Articles

Alu SINE analyses of 3,000-year-old human skeletal remains: a pilot study

As Short Interspersed Elements (SINEs), human-specific Alu elements can be used for population genetic studies. Very recent inserts are polymorphic within and between human populations. In a sample of 30 elements...

Authors: Maximilian Kothe, Verena Seidenberg, Susanne Hummel and Oliver Piskurek

Active recombinant Tol2 transposase for gene transfer and gene discovery applications

The revolutionary concept of “jumping genes” was conceived by McClintock in the late 1940s while studying the Activator/Dissociation (Ac/Ds) system in maize. Transposable elements (TEs) represent the most abundan...

Authors: Jun Ni, Kirk J. Wangensteen, David Nelsen, Darius Balciunas, Kimberly J. Skuster, Mark D. Urban and Stephen C. Ekker

Erratum to: ribosomal protein and biogenesis factors affect multiple steps during movement of the Saccharomyces cerevisiae Ty1 retrotransposon

Authors: Susmitha Suresh, Hyo Won Ahn, Kartikeya Joshi, Arun Dakshinamurthy, Arun Kannanganat, David J. Garfinkel and Philip J. Farabaugh

The contribution of transposable elements to size variations between four teleost genomes

Teleosts are unique among vertebrates, with a wide range of haploid genome sizes in very close lineages, varying from less than 400 mega base pairs (Mb) for pufferfish to over 3000 Mb for salmon. The cause of ...

Authors: Bo Gao, Dan Shen, Songlei Xue, Cai Chen, Hengmi Cui and Chengyi Song

Genome ARTIST: a robust, high-accuracy aligner tool for mapping transposon insertions and self-insertions

A critical topic of insertional mutagenesis experiments performed on model organisms is mapping the hits of artificial transposons (ATs) at nucleotide level accuracy. Mapping errors may occur when sequencing a...

Authors: Alexandru Al. Ecovoiu, Iulian Constantin Ghionoiu, Andrei Mihai Ciuca and Attila Cristian Ratiu

Phylogenomic analysis reveals genome-wide purifying selection on TBE transposons in the ciliate Oxytricha

Transposable elements are a major player contributing to genetic variation and shaping genome evolution. Multiple independent transposon domestication events have occurred in ciliates, recruiting transposases ...

Authors: Xiao Chen and Laura F. Landweber

Isolation and characterization of putative functional long terminal repeat retrotransposons in the Pyrus genome

Long terminal repeat (LTR)-retrotransposons constitute 42.4 % of the genome of the ‘Suli’ pear (Pyrus pyrifolia white pear group), implying that retrotransposons have played important roles in Pyrus evolution. Th...

Authors: Shuang Jiang, Danying Cai, Yongwang Sun and Yuanwen Teng

Transposable element detection from whole genome sequence data

The number of software tools available for detecting transposable element insertions from whole genome sequence data has been increasing steadily throughout the last ~5 years. Some of these methods have unique...

Authors: Adam D. Ewing

The making of a genomic parasite - the Mothra family sheds light on the evolution of Helitrons in plants

Helitrons are Class II transposons which are highly abundant in almost all eukaryotes. However, most Helitrons lack protein coding sequence. These non-autonomous elements are thought to hijack recombinase/heli...

Authors: Stefan Roffler, Fabrizio Menardo and Thomas Wicker

Ribosomal protein and biogenesis factors affect multiple steps during movement of the Saccharomyces cerevisiae Ty1 retrotransposon

A large number of Saccharomyces cerevisiae cellular factors modulate the movement of the retrovirus-like transposon Ty1. Surprisingly, a significant number of chromosomal genes required for Ty1 transposition enco...

Authors: Susmitha Suresh, Hyo Won Ahn, Kartikeya Joshi, Arun Dakshinamurthy, Arun Kannanganat, David J. Garfinkel and Philip J. Farabaugh

Transposable element polymorphisms recapitulate human evolution

The human genome contains several active families of transposable elements (TE): Alu, L1 and SVA. Germline transposition of these elements can lead to polymorphic TE (polyTE) loci that differ between individua...

Authors: Lavanya Rishishwar, Carlos E. Tellez Villa and I. King Jordan

First international workshop on human endogenous retroviruses and diseases, HERVs & disease 2015

The First International Scientific Conference on Human Endogenous Retroviruses (HERVs) and Disease, Lyon-France, May 26-27^th 2015, brought together scientific and medical specialists from around the world investi...

Authors: Avindra Nath, Patrick Küry, Guilherme Sciascia do Olival, Antonina Dolei, Håkan Karlsson, Laurent Groc, Marion Schneider, John Kriesel, Jean-Louis Touraine, François Mallet, Patrice N. Marche, Frederick Arnaud, Cédric Feschotte and Hervé Perron

A long terminal repeat retrotransposon of Schizosaccharomyces japonicus integrates upstream of RNA pol III transcribed genes

Transposable elements (TEs) are common constituents of centromeres. However, it is not known what causes this relationship. Schizosaccharomyces japonicus contains 10 families of Long Terminal Repeat (LTR)-retrotr...

Authors: Yabin Guo, Parmit Kumar Singh and Henry L. Levin

Identification and characterization of a minisatellite contained within a novel miniature inverted-repeat transposable element (MITE) of Porphyromonas gingivalis

Repetitive regions of DNA and transposable elements have been found to constitute large percentages of eukaryotic and prokaryotic genomes. Such elements are known to be involved in transcriptional regulation, ...

Authors: Brian A. Klein, Tsute Chen, Jodie C. Scott, Andrea L. Koenigsberg, Margaret J. Duncan and Linden T. Hu

Spotting the enemy within: Targeted silencing of foreign DNA in mammalian genomes by the Krüppel-associated box zinc finger protein family

Tandem C2H2-type zinc finger proteins (ZFPs) constitute the largest transcription factor family in animals. Tandem-ZFPs bind DNA in a sequence-specific manner through arrays of multiple zinc finger domains tha...

Authors: Gernot Wolf, David Greenberg and Todd S. Macfarlan

Comparative paleovirological analysis of crustaceans identifies multiple widespread viral groups

The discovery of many fragments of viral genomes integrated in the genome of their eukaryotic host (endogenous viral elements; EVEs) has recently opened new avenues to further our understanding of viral evolut...

Authors: Gabriel Metegnier, Thomas Becking, Mohamed Amine Chebbi, Isabelle Giraud, Bouziane Moumen, Sarah Schaack, Richard Cordaux and Clément Gilbert

Precise repair of mPing excision sites is facilitated by target site duplication derived microhomology

A key difference between the Tourist and Stowaway families of miniature inverted repeat transposable elements (MITEs) is the manner in which their excision alters the genome. Upon excision, Stowaway-like MITEs an...

Authors: David M. Gilbert, M. Catherine Bridges, Ashley E. Strother, Courtney E. Burckhalter, James M. Burnette III and C. Nathan Hancock

A host factor supports retrotransposition of the TRE5-A population in Dictyostelium cells by suppressing an Argonaute protein

In the compact and haploid genome of Dictyostelium discoideum control of transposon activity is of particular importance to maintain viability. The non-long terminal repeat retrotransposon TRE5-A amplifies contin...

Authors: Anika Schmith, Thomas Spaller, Friedemann Gaube, Åsa Fransson, Benjamin Boesler, Sandeep Ojha, Wolfgang Nellen, Christian Hammann, Fredrik Söderbom and Thomas Winckler

A call for benchmarking transposable element annotation methods

DNA derived from transposable elements (TEs) constitutes large parts of the genomes of complex eukaryotes, with major impacts not only on genomic research but also on how organisms evolve and function. Althoug...

Authors: Douglas R. Hoen, Glenn Hickey, Guillaume Bourque, Josep Casacuberta, Richard Cordaux, Cédric Feschotte, Anna-Sophie Fiston-Lavier, Aurélie Hua-Van, Robert Hubley, Aurélie Kapusta, Emmanuelle Lerat, Florian Maumus, David D. Pollock, Hadi Quesneville, Arian Smit, Travis J. Wheeler…

The diversification of PHIS transposon superfamily in eukaryotes

PHIS transposon superfamily belongs to DNA transposons and includes PIF/Harbinger, ISL2EU, and Spy transposon groups. These three groups have similar DDE domain-containing transposases; however, their coding capa...

Authors: Min-Jin Han, Chu-Lin Xiong, Hong-Bo Zhang, Meng-Qiang Zhang, Hua-Hao Zhang and Ze Zhang

Repbase Update, a database of repetitive elements in eukaryotic genomes

Repbase Update (RU) is a database of representative repeat sequences in eukaryotic genomes. Since its first development as a database of human repetitive sequences in 1992, RU has been serving as a well-curate...

Authors: Weidong Bao, Kenji K. Kojima and Oleksiy Kohany

Differential SINE evolution in vesper and non-vesper bats

Short interspersed elements (SINEs) have a powerful influence on genome evolution and can be useful markers for phylogenetic inference and population genetic analyses. In this study, we examined survey sequenc...

Authors: David A Ray, Heidi JT Pagan, Roy N Platt II, Ashley R Kroll, Sarah Schaack and Richard D Stevens

Mechanism of spacer integration links the CRISPR/Cas system to transposition as a form of mobile DNA

It has recently become clear that many bacterial and archaeal species possess adaptive immune systems. These are typified by multiple copies of DNA sequences known as clustered regularly interspaced short pali...

Authors: Fred Dyda and Alison B Hickman

Genome-wide comparison of Asian and African rice reveals high recent activity of DNA transposons

DNA (Class II) transposons are ubiquitous in plant genomes. However, unlike for (Class I) retrotransposons, only little is known about their proliferation mechanisms, activity, and impact on genomes. Asian and...

Authors: Stefan Roffler and Thomas Wicker

Evolution of group II introns

Present in the genomes of bacteria and eukaryotic organelles, group II introns are an ancient class of ribozymes and retroelements that are believed to have been the ancestors of nuclear pre-mRNA introns. Desp...

Authors: Steven Zimmerly and Cameron Semper

Reviewer acknowledgement 2015

The Editors of Mobile DNA would like to thank all our reviewers who have contributed to the journal in volume 5 (2014).

Authors: Nancy L Craig, Thomas H Eikbush, Cédric Feschotte and Henry Levin

Transposable elements in a clade of three tetraploids and a diploid relative, focusing on Gypsy amplification

Polyploidization can activate specific transposable elements, leading to their accumulation. At the same time, the preferential loss of repetitive elements in polyploids may be central to diploidization. The p...

Authors: Mathieu Piednoël, Aretuza Sousa and Susanne S Renner

HERV-K(HML-2) rec and np9 transcripts not restricted to disease but present in many normal human tissues

Human endogenous retroviruses of the HERV-K(HML-2) group have been associated with the development of tumor diseases. Various HERV-K(HML-2) loci encode retrovirus-like proteins, and expression of such proteins...

Authors: Katja Schmitt, Kristina Heyne, Klaus Roemer, Eckart Meese and Jens Mayer

Repeated horizontal transfers of four DNA transposons in invertebrates and bats

Horizontal transfer (HT) of transposable elements (TEs) into a new genome is considered as an important force to drive genome variation and biological innovation. However, most of the HT of DNA transposons pre...

Authors: Zhou Tang, Hua-Hao Zhang, Ke Huang, Xiao-Gu Zhang, Min-Jin Han and Ze Zhang

Jerzy Jurka: June 4, 1950 – July 19, 2014

Authors: Elzbieta Jurka

Jerzy Jurka – 1950–2014

Authors: Prescott Deininger

A droplet digital PCR detection method for rare L1 insertions in tumors

The active human mobile element, long interspersed element 1 (L1) currently populates human genomes in excess of 500,000 copies per haploid genome. Through its mobility via a process called target primed rever...

Authors: Travis B White, Adam M McCoy, Vincent A Streva, Joshua Fenrich and Prescott L Deininger

Development of a monoclonal antibody specific to the endonuclease domain of the human LINE-1 ORF2 protein

LINE-1 (L1) retrotransposons are common occupants of mammalian genomes representing about a fifth of the genetic content. Ongoing L1 retrotransposition in the germ line and somatic tissues has contributed to s...

Authors: Mark Sokolowski, Cecily B DeFreece, Geraldine Servant, Kristine J Kines, Dawn L deHaro and Victoria P Belancio

Distinct features of the piRNA pathway in somatic and germ cells: from piRNA cluster transcription to piRNA processing and amplification

Transposable elements (TEs) are major components of genomes. Their mobilization may affect genomic expression and be a threat to genetic stability. This is why they have to be tightly regulated by a dedicated ...

Authors: Emmanuelle Théron, Cynthia Dennis, Emilie Brasset and Chantal Vaury

Tn5 transposition in Escherichia coli is repressed by Hfq and activated by over-expression of the small non-coding RNA SgrS

Hfq functions in post-transcriptional gene regulation in a wide range of bacteria, usually by promoting base pairing of mRNAs with trans-encoded sRNAs. It was previously shown that Hfq down-regulates Tn10 transpo...

Authors: Joseph A Ross, Ryan S Trussler, Morgan D Black, Crystal R McLellan and David B Haniford

Mobile genetic elements and genome evolution 2014

The Mobile Genetic Elements and Genome Evolution conference was hosted by Keystone Symposia in Santa Fe, NM USA, 9 March through 14 March 2014. The goal of this conference was to bring together scientists from...

Authors: Parmit Kumar Singh, Guillaume Bourque, Nancy L Craig, Josh T Dubnau, Cédric Feschotte, Diane A Flasch, Kevin L Gunderson, Harmit Singh Malik, John V Moran, Joseph E Peters, R Keith Slotkin and Henry L Levin

Molecular characterization of a new member of the lariat capping twin-ribozyme introns

Twin-ribozyme introns represent a complex class of mobile group I introns that harbour a lariat capping (LC) ribozyme and a homing endonuclease gene embedded in a conventional self-splicing group I ribozyme (G...

Authors: Yunjia Tang, Henrik Nielsen, Benoît Masquida, Paul P Gardner and Steinar D Johansen

Analysis of CACTA transposases reveals intron loss as major factor influencing their exon/intron structure in monocotyledonous and eudicotyledonous hosts

CACTA elements are DNA transposons and are found in numerous organisms. Despite their low activity, several thousand copies can be identified in many genomes. CACTA elements transpose using a ‘cut-and-paste’ mech...

Authors: Jan P Buchmann, Ari Löytynoja, Thomas Wicker and Alan H Schulman

CRISPR-Cas immunity and mobile DNA: a new superfamily of DNA transposons encoding a Cas1 endonuclease

Mobile genetic elements such as DNA transposons are a feature of most genomes. The existence of novel DNA transposons can be inferred when whole genome sequencing reveals the presence of hallmarks of mobile el...

Authors: Alison B Hickman and Fred Dyda

piRNA clusters and open chromatin structure

Transposable elements (TEs) are major structural components of eukaryotic genomes; however, mobilization of TEs generally has negative effects on the host genome. To counteract this threat, host cells have evo...

Authors: Soichiro Yamanaka, Mikiko C Siomi and Haruhiko Siomi

The Drosophila mojavensis Bari3 transposon: distribution and functional characterization

Bari-like transposons belong to the Tc1-mariner superfamily, and they have been identified in several genomes of the Drosophila genus. This transposon’s family has been used as paradigm to investigate the complex...

Authors: Antonio Palazzo, Roberta Moschetti, Ruggiero Caizzi and René Massimiliano Marsano

Processed pseudogene insertions in somatic cells

Processed pseudogenes are copies of messenger RNAs that have been reverse transcribed into DNA and inserted into the genome using the enzymatic activities of active L1 elements. Processed pseudogenes generally...

Authors: Haig H Kazazian Jr

Modular organization and reticulate evolution of the ORF1 of Jockey superfamily transposable elements

Long interspersed nuclear elements (LINES) are the most common transposable element (TE) in almost all metazoan genomes examined. In most LINE superfamilies there are two open reading frames (ORFs), and both a...

Authors: Cushla J Metcalfe and Didier Casane

Mobile DNA: an evolving field

During the Mobile Genetic Elements and Genome Evolution Keystone Symposium in March 2014, the Editors of Mobile DNA caught up with a panel of conference speakers to select key advances in the field, and hear thei...

Authors: Marlene Belfort, Luciano Marraffini, Todd Macfarlan, Jef Boeke, Keith Slotkin, Harmit Malik and Lynne Maquat

DINE-1, the highest copy number repeats in Drosophila melanogaster are non-autonomous endonuclease-encoding rolling-circle transposable elements (Helentrons)

The Drosophila INterspersed Elements-1 (DINE-1/INE1) transposable elements (TEs) are the most abundant component of the Drosophila melanogaster genome and have been associated with functional gene duplications. D...

Authors: Jainy Thomas, Komal Vadnagara and Ellen J Pritham

Tc 1-like transposable elements in plant genomes

The Tc1/mariner superfamily of transposable elements (TEs) is widespread in animal genomes. Mariner-like elements, which bear a DDD triad catalytic motif, have been identified in a wide range of flowering plant s...

Authors: Yuan Liu and Guojun Yang

Blood from ‘junk’: the LTR chimeric transcript Pu.2 promotes erythropoiesis

Transposable elements (TEs) are a prominent feature of most eukaryotic genomes. Despite rapidly accumulating evidence for the role of TE-driven insertional mutagenesis and structural variation in genome evolut...

Authors: Kyle R Upton and Geoffrey J Faulkner

Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression

Mammalian-wide interspersed repeats (MIRs) are the most ancient family of transposable elements (TEs) in the human genome. The deep conservation of MIRs initially suggested the possibility that they had been e...

Authors: Daudi Jjingo, Andrew B Conley, Jianrong Wang, Leonardo Mariño-Ramírez, Victoria V Lunyak and I King Jordan

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

Of the different bioinformatic methods used to recover transposable elements (TEs) in genome sequences, one of the most commonly used procedures is the homology-based method proposed by the RepeatMasker progra...

Authors: Marc Bailly-Bechet, Annabelle Haudry and Emmanuelle Lerat

The Tc1/mariner transposable element family shapes genetic variation and gene expression in the protist Trichomonas vaginalis

Trichomonas vaginalis is the most prevalent non-viral sexually transmitted parasite. Although the protist is presumed to reproduce asexually, 60% of its haploid genome contains transposable elements (TEs), known ...

Authors: Martina Bradic, Sally D Warring, Vivien Low and Jane M Carlton