A Field Guide to Eukaryotic Transposable Elements

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RepeatModeler2 for automated genomic discovery of transposable element families

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A unified classification system for eukaryotic transposable elements

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Repeated Sequences in DNA

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The origins of genome complexity

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Alu repeats and human genomic diversity

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The Norway spruce genome sequence and conifer genome evolution

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Ten things you should know about transposable elements

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Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline

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Origin and evolution of retroelements based upon their reverse transcriptase sequences

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Regulatory activities of transposable elements: from conflicts to benefits

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DNA transposons and the evolution of eukaryotic genomes.

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Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition

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Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition

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The Piwi-piRNA Pathway Provides an Adaptive Defense in the Transposon Arms Race

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High frequency retrotransposition in cultured mammalian cells

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The new tree of eukaryotes

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Endogenous viruses: insights into viral evolution and impact on host biology

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Eukaryotic transposable elements and genome evolution

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Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis

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Genome Size Reduction through Illegitimate Recombination Counteracts Genome Expansion in <i>Arabidopsis</i>

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Roles for retrotransposon insertions in human disease

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The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein that Mediates Intercellular RNA Transfer

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Transposable Elements, Epigenetics, and Genome Evolution

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Analyses of LTR-Retrotransposon Structures Reveal Recent and Rapid Genomic DNA Loss in RicePreprint

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The axolotl genome and the evolution of key tissue formation regulators

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Rolling-circle transposons in eukaryotes

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An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

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Unexpected consequences of a sudden and massive transposon amplification on rice gene expression

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Dynamics of genome size evolution in birds and mammals

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High-frequency P element loss in Drosophila is homolog dependent

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Finding the missing honey bee genes: lessons learned from a genome upgrade

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Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification

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Active Transposition in Genomes

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Ancestral, Mammalian-wide Subfamilies of LINE-1 Repetitive Sequences

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Retroviruses in invertebrates: the gypsyretrotransposon is apparently an infectious retrovirus of Drosophilamelanogaster.

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Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primatesPreprint

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SVA Elements: A Hominid-specific Retroposon Family

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Retroelement Distributions in the Human Genome: Variations Associated With Age and Proximity to GenesPreprint

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The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements

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A proposed superfamily of transposase genes: transposon-like elements in ciliated protozoa and a common "D35E" motif.

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Modeling of TREX1-dependent autoimmune disease using human stem cells highlights L1 accumulation as a source of neuroinflammation

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Transposases are the most abundant, most ubiquitous genes in nature

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The outs and ins of transposition: from Mu to Kangaroo

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The Influence of LINE-1 and SINE Retrotransposons on Mammalian Genomes

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Coevolution between transposable elements and recombination

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A Virophage at the Origin of Large DNA Transposons

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Host–transposon interactions: conflict, cooperation, and cooptionPreprint

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Self-synthesizing DNA transposons in eukaryotes

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Reconstruction and analysis of human alu genes

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A triptych of the evolution of plant transposable elements

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The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies

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Integration site selection by retroviruses and transposable elements in eukaryotes

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Transposable elements are the primary source of novelty in primate gene regulationPreprint

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Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses

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Everyman's Guide to Bacterial Insertion Sequences

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Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses

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The complete sequence of the smallest known nuclear genome from the microsporidian Encephalitozoon intestinalis

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Massive horizontal transfer of transposable elements in insects

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Origins and Evolution of Retrotransposons

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Dramatic amplification of a rice transposable element during recent domestication

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The non-autonomous retrotransposon SVA is trans -mobilized by the human LINE-1 protein machinery

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Evolutionary history of 7SL RNA-derived SINEs in Supraprimates

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Origin of viruses: primordial replicators recruiting capsids from hosts

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Requirement of RNA Polymerase III Transcription Factors for in Vitro Position-Specific Integration of a Retroviruslike Element

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Transposition favors the generation of large effect mutations that may facilitate rapid adaption

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Mu Transposon Insertion Sites and Meiotic Recombination Events Co-Localize with Epigenetic Marks for Open Chromatin across the Maize Genome

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Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution

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Effects of Recombination Rate and Gene Density on Transposable Element Distributions in Arabidopsis thalianaPreprint

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Co-option of endogenous viral sequences for host cell function

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Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids

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Origin and evolution of SINEs in eukaryotic genomes

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Retrotransposition of marked SVA elements by human L1s in cultured cells

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Evolution of group II introns

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Miniature Inverted‐Repeat Transposable Elements and Their Relationship to Established DNA Transposons

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Massive amplification of rolling-circle transposons in the lineage of the bat Myotis lucifugus

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SINEs and LINEs: symbionts of eukaryotic genomes with a common tail

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Horizontal acquisition of transposable elements and viral sequences: patterns and consequences

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Host genome integration and giant virus-induced reactivation of the virophage mavirus

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Non-LTR retrotransposons encode noncanonical RRM domains in their first open reading frame

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Tuned for Transposition: Molecular Determinants Underlying the Hyperactivity of a Stowaway MITE

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Targeting of the Yeast Ty5 Retrotransposon to Silent Chromatin Is Mediated by Interactions between Integrase and Sir4p

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The Landscape of L1 Retrotransposons in the Human Genome Is Shaped by Pre-insertion Sequence Biases and Post-insertion Selection

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Penelope , a new family of transposable elements and its possible role in hybrid dysgenesis in Drosophila virilis

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Trimeric structure and flexibility of the L1ORF1 protein in human L1 retrotransposition

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Comparative Genomic Paleontology across Plant Kingdom Reveals the Dynamics of TE-Driven Genome Evolution

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Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration

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The genomic ecosystem of transposable elements in maize

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Did Genetic Drift Drive Increases in Genome Complexity?

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Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals

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On the Population Dynamics of Junk: A Review on the Population Genomics of Transposable Elements

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The Site-Specific Ribosomal Insertion Element Type II of Bombyx mori (R2Bm) Contains the Coding Sequence for a Reverse Transcriptase-Like Enzyme

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Transposons but Not Retrotransposons Are Located Preferentially in Regions of High Recombination Rate in Caenorhabditis elegans

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Evolution and diversity of transposable elements in fish genomes

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Env -less endogenous retroviruses are genomic superspreaders

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Retroelements containing introns in diverse invertebrate taxa

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Retrotransposons as Drivers of Mammalian Brain Evolution

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The Role of Retrotransposons and Endogenous Retroviruses in Age-Dependent Neurodegenerative Disorders

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Systemic interindividual epigenetic variation in humans is associated with transposable elements and under strong genetic control

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Constitutive Heterochromatin in Eukaryotic Genomes: A Mine of Transposable Elements

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Making the Genome Huge: The Case of Triatoma delpontei, a Triatominae Species with More than 50% of Its Genome Full of Satellite DNA

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The Evolutionary Volte-Face of Transposable Elements: From Harmful Jumping Genes to Major Drivers of Genetic Innovation

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Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration

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From Chaos Comes Order: Genetics and Genome Biology of Arbuscular Mycorrhizal Fungi

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Retrotransposon addiction promotes centromere function via epigenetically activated small RNAs

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The power of “controllers”: Transposon-mediated duplicated genes evolve towards neofunctionalization

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The Diverse Evolutionary Histories of Domesticated Metaviral Capsid Genes in Mammals

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Heterologous survey of 130 DNA transposons in human cells highlights their functional divergence and expands the genome engineering toolbox

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

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HERV-W Envelope Triggers Abnormal Dopaminergic Neuron Process through DRD2/PP2A/AKT1/GSK3 for Schizophrenia Risk

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Repeat Age Decomposition Informs an Ancient Set of Repeats Associated With Coleoid Cephalopod Divergence

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Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly

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Shedding light on DNA methylation and its clinical implications: the impact of long-read-based nanopore technology

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Transposable elements are vectors of recurrent transgenerational epigenetic inheritance

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Genomic insights into the adaptation and evolution of the nautilus, an ancient but evolving “living fossil”

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Transposable Elements Co-Option in Genome Evolution and Gene Regulation

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Human Endogenous Retroviruses: Our Genomic Fossils and Companions

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Retroelement decay by the exonuclease XRN1 is a viral mimicry dependency in cancer

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Chronic Viral Mimicry Induction following p53 Loss Promotes Immune Evasion

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The Dynamic Interplay Between Ribosomal DNA and Transposable Elements: A Perspective From Genomics and Cytogenetics

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Gag proteins encoded by endogenous retroviruses are required for zebrafish development

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Recent reactivation of a pathogenicity-associated transposable element is associated with major chromosomal rearrangements in a fungal wheat pathogen

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Transposable Element Interactions Shape the Ecology of the Deer Mouse Genome

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Jump-starting life: balancing transposable element co-option and genome integrity in the developing mammalian embryo

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Ten things you should know about transposable elements

Bourque, G., Burns, K. H., Gehring, M. A., Gorbunova, V., Seluanov, A., Hammell, M., Imbeault, M., Izsvák, Z., Levin, H. L., Macfarlan, T. S., et al. (2018) · Open Collections · doi:10.14288/1.0374202