McClintock, B. The origin and behavior of mutable loci in maize. Proc. Natl Acad. Sci. USA 36, 344–355 (1950).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Britten, R. J. & Davidson, E. H. Gene regulation for higher cells: a theory. Science 165, 349–357 (1969).

CAS  PubMed  Article  Google Scholar 

Nurk, S. et al. The complete sequence of a human genome. Science 376, 44–53 (2022).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).

CAS  PubMed  Article  Google Scholar 

Craig Venter, J. et al. The sequence of the human genome. Science 291, 1304–1351 (2001).

Article  Google Scholar 

Waterston, R. H. et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562 (2002).

CAS  PubMed  Article  Google Scholar 

Wicker, T. et al. A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet. 8, 973–982 (2007).

CAS  PubMed  Article  Google Scholar 

Jangam, D., Feschotte, C. & Betrán, E. Transposable element domestication as an adaptation to evolutionary conflicts. Trends Genet. 33, 817–831 (2017).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Feschotte, C. & Pritham, E. J. DNA transposons and the evolution of eukaryotic genomes. Annu Rev. Genet. 41, 331–368 (2007).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Levin, H. L. & Moran, J. V. Dynamic interactions between transposable elements and their hosts. Nat. Rev. Genet. 12, 615–627 (2011).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Doolittle, W. F. & Sapienza, C. Selfish genes, the phenotype paradigm and genome evolution. Nature 284, 601–603 (1980).

CAS  PubMed  Article  Google Scholar 

Capy, P. Taming, domestication and exaptation: trajectories of transposable elements in genomes. Cells 10, 3590 (2021).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Polak, P. & Domany, E. Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes. BMC Genomics 7, 133–148 (2006).

PubMed  PubMed Central  Article  CAS  Google Scholar 

Gifford, W. D., Pfaff, S. L. & Macfarlan, T. S. Transposable elements as genetic regulatory substrates in early development. Trends Cell Biol. 23, 218–226 (2013).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Garcia-Perez, J. R., Widmann, T. J. & Adams, I. R. The impact of transposable elements on mammalian development. Development 143, 4101–4114 (2016).

CAS  PubMed  Article  Google Scholar 

van de Lagemaat, L. N., Landry, J.-R., Mager, D. L. & Medstrand, P. Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions. Trends Genet. 19, 530–536 (2003).

PubMed  Article  CAS  Google Scholar 

Simonti, C. N., Pavličev, M. & Capra, J. A. Transposable element exaptation into regulatory regions is rare, influenced by evolutionary age, and subject to pleiotropic constraints. Mol. Biol. Evol. 34, 2856–2869 (2017).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Miyawaki, S. et al. The mouse Sry locus harbors a cryptic exon that is essential for male sex determination. Science 370, 121–124 (2020).

CAS  PubMed  Article  Google Scholar 

Flemr, M. et al. A retrotransposon-driven dicer isoform directs endogenous small interfering RNA production in mouse oocytes. Cell 155, 807–816 (2013).

CAS  PubMed  Article  Google Scholar 

Sakashita, A. et al. Endogenous retroviruses drive species-specific germline transcriptomes in mammals. Nat. Struct. Mol. Biol. 27, 967–977 (2020).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Modzelewski, A. J. et al. A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development. Cell 184, 5541–5558.e22 (2021).

CAS  PubMed  Article  Google Scholar 

Senft, A. D. & Macfarlan, T. S. Transposable elements shape the evolution of mammalian development. Nat. Rev. Genet. 22, 691–711 (2021).

CAS  PubMed  Article  Google Scholar 

Chuong, E. B., Elde, N. C. & Feschotte, C. Regulatory activities of transposable elements: from conflicts to benefits. Nat. Rev. Genet. 18, 71–86 (2017).

CAS  PubMed  Article  Google Scholar 

Ito, J. et al. Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses. PLoS Genet. 13, e1006883 (2017).

PubMed  PubMed Central  Article  CAS  Google Scholar 

Notwell, J. H., Chung, T., Heavner, W. & Bejerano, G. A family of transposable elements co-opted into developmental enhancers in the mouse neocortex. Nat. Commun. 6, 6644 (2015).

CAS  PubMed  Article  Google Scholar 

Chuong, E. B., Elde, N. C. & Feschotte, C. Regulatory evolution of innate immunity through co-option of endogenous retroviruses. Science 351, 1083–1087 (2016).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Ye, M. et al. Specific subfamilies of transposable elements contribute to different domains of T lymphocyte enhancers. Proc. Natl Acad. Sci. USA 117, 7905–7916 (2020).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Peaston, A. E. et al. Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev. Cell 7, 597–606 (2004).

CAS  PubMed  Article  Google Scholar 

Macfarlan, T. S. et al. Embryonic stem cell potency fluctuates with endogenous retrovirus activity. Nature 487, 57–63 (2012).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Franke, V. et al. Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes. Genome Res. 27, 1384–1394 (2017).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Hasuwa, H. et al. Production of functional oocytes requires maternally expressed PIWI genes and piRNAs in golden hamsters. Nat. Cell Biol. 23, 1002–1012 (2021).

CAS  PubMed  Article  Google Scholar 

Gerlo, S., Davis, J. R. E., Mager, D. L. & Kooijman, R. Prolactin in man: a tale of two promoters. BioEssays 28, 1051–1055 (2006).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Emera, D. et al. Convergent evolution of endometrial prolactin expression in primates, mice, and elephants through the independent recruitment of transposable elements. Mol. Biol. Evol. 29, 239–247 (2012).

CAS  PubMed  Article  Google Scholar 

Davis, M. P. et al. Transposon-driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution. EMBO Rep. 18, 1231–1247 (2017).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Beyer, U., Moll-Rocek, J., Moll, U. M. & Dobbelstein, M. Endogenous retrovirus drives hitherto unknown proapoptotic p63 isoforms in the male germ line of humans and great apes. Proc. Natl Acad. Sci. USA 108, 3624–3629 (2011).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Pi, W. et al. The LTR enhancer of ERV-9 human endogenous retrovirus is active in oocytes and progenitor cells in transgenic zebrafish and humans. Proc. Natl Acad. Sci. USA 101, 805–810 (2004).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Hu, T. et al. Long non-coding RNAs transcribed by ERV-9 LTR retrotransposon act in cis to modulate long-range LTR enhancer function. Nucleic Acids Res. 45, 4479–4492 (2017).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Feschotte, C. Transposable elements and the evolution of regulatory networks. Nat. Rev. Genet. 9, 397–405 (2008).

CAS