Browse > Article
http://dx.doi.org/10.5483/BMBRep.2022.55.7.088

Ongoing endeavors to detect mobilization of transposable elements  

Lee, Yujeong (Department of Biological Sciences, Kangwon National University)
Ha, Una (Department of Biological Sciences, Kangwon National University)
Moon, Sungjin (Department of Biological Sciences, Kangwon National University)
Publication Information
BMB Reports / v.55, no.7, 2022 , pp. 305-315 More about this Journal
Abstract
Transposable elements (TEs) are DNA sequences capable of mobilization from one location to another in the genome. Since the discovery of 'Dissociation (Dc) locus' by Barbara McClintock in maize (1), mounting evidence in the era of genomics indicates that a significant fraction of most eukaryotic genomes is composed of TE sequences, involving in various aspects of biological processes such as development, physiology, diseases and evolution. Although technical advances in genomics have discovered numerous functional impacts of TE across species, our understanding of TEs is still ongoing process due to challenges resulted from complexity and abundance of TEs in the genome. In this mini-review, we briefly summarize biology of TEs and their impacts on the host genome, emphasizing importance of understanding TE landscape in the genome. Then, we introduce recent endeavors especially in vivo retrotransposition assays and long read sequencing technology for identifying de novo insertions/TE polymorphism, which will broaden our knowledge of extraordinary relationship between genomic cohabitants and their host.
Keywords
In vivo retrotranposition assay; Oxford nanopore technology (ONT); Transposable elements; Transposition;
Citations & Related Records
Times Cited By KSCI : 3  (Citation Analysis)
연도 인용수 순위
1 Ferreri GC, Brown JD, Obergfell C et al (2011) Recent amplification of the kangaroo endogenous retrovirus, KERV, limited to the centromere. J Virol 85, 4761-4771   DOI
2 Flasch DA, Macia A, Sanchez L et al (2019) Genomewide de novo L1 retrotransposition connects endonuclease activity with replication. Cell 177, 837-851 e828   DOI
3 Marlor RL, Parkhurst SM and Corces VG (1986) The Drosophila melanogaster gypsy transposable element encodes putative gene products homologous to retroviral proteins. Mol Cell Biol 6, 1129-1134   DOI
4 van Dijk EL, Jaszczyszyn Y, Naquin D and Thermes C (2018) The third revolution in sequencing technology. Trends Genet 34, 666-681   DOI
5 Kasianowicz JJ, Brandin E, Branton D and Deamer DW (1996) Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci U S A 93, 13770-13773   DOI
6 Jain M, Olsen HE, Paten B and Akeson M (2016) The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol 17, 239   DOI
7 Kannan M, Li J, Fritz SE et al (2017) Dynamic silencing of somatic L1 retrotransposon insertions reflects the developmental and cellular contexts of their genomic integration. Mob DNA 8, 8   DOI
8 Kopera HC, Larson PA, Moldovan JB, Richardson SR, Liu Y and Moran JV (2016) LINE-1 cultured cell retrotransposition assay. Methods Mol Biol 1400, 139-156   DOI
9 Fort-Aznar L, Ugbode C and Sweeney ST (2020) Retrovirus reactivation in CHMP2BIntron5 models of frontotemporal dementia. Hum Mol Genet 29, 2637-2646   DOI
10 Payne A, Holmes N, Rakyan V and Loose M (2019) BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files. Bioinformatics 35, 2193-2198   DOI
11 Jain M, Koren S, Miga KH et al (2018) Nanopore sequencing and assembly of a human genome with ultralong reads. Nat Biotechnol 36, 338-345   DOI
12 Pradhan B, Cajuso T, Katainen R et al (2017) Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing. Sci Rep 7, 14521   DOI
13 Siudeja K, van den Beek M, Riddiford N et al (2021) Unraveling the features of somatic transposition in the Drosophila intestine. EMBO J 40, e106388   DOI
14 Goodwin S, Gurtowski J, Ethe-Sayers S, Deshpande P, Schatz MC and McCombie WR (2015) Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome. Genome Res 25, 1750-1756   DOI
15 Haggerty C, Kretzmer H, Riemenschneider C et al (2021) Dnmt1 has de novo activity targeted to transposable elements. Nat Struct Mol Biol 28, 594-603   DOI
16 Dupuy AJ, Akagi K, Largaespada DA, Copeland NG and Jenkins NA (2005) Mammalian mutagenesis using a highly mobile somatic Sleeping Beauty transposon system. Nature 436, 221-226   DOI
17 Moran JV, Holmes SE, Naas TP, DeBerardinis RJ, Boeke JD and Kazazian HH Jr (1996) High frequency retrotrans-position in cultured mammalian cells. Cell 87, 917-927   DOI
18 Cherf GM, Lieberman KR, Rashid H, Lam CE, Karplus K and Akeson M (2012) Automated forward and reverse ratcheting of DNA in a nanopore at 5-A precision. Nat Biotechnol 30, 344-348   DOI
19 Amarasinghe SL, Ritchie ME and Gouil Q (2021) longread-tools.org: an interactive catalogue of analysis methods for long-read sequencing data. Gigascience 10, giab003   DOI
20 Gong L, Wong CH, Cheng WC et al (2018) Picky comprehensively detects high-resolution structural variants in nanopore long reads. Nat Methods 15, 455-460   DOI
21 David M, Dursi LJ, Yao D, Boutros PC and Simpson JT (2017) Nanocall: an open source basecaller for Oxford Nanopore sequencing data. Bioinformatics 33, 49-55   DOI
22 Gong L, Wong CH, Idol J, Ngan CY and Wei CL (2019) Ultra-long read sequencing for whole genomic DNA analysis. J Vis Exp 145, e58954
23 Branton D and Deamer DW (2018) Nanopore sequencing: an introduction, World Scientific, New Jersey.
24 Muotri AR, Chu VT, Marchetto MC, Deng W, Moran JV and Gage FH (2005) Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. Nature 435, 903-910   DOI
25 Wei W, Morrish TA, Alisch RS and Moran JV (2000) A transient assay reveals that cultured human cells can accommodate multiple LINE-1 retrotransposition events. Anal Biochem 284, 435-438   DOI
26 Moon S, Cassani M, Lin YA, Wang L, Dou K and Zhang ZZ (2018) A robust transposon-endogenizing response from germline stem cells. Dev Cell 47, 660-671 e663   DOI
27 Rebollo R, Farivar S and Mager DL (2012) C-GATE - catalogue of genes affected by transposable elements. Mob DNA 3, 9   DOI
28 Morrish TA, Gilbert N, Myers JS et al (2002) DNA repair mediated by endonuclease-independent LINE-1 retrotransposition. Nat Genet 31, 159-165   DOI
29 Feng Q, Moran JV, Kazazian HH Jr and Boeke JD (1996) Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87, 905-916   DOI
30 An W, Han JS, Wheelan SJ et al (2006) Active retrotransposition by a synthetic L1 element in mice. Proc Natl Acad Sci U S A 103, 18662-18667   DOI
31 Sousa-Victor P, Ayyaz A, Hayashi R et al (2017) Piwi is required to limit exhaustion of aging somatic stem cells. Cell Rep 20, 2527-2537   DOI
32 Tubio JMC, Li Y, Ju YS et al (2014) Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes. Science 345, 1251343   DOI
33 Kofler R, Senti KA, Nolte V, Tobler R and Schlotterer C (2018) Molecular dissection of a natural transposable element invasion. Genome Res 28, 824-835   DOI
34 Boza V, Brejova B and Vinar T (2017) DeepNano: deep recurrent neural networks for base calling in MinION nanopore reads. PLoS One 12, e0178751   DOI
35 Nicholls SM, Quick JC, Tang S and Loman NJ (2019) Ultra-deep, long-read nanopore sequencing of mock microbial community standards. Gigascience 8, giz043   DOI
36 de Souza FS, Franchini LF and Rubinstein M (2013) Exaptation of transposable elements into novel cis-regulatory elements: is the evidence always strong? Mol Biol Evol 30, 1239-1251   DOI
37 De Coster W, De Rijk P, De Roeck A et al (2019) Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome. Genome Res 29, 1178-1187   DOI
38 De Roeck A, De Coster W, Bossaerts L et al (2019) NanoSatellite: accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION. Genome Biol 20, 239   DOI
39 Hill T, Schlotterer C and Betancourt AJ (2016) Hybrid dysgenesis in Drosophila simulans associated with a rapid invasion of the P-element. PLoS Genet 12, e1005920   DOI
40 Richardson SR, Doucet AJ, Kopera HC, Moldovan JB, Garcia-Perez JL and Moran JV (2015) The Influence of LINE-1 and SINE retrotransposons on mammalian genomes. Microbiol Spectr 3, MDNA3-0061-2014
41 Cordaux R and Batzer MA (2009) The impact of retrotransposons on human genome evolution. Nat Rev Genet 10, 691-703   DOI
42 Ostertag EM and Kazazian HH Jr (2001) Biology of mammalian L1 retrotransposons. Annu Rev Genet 35, 501-538   DOI
43 Ewing AD and Kazazian HH Jr (2010) High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. Genome Res 20, 1262-1270   DOI
44 Tarlinton RE, Meers J and Young PR (2006) Retroviral invasion of the koala genome. Nature 442, 79-81   DOI
45 Lander ES, Linton LM, Birren B et al (2001) Initial sequencing and analysis of the human genome. Nature 409, 860-921   DOI
46 Khurana JS, Wang J, Xu J et al (2011) Adaptation to P element transposon invasion in Drosophila melanogaster. Cell 147, 1551-1563   DOI
47 Huang S, Tao X, Yuan S et al (2016) Discovery of an active RAG transposon illuminates the origins of V(D)J recombination. Cell 166, 102-114   DOI
48 Michael TP, Jupe F, Bemm F et al (2018) High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell. Nat Commun 9, 541   DOI
49 Fujimoto A, Wong JH, Yoshii Y et al (2021) Whole-genome sequencing with long reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer. Genome Med 13, 65   DOI
50 Kapitonov VV and Jurka J (2005) RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. PLoS Biol 3, e181   DOI
51 Tyson JR, O'Neil NJ, Jain M, Olsen HE, Hieter P and Snutch TP (2018) MinION-based long-read sequencing and assembly extends the Caenorhabditis elegans reference genome. Genome Res 28, 266-274   DOI
52 Notwell JH, Chung T, Heavner W and Bejerano G (2015) A family of transposable elements co-opted into developmental enhancers in the mouse neocortex. Nat Commun 6, 6644   DOI
53 Huang CR, Burns KH and Boeke JD (2012) Active transposition in genomes. Annu Rev Genet 46, 651-675   DOI
54 Kofler R, Hill T, Nolte V, Betancourt AJ and Schlotterer C (2015) The recent invasion of natural Drosophila simulans populations by the P-element. Proc Natl Acad Sci U S A 112, 6659-6663   DOI
55 Bellen HJ, Levis RW, He Y et al (2011) The Drosophila gene disruption project: progress using transposons with distinctive site specificities. Genetics 188, 731-743   DOI
56 Manrao EA, Derrington IM, Laszlo AH et al (2012) Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nat Biotechnol 30, 349-353   DOI
57 Labrador M, Sha K, Li A and Corces VG (2008) Insulator and Ovo proteins determine the frequency and specificity of insertion of the gypsy retrotransposon in Drosophila melanogaster. Genetics 180, 1367-1378   DOI
58 Mevel-Ninio M, Mariol MC and Gans M (1989) Mobilization of the gypsy and copia retrotransposons in Drosophila melanogaster induces reversion of the ovo dominant female-sterile mutations: molecular analysis of revertant alleles. EMBO J 8, 1549-1558   DOI
59 Spradling AC, Bellen HJ and Hoskins RA (2011) Drosophila P elements preferentially transpose to replication origins. Proc Natl Acad Sci U S A 108, 15948-15953   DOI
60 Eickbush TH and Eickbush DG (2015) Integration, regulation, and long-term stability of R2 retrotransposons. Microbiol Spectr 3, MDNA3-0011-2014
61 Studer A, Zhao Q, Ross-Ibarra J and Doebley J (2011) Identification of a functional transposon insertion in the maize domestication gene tb1. Nat Genet 43, 1160-1163   DOI
62 Kissinger JC and DeBarry J (2011) Genome cartography: charting the apicomplexan genome. Trends Parasitol 27, 345-354   DOI
63 Van't Hof AE, Campagne P, Rigden DJ et al (2016) The industrial melanism mutation in British peppered moths is a transposable element. Nature 534, 102-105   DOI
64 Lisch D (2013) How important are transposons for plant evolution? Nat Rev Genet 14, 49-61   DOI
65 Chang CH, Chavan A, Palladino J et al (2019) Islands of retroelements are major components of Drosophila centromeres. PLoS Biol 17, e3000241   DOI
66 Glockner G and Heidel AJ (2009) Centromere sequence and dynamics in Dictyostelium discoideum. Nucleic Acids Res 37, 1809-1816   DOI
67 Kim HS, Jeon S, Kim C et al (2019) Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information. Gigascience 8, giz125   DOI
68 Dej KJ, Gerasimova T, Corces VG and Boeke JD (1998) A hotspot for the Drosophila gypsy retroelement in the ovo locus. Nucleic Acids Res 26, 4019-4025   DOI
69 Kim A, Terzian C, Santamaria P, Pelisson A, Purd'homme N and Bucheton A (1994) Retroviruses in invertebrates: the gypsy retrotransposon is apparently an infectious retrovirus of Drosophila melanogaster. Proc Natl Acad Sci U S A 91, 1285-1289   DOI
70 Song SU, Gerasimova T, Kurkulos M, Boeke JD and Corces VG (1994) An env-like protein encoded by a Drosophila retroelement: evidence that gypsy is an infectious retrovirus. Genes Dev 8, 2046-2057   DOI
71 Li W, Prazak L, Chatterjee N et al (2013) Activation of transposable elements during aging and neuronal decline in Drosophila. Nat Neurosci 16, 529-531   DOI
72 Wang Y, Zhao Y, Bollas A, Wang Y and Au KF (2021) Nanopore sequencing technology, bioinformatics and applications. Nat Biotechnol 39, 1348-1365   DOI
73 Beck CR, Collier P, Macfarlane C et al (2010) LINE-1 retrotransposition activity in human genomes. Cell 141, 1159-1170   DOI
74 Sun W, Samimi H, Gamez M, Zare H and Frost B (2018) Pathogenic tau-induced piRNA depletion promotes neuronal death through transposable element dysregulation in neurodegenerative tauopathies. Nat Neurosci 21, 1038-1048   DOI
75 Kim J, Hu C, Moufawad El Achkar C et al (2019) Patient-customized oligonucleotide therapy for a rare genetic disease. N Engl J Med 381, 1644-1652   DOI
76 Logsdon GA, Vollger MR and Eichler EE (2020) Long-read human genome sequencing and its applications. Nat Rev Genet 21, 597-614   DOI
77 Song L, Hobaugh MR, Shustak C, Cheley S, Bayley H and Gouaux JE (1996) Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore. Science 274, 1859-1866   DOI
78 Solares EA, Chakraborty M, Miller DE et al (2018) Rapid low-cost assembly of the Drosophila melanogaster reference genome using low-coverage, long-read sequencing. G3 (Bethesda) 8, 3143-3154   DOI
79 Jain M, Olsen HE, Turner DJ et al (2018) Linear assembly of a human centromere on the Y chromosome. Nat Biotechnol 36, 321-323   DOI
80 Sotero-Caio CG, Platt RN 2nd, Suh A and Ray DA (2017) Evolution and diversity of transposable elements in vertebrate genomes. Genome Biol Evol 9, 161-177   DOI
81 Houwing S, Kamminga LM, Berezikov E et al (2007) A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish. Cell 129, 69-82   DOI
82 Chang YH, Keegan RM, Prazak L and Dubnau J (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, e3000278   DOI
83 Jones BC, Wood JG, Chang C et al (2016) A somatic piRNA pathway in the Drosophila fat body ensures metabolic homeostasis and normal lifespan. Nat Commun 7, 13856   DOI
84 Wood JG, Jones BC, Jiang N et al (2016) Chromatin-modifying genetic interventions suppress age-associated transposable element activation and extend life span in Drosophila. Proc Natl Acad Sci U S A 113, 11277-11282   DOI
85 Penke TJ, McKay DJ, Strahl BD, Matera AG and Duronio RJ (2016) Direct interrogation of the role of H3K9 in metazoan heterochromatin function. Genes Dev 30, 1866-1880   DOI
86 Deininger PL and Batzer MA (1999) Alu repeats and human disease. Mol Genet Metab 67, 183-193   DOI
87 Duffy JB (2002) GAL4 system in Drosophila: a fly geneticist's Swiss army knife. Genesis 34, 1-15   DOI
88 Lee E, Iskow R, Yang L et al (2012) Landscape of somatic retrotransposition in human cancers. Science 337, 967-971   DOI
89 Shukla R, Upton KR, Munoz-Lopez M et al (2013) Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell 153, 101-111   DOI
90 Bailey JA, Liu G and Eichler EE (2003) An Alu transposition model for the origin and expansion of human segmental duplications. Am J Hum Genet 73, 823-834   DOI
91 Deniz O, Frost JM and Branco MR (2019) Regulation of transposable elements by DNA modifications. Nat Rev Genet 20, 417-431   DOI
92 Yang P, Wang Y and Macfarlan TS (2017) The role of KRAB-ZFPs in transposable element repression and mammalian evolution. Trends Genet 33, 871-881   DOI
93 Wang L, Dou K, Moon S, Tan FJ and Zhang ZZ (2018) Hijacking oogenesis enables massive propagation of LINE and retroviral transposons. Cell 174, 1082-1094 e1012   DOI
94 Carmell MA, Girard A, van de Kant HJ et al (2007) MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Dev Cell 12, 503-514   DOI
95 Siudeja K, van den Beek M, Riddiford N et al (2021) Unraveling the features of somatic transposition in the Drosophila intestine. EMBO J 40, e106388   DOI
96 Neumann P, Navratilova A, Koblizkova A et al (2011) Plant centromeric retrotransposons: a structural and cytogenetic perspective. Mob DNA 2, 4   DOI
97 Abad JP, De Pablos B, Osoegawa K, De Jong PJ, Martin-Gallardo A and Villasante A (2004) TAHRE, a novel telomeric retrotransposon from Drosophila melanogaster, reveals the origin of Drosophila telomeres. Mol Biol Evol 21, 1620-1624   DOI
98 Villasante A, Abad JP, Planello R, Mendez-Lago M, Celniker SE and de Pablos B (2007) Drosophila telomeric retrotransposons derived from an ancestral element that was recruited to replace telomerase. Genome Res 17, 1909-1918   DOI
99 Agudo M, Losada A, Abad JP, Pimpinelli S, Ripoll P and Villasante A (1999) Centromeres from telomeres? The centromeric region of the Y chromosome of Drosophila melanogaster contains a tandem array of telomeric HeT-A-and TART-related sequences. Nucleic Acids Res 27, 3318-3324   DOI
100 Babaian A and Mager DL (2016) Endogenous retroviral promoter exaptation in human cancer. Mob DNA 7, 24   DOI
101 Montgomery EA, Huang SM, Langley CH and Judd BH (1991) Chromosome rearrangement by ectopic recombination in Drosophila melanogaster: genome structure and evolution. Genetics 129, 1085-1098   DOI
102 Ozata DM, Gainetdinov I, Zoch A, O'Carroll D and Zamore PD (2019) PIWI-interacting RNAs: small RNAs with big functions. Nat Rev Genet 20, 89-108   DOI
103 Bourc'his D and Bestor TH (2004) Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431, 96-99   DOI
104 Garg S, Fungtammasan A, Carroll A et al (2021) Chromosome-scale, haplotype-resolved assembly of human genomes. Nat Biotechnol 39, 309-312   DOI
105 Miller DE, Staber C, Zeitlinger J and Hawley RS (2018) Highly contiguous genome assemblies of 15 Drosophila species generated using Nanopore sequencing. G3 (Bethesda) 8, 3131-3141   DOI
106 Miga KH, Koren S, Rhie A et al (2020) Telomere-to-telomere assembly of a complete human X chromosome. Nature 585, 79-84   DOI
107 Chernyavskaya Y, Zhang X, Liu J and Blackburn J (2022) Long-read sequencing of the zebrafish genome reorganizes genomic architecture. BMC Genomics 23, 116   DOI
108 Kirov I, Merkulov P, Dudnikov M et al (2021) Transposons hidden in Arabidopsis thaliana genome assembly gaps and mobilization of non-autonomous LTR retrotransposons unravelled by nanotei pipeline. Plants (Basel) 10, 2681
109 Mohamed M, Dang NT, Ogyama Y et al (2020) A transposon story: from TE content to TE dynamic invasion of Drosophila genomes using the single-molecule sequencing technology from Oxford Nanopore. Cells 9, 1776   DOI
110 Ellison CE and Cao W (2020) Nanopore sequencing and Hi-C scaffolding provide insight into the evolutionary dynamics of transposable elements and piRNA production in wild strains of Drosophila melanogaster. Nucleic Acids Res 48, 290-303   DOI
111 Frommer M, McDonald LE, Millar DS et al (1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci U S A 89, 1827-1831   DOI
112 Hancks DC and Kazazian HH Jr (2016) Roles for retrotransposon insertions in human disease. Mob DNA 7, 9   DOI
113 Brouha B, Schustak J, Badge RM et al (2003) Hot L1s account for the bulk of retrotransposition in the human population. Proc Natl Acad Sci U S A 100, 5280-5285   DOI
114 Hancks DC, Goodier JL, Mandal PK, Cheung LE and Kazazian HH Jr (2011) Retrotransposition of marked SVA elements by human L1s in cultured cells. Hum Mol Genet 20, 3386-3400   DOI
115 Kazazian HH Jr and Moran JV (2017) Mobile DNA in health and disease. N Engl J Med 377, 361-370   DOI
116 Mager DL and Stoye JP (2015) Mammalian endogenous retroviruses. Microbiol Spectr 3, MDNA3-0009-2014
117 Clark JB and Kidwell MG (1997) A phylogenetic perspective on P transposable element evolution in Drosophila. Proc Natl Acad Sci U S A 94, 11428-11433   DOI
118 Song SU, Kurkulos M, Boeke JD and Corces VG (1997) Infection of the germ line by retroviral particles produced in the follicle cells: a possible mechanism for the mobilization of the gypsy retroelement of Drosophila. Development 124, 2789-2798   DOI
119 Mc CB (1950) The origin and behavior of mutable loci in maize. Proc Natl Acad Sci U S A 36, 344-355   DOI
120 Keegan RM, Talbot LR, Chang YH, Metzger MJ and Dubnau J (2021) Intercellular viral spread and intracellular transposition of Drosophila gypsy. PLoS Genet 17, e1009535   DOI
121 Chang YH and Dubnau J (2019) The gypsy endogenous retrovirus drives non-cell-autonomous propagation in a Drosophila TDP-43 model of neurodegeneration. Curr Biol 29, 3135-3152 e3134   DOI
122 Wensink PC, Tabata S and Pachl C (1979) The clustered and scrambled arrangement of moderately repetitive elements in Drosophila DNA. Cell 18, 1231-1246   DOI
123 Potter S, Truett M, Phillips M and Maher A (1980) Eucaryotic transposable genetic elements with inverted terminal repeats. Cell 20, 639-647   DOI
124 Biemont C, Ronsseray S, Anxolabehere D, Izaabel H and Gautier C (1990) Localization of P elements, copy number regulation, and cytotype determination in Drosophila melanogaster. Genet Res 56, 3-14   DOI
125 Badge RM, Alisch RS and Moran JV (2003) ATLAS: a system to selectively identify human-specific L1 insertions. Am J Hum Genet 72, 823-838   DOI
126 Sheen FM, Sherry ST, Risch GM et al (2000) Reading between the LINEs: human genomic variation induced by LINE-1 retrotransposition. Genome Res 10, 1496-1508   DOI
127 Raiz J, Damert A, Chira S et al (2012) The non-autonomous retrotransposon SVA is trans-mobilized by the human LINE-1 protein machinery. Nucleic Acids Res 40, 1666-1683   DOI
128 Ewing AD, Smits N, Sanchez-Luque FJ et al (2020) Nano-pore sequencing enables comprehensive transposable element epigenomic profiling. Mol Cell 80, 915-928 e915   DOI
129 Jiang F, Zhang J, Liu Q et al (2019) Long-read direct RNA sequencing by 5'-Cap capturing reveals the impact of Piwi on the widespread exonization of transposable elements in locusts. RNA Biol 16, 950-959   DOI
130 Kirov I, Dudnikov M, Merkulov P et al (2020) Nanopore RNA sequencing revealed long non-coding and LTR retrotransposon-related RNAs expressed at early stages of triticale SEED development. Plants (Basel) 9, 1794
131 Boeke JD, Garfinkel DJ, Styles CA and Fink GR (1985) Ty elements transpose through an RNA intermediate. Cell 40, 491-500   DOI
132 Ostertag EM, Prak ET, DeBerardinis RJ, Moran JV and Kazazian HH Jr (2000) Determination of L1 retrotransposition kinetics in cultured cells. Nucleic Acids Res 28, 1418-1423   DOI
133 Levis RW, Ganesan R, Houtchens K, Tolar LA and Sheen FM (1993) Transposons in place of telomeric repeats at a Drosophila telomere. Cell 75, 1083-1093   DOI
134 Pornthanakasem W and Mutirangura A (2004) LINE-1 insertion dimorphisms identification by PCR. Biotechniques 37, 750, 752
135 Kim EY, Fan W and Cho J (2021) Determination of TE insertion positions using transposon display. Methods Mol Biol 2250, 115-121   DOI
136 Traverse KL and Pardue ML (1988) A spontaneously opened ring chromosome of Drosophila melanogaster has acquired He-T DNA sequences at both new telomeres. Proc Natl Acad Sci U S A 85, 8116-8120   DOI
137 Treiber CD and Waddell S (2017) Resolving the prevalence of somatic transposition in Drosophila. Elife 6, e28297   DOI
138 Sundaram V, Cheng Y, Ma Z et al (2014) Widespread contribution of transposable elements to the innovation of gene regulatory networks. Genome Res 24, 1963-1976   DOI
139 Lee SC, Ernst E, Berube B et al (2020) Arabidopsis retrotransposon virus-like particles and their regulation by epigenetically activated small RNA. Genome Res 30, 576-588   DOI
140 Panda K and Slotkin RK (2020) Long-read cDNA sequencing enables a "gene-like" transcript annotation of transposable elements. Plant Cell 32, 2687-2698   DOI
141 Sultana T, van Essen D, Siol O et al (2019) The landscape of L1 retrotransposons in the human genome is shaped by pre-insertion sequence biases and post-insertion selection. Mol Cell 74, 555-570 e557   DOI
142 Xie Y, Rosser JM, Thompson TL, Boeke JD and An W (2011) Characterization of L1 retrotransposition with highthroughput dual-luciferase assays. Nucleic Acids Res 39, e16   DOI
143 Newkirk SJ, Lee S, Grandi FC et al (2017) Intact piRNA pathway prevents L1 mobilization in male meiosis. Proc Natl Acad Sci U S A 114, E5635-E5644
144 Jensen S and Heidmann T (1991) An indicator gene for detection of germline retrotransposition in transgenic Drosophila demonstrates RNA-mediated transposition of the LINE I element. EMBO J 10, 1927-1937   DOI
145 Nagirnaja L, Morup N, Nielsen JE et al (2021) Variant PNLDC1, defective piRNA processing, and azoospermia. N Engl J Med 385, 707-719   DOI
146 Goerner-Potvin P and Bourque G (2018) Computational tools to unmask transposable elements. Nat Rev Genet 19, 688-704   DOI
147 Berrens RV, Yang A, Laumer CE et al (2021) Locus-specific expression of transposable elements in single cells with CELLO-seq. Nat Biotechnol 40, 546-554   DOI
148 Maringer K, Yousuf A, Heesom KJ et al (2017) Proteomics informed by transcriptomics for characterising active transposable elements and genome annotation in Aedes aegypti. BMC Genomics 18, 101   DOI
149 Lynch VJ, Leclerc RD, May G and Wagner GP (2011) Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals. Nat Genet 43, 1154-1159   DOI
150 Rad R, Rad L, Wang W et al (2010) PiggyBac transposon mutagenesis: a tool for cancer gene discovery in mice. Science 330, 1104-1107   DOI