Wells, J. N. & Feschotte, C. A field guide to eukaryotic transposable elements. Ann. Rev. Genet. 54, 539–561 (2020).
Kazazian, H. H. Jr. & Moran, J. V. Mobile DNA in health and disease. New Engl. J. Med. 377, 361–370 (2017).
Fueyo, R., Judd, J., Feschotte, C. & Wysocka, J. Roles of transposable elements in the regulation of mammalian transcription. Nat. Rev. Mol. Cell Biol. 23, 481–497 (2022).
Frank, J. A. et al. Evolution and antiviral activity of a human protein of retroviral origin. Science 378, 422–428 (2022).
Wang, L. et al. Retrotransposon activation during Drosophila metamorphosis conditions adult antiviral responses. Nat. Genet. 54, 1933–1945 (2022).
Telesnitsky, A. & Goff, S. P. in Retroviruses (eds Coffin, J. M. et al.) 121–160 (Cold Spring Harbor Laboratory Press, 1997).
Wang, L., Dou, K., Moon, S., Tan, F. J. & Zhang, Z. Z. Hijacking oogenesis enables massive propagation of LINE and retroviral transposons. Cell 174, 1082–1094 (2018).
Xie, T. & Spradling, A. C. A niche maintaining germ line stem cells in the Drosophila ovary. Science 290, 328–330 (2000).
Kaminker, J. S. et al. The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol. 3, research0084.1 (2002).
Wicker, T. et al. A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet. 8, 973–982 (2007).
Lammel, U. & Klambt, C. Specific expression of the Drosophila midline-jumper retro-transposon in embryonic CNS midline cells. Mech. Dev. 100, 339–342 (2001).
Siomi, M. C., Sato, K., Pezic, D. & Aravin, A. A. PIWI-interacting small RNAs: the vanguard of genome defence. Nat. Rev. Mol. Cell Biol. 12, 246–258 (2011).
Li, C. et al. Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell 137, 509–521 (2009).
Vagin, V. V. et al. A distinct small RNA pathway silences selfish genetic elements in the germline. Science 313, 320–324 (2006).
Wang, Y. et al. eccDNAs are apoptotic products with high innate immunostimulatory activity. Nature 599, 308–314 (2021).
Henriksen, R. A. et al. Circular DNA in the human germline and its association with recombination. Mol. Cell 82, 209–217 (2022).
Boeke, J. D., Garfinkel, D. J., Styles, C. A. & Fink, G. R. Ty elements transpose through an RNA intermediate. Cell 40, 491–500 (1985).
Shoshani, O. et al. Chromothripsis drives the evolution of gene amplification in cancer. Nature 591, 137–141 (2021).
Libuda, D. E. & Winston, F. Amplification of histone genes by circular chromosome formation in Saccharomyces cerevisiae. Nature 443, 1003–1007 (2006).
Moller, H. D. et al. Formation of extrachromosomal circular DNA from long terminal repeats of retrotransposons in Saccharomyces cerevisiae. G3 6, 453–462 (2015).
Brown, P. O. in Retroviruses (eds Coffin, J. M. et al.) 161–204 (Cold Spring Harbor Laboratory Press, 1997).
Brambati, A., Barry, R. M. & Sfeir, A. DNA polymerase theta (Polθ)—an error-prone polymerase necessary for genome stability. Curr. Opin. Genet. Dev. 60, 119–126 (2020).
Mateos-Gomez, P. A. et al. Mammalian polymerase θ promotes alternative NHEJ and suppresses recombination. Nature 518, 254–257 (2015).
Ramsden, D. A., Carvajal-Garcia, J. & Gupta, G. P. Mechanism, cellular functions and cancer roles of polymerase-theta-mediated DNA end joining. Nat. Rev. Mol. Cell Biol. 23, 125–140 (2022).
Lauermann, V. & Boeke, J. D. Plus-strand strong-stop DNA transfer in yeast Ty retrotransposons. EMBO J. 16, 6603–6612 (1997).
Heyman, T., Agoutin, B., Friant, S., Wilhelm, F. X. & Wilhelm, M. L. Plus-strand DNA synthesis of the yeast retrotransposon Ty1 is initiated at two sites, PPT1 next to the 3′ LTR and PPT2 within the pol gene. PPT1 is sufficient for Ty1 transposition. J. Mol. Biol. 253, 291–303 (1995).
Tanese, N., Telesnitsky, A. & Goff, S. P. Abortive reverse transcription by mutants of Moloney murine leukemia virus deficient in the reverse transcriptase-associated RNase H function. J. Virol. 65, 4387–4397 (1991).
Finston, W. I. & Champoux, J. J. RNA-primed initiation of Moloney murine leukemia virus plus strands by reverse transcriptase in vitro. J. Virol. 51, 26–33 (1984).
Rhim, H., Park, J. & Morrow, C. D. Deletions in the tRNA(Lys) primer-binding site of human immunodeficiency virus type 1 identify essential regions for reverse transcription. J. Virol. 65, 4555–4564 (1991).
Le Grice, S. F. “In the beginning”: initiation of minus strand DNA synthesis in retroviruses and LTR-containing retrotransposons. Biochemistry 42, 14349–14355 (2003).
Hu, Z., Leppla, S. H., Li, B. & Elkins, C. A. Antibodies specific for nucleic acids and applications in genomic detection and clinical diagnostics. Expert Rev. Mol. Diagn. 14, 895–916 (2014).
Gagnier, L., Belancio, V. P. & Mager, D. L. Mouse germ line mutations due to retrotransposon insertions. Mobile DNA 10, 15 (2019).
Dewannieux, M., Dupressoir, A., Harper, F., Pierron, G. & Heidmann, T. Identification of autonomous IAP LTR retrotransposons mobile in mammalian cells. Nat. Genet. 36, 534–539 (2004).
Schorn, A. J., Gutbrod, M. J., LeBlanc, C. & Martienssen, R. LTR-retrotransposon control by tRNA-derived small RNAs. Cell 170, 61–71 (2017).
Shank, P. R. et al. Mapping unintegrated avian sarcoma virus DNA: termini of linear DNA bear 300 nucleotides present once or twice in two species of circular DNA. Cell 15, 1383–1395 (1978).
Grow, E. J. et al. Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells. Nature 522, 221–225 (2015).
Wang, J. et al. Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells. Nature 516, 405–409 (2014).
Macfarlan, T. S. et al. Embryonic stem cell potency fluctuates with endogenous retrovirus activity. Nature 487, 57–63 (2012).
Pang, M., McConnell, M. & Fisher, P. A. The Drosophila mus308 gene product, implicated in tolerance of DNA interstrand crosslinks, is a nuclear protein found in both ovaries and embryos. DNA Repair 4, 971–982 (2005).
Vaidya, A. et al. Knock-in reporter mice demonstrate that DNA repair by non-homologous end joining declines with age. PLoS Genet. 10, e1004511 (2014).
Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience 10, giab008 (2021).
Gu, Z., Gu, L., Eils, R., Schlesner, M. & Brors, B. circlize implements and enhances circular visualization in R. Bioinformatics 30, 2811–2812 (2014).
Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparinggenomic features. Bioinformatics 26, 841–842 (2010).
Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011).
More News
Reinvent oil refineries for a net-zero future
This Earth-like exoplanet is the first confirmed to have an atmosphere
Retuning of hippocampal representations during sleep – Nature