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Locus-Specific DNA Methylation Profiling of Human LINE-1 Retrotransposons

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Genomic Structural Variants in Nervous System Disorders

Abstract

Long Interspersed Element 1 (LINE-1 or L1) retrotransposons are the only active and autonomous mobile genetic elements present in the human genome. They are responsible for insertional mutagenesis traced to the germline and early embryo, cancer cells and healthy somatic tissues, such as the brain. L1 insertions can therefore impact both the heritable and somatic genome, with the potential to lead to pathogenesis in either context. The mobility of any given L1 copy is highly dependent on its ability to escape epigenetic repression and be transcribed to produce the intermediary RNA necessary for retrotransposition. L1 transcription is typically driven by an internal promoter encoded within the L1 5′ untranslated region, which contains a CpG island that is in turn subject to epigenetic silencing mediated by DNA methylation. In each of us, there are ~350 transcriptional units of the most recent (and potentially mobile) L1s, with many of these only being found in small human populations. In certain cell types, such as neurons, somatic L1 insertions can arise and incorporate new L1 transcriptional units. The technique presented here allows en masse DNA methylation profiling of multiple L1s in a manner allowing locus-specific resolution of individual L1 copies escaping repression in the brain, other healthy tissues, cancer biopsies, and cultured neural cells, among others.

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References

  1. Feusier J, Watkins WS, Thomas J, Farrell A, Witherspoon DJ, Baird L, Ha H, Xing J, Jorde LB (2019) Pedigree-based estimation of human mobile element retrotransposition rates. Genome Res 29(10):1567–1577. https://doi.org/10.1101/gr.247965.118

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Ewing AD, Kazazian HH (2010) High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. Genome Res 20(9):1262–1270. https://doi.org/10.1101/gr.106419.110

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Richardson SR, Gerdes P, Gerhardt DJ, Sanchez-Luque FJ, Bodea GO, Muñoz-Lopez M, Jesuadian JS, Kempen M-JHC, Carreira PE, Jeddeloh JA et al (2017) Heritable L1 retrotransposition in the mouse primordial germline and early embryo. Genome Res 27(8):1395–1405. https://doi.org/10.1101/gr.219022.116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Sanchez-Luque FJ, Kempen M-JHC, Gerdes P, Vargas-Landin DB, Richardson SR, Troskie R-L, Jesuadian JS, Cheetham SW, Carreira PE, Salvador-Palomeque C et al (2019) LINE-1 evasion of epigenetic repression in humans. Mol Cell 75(3):590–604.e12. https://doi.org/10.1016/j.molcel.2019.05.024

    Article  CAS  PubMed  Google Scholar 

  5. Upton KR, Gerhardt DJ, Jesuadian JS, Richardson SR, Sánchez-Luque FJ, Bodea GO, Ewing AD, Salvador-Palomeque C, Van Der Knaap MS, Brennan PM et al (2015) Ubiquitous L1 mosaicism in hippocampal neurons. Cell 161(2):228–239. https://doi.org/10.1016/j.cell.2015.03.026

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Evrony GD, Lee E, Mehta BK, Benjamini Y, Johnson RM, Cai X, Yang L, Haseley P, Lehmann HS, Park PJ et al (2015) Cell lineage analysis in human brain using endogenous retroelements. Neuron 85(1):49–59. https://doi.org/10.1016/j.neuron.2014.12.028

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Scott EC, Gardner EJ, Masood A, Chuang NT, Vertino PM, Devine SE (2016) A hot L1 retrotransposon evades somatic repression and initiates human colorectal cancer. Genome Res 26(6):745–755. https://doi.org/10.1101/gr.201814.115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Tubio JMC, Li Y, Ju YS, Martincorena I, Cooke SL, Tojo M, Gundem G, Pipinikas CP, Zamora J, Raine K et al (2014) Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes. Science 345(6196):1251343. https://doi.org/10.1126/science.1251343

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Shukla R, Upton KR, Muñoz-Lopez M, Gerhardt DJ, Fisher ME, Nguyen T, Brennan PM, Baillie JK, Collino A, Ghisletti S et al (2013) Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell 153(1):101–111. https://doi.org/10.1016/j.cell.2013.02.032

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Nguyen THM, Carreira PE, Sanchez-Luque FJ, Schauer SN, Fagg AC, Richardson SR, Davies CM, Jesuadian JS, Kempen M-JHC, Troskie RL et al (2018) L1 retrotransposon heterogeneity in ovarian tumor cell evolution. Cell Rep 23(13):3730–3740. https://doi.org/10.1016/j.celrep.2018.05.090

    Article  CAS  PubMed  Google Scholar 

  11. Salvador-Palomeque C, Sanchez-Luque FJ, Fortuna PRJ, Ewing AD, Wolvetang EJ, Richardson SR, Faulkner GJ (2019) Dynamic methylation of an L1 transduction family during reprogramming and neurodifferentiation. Mol Cell Biol 39(7):e00499–e00418. https://doi.org/10.1128/mcb.00499-18

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Ewing AD, Smits N, Sanchez-Luque FJ, Faivre J, Brennan PM, Richardson SR, Cheetham SW, Faulkner GJ (2020) Nanopore sequencing enables comprehensive transposable element epigenomic profiling. Mol Cell 80(5):915–928.e5. https://doi.org/10.1016/j.molcel.2020.10.024

    Article  CAS  PubMed  Google Scholar 

  13. Kazazian HH, Moran JV (2017) Mobile DNA in health and disease. N Engl J Med 377(4):361–370. https://doi.org/10.1056/nejmra1510092

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, Fitzhugh W et al (2001) Initial sequencing and analysis of the human genome. Nature 409(6822):860–921. https://doi.org/10.1038/35057062

    Article  CAS  PubMed  Google Scholar 

  15. Boissinot S, Sookdeo A (2016) The evolution of LINE-1 in vertebrates. Genome Biol Evol 8(12):3485–3507. https://doi.org/10.1093/gbe/evw247

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Cordaux R, Batzer MA (2009) The impact of retrotransposons on human genome evolution. Nat Rev Genet 10(10):691–703. https://doi.org/10.1038/nrg2640

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Moran JV, Holmes SE, Naas TP, DeBerardinis RJ, Boeke JD, Kazazian HH (1996) High frequency retrotransposition in cultured mammalian cells. Cell 87(5):917–927. https://doi.org/10.1016/S0092-8674(00)81998-4

    Article  CAS  PubMed  Google Scholar 

  18. Gilbert N, Lutz S, Morrish TA, Moran JV (2005) Multiple fates of L1 retrotransposition intermediates in cultured human cells. Mol Cell Biol 25(17):7780–7795. https://doi.org/10.1128/mcb.25.17.7780-7795.2005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Brouha B, Schustak J, Badge RM, Lutz-Prigge S, Farley AH, Morant JV, Kazazian HH (2003) Hot L1s account for the bulk of retrotransposition in the human population. Proc Natl Acad Sci U S A 100(9):5280–5285. https://doi.org/10.1073/pnas.0831042100

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Jacobs FMJ, Greenberg D, Nguyen N, Haeussler M, Ewing AD, Katzman S, Paten B, Salama SR, Haussler D (2014) An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons. Nature 516(7530):242–245. https://doi.org/10.1038/nature13760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Castro-Diaz N, Ecco G, Coluccio A, Kapopoulou A, Yazdanpanah B, Friedli M, Duc J, Jang SM, Turelli P, Trono D (2014) Evolutionally dynamic L1 regulation in embryonic stem cells. Genes Dev 28(13):1397–1409. https://doi.org/10.1101/gad.241661.114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Hata K, Sakaki Y (1997) Identification of critical CpG sites for repression of L1 transcription by DNA methylation. Gene 189(2):227–234. https://doi.org/10.1016/S0378-1119(96)00856-6

    Article  CAS  PubMed  Google Scholar 

  23. Coufal NG, Garcia-Perez JL, Peng GE, Yeo GW, Mu Y, Lovci MT, Morell M, O’Shea KS, Moran JV, Gage FH (2009) L1 retrotransposition in human neural progenitor cells. Nature 460(7259):1127–1131. https://doi.org/10.1038/nature08248

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Muotri AR, Marchetto MCN, Coufal NG, Oefner R, Yeo G, Nakashima K, Gage FH (2010) L1 retrotransposition in neurons is modulated by MeCP2. Nature 468(7322):443–446. https://doi.org/10.1038/nature09544

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Rowe HM, Jakobsson J, Mesnard D, Rougemont J, Reynard S, Aktas T, Maillard PV, Layard-Liesching H, Verp S, Marquis J et al (2010) KAP1 controls endogenous retroviruses in embryonic stem cells. Nature 463(7278):237–240. https://doi.org/10.1038/nature08674

    Article  CAS  PubMed  Google Scholar 

  26. Klawitter S, Fuchs NV, Upton KR, Muñoz-Lopez M, Shukla R, Wang J, Garcia-Cañadas M, Lopez-Ruiz C, Gerhardt DJ, Sebe A et al (2016) Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells. Nat Commun 7:10286. https://doi.org/10.1038/ncomms10286

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Wissing S, Mũoz-lopez M, Macia A, Yang Z, Montano M, Collins W, Garcia-perez JL, Moran JV, Greene WC (2012) Reprogramming somatic cells into ips cells activates line-1 retroelement mobility. Hum Mol Genet 21(1):208–218. https://doi.org/10.1093/hmg/ddr455

    Article  CAS  PubMed  Google Scholar 

  28. Macia A, Widmann TJ, Heras SR, Ayllon V, Sanchez L, Benkaddour-Boumzaouad M, Muñoz-Lopez M, Rubio A, Amador-Cubero S, Blanco-Jimenez E et al (2017) Engineered LINE-1 retrotransposition in nondividing human neurons. Genome Res 27(3):335–348. https://doi.org/10.1101/gr.206805.116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Schauer SN, Carreira PE, Shukla R, Gerhardt DJ, Gerdes P, Sanchez-Luque FJ, Nicoli P, Kindlova M, Ghisletti S, Dos Santos AD et al (2018) L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis. Genome Res 28(5):639–653. https://doi.org/10.1101/gr.226993.117

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Magoč T, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27(21):2957–2963. https://doi.org/10.1093/bioinformatics/btr507

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

F.J.S-L. acknowledges the support of the Fundación Pública Andaluza “Progreso y Salud” and the Junta de Andalucía EMERGIA Grant (20_00225). M.H.C.K acknowledges the support of the College of Medicine and Veterinary Medicine (University of Edinburgh). G.J.F. acknowledges the support of a CSL Centenary Fellowship, an NHMRC Investigator Grant (GNT1173711), and the Mater Foundation.

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Correspondence to Francisco J. Sanchez-Luque .

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Sanchez-Luque, F.J., Kempen, MJ.H.C., Faulkner, G.J. (2022). Locus-Specific DNA Methylation Profiling of Human LINE-1 Retrotransposons. In: Proukakis, C. (eds) Genomic Structural Variants in Nervous System Disorders. Neuromethods, vol 182. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2357-2_11

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  • DOI: https://doi.org/10.1007/978-1-0716-2357-2_11

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  • Publisher Name: Humana, New York, NY

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