Transposable elements and their role in aging

Ade, 2013, Alu elements: an intrinsic source of human genome instability, Curr. Opin. Virol., 3, 639, 10.1016/j.coviro.2013.09.002 Alseth, 2014, Inosine in DNA and RNA, Curr. Opin. Genet. Dev., 26, 116, 10.1016/j.gde.2014.07.008 Ambati, 2020, Repurposing anti-inflammasome NRTIs for improving insulin sensitivity and reducing type 2 diabetes development, Nat. Commun., 11, 4737, 10.1038/s41467-020-18528-z Andrenacci, 2020, The role of transposable elements activity in aging and their possible involvement in laminopathic diseases, Ageing Res. Rev., 57, 10.1016/j.arr.2019.100995 Aravin, 2007, The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race, Science, 318, 761, 10.1126/science.1146484 Aravin, 2008, A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice, Mol. Cell., 31, 785, 10.1016/j.molcel.2008.09.003 Ariumi, 2016, Guardian of the human genome: host defense mechanisms against LINE-1 retrotransposition, Front. Chem., 4, 28, 10.3389/fchem.2016.00028 Babaian, 2016, Endogenous retroviral promoter exaptation in human cancer, Mob. DNA, 7, 24, 10.1186/s13100-016-0080-x Badal, 2013, FB-NOF is a non-autonomous transposable element, expressed in Drosophila melanogaster and present only in the melanogaster group, Gene, 526, 459, 10.1016/j.gene.2013.04.082 Bazak, 2014, A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes, Genome Res, 24, 365, 10.1101/gr.164749.113 Bire, 2013, Transposase concentration controls transposition activity: myth or reality?, Gene, 530, 165, 10.1016/j.gene.2013.08.039 Bogerd, 2006, APOBEC3A and APOBEC3B are potent inhibitors of LTR-retrotransposon function in human cells, Nucl. Acids Res, 34, 89, 10.1093/nar/gkj416 Bourque, 2018, Ten things you should know about transposable elements, Genome Biol., 19, 199, 10.1186/s13059-018-1577-z Bouuaert, 2013, The autoregulation of a eukaryotic DNA transposon, eLife, 2 Bravo, 2020, Transposable elements, circular RNAs and mitochondrial transcription in age-related genomic regulation, Development, 147, 10.1242/dev.175786 Brouwer, 2011, Genetic organization, mobility and predicted functions of genes on integrated, mobile genetic elements in sequenced strains of clostridium difficile, PLOS ONE, 6, 10.1371/journal.pone.0023014 Brown, 1991, Expression of the intracisternal-A particle endogenous retro-virus genes over the lifetime of mouse and Syrian hamster. Arch, Gerontol. Geriatr., 13, 15 Campos-Sanchez, 2014, Genomic landscape of human, bat, and ex vivo DNA transposon integrations, Genome Biol. Evol., 31, 1816, 10.1093/molbev/msu138 Casacuberta, 2013, The impact of transposable elements in environmental adaptation, Mol. Ecol., 22, 1503, 10.1111/mec.12170 Casola, 2007, Convergent domestication of pogo-like transposases into centromere-binding proteins in fission yeast and mammals, Mol. Biol. Evol., 25, 29, 10.1093/molbev/msm221 Chang, 2019, Cellular labeling of endogenous retrovirus replication (CLEVR) reveals de novo insertions of the gypsy retrotransposable element in cell culture and in both neurons and glial cells of aging fruit flies, PLOS Biol., 17, 10.1371/journal.pbio.3000278 Charlesworth, 1983, The population dynamics of transposable elements, Genet. Res., 42, 1, 10.1017/S0016672300021455 Chen, 2016, Age-associated de-repression of retrotransposons in the Drosophila fat body, its potential cause and consequence, Aging Cell, 15, 542, 10.1111/acel.12465 Chen, 2008, Gene regulation by SINEs and inosines: Biological consequences of A-to-I editing of Alu element inverted repeats, Cell Cycle, 7, 3294, 10.4161/cc.7.21.6927 Chen, 2009, Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: Functional role of a nuclear noncoding RNA, Mol. Cell, 35, 467, 10.1016/j.molcel.2009.06.027 Chen, 2008, Alu element-mediated gene silencing, EMBO J., 27, 1694, 10.1038/emboj.2008.94 Chiappinelli, 2015, Inhibiting DNA methylation causes an interferon response in cancer via dsRNA including endogenous retroviruses, Cell, 162, 974, 10.1016/j.cell.2015.07.011 Chung, 2007, Cis-regulatory elements in the Accord retrotransposon result in tissue-specific expression of the Drosophila melanogaster insecticide resistance gene Cyp6g1., Genetics, 175, 1071, 10.1534/genetics.106.066597 Chuong, 2016, Regulatory evolution of innate immunity through co-option of endogenous retroviruses, Science, 351, 1083, 10.1126/science.aad5497 Chuong, 2017, Regulatory activities of transposable elements: from conflicts to benefits, Nat. Rev. Genet., 18, 71, 10.1038/nrg.2016.139 Conrad, 1997, A human endogenous retroviral superantigen as candidate autoimmune gene in type I diabetes, Cell, 90, 303, 10.1016/S0092-8674(00)80338-4 Cornelis, 2015, Retroviral envelope gene captures and syncytin exaptation for placentation in marsupials, Proc. Natl. Acad. Sci. USA, 112, E487, 10.1073/pnas.1417000112 Cornelis, 2017, An endogenous retroviral envelope syncytin and its cognate receptor identified in the viviparous placental Mabuya lizard, Proc. Natl. Acad. Sci. USA, 114, E10991, 10.1073/pnas.1714590114 Crabbe, 2012, Human telomeres are tethered to the nuclear envelope during post-mitotic nuclear assembly, Cell Rep., 2, 1521, 10.1016/j.celrep.2012.11.019 Crow, 2015, Aicardi–Goutières syndrome and the type I interferonopathies, Nat. Rev. Immunol., 15, 429, 10.1038/nri3850 Curinha, 2014, Implications of polyadenylation in health and disease, Nucleus, 5, 508, 10.4161/nucl.36360 De Cecco, 2013, Transposable elements become active and mobile in the genomes of aging mammalian somatic tissues, Aging (Albany NY), 5, 867, 10.18632/aging.100621 De Cecco, 2013, Genomes of replicatively senescent cells undergo global epigenetic changes leading to gene silencing and activation of transposable elements, Aging Cell, 12, 247, 10.1111/acel.12047 De Cecco, 2019, L1 drives IFN in senescent cells and promotes age-associated inflammation, Nature, 566, 73, 10.1038/s41586-018-0784-9 De Koning, 2011, Repetitive elements may comprise over two-thirds of the human genome, PLoS Genet, 7, 10.1371/journal.pgen.1002384 Dennis, 2012, C. elegans germ cells show temperature and age-dependent expression of Cer1, a Gypsy/Ty3-related retrotransposon, PloS Pathog., 8, 10.1371/journal.ppat.1002591 Di Giorgio, 2022, Endogenous retroviruses (ERVs): Does RLR (RIG-I-like receptors)-MAVS pathway directly control senescence and aging as a consequence of ERV de-repression, Front. Immunol., 13, 10.3389/fimmu.2022.917998 Di Ruocco, 2018, Alu RNA accumulation induces epithelial-to-mesenchymal transition by modulating miR-566 and is associated with cancer progression, Oncogene, 37, 627, 10.1038/onc.2017.369 Dias, 2014, Tetris Is a Foldback transposon that provided the building blocks for an emerging satellite DNA of Drosophila virilis, Genome Biol. Evol., 6, 1302, 10.1093/gbe/evu108 Domingues, 2017, Functional insights into ANP32A-dependent influenza A virus polymerase host restriction, Cell Reports, 20, 2538, 10.1016/j.celrep.2017.08.061 Doucet-O'Hare, 2015, LINE-1 expression and retrotransposition in Barrett's esophagus and esophageal carcinoma, Proc. Natl. Acad. Sci. USA, 112, E4894, 10.1073/pnas.1502474112 Dramard, 2007, Natural epigenetic protection against the I-factor, a Drosophila LINE retrotransposon, by remnants of ancestral invasions, PloS One, 2, 10.1371/journal.pone.0000304 Driver, 1992, Transposable elements as a factor in aging of Drosophila melanogaster, Ann. N. Y. Acad. Sci., 673, 83, 10.1111/j.1749-6632.1992.tb27439.x Driver, 1994, Apparent retardation of aging in Drosophila melanogaster by inhibitors of reverse transcriptase, Ann. N. Y. Acad. Sci., 717, 189, 10.1111/j.1749-6632.1994.tb12087.x Dupeyron, 2014, Horizontal transfer of transposons between and within crustaceans and insects, Mob. DNA, 5, 1 Durruthy-Durruthy, 2015, The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming, NatGenet, 48, 44 Dutrieux, 2015, PML/TRIM19–dependent inhibition of retroviral reverse‐transcription by Daxx, PLoS Pathog., 11, 10.1371/journal.ppat.1005280 Ecco, 2017, KRAB zinc finger proteins, Development, 144, 2719, 10.1242/dev.132605 Elbarbary, 2016, Retrotransposons as regulators of gene expression, Science, 351, 10.1126/science.aac7247 Elsner, 2018, Longevity and transposon defense, the case of termite reproductives, PNAS, 115, 5504, 10.1073/pnas.1804046115 2012, An integrated encyclopedia of DNA elements in the human genome, Nature, 489, 57, 10.1038/nature11247 Erwin, 2019, Aging in the Drosophila ovary: contrasting changes in the expression of the piRNA machinery and mitochondria but no global release of transposable elements, BMC Genom., 20, 305, 10.1186/s12864-019-5668-3 Fabian, 2021, Transposable element landscape in Drosophila populations selected for longevity, Genome Biol. Evol., 13, 10.1093/gbe/evab031 Farkash, 2006, Gamma radiation increases endonuclease-dependent L1 retrotransposition in a cultured cell assay, Nucl. Acids Res., 34, 1196, 10.1093/nar/gkj522 Feng, 2017, Deamination-independent restriction of LINE-1 retrotransposition by APOBEC3H, Sci. Rep., 7, 10881, 10.1038/s41598-017-11344-4 Fernandes, 2018, Long non-coding RNAs in neuronal aging, Non-coding RNA, 4, 12, 10.3390/ncrna4020012 Feschotte, 2012, Endogenous viruses: insights into viral evolution and impact on host biology, Nat. Rev. Genet., 13, 283, 10.1038/nrg3199 Feschotte, 2007, DNA transposons and the evolution of eukaryotic genomes, Ann. Rev. Genet., 41, 331, 10.1146/annurev.genet.40.110405.090448 Franchini, L.F., López-Leal, R., Nasif, S., Beati, P., Gelman, D.M., Low, M.J., de Souza, F.J., Rubinstein, M., 2011. Convergent evolution of two mammalian neuronal enhancers by sequential exaptation of unrelated retroposons. Proc. Nat. Acad. Sci. USA. 108, 15270–15275. https://doi.org/10.1073/pnas.1104997108. Frank, 2017, Co-option of endogenous viral sequences for host cell function, Curr. Opin. Virol., 25, 81, 10.1016/j.coviro.2017.07.021 Fukuda, 2021, Cytoplasmic synthesis of endogenous Alu complementary DNA via reverse transcription and implications in age-related macular degeneration, PNAS, 118, 10.1073/pnas.2022751118 Fulcher, 2014, If the cap fits, wear it: an overview of telomeric structures over evolution, Cell. Mol. Life Sci., 71, 847, 10.1007/s00018-013-1469-z Gamdzyk, 2020, cGAS/STING pathway activation contributes to delayed neurodegeneration in neonatal hypoxia-ischemia rat model: Possible involvement of LINE-1., Mol. Neurobiol., 57, 2600, 10.1007/s12035-020-01904-7 Gao, 2012, Characterization and functional annotation of nested transposable elements in eukaryotic genomes, Genomics, 100, 222, 10.1016/j.ygeno.2012.07.004 Girard, 2006, A germline-specific class of small RNAs binds mammalian Piwi proteins, Nature, 442, 199, 10.1038/nature04917 Gkountela, 2013, The ontogeny of cKIT+ human primordial germ cells proves to be a resource for human germline reprogramming, imprint erasure and in vitro differentiation, Nat. Cell. Biol., 15, 113, 10.1038/ncb2638 Gkountela, 2015, DNA demethylation dynamics in the human prenatal germline, Cell, 161, 1425, 10.1016/j.cell.2015.05.012 González, 2009, The adaptive role of transposable elements in the Drosophila genome, Gene, 448, 124, 10.1016/j.gene.2009.06.008 González, 2009, A recent adaptive transposable element insertion near highly conserved developmental loci in Drosophila melanogaster., Mol. Biol. Evol., 26, 1949, 10.1093/molbev/msp107 Goodier, 2016, Restricting retrotransposons: a review, Mob. DNA, 7, 16, 10.1186/s13100-016-0070-z Grundy, 2021, Transposable element regulation and expression in cancer, FEBS J. Guio, 2014, The transposable element Bari-Jheh mediates oxidative stress response in Drosophila, MolEcol, 23, 2020 Guo, 2015, The transcriptome and DNA methylome landscapes of human primordial germ cells, Cell, 161, 1437, 10.1016/j.cell.2015.05.015 Hall, 2012, Detection and interpretation of genomic structural variation in mammals, Methods Mol. Biol. (Clifton N. J. ), 838, 225, 10.1007/978-1-61779-507-7_11 Hammond, 2001, Argonaute2, a link between genetic and biochemical analyses of RNAi, Science, 293, 1146, 10.1126/science.1064023 Han, 2008, L1 recombination-associated deletions generate human genomic variation, Proc. Natl. Acad. Sci. USA, 105, 19366, 10.1073/pnas.0807866105 Haney, 2009, Contrasting patterns of transposable element insertions in Drosophila heat-shock promoters, PLOS One, 4, 10.1371/journal.pone.0008486 Hari, 2019, The innate immune sensor Toll-like receptor 2 controls the senescence-associated secretory phenotype, Sci. Adv., 5, 10.1126/sciadv.aaw0254 Hata, 1997, Identification of critical CpG sites for repression of L1 transcription by DNA methylation, Gene, 189, 227, 10.1016/S0378-1119(96)00856-6 Hedges, 2007, Inviting instability: transposable elements, double strand breaks, and the maintenance of genome integrity, Mutat. Res. Mol. Mech. Mutagen., 616, 46, 10.1016/j.mrfmmm.2006.11.021 Heestand, 2018, Deficiency for Piwi results in transmission of a heritable stress that promotes longevity via DAF-16/Foxo, BioRxiv Hemler, 2014, Tetraspanin proteins promote multiple cancer stages, Nat. Rev. Cancer, 14, 49, 10.1038/nrc3640 Holoch, 2015, RNA-mediated epigenetic regulation of gene expression, Nat. Rev. Genet., 16, 71, 10.1038/nrg3863 Hu, 2014, Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging, Genes Dev., 28, 396, 10.1101/gad.233221.113 Huang, 2012, Active transposition in genomes, Annu. Rev. Genet., 46, 651, 10.1146/annurev-genet-110711-155616 Huang, 2005, The phylogenetic analysis of tetraspanins projects the evolution of cell-cell interactions from unicellular to multicellular organisms, Genomics, 86, 674, 10.1016/j.ygeno.2005.08.004 Huang, 2016, Discovery of an active RAG transposon illuminates the origins of V(D)J recombination, Cell, 166, 102, 10.1016/j.cell.2016.05.032 Hwang, 2019, Oxidative stress causes Alu RNA accumulation via PIWIL4 sequestration into stress granules, BMB Rep., 52, 196, 10.5483/BMBRep.2019.52.3.146 Jachowicz, 2017, LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo, Nat. Genet., 49, 1502, 10.1038/ng.3945 Janic, 2010, Ectopic expression of germline genes drives malignant brain tumor growth in Drosophila, Science, 330, 1824, 10.1126/science.1195481 Jones, 2016, A somatic piRNA pathway in the Drosophila fat body ensures metabolic homeostasis and normal lifespan, Nat. Commun., 7, 13856, 10.1038/ncomms13856 Juliano, 2014, PIWI proteins and PIWI-interacting RNAs function in Hydra somatic stem cells, Proc. Natl. Acad. Sci. USA, 111, 337, 10.1073/pnas.1320965111 Jurka, 2007, Repetitive sequences in complex genomes: structure and evolution, Annu. Rev. Genom. Hum. Genet., 8, 241, 10.1146/annurev.genom.8.080706.092416 Kapitonov, 2008, A universal classification of eukaryotic transposable elements implemented in Repbase, Nat. Rev. Genet., 9, 411, 10.1038/nrg2165-c1 Kapitonov, 2015, Evolution of the RAG1–RAG2 locus: both proteins came from the same transposon, Biol. Direct, 10, 20, 10.1186/s13062-015-0055-8 Kapusta, 2013, Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs, PLoS Genet, 9, 10.1371/journal.pgen.1003470 Kassiotis, 2014, Endogenous retroviruses and the development of cancer, J. Immunol., 192, 1343, 10.4049/jimmunol.1302972 Kassiotis, 2016, Immune responses to endogenous retroelements: taking the bad with the good, Nat. Rev. Immunol., 16, 207, 10.1038/nri.2016.27 Kassiotis, 2017, Making a virtue of necessity: the pleiotropic role of human endogenous retroviruses in cancer, Philos. Trans. R. Soc. Lond. B. Biol. Sci., 372, 10.1098/rstb.2016.0277 Kawamura, 2019, Extracellular vesicles mediate the horizontal transfer of an active LINE-1 retrotransposon, J. Extracell. Vesicles, 8, 10.1080/20013078.2019.1643214 Kedersha, 2002, Stress granules: sites of mRNA triage that regulate mRNA stability and translatability, Biochem. Soc. Trans., 30, 963, 10.1042/bst0300963 Kedersha, 1999, RNA-binding proteins TIA-1 and TIAR link the phosphorylation of eIF-2 alpha to the assembly of mammalian stress granules, J. Cell Biol., 147, 1431, 10.1083/jcb.147.7.1431 Keegan, 2004, Adenosine deaminases acting on RNA (ADARs): RNA-editing enzymes, Genome Biol., 5, 209, 10.1186/gb-2004-5-2-209 Kelley, 2012, Transposable elements reveal a stem cell specific class of long noncoding RNAs, Genome Biol., 13, R107, 10.1186/gb-2012-13-11-r107 Kerur, 2017, cGAS drives noncanonical-inflammasome activation in age-related macular degeneration, Nat. Med., 24, 50, 10.1038/nm.4450 Khatua, 2010, Inhibition of LINE-1 and Alu retrotransposition by exosomes encapsidating APOBEC3G and APOBEC3F, Virology, 400, 68, 10.1016/j.virol.2010.01.021 Kim, 2014, Foldback intercoil DNA and the mechanism of DNA transposition, Genom. Inf., 12, 80, 10.5808/GI.2014.12.3.80 Kines, 2012, Expressing genes do not forget their LINEs: transposable elements and gene expression, Front. Biosci., 17, 1329, 10.2741/3990 Kirkwood, 1977, Evolution of ageing, Nature, 170, 201 Klenov, 2011, Separation of stem cell maintenance and transposon silencing functions of Piwi protein, PNAS, 108, 18760, 10.1073/pnas.1106676108 Krichevsky, 2001, Neuronal RNA granules: a link between RNA localization and stimulation-dependent translation, Neuron, 32, 683, 10.1016/S0896-6273(01)00508-6 Kursel, 2016, Centromeres, Curr. Biol., 26, R487, 10.1016/j.cub.2016.05.031 LaRocca, 2020, Repetitive elements as a transcriptomic marker of aging: Evidence in multiple datasets and models, Aging Cell, 19, 10.1111/acel.13167 Le Manh, 2017, Natural and laboratory mutations in kuzbanian are associated with zinc stress phenotypes in Drosophila melanogaster, Sci. Rep., 7, 42663, 10.1038/srep42663 Leboyer, 2013, Human endogenous retrovirus type W(HERV-W) in schizophrenia: a new avenue of research at the gene–environment interface. World J, Biol. Psychiatry, 14, 80 Lee, 2012, Landscape of somatic retrotransposition in human cancers, Science, 337, 967, 10.1126/science.1222077 Lee, 2007, A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders, Cell, 131, 1235, 10.1016/j.cell.2007.11.037 Lenart, 2018, PIWI-piRNA pathway: Setting the pace of aging by reducing DNA damage, Mech. Ageing Dev., 173, 29, 10.1016/j.mad.2018.03.009 Levanon, 2014, Does RNA editing compensate for Alu invasion of the primate genome?, Bioessays, 37, 175, 10.1002/bies.201400163 Li, 2017, Aicardi–Goutières syndrome protein TREX1 suppresses L1 and maintains genome integrity through exonuclease-independent ORF1p depletion, Nucl. Acids Res, 45, 4619, 10.1093/nar/gkx178 Li, 2013, Activation of transposable elements during aging and neuronal decline in Drosophila, Nat. Neurosci., 16, 529, 10.1038/nn.3368 Li, 2015, Human endogenous retrovirus-K contributes to motor neuron disease, Sci. Transl. Med., 7, 307ra153, 10.1126/scitranslmed.aac8201 Liu, 2023, Resurrection of endogenous retroviruses during aging reinforces senescence, Cell, 186, 1, 10.1016/j.cell.2022.12.017 Liu, 2019, The emerging role of the piRNA/piwi complex in cancer, Mol. Cancer, 18, 123, 10.1186/s12943-019-1052-9 López-Otín, 2013, The hallmarks of aging, Cell, 153, 1194, 10.1016/j.cell.2013.05.039 Lou, 2020, A potential new mechanism for pregnancy loss: considering the role of LINE-1 retrotransposons in early spontaneous miscarriage, Reprod. Biol. Endocrin., 18, 6, 10.1186/s12958-020-0564-x Lu, 2014, The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity, Nat. Struct. Mol. Biol., 21, 423, 10.1038/nsmb.2799 Lynch, 2011, Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals, Nat. Genet., 43, 1154, 10.1038/ng.917 Lynch, 2015, Ancient transposable elements transformed the uterine regulatory landscape and transcriptome during the evolution of mammalian pregnancy, Cell Rep., 10, 551, 10.1016/j.celrep.2014.12.052 Mager, 1999, Endogenous retroviruses provide the primary polyadenylation signal for two new human genes (HHLA2 and HHLA3), Genomics, 59, 255, 10.1006/geno.1999.5877 Magwire, 2011, Successive increases in the resistance of Drosophila to viral infection through a transposon insertion followed by a duplication, PLoS Genet, 7, 10.1371/journal.pgen.1002337 Majumdar, 2015, P transposable elements in Drosophila and other eukaryotic organisms, Microbiol. Spectr., 3 Majumdar, 2013, The human THAP9 gene encodes an active P-element DNA transposase, Science, 339, 446, 10.1126/science.1231789 Makarevitch, 2015, Transposable elements contribute to activation of maize genes in response to abiotic stress, PLoS Genet, 11 Makhnovskii, 2020, Domesticated gag gene of Drosophila LTR retrotransposons is involved in response to oxidative stress, Genes, 11, 396, 10.3390/genes11040396 Martens, 2005, The profile of repeat-associated histone lysine methylation states in the mouse epigenome, EMBO J., 24, 800, 10.1038/sj.emboj.7600545 Martinez, 2017, tRNA-derived small RNAs target transposable element transcripts, Nucleic Acids Res, 45, 5142, 10.1093/nar/gkx103 Mateo, 2014, A transposable element insertion confers xenobiotic resistance in Drosophila, PLoS Genet, 10, 10.1371/journal.pgen.1004560 Maxwell, 2011, Retrotransposition is associated with genome instability during chronological aging, Proc. Natl. Acad. Sci. USA, 108, 20376, 10.1073/pnas.1100271108 McClintock, 1984, The significance of responses of the genome to challenge, Science, 226, 792, 10.1126/science.15739260 McCue, 2012, Transposable element small RNAs as regulators of gene expression, Trends Genet, 28, 616, 10.1016/j.tig.2012.09.001 Menzel, 2014, The diversification and activity of hAT transposons in Musa genomes, Chromosome Res, 22, 559, 10.1007/s10577-014-9445-5 Merenciano, 2016, Multiple independent retroelement insertions in the promoter of a stress response gene have variable molecular and functional effects in Drosophila, PLoS Genet, 12, 10.1371/journal.pgen.1006249 Metcalfe, 2012, Evolution of the Australian lungfish (Neoceratodus forsteri) genome: a major role for CR1 and L2 LINE elements, Mol. Biol. Evol., 29, 3529, 10.1093/molbev/mss159 Meyer, 2021, Giant lungfish genome elucidates the conquest of land by vertebrates, Nature, 590, 284, 10.1038/s41586-021-03198-8 Mita, 2016, How retrotransposons shape genome regulation, Curr. Opin. Genet. Dev., 37, 90, 10.1016/j.gde.2016.01.001 Mita, 2020, BRCA1 and S phase DNA repair pathways restrict LINE-1 retrotransposition in human cells, Nat. Struct. Mol. Biol., 27, 179, 10.1038/s41594-020-0374-z Møller, 2020, Near-random distribution of chromosome-derived circular DNA in the condensed genome of pigeons and the larger, more repeat-rich human genome, Genome Biol. Evol., 12, 3762, 10.1093/gbe/evz281 Morgan, 1999, Epigenetic inheritance at the agouti locus in the mouse, Nat. Genet., 23, 314, 10.1038/15490 Murray, 1990, Hypothesis. Are transposons a cause of ageing?, Mut. Res, 237, 59, 10.1016/0921-8734(90)90011-F Myers, 2005, A fine-scale map of recombination rates and hotspots across the human genome, Science, 310, 321, 10.1126/science.1117196 Naville, 2016, Not so bad after all: retroviruses and long terminal repeat retrotransposons as a source of new genes in vertebrates, Clin. Microbiol. Infect., 22, 312, 10.1016/j.cmi.2016.02.001 Nelson, 2021, The retrotransposon R2 maintains Drosophila ribosomal DNA repeats, BioRxiv, 2021 Nikitin, 1995, Somatic movement of the mariner transposable element and lifespan of Drosophila species, Mut. Res., 338, 43, 10.1016/0921-8734(95)00010-4 2006, meets silencer: Crosstalk between RNA editing and RNA interference, 7, 919 Notwell, 2015, A family of transposable elements co-opted into developmental enhancers in the mouse neocortex, Nat. Commun., 6, 6644, 10.1038/ncomms7644 Nowoshilow, 2018, The axolotl genome and the evolution of key tissue formation regulators, Nature, 554, 50, 10.1038/nature25458 Nozawa, 2000, In vitro expansion of mammalian telomere repeats by DNA polymerase alpha-primase, Nucleic Acids Res, 28, 3117, 10.1093/nar/28.16.3117 Nurk, 2022, The complete sequence of a human genome, Science, 376, 44, 10.1126/science.abj6987 Oberdoerffer, 2008, DNA damage-induced alterations in chromatin contribute to genomic integrity and age-related changes in gene expression, Cell, 135, 907, 10.1016/j.cell.2008.10.025 Orr, 2016, Tightening the connection between transposable element mobilization and aging, Proc. Natl. Acad. Sci. USA, 113, 11069, 10.1073/pnas.1613350113 Ozata, 2019, PIWI- interacting RNAs: small RNAs with big functions, Nat. Rev. Genet., 20, 89, 10.1038/s41576-018-0073-3 Pappalardo, 2021, Transposable elements and stress in vertebrates: An overview, Int. J. Mol. Sci., 22, 1970, 10.3390/ijms22041970 Pardue, 2011, Retrotransposons that maintain chromosome ends, Proc. Natl. Acad. Sci. USA, 108, 20317, 10.1073/pnas.1100278108 Pastuzyn, 2018, The neuronal gene arc encodes a repurposed retrotransposon Gag protein that mediates intercellular RNA transfer, Cell, 172, 275, 10.1016/j.cell.2017.12.024 Patterson, 2015, Preferential retrotransposition in aging yeast mother cells is correlated with increased genome instability, DNA Repair (Amst. ), 34, 18, 10.1016/j.dnarep.2015.07.004 Paz-Yaacov, 2010, Adenosine-to-inosine RNA editing shapes transcriptome diversity in primates, PNAS, 107, 12174, 10.1073/pnas.1006183107 Pehrsson, 2019, The epigenomic landscape of transposable elements across normal human development and anatomy, Nat. Commun., 10, 5640, 10.1038/s41467-019-13555-x Percharde, 2018, A LINE1-nucleolin partnership regulates early development and ESC identity, Cell, 174, 391, 10.1016/j.cell.2018.05.043 Perepelitsa-Belancio, 2003, RNA truncation by premature polyadenylation attenuates human mobile element activity, Nat. Genet., 35, 363, 10.1038/ng1269 Perrat, 2013, Transposition-driven genomic heterogeneity in the Drosophila brain, Science, 340, 91, 10.1126/science.1231965 Perron, 2001, Multiple sclerosis retrovirus particles and recombinant envelope trigger an abnormal immune response in vitro, by inducing polyclonal Vβ16 T-lymphocyte activation, Virology, 287, 321, 10.1006/viro.2001.1045 Perry, 2010, Shadow enhancers foster robustness of Drosophila gastrulation, Curr. Biol., 20, 1562, 10.1016/j.cub.2010.07.043 Piégu, 2015, A survey of transposable element classification systems--a call for a fundamental update to meet the challenge of their diversity and complexity, Mol. Phylogenet. Evol., 86, 90, 10.1016/j.ympev.2015.03.009 Pinto, 2016, Transient mitochondrial DNA double strand breaks in mice cause accelerated aging phenotypes in a ROS-dependent but p53/p21-independent manner, Cell Death Differ., 24, 288, 10.1038/cdd.2016.123 Piriyapongsa, 2007, Origin and evolution of human microRNAs from transposable elements, Genetics, 176, 1323, 10.1534/genetics.107.072553 Platt, 2014, Large numbers of novel miRNAs originate from DNA transposons and are coincident with a large species radiation in bats, Mol. Biol. Evol., 31, 1536, 10.1093/molbev/msu112 Platt, 2018, Mammalian transposable elements and their impacts on genome evolution, Chromosome Res, 26, 25, 10.1007/s10577-017-9570-z Playfoot, 2021, Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain, Genome Res, 31, 1, 10.1101/gr.275133.120 Pradhan, 2022, Transposons: Unexpected players in cancer, Gene, 808, 10.1016/j.gene.2021.145975 Prasanth, 2005, Regulating gene expression through RNA nuclear retention, Cell, 123, 249, 10.1016/j.cell.2005.08.033 Pritham, 2007, Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses, Gene, 390, 3, 10.1016/j.gene.2006.08.008 Qiu, 2021, The decreased exclusion of nuclear eccDNA: From molecular and subcellular levels to human aging and age-related diseases, Ageing Res. Rev., 67, 10.1016/j.arr.2021.101306 Quadrana, 2019, Transposition favors the generation of large effect mutations that may facilitate rapid adaptation, Nat. Commun., 10, 3421, 10.1038/s41467-019-11385-5 Rebollo, 2011, Retrotransposon-induced heterochromatin spreading in the mouse revealed by insertional polymorphisms, PLOS Genet, 7, 10.1371/journal.pgen.1002301 Reddien, 2005, SMEDWI-2 is a PIWI-like protein that regulates planarian stem cells, Science, 310, 1327, 10.1126/science.1116110 Reznik, 2019, Heterogeneity of transposon expression and activation of the repressive network in human fetal germ cells, Development, 146 Ross, 2014, PIWI proteins and PIWI-interacting RNAs in the soma, Nature, 505, 353, 10.1038/nature12987 Roulois, 2015, DNA demethylating agents target colorectal cancer cells by inducing viral mimicry by endogenous transcripts, Cell, 162, 961, 10.1016/j.cell.2015.07.056 Russell, 2018, Transposons and the PIWI pathway: genome defense in gametes and embryos, Reproduction, 156, R111 Savva, 2012, The ADAR protein family, Genome Biol., 13, 252, 10.1186/gb-2012-13-12-252 Scalvenzi, 2014, Insights on genome size evolution from a miniature inverted repeat transposon driving a satellite DNA, Mol. Phylogenet. Evol., 81, 1, 10.1016/j.ympev.2014.08.014 Schneider, 2021, Combination of antiretroviral drugs zidovudine and efavirenz impairs tumor growths in a mouse model of cancer, Viruses, 13, 2396, 10.3390/v13122396 Schorn, 2017, LTR-retrotransposon control by tRNA-derived small RNAs, Cell, 170, 61, 10.1016/j.cell.2017.06.013 Seim, 2013, Genome analysis reveals insights into physiology and longevity of the Brandt's bat Myotis brandtii, Nat. Commun., 4, 2212, 10.1038/ncomms3212 Sekar, 2016, Schizophrenia risk from complex variation of complement component 4, Nature, 530, 177, 10.1038/nature16549 Sienski, 2012, Transcriptional silencing of transposons by Piwi and maelstrom and its impact on chromatin state and gene expression, Cell, 151, 964, 10.1016/j.cell.2012.10.040 Sigurdsson, 2009, HapMap methylation-associated SNPs, markers of germline DNA methylation, positively correlate with regional levels of human meiotic recombination, Genome Res, 19, 581, 10.1101/gr.086181.108 Sigurdsson, 2012, Distribution of a marker of germline methylation differs between major families of transposon-derived repeats in the human genome, Gene, 492, 104, 10.1016/j.gene.2011.10.046 Simon, 2019, LINE1 Derepression in aged wild-type and SIRT6-deficient mice drives inflammation, Cell Metab., 29, 871, 10.1016/j.cmet.2019.02.014 Singer, 2010, LINE-1 retrotransposons: mediators of somatic variation in neuronal genomes?, Cell, 33, 346 Siudeja, 2021, Unraveling the features of somatic transposition in the Drosophila intestine, EMBO J., 40, 10.15252/embj.2020106388 Slotkin, 2007, Transposable elements and the epigenetic regulation of the genome, Nature, 8, 272 Smith, 2019, A chromosome-scale assembly of the axolotl genome, Genome Res, 29, 317, 10.1101/gr.241901.118 Sousa-Victor, 2017, Piwi is required to limit exhaustion of aging somatic stem cells, Cell Rep., 20, 2527, 10.1016/j.celrep.2017.08.059 Staveley, 1995, Protected P-element termini suggest a role for inverted-repeat-binding protein in transposase-induced gap repair in Drosophila melanogaster, Genetics, 139, 1321, 10.1093/genetics/139.3.1321 Stenglein, 2006, APOBEC3B and APOBEC3F inhibit L1 retrotransposition by a DNA deamination-independent mechanism, J. Biol. Chem., 281, 16837, 10.1074/jbc.M602367200 Stetson, 2008, Trex1 prevents cell-intrinsic initiation of autoimmunity, Cell, 134, 587, 10.1016/j.cell.2008.06.032 Storci, 2020, Ribosomal DNA instability: an evolutionary conserved fuel for inflammaging, Ageing Res. Rev., 58, 10.1016/j.arr.2020.101018 Sturm, 2015, The mechanism of ageing: primary role of transposable elements in genome disintegration. Cell, Molec. Life Sci., 72, 1839, 10.1007/s00018-015-1896-0 Sun, 2018, Pathogenic tau-induced piRNA depletion promotes neuronal death through transposable element dysregulation in neurodegenerative tauopathies, Nat. Neurosci., 21, 1038, 10.1038/s41593-018-0194-1 Sun, 2018, Transcription factor profiling reveals molecular choreography and key regulators of human retrotransposon expression, Proc. Natl. Acad. Sci. USA, 115, E5526, 10.1073/pnas.1722565115 Sun, 2014, Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development, BMC Genom., 15, 186, 10.1186/1471-2164-15-186 Suntsova, 2013, Human-specific endogenous retroviral insert serves as an enhancer for the schizophrenia-linked gene PRODH, Proc. Natl. Acad. Sci. USA, 110, 19472, 10.1073/pnas.1318172110 Szabo, 2021, The effects of flavonoids, green tea polyphenols and coffee on DMBA induced LINE-1 DNA hypomethylation, PLoS ONE, 16, 10.1371/journal.pone.0250157 Tam, 2019, Diseases of the nERVous system: retrotransposon activity in neurodegenerative disease, Mob. DNA, 10, 32, 10.1186/s13100-019-0176-1 Tang, 2015, A unique gene regulatory network resets the human germline epigenome for development, Cell, 161, 1453, 10.1016/j.cell.2015.04.053 Tang, 2016, Specification and epigenetic programming of the human germ line, Nat. Rev. Genet., 17, 585, 10.1038/nrg.2016.88 Tarallo, 2012, DICER1 loss and Alu RNA induce age-related macular degeneration via the NLRP3 inflammasome and MyD88, Cell, 149, 847, 10.1016/j.cell.2012.03.036 Tasnim, 2018, p53 is required for female germline stem cell maintenance in P-element hybrid dysgenesis, Dev. Biol., 434, 215, 10.1016/j.ydbio.2017.12.021 Thomas, 2017, Modeling of TREX1-dependent autoimmune disease using human stem cells highlights L1 accumulation as a source of neuroinflammation, Cell. Stem. Cell., 21, 319, 10.1016/j.stem.2017.07.009 Tiwawech, 2014, Alu methylation in serum from patients with nasopharyngeal carcinoma, Asian Pac. J. Cancer Prev., 15, 9797, 10.7314/APJCP.2014.15.22.9797 Trizzino, 2017, Transposable elements are the primary source of novelty in primate gene regulation, Genome Res, 27, 1623, 10.1101/gr.218149.116 Tsurumi, 2012, Global heterochromatin loss: a unifying theory of aging, Epigenetics, 7, 680, 10.4161/epi.20540 Urrutia, 2003, KRAB-containing zinc-finger repressor proteins, Genome Biol., 4, 231, 10.1186/gb-2003-4-10-231 Vagin, 2006, A distinct small RNA pathway silences selfish genetic element in the germline, Science, 313, 320, 10.1126/science.1129333 Van Houte, 2014, Extension of Saccharomyces paradoxus chronological lifespan by retrotransposons in certain media conditions is associated with changes in reactive oxygen species, Genetics, 198, 531, 10.1534/genetics.114.168799 Van Meter, 2014, SIRT6 represses LINE1 retrotransposons by ribosylating KAP1 but this repression fails with stress and age, Nat. Commun., 23, 5011, 10.1038/ncomms6011 van Wyk, 2021, Genome-wide analyses of repeat-induced point mutations in the Ascomycota, Front. Microbiol., 11, 10.3389/fmicb.2020.622368 Villeponteau, 1997, The heterochromatin loss model of aging, Exp. Gerontol., 32, 383, 10.1016/S0531-5565(96)00155-6 Volkman, 2014, The enemy within: endogenous retroelements and autoimmune disease, Nat. Immunol., 15, 415, 10.1038/ni.2872 Wan, 2020, Research advances in how the cGAS-STING pathway controls the cellular inflammatory response, Front. Immunol., 11, 615, 10.3389/fimmu.2020.00615 Wang, 2011, Inhibition of activated pericentromeric SINE/Alu repeat transcription in senescent human adult stem cells reinstates self-renewal, Cell Cycle, 10, 3016, 10.4161/cc.10.17.17543 Wang, 2014, Primatespecific endogenous retrovirus-driven transcription defines naive-like stem cells, Nature, 516, 405, 10.1038/nature13804 Wang, 2015, MIR retrotransposon sequences provide insulators to the human genome, Proc. Natl. Acad. Sci. USA, 112, E4428 White, 2015, Controlled induction of DNA double-strand breaks in the mouse liver induces features of tissue ageing, Nat. Commun., 6, 6790, 10.1038/ncomms7790 Wicker, 2007, A unified classification system for eukaryotic transposable elements, Nat. Rev. Genet., 8, 973, 10.1038/nrg2165 Wood, 2016, Chromatin-modifying genetic interventions suppress age-associated transposable element activation and extend life span in Drosophila, Proc. Natl. Acad. Sci. USA, 113, 11277, 10.1073/pnas.1604621113 Woodard, 2017, Temporal self-regulation of transposition through host-independent transposase rodlet formation, Nucleic Acids Res, 45, 353, 10.1093/nar/gkw1115 Woodruff, 1992, Transposable DNA and life history traits. 1. Transposition of P DNA elements in somatic cells reduces the lifespan of Drosophila melanogaster, Genetica, 86, 143, 10.1007/BF00133717 Woodruff, 1995, P DNA element movement in somatic cells reduces lifespan in Drosophila melanogaster: evidence in support of the somatic mutation theory of aging, Mutat. Res., 338, 35, 10.1016/0921-8734(95)00009-U Wylie, 2016, p53 genes function to restrain mobile elements, Genes Dev., 30, 64, 10.1101/gad.266098.115 Yang, 2022, Transposable element landscapes in aging Drosophila, PLoS Genet, 18, 10.1371/journal.pgen.1010024 Yushkova, 2020, Involvement of DNA repair genes and system of radiation-induced activation of transposons in formation of transgenerational effects, Front. Genet, 11, 10.3389/fgene.2020.596947 Yushkova, 2016, Interaction between gene repair and mobile elements induced activity systems after low-dose irradiation, Int. J. Rad. Biol., 92, 485, 10.1080/09553002.2016.1206221 Zainullin, 2010, The radiationally induced change of level of double-stranded breaks DNA in neyroblastes of larvae and frequency of lethal mutations in sex cells of males Drosophila melanogaster, Rus. J. Radiat. Biol. Radioecol., 50, 523 Zeng, 2018, Prospectively isolated tetraspanin+ neoblasts are adult pluripotent stem cells underlying Planaria regeneration, Cell, 173, 1593, 10.1016/j.cell.2018.05.006 Zhang, 2015, MIWI and piRNA-mediated cleavage of messenger RNAs in mouse testes, Cell Res, 25, 193, 10.1038/cr.2015.4 Zhao, 2013, Modulation of LINE-1 and Alu/SVA retrotransposition by Aicardi–Goutières syndrome-related SAMHD1, Cell Rep., 4, 1108, 10.1016/j.celrep.2013.08.019 Zhu, 2019, Modeling of genome-wide polyadenylation signals in Xenopus tropicalis, Front. Genet., 10, 647, 10.3389/fgene.2019.00647 Zhu, 2012, Activation of germline-specific genes is required for limb regeneration in the Mexican axolotl, Dev. Biol., 370, 42, 10.1016/j.ydbio.2012.07.021 Zuo, 2016, piRNAs and their functions in the brain, Int. J. Hum. Genet, 16, 53, 10.1080/09723757.2016.11886278 Zuo, 2020, Repetitive elements: different subtypes hint at distinct functions, Trends Genet, 36, 385, 10.1016/j.tig.2020.03.008