A Field Guide to Eukaryotic Transposable Elements

The zebrafish reference genome sequence and its relationship to the human genome.

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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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Gene Regulation for Higher Cells: A Theory

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The origins of genome complexity

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Alu repeats and human genomic diversity

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

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Regulatory activities of transposable elements: from conflicts to benefits

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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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Origin and evolution of retroelements based upon their reverse transcriptase sequences

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

Feschotte, C., & Gilbert, C. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3199 · Cited by 918

The new tree of eukaryotes

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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 Arabidopsis

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Roles for retrotransposon insertions in human disease

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Transposable Elements, Epigenetics, and Genome Evolution

Fedoroff, N. V. (2012) · Science · doi:10.1126/science.338.6108.758 · Cited by 634

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

Kapitonov, V. V., & Jurka, J. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.151269298 · Cited by 528

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

Kapusta, A., Suh, A., & Feschotte, C. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1616702114 · Cited by 466

High-frequency P element loss in Drosophila is homolog dependent

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Active Transposition in Genomes

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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

Neumann, P., Novák, P., Hoštáková, N., & Macas, J. (2019) · Mobile DNA · doi:10.1186/s13100-018-0144-1 · Cited by 413

SVA Elements: A Hominid-specific Retroposon Family

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

Smit, A. F. A., Tóth, G. J., Riggs, A. D., & Jurka, J. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.0095 · Cited by 384

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

Khan, H., Smit, A. F. A., & Boissinot, S. (2005) · Genome Research · doi:10.1101/gr.4001406 · Cited by 369

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

Jacques, P., Jeyakani, J., & Bourque, G. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003504 · Cited by 360

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

Medstrand, P., van de Lagemaat, L. N., & Mager, D. L. (2002) · Genome Research · doi:10.1101/gr.388902 · Cited by 352

Transposases are the most abundant, most ubiquitous genes in nature

Aziz, R. K., Breitbart, M., & Edwards, R. A. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq140 · Cited by 339

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

Richardson, S. R., Doucet, A. J., Kopera, H. C., Moldovan, J. B., Garcia-Perez, J. L., & Moran, J. V. (2015) · Microbiology Spectrum · doi:10.1128/microbiolspec.mdna3-0061-2014 · Cited by 338

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

Doak, T. G., Doerder, F. P., Jahn, C. L., & Herrick, G. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.3.942 · Cited by 333

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

Thomas, C. A., Tejwani, L., Trujillo, C. A., Negraes, P. D., Herai, R. H., Mesci, P., Macia, A., Crow, Y. J., & Muotri, A. R. (2017) · Cell Stem Cell · doi:10.1016/j.stem.2017.07.009 · Cited by 330

The outs and ins of transposition: from Mu to Kangaroo

Curcio, M. J., & Derbyshire, K. M. (2003) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1241 · Cited by 319

Coevolution between transposable elements and recombination

Kent, T. V., Uzunović, J., & Wright, S. I. (2017) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2016.0458 · Cited by 312

Host–transposon interactions: conflict, cooperation, and cooptionPreprint

Cosby, R. L., Chang, N., & Feschotte, C. (2019) · Genes & Development · doi:10.1101/gad.327312.119 · Cited by 300

A Virophage at the Origin of Large DNA Transposons

Fischer, M., & Suttle, C. A. (2011) · Science · doi:10.1126/science.1199412 · Cited by 297

A triptych of the evolution of plant transposable elements

Tenaillon, M. I., Hollister, J. D., & Gaut, B. S. (2010) · Trends in Plant Science · doi:10.1016/j.tplants.2010.05.003 · Cited by 291

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

Trizzino, M., Park, Y., Beltrame, M. H., Aracena, K. A., Mika, K. M., Çalışkan, M., Perry, G. H., Lynch, V. J., & Brown, C. D. (2017) · Genome Research · doi:10.1101/gr.218149.116 · Cited by 286

Self-synthesizing DNA transposons in eukaryotes

Kapitonov, V. V., & Jurka, J. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0600833103 · Cited by 286

Reconstruction and analysis of human alu genes

Jurka, J., & Milosavljević, A. (1991) · Journal of Molecular Evolution · doi:10.1007/bf02515383 · Cited by 286

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

Pritham, E. J., Sharma, T. P., & Feschotte, C. (2006) · Gene · doi:10.1016/j.gene.2006.08.008 · Cited by 276

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

Yuan, Y., & Wessler, S. R. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1104208108 · Cited by 276

Integration site selection by retroviruses and transposable elements in eukaryotes

Sultana, T., Zamborlini, A., Cristofari, G., & Lesage, P. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.7 · Cited by 275

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

Malik, H. S., & Eickbush, T. H. (2001) · Genome Research · doi:10.1101/gr.185101 · Cited by 248

Massive horizontal transfer of transposable elements in insects

Peccoud, J., Loiseau, V., Cordaux, R., & Gilbert, C. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1621178114 · Cited by 248

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

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Origins and Evolution of Retrotransposons

Eickbush, T. H., & Malik, H. S. (2007) · Wiley eBooks · doi:10.1128/9781555817954.ch49 · Cited by 240

Dramatic amplification of a rice transposable element during recent domestication

Naito, K., Cho, E., Yang, G., Campbell, M. A., Yano, K., Okumoto, Y., Tanisaka, T., & Wessler, S. R. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605421103 · Cited by 239

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

Kriegs, J. O., Churakov, G., Jurka, J., Brosius, J., & Schmitz, J. (2007) · Trends in Genetics · doi:10.1016/j.tig.2007.02.002 · Cited by 234

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

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

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Origin of viruses: primordial replicators recruiting capsids from hosts

Krupovìč, M., Dolja, V. V., & Koonin, E. V. (2019) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0205-6 · Cited by 213

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

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

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Co-option of endogenous viral sequences for host cell function

Frank, J. A., & Feschotte, C. (2017) · Current Opinion in Virology · doi:10.1016/j.coviro.2017.07.021 · Cited by 207

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

Krupovìč, M., & Koonin, E. V. (2014) · Nature Reviews Microbiology · doi:10.1038/nrmicro3389 · Cited by 206

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

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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

Kramerov, D. A., & Vassetzky, N. S. (2011) · Heredity · doi:10.1038/hdy.2011.43 · Cited by 198

Retrotransposition of marked SVA elements by human L1s in cultured cells

Hancks, D. C., Goodier, J. L., Mandal, P. K., Cheung, L. E., & Kazazian, H. H. (2011) · Human Molecular Genetics · doi:10.1093/hmg/ddr245 · Cited by 191

Evolution of group II introns

Zimmerly, S., & Semper, C. (2015) · Mobile DNA · doi:10.1186/s13100-015-0037-5 · Cited by 189

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

Gilbert, C., & Feschotte, C. (2018) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2018.02.007 · Cited by 174

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

Khazina, E., Truffault, V., Büttner, R., Schmidt, S., Coles, M. P., & Weichenrieder, O. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2097 · Cited by 170

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

Pritham, E. J., & Feschotte, C. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0609601104 · Cited by 169

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

Ohshima, K., & Okada, N. (2005) · Cytogenetic and Genome Research · doi:10.1159/000084981 · Cited by 166

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

Fischer, M., & Hackl, T. (2016) · Nature · doi:10.1038/nature20593 · Cited by 164

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

Khazina, E., & Weichenrieder, O. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0809964106 · Cited by 160

Islands of retroelements are major components of Drosophila centromeres

Chang, C.-H., Chavan, A., Palladino, J., Wei, X., Martins, N. M. C., Santinello, B., Chen, C.-C., Erceg, J., Beliveau, B. J., Wu, C.-T., et al. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000241 · Cited by 159

The genomic ecosystem of transposable elements in maize

Stitzer, M. C., Anderson, S. N., Springer, N. M., & Ross‐Ibarra, J. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009768 · Cited by 159

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

Yang, G., Nagel, D. H., Feschotte, C., Hancock, C. N., & Wessler, S. R. (2009) · Science · doi:10.1126/science.1175688 · Cited by 158

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

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

Xie, W., Gai, X., Zhu, Y., Zappulla, D. C., Sternglanz, R., & Voytas, D. F. (2001) · Molecular and Cellular Biology · doi:10.1128/mcb.21.19.6606-6614.2001 · Cited by 156

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

Sultana, T., van Essen, D., Siol, O., Bailly-Bechet, M., Philippe, C., Zine El Aabidine, A., Pioger, L., Nigumann, P., Saccani, S., Andrau, J.-C., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.02.036 · Cited by 154

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

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

Baidouri, M. E., & Panaud, O. (2013) · Genome Biology and Evolution · doi:10.1093/gbe/evt025 · Cited by 151

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

Bourgeois, Y., & Boissinot, S. (2019) · Genes · doi:10.3390/genes10060419 · Cited by 149

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

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Did Genetic Drift Drive Increases in Genome Complexity?

Whitney, K. D., & Garland, T. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001080 · Cited by 142

Evolution and diversity of transposable elements in fish genomes

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Env -less endogenous retroviruses are genomic superspreaders

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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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Retroelements containing introns in diverse invertebrate taxa

Arkhipova, I. R., Pyatkov, K. I., Meselson, M. S., & Evgen’ev, M. B. (2003) · Nature Genetics · doi:10.1038/ng1074 · Cited by 131

Structural and sequence diversity of eukaryotic transposable elements

Kojima, K. K. (2018) · Genes & Genetic Systems · doi:10.1266/ggs.18-00024 · Cited by 131

Genome-wide de novo L1 Retrotransposition Connects Endonuclease Activity with Replication

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DNA Transposition at Work

Hickman, A. B., & Dyda, F. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.6b00003 · Cited by 123

Abortive Gap Repair: Underlying Mechanism for Ds element Formation

Rubin, E., & Levy, A. A. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.11.6294 · Cited by 123

Helitrons , the Eukaryotic Rolling-circle Transposable Elements

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A Helitron transposon reconstructed from bats reveals a novel mechanism of genome shuffling in eukaryotes

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