Wells JN, Feschotte C (2020) A field guide to eukaryotic transposable elements. Annu Rev Genet 54:539–561

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lander ES et al (2001) Initial sequencing and analysis of the human genome. Nature 409(6822):860–921

Article  CAS  PubMed  Google Scholar 

Venter JC et al (2001) The sequence of the human genome. Science 291(5507):1304–1351

Article  CAS  PubMed  Google Scholar 

Ågren JA, Clark AG (2018) Selfish genetic elements. PLoS Genet 14(11):e1007700

Article  PubMed  PubMed Central  Google Scholar 

McClintock B (1956) Controlling elements and the gene. Cold Spring Harb Symp Quant Biol 21:197–216

Article  CAS  PubMed  Google Scholar 

Chuong EB, Elde NC, Feschotte C (2017) Regulatory activities of transposable elements: from conflicts to benefits. Nat Rev Genet 18(2):71–86

Article  CAS  PubMed  Google Scholar 

Gemayel R et al (2010) Variable tandem repeats accelerate evolution of coding and regulatory sequences. Annu Rev Genet 44:445–477

Article  CAS  PubMed  Google Scholar 

Hannan AJ (2018) Tandem repeats mediating genetic plasticity in health and disease. Nat Rev Genet 19(5):286–298

Article  CAS  PubMed  Google Scholar 

Garcia-Montojo M et al (2018) Human endogenous retrovirus-K (HML-2): a comprehensive review. Crit Rev Microbiol 44(6):715–738

Article  PubMed  PubMed Central  Google Scholar 

Johnson WE (2019) Origins and evolutionary consequences of ancient endogenous retroviruses. Nat Rev Microbiol 17(6):355–370

Article  CAS  PubMed  Google Scholar 

Stocking C, Kozak CA (2008) Murine endogenous retroviruses. Cell Mol Life Sci 65(21):3383–3398

Article  CAS  PubMed  PubMed Central  Google Scholar 

Beck CR et al (2011) LINE-1 elements in structural variation and disease. Annu Rev Genomics Hum Genet 12:187–215

Article  CAS  PubMed  PubMed Central  Google Scholar 

Brouha B et al (2003) Hot L1s account for the bulk of retrotransposition in the human population. Proc Natl Acad Sci U S A 100(9):5280–5285

Article  CAS  PubMed  PubMed Central  Google Scholar 

Beck CR et al (2010) LINE-1 retrotransposition activity in human genomes. Cell 141(7):1159–1170

Article  CAS  PubMed  PubMed Central  Google Scholar 

Feusier J et al (2019) Pedigree-based estimation of human mobile element retrotransposition rates. Genome Res 29(10):1567–1577

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lavie L et al (2004) The human L1 promoter: variable transcription initiation sites and a major impact of upstream flanking sequence on promoter activity. Genome Res 14(11):2253–2260

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hermant C, Torres-Padilla ME (2021) TFs for TEs: the transcription factor repertoire of mammalian transposable elements. Genes Dev 35(1–2):22–39

Article  CAS  PubMed  PubMed Central  Google Scholar 

Athanikar JN, Badge RM, Moran JV (2004) A YY1-binding site is required for accurate human LINE-1 transcription initiation. Nucleic Acids Res 32(13):3846–3855

Article  CAS  PubMed  PubMed Central  Google Scholar 

Han JS, Szak ST, Boeke JD (2004) Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature 429(6989):268–274

Article  CAS  PubMed  Google Scholar 

Perepelitsa-Belancio V, Deininger P (2003) RNA truncation by premature polyadenylation attenuates human mobile element activity. Nat Genet 35(4):363–366

Article  CAS  PubMed  Google Scholar 

Ilık İA et al (2024) Autonomous transposons tune their sequences to ensure somatic suppression. Nature 626:1116

Article  PubMed  PubMed Central  Google Scholar 

Susan Lindtner BKF, Jørgen K (2002) An element in the 3’ untranslated region of human LINE-1 retrotransposon mRNA binds NXF1(TAP) and can function as a nuclear export element. RNA 8(3):345–356

Article  PubMed  PubMed Central  Google Scholar 

Martin SL (2010) Nucleic acid chaperone properties of ORF1p from the non-LTR retrotransposon, LINE-1. RNA Biol 7(6):706–711

Article  CAS  PubMed  PubMed Central  Google Scholar 

Feng Q et al (1996) Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87(5):905–916

Article  CAS  PubMed  Google Scholar 

Mathias SL et al (1991) Reverse transcriptase encoded by a human transposable element. Science 254(5039):1808–1810

Article  CAS  PubMed  Google Scholar 

Ardeljan D et al (2020) LINE-1 ORF2p expression is nearly imperceptible in human cancers. Mob DNA 11:1

Article  CAS  PubMed  Google Scholar 

Wei W et al (2001) Human L1 retrotransposition: cis preference versus trans complementation. Mol Cell Biol 21(4):1429–1439

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kulpa DA, Moran JV (2006) Cis-preferential LINE-1 reverse transcriptase activity in ribonucleoprotein particles. Nat Struct Mol Biol 13(7):655–660

Article  CAS  PubMed  Google Scholar 

Deininger P (2011) Alu elements: know the SINEs. Genome Biol 12(12):236

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hancks DC, Kazazian HH Jr (2010) SVA retrotransposons: evolution and genetic instability. Semin Cancer Biol 20(4):234–245

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chu C et al (2023) The landscape of human SVA retrotransposons. Nucleic Acids Res 51:11453

Article  CAS  PubMed  PubMed Central  Google Scholar 

Britten RJ, Davidson EH (1969) Gene regulation for higher cells: a theory. Science 165(3891):349–357

Article  CAS  PubMed  Google Scholar 

Lynch VJ et al (2015) Ancient transposable elements transformed the uterine regulatory landscape and transcriptome during the evolution of mammalian pregnancy. Cell Rep 10(4):551–561

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chuong EB, Elde NC, Feschotte C (2016) Regulatory evolution of innate immunity through co-option of endogenous retroviruses. Science 351(6277):1083–1087

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kunarso G et al (2010) Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat Genet 42(7):631–634

Article  CAS  PubMed  Google Scholar 

Cao Y et al (2019) Widespread roles of enhancer-like transposable elements in cell identity and long-range genomic interactions. Genome Res 29(1):40–52

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fuentes DR, Swigut T, Wysocka J (2018) Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation. Elife 7:e35989

Article  PubMed  PubMed Central