Articles

Insertion and deletion polymorphisms of the ancient AluS family in the human genome

Polymorphic Alu elements account for 17% of structural variants in the human genome. The majority of these belong to the youngest AluY subfamilies, and most structural variant discovery efforts have focused on id...

Authors: Maria S. Kryatova, Jared P. Steranka, Kathleen H. Burns and Lindsay M. Payer

LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences

Population genomic analysis of transposable elements has greatly benefited from recent advances of sequencing technologies. However, the short size of the reads and the propensity of transposable elements to n...

Authors: Eric Disdero and Jonathan Filée

Convergence of retrotransposons in oomycetes and plants

Retrotransposons comprise a ubiquitous and abundant class of eukaryotic transposable elements. All members of this class rely on reverse transcriptase activity to produce a DNA copy of the element from the RNA...

Authors: Kirill Ustyantsev, Alexandr Blinov and Georgy Smyshlyaev

Considerations and complications of mapping small RNA high-throughput data to transposable elements

High-throughput sequencing (HTS) has revolutionized the way in which epigenetic research is conducted. When coupled with fully-sequenced genomes, millions of small RNA (sRNA) reads are mapped to regions of int...

Authors: Alexandros Bousios, Brandon S. Gaut and Nikos Darzentas

Chicken (Gallus gallus) endogenous retrovirus generates genomic variations in the chicken genome

Transposable elements (TEs) comprise ~10% of the chicken (Gallus gallus) genome. The content of TEs is much lower than that of mammalian genomes, where TEs comprise around half of the genome. Endogenous retroviru...

Authors: Jinmin Lee, Seyoung Mun, Dong Hee Kim, Chun-Sung Cho, Dong-Yep Oh and Kyudong Han

Functional characterization of the active Mutator-like transposable element, Muta1 from the mosquito Aedes aegypti

Mutator-like transposable elements (MULEs) are widespread with members in fungi, plants, and animals. Most of the research on the MULE superfamily has focused on plant MULEs where they...

Authors: Kun Liu and Susan R. Wessler

Non-canonical Helitrons in Fusarium oxysporum

Helitrons are eukaryotic rolling circle transposable elements that can have a large impact on host genomes due to their copy-number and their ability to capture and copy genes and regulatory elements. They occ...

Authors: Biju Vadakkemukadiyil Chellapan, Peter van Dam, Martijn Rep, Ben J. C. Cornelissen and Like Fokkens

The intron-enriched HERV-K(HML-10) family suppresses apoptosis, an indicator of malignant transformation

Human endogenous retroviruses (HERVs) constitute 8% of the human genome and contribute substantially to the transcriptome. HERVs have been shown to generate RNAs that modulate host gene expression. However, ex...

Authors: Felix Broecker, Roger Horton, Jochen Heinrich, Alexandra Franz, Michal-Ruth Schweiger, Hans Lehrach and Karin Moelling

TE studies in Japan: The third Japanese meeting on host-transposon interactions

The third Japanese meeting entitled “Biological Function and Evolution through Interactions between Hosts and Transposable Elements (TEs)” was held on 5–6 September 2016 at National Institute of Genetics (NIG)...

Authors: Kenji Ichiyanagi

Endogenous retroviral promoter exaptation in human cancer

Cancer arises from a series of genetic and epigenetic changes, which result in abnormal expression or mutational activation of oncogenes, as well as suppression/inactivation of tumor suppressor genes. Aberrant...

Authors: Artem Babaian and Dixie L. Mager

Deciphering fact from artifact when using reporter assays to investigate the roles of host factors on L1 retrotransposition

The Long INterspersed Element-1 (L1, LINE-1) is the only autonomous mobile DNA element in humans and has generated as much as half of the genome. Due to increasing clinical interest in the roles of L1 in cance...

Authors: Pamela R. Cook and G. Travis Tabor

Somatic retrotransposition is infrequent in glioblastomas

Gliomas are the most common primary brain tumors in adults. We sought to understand the roles of endogenous transposable elements in these malignancies by identifying evidence of somatic retrotransposition in ...

Authors: Pragathi Achanta, Jared P. Steranka, Zuojian Tang, Nemanja Rodić, Reema Sharma, Wan Rou Yang, Sisi Ma, Mark Grivainis, Cheng Ran Lisa Huang, Anna M. Schneider, Gary L. Gallia, Gregory J. Riggins, Alfredo Quinones-Hinojosa, David Fenyö, Jef D. Boeke and Kathleen H. Burns

Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme

LINE-1 (L1) retrotransposons are a notable endogenous source of mutagenesis in mammals. Notably, cancer cells can support unusual L1 retrotransposition and L1-associated sequence rearrangement mechanisms follo...

Authors: Patricia E. Carreira, Adam D. Ewing, Guibo Li, Stephanie N. Schauer, Kyle R. Upton, Allister C. Fagg, Santiago Morell, Michaela Kindlova, Patricia Gerdes, Sandra R. Richardson, Bo Li, Daniel J. Gerhardt, Jun Wang, Paul M. Brennan and Geoffrey J. Faulkner

A map of mobile DNA insertions in the NCI-60 human cancer cell panel

The National Cancer Institute-60 (NCI-60) cell lines are among the most widely used models of human cancer. They provide a platform to integrate DNA sequence information, epigenetic data, RNA and protein expre...

Authors: John G. Zampella, Nemanja Rodić, Wan Rou Yang, Cheng Ran Lisa Huang, Jane Welch, Veena P. Gnanakkan, Toby C. Cornish, Jef D. Boeke and Kathleen H. Burns

International Congress on Transposable elements (ICTE 2016) in Saint Malo: mobile elements under the sun of Brittany

The third international conference on Transposable Elements (ICTE) was held 16–19 April 2016 in Saint Malo, France. Organized by the French Transposition Community (Research group of the CNRS: “Mobile genetic ...

Authors: Pascale Lesage, Mireille Bétermier, Antoine Bridier-Nahmias, Michael Chandler, Séverine Chambeyron, Gael Cristofari, Nicolas Gilbert, Hadi Quesneville, Chantal Vaury and Jean-Nicolas Volff

Functional opsin retrogene in nocturnal moth

Retrotransposed genes are different to other types of genes as they originate from a processed mRNA and are then inserted back into the genome. For a long time, the contribution of this mechanism to the origin...

Authors: Pengjun Xu, Roberto Feuda, Bin Lu, Haijun Xiao, Robert I. Graham and Kongming Wu

Convergent evolution of tRNA gene targeting preferences in compact genomes

In gene-dense genomes, mobile elements are confronted with highly selective pressure to amplify without causing excessive damage to the host. The targeting of tRNA genes as potentially safe integration sites h...

Authors: Thomas Spaller, Eva Kling, Gernot Glöckner, Falk Hillmann and Thomas Winckler

Restricting retrotransposons: a review

Retrotransposons have generated about 40 % of the human genome. This review examines the strategies the cell has evolved to coexist with these genomic “parasites”, focussing on the non-long terminal repeat ret...

Authors: John L. Goodier

Identification of polymorphic SVA retrotransposons using a mobile element scanning method for SVA (ME-Scan-SVA)

Mobile element insertions are a major source of human genomic variation. SVA (SINE-R/VNTR/Alu) is the youngest retrotransposon family in the human genome and a number of diseases are known to be caused by SVA ...

Authors: Hongseok Ha, Jui Wan Loh and Jinchuan Xing

Virus-like attachment sites as structural landmarks of plants retrotransposons

The genomic data available nowadays has enabled the study of repetitive sequences and their relationship to viruses. Among them, long terminal repeat retrotransposons (LTR-RTs) are the largest component of mos...

Authors: Edgar Andres Ochoa Cruz, Guilherme Marcello Queiroga Cruz, Andréia Prata Vieira and Marie-Anne Van Sluys

Christophe Terzian (1959-2016)

Authors:

Pinpointing the vesper bat transposon revolution using the Miniopterus natalensis genome

Around 40 million years ago DNA transposons began accumulating in an ancestor of bats in the family Vespertilionidae. Since that time, Class II transposons have been continuously reinvading and accumulating in...

Authors: Roy N. Platt II, Sarah F. Mangum and David A. Ray

Distribution of the DNA transposon family, Pokey in the Daphnia pulex species complex

The Pokey family of DNA transposons consists of two putatively autonomous groups, PokeyA and PokeyB, and two groups of Miniature Inverted-repeat Transposable Elements (MITEs), mPok1 and mPok2. This TE family is u...

Authors: Shannon H. C. Eagle and Teresa J. Crease

Roles for retrotransposon insertions in human disease

Over evolutionary time, the dynamic nature of a genome is driven, in part, by the activity of transposable elements (TE) such as retrotransposons. On a shorter time scale it has been established that new TE in...

Authors: Dustin C. Hancks and Haig H. Kazazian Jr.

Genomic analysis of mouse VL30 retrotransposons

Retrotransposons are mobile elements that have a high impact on shaping the mammalian genomes. Since the availability of whole genomes, genomic analyses have provided novel insights into retrotransposon biolog...

Authors: Georgios Markopoulos, Dimitrios Noutsopoulos, Stefania Mantziou, Demetrios Gerogiannis, Soteroula Thrasyvoulou, Georgios Vartholomatos, Evangelos Kolettas and Theodore Tzavaras

The endonuclease domain of the LINE-1 ORF2 protein can tolerate multiple mutations

Approximately 17 % of the human genome is comprised of the Long INterspersed Element-1 (LINE-1 or L1) retrotransposon, the only currently active autonomous family of retroelements. Though L1 elements have helped ...

Authors: Kristine J. Kines, Mark Sokolowski, Dawn L. deHaro, Claiborne M. Christian, Melody Baddoo, Madison E. Smither and Victoria P. Belancio

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

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

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

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