbour a ...

Authors: Birgit Henrich, Stephanie Hammerlage, Sebastian Scharf, Diana Haberhausen, Ursula Fürnkranz, Karl Köhrer, Lena Peitzmann, Pier Luigi Fiori, Joachim Spergser, Klaus Pfeffer and Alexander T. Dilthey

Comprehensive genomic analysis reveals dynamic evolution of endogenous retroviruses that code for retroviral-like protein domains

Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections of mammalian germline cells. A large proportion of ERVs lose their open reading frames (ORFs), while others retain them and become e...

Authors: Mahoko Takahashi Ueda, Kirill Kryukov, Satomi Mitsuhashi, Hiroaki Mitsuhashi, Tadashi Imanishi and So Nakagawa

Twenty years of transposable element analysis in the Arabidopsis thaliana genome

Transposable elements (TEs) are mobile repetitive DNA sequences shown to be major drivers of genome evolution. As the first plant to have its genome sequenced and analyzed at the genomic scale, Arabidopsis thalia...

Authors: Hadi Quesneville

Evolution of pogo, a separate superfamily of IS630-Tc1-mariner transposons, revealing recurrent domestication events in vertebrates

Tc1/mariner and Zator, as two superfamilies of IS630-Tc1-mariner (ITm) group, have been well-defined. However, the molecular evolution and domestication of pogo transposons, once designated as an important family...

Authors: Bo Gao, Yali Wang, Mohamed Diaby, Wencheng Zong, Dan Shen, Saisai Wang, Cai Chen, Xiaoyan Wang and Chengyi Song

LINE-1 ORF1p does not determine substrate preference for human/orangutan SVA and gibbon LAVA

Non-autonomous VNTR (Variable Number of Tandem Repeats) composite retrotransposons – SVA (SINE-R-VNTR-Alu) and LAVA (L1-Alu-VNTR-Alu) – are specific to hominoid primates. SVA expanded in great apes, LAVA in gibbo...

Authors: Annette Damert

Deep sequencing reveals new roles for MuB in transposition immunity and target-capture, and redefines the insular Ter region of E. coli

The target capture protein MuB is responsible for the high efficiency of phage Mu transposition within the E. coli genome. However, some targets are off-limits, such as regions immediately outside the Mu ends (ci...

Authors: David M. Walker and Rasika M. Harshey

IS982 and kin: new insights into an old IS family

Insertion sequences (IS) are ubiquitous transposable elements with a very simple organization: two inverted repeats flanking a transposase coding gene. IS982 is one of 26 insertion sequence families known so far....

Authors: Nancy Fayad, Mireille Kallassy Awad and Jacques Mahillon

Transposable elements in Drosophila

Drosophila has been studied as a biological model for many years and many discoveries in biology rely on this species. Research on transposable elements (TEs) is not an exception. Drosophila has contributed signi...

Authors: Vincent Mérel, Matthieu Boulesteix, Marie Fablet and Cristina Vieira

Identification and characterisation of endogenous Avian Leukosis Virus subgroup E (ALVE) insertions in chicken whole genome sequencing data

Endogenous retroviruses (ERVs) are the remnants of retroviral infections which can elicit prolonged genomic and immunological stress on their host organism. In chickens, endogenous Avian Leukosis Virus subgrou...

Authors: Andrew S. Mason, Ashlee R. Lund, Paul M. Hocking, Janet E. Fulton and David W. Burt

Phylogenetic analysis of the Tc1/mariner superfamily reveals the unexplored diversity of pogo-like elements

Tc1/mariner transposons are widespread DNA transposable elements (TEs) that have made important contributions to the evolution of host genomic complexity in metazoans. However, the evolution and diversity of the

Authors: Mathilde Dupeyron, Tobias Baril, Chris Bass and Alexander Hayward

Transposons and satellite DNA: on the origin of the major satellite DNA family in the Chenopodium genome

Extensive and complex links exist between transposable elements (TEs) and satellite DNA (satDNA), which are the two largest fractions of eukaryotic genome. These relationships have a crucial effect on genome s...

Authors: Alexander Belyayev, Jiřina Josefiová, Michaela Jandová, Václav Mahelka, Karol Krak and Bohumil Mandák

Transposable element abundance correlates with mode of transmission in microsporidian parasites

The extreme genome reduction and physiological simplicity of some microsporidia has been attributed to their intracellular, obligate parasitic lifestyle. Although not all microsporidian genomes are small (size...

Authors: Nathalia Rammé Medeiros de Albuquerque, Dieter Ebert and Karen Luisa Haag

Hagfish genome reveals parallel evolution of 7SL RNA-derived SINEs

Short interspersed elements (SINEs) are ubiquitous components of eukaryotic genomes. SINEs are composite transposable elements that are mobilized by non-long terminal repeat (non-LTR) retrotransposons, also ca...

Authors: Kenji K. Kojima

Identification of RAG-like transposons in protostomes suggests their ancient bilaterian origin

V(D) J recombination is essential for adaptive immunity in jawed vertebrates and is initiated by the RAG1-RAG2 endonuclease. The RAG1 and RAG2 genes are thought to have evolved from a RAGL (RAG-like) transposon c...

Authors: Eliza C. Martin, Célia Vicari, Louis Tsakou-Ngouafo, Pierre Pontarotti, Andrei J. Petrescu and David G. Schatz

Diverse transposable element landscapes in pathogenic and nonpathogenic yeast models: the value of a comparative perspective

Genomics and other large-scale analyses have drawn increasing attention to the potential impacts of transposable elements (TEs) on their host genomes. However, it remains challenging to transition from identif...

Authors: Patrick H. Maxwell

AcademH, a lineage of Academ DNA transposons encoding helicase found in animals and fungi

DNA transposons are ubiquitous components of eukaryotic genomes. Academ superfamily of DNA transposons is one of the least characterized DNA transposon superfamilies in eukaryotes. DNA transposons belonging to th...

Authors: Kenji K. Kojima

Variation in base composition underlies functional and evolutionary divergence in non-LTR retrotransposons

Non-LTR retrotransposons often exhibit base composition that is markedly different from the nucleotide content of their host’s gene. For instance, the mammalian L1 element is AT-rich with a strong A bias on th...

Authors: Robert P. Ruggiero and Stéphane Boissinot

The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families

Nearly half the human genome consists of repeat elements, most of which are retrotransposons, and many of which play important biological roles. However repeat elements pose several unique challenges to curren...

Authors: Jason D. Fernandes, Armando Zamudio-Hurtado, Hiram Clawson, W. James Kent, David Haussler, Sofie R. Salama and Maximilian Haeussler

Integrated Mobile Element Scanning (ME-Scan) method for identifying multiple types of polymorphic mobile element insertions

Mobile elements are ubiquitous components of mammalian genomes and constitute more than half of the human genome. Polymorphic mobile element insertions (pMEIs) are a major source of human genomic variation and...

Authors: Jui Wan Loh, Hongseok Ha, Timothy Lin, Nawei Sun, Kathleen H. Burns and Jinchuan Xing

Finding and extending ancient simple sequence repeat-derived regions in the human genome

Previously, 3% of the human genome has been annotated as simple sequence repeats (SSRs), similar to the proportion annotated as protein coding. The origin of much of the genome is not well annotated, however, ...

Authors: Jonathan A. Shortt, Robert P. Ruggiero, Corey Cox, Aaron C. Wacholder and David D. Pollock

Hybrid dysgenesis in Drosophila virilis results in clusters of mitotic recombination and loss-of-heterozygosity but leaves meiotic recombination unaltered

Transposable elements (TEs) are endogenous mutagens and their harmful effects are especially evident in syndromes of hybrid dysgenesis. In Drosophila virilis, hybrid dysgenesis is a syndrome of incomplete gonadal...

Authors: Lucas W. Hemmer, Guilherme B. Dias, Brittny Smith, Kelley Van Vaerenberghe, Ashley Howard, Casey M. Bergman and Justin P. Blumenstiel

Characterising a human endogenous retrovirus(HERV)-derived tumour-associated antigen: enriched RNA-Seq analysis of HERV-K(HML-2) in mantle cell lymphoma cell lines

The cell-surface attachment protein (Env) of the HERV-K(HML-2) lineage of endogenous retroviruses is a potentially attractive tumour-associated antigen for anti-cancer immunotherapy. The human genome contains ...

Authors: Witold Tatkiewicz, James Dickie, Franchesca Bedford, Alexander Jones, Mark Atkin, Michele Kiernan, Emmanuel Atangana Maze, Bora Agit, Garry Farnham, Alexander Kanapin and Robert Belshaw

Integrating transposable elements in the 3D genome

Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) however, the spatial information of...

Authors: Alexandros Bousios, Hans-Wilhelm Nützmann, Dorothy Buck and Davide Michieletto

LUMI-PCR: an Illumina platform ligation-mediated PCR protocol for integration site cloning, provides molecular quantitation of integration sites

Ligation-mediated PCR protocols have diverse uses including the identification of integration sites of insertional mutagens, integrating vectors and naturally occurring mobile genetic elements. For approaches ...

Authors: Joanna C. Dawes, Philip Webster, Barbara Iadarola, Claudia Garcia-Diaz, Marian Dore, Bruce J. Bolt, Hamlata Dewchand, Gopuraja Dharmalingam, Alex P. McLatchie, Jakub Kaczor, Juan J. Caceres, Alberto Paccanaro, Laurence Game, Simona Parrinello and Anthony G. Uren