Skip to main content

Retrotransposons and the Mammalian Germline

  • Chapter
  • First Online:
Human Retrotransposons in Health and Disease

Abstract

Retrotransposons are an abundant class of mobile genetic elements in mammalian genomes that contribute to genetic instability and variation in the population by integrating at new sites in the genome. Retrotransposons need to be active in the germline so that new retrotransposon integrations can accumulate in the genome during evolution and therefore retrotransposons contain sequences to drive their expression in cells in the germline. While mammals appear to have evolved mechanisms in the germline to limit retrotransposon activity and the resulting mutational load, retrotransposons also appear to be contributing to the regulation of gene expression and driving evolution of transcriptional networks in germline cells. This review will discuss the interplay between retrotransposons and their host cells in the mammalian germline, the genome defence systems that germ cells and pluripotent cells use to limit the mutagenic activity of retrotransposons, and the impact that retrotransposons are having on the biology of mammalian germ cells and pluripotent cells.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  • Adams IR, McLaren A (2002) Sexually dimorphic development of mouse primordial germ cells: switching from oogenesis to spermatogenesis. Development 129:1155–1164

    CAS  PubMed  Google Scholar 

  • Ahl V, Keller H, Schmidt S, Weichenrieder O (2015) Retrotransposition and crystal structure of an Alu RNP in the ribosome-stalling conformation. Mol Cell 60:715–727. doi:10.1016/j.molcel.2015.10.003

    Article  CAS  PubMed  Google Scholar 

  • Ancelin K, Lange UC, Hajkova P, Schneider R, Bannister AJ, Kouzarides T, Surani MA (2006) Blimp1 associates with Prmt5 and directs histone arginine methylation in mouse germ cells. Nat Cell Biol 8:623–630. doi:10.1038/ncb1413

    Article  CAS  PubMed  Google Scholar 

  • Aravin AA, Sachidanandam R, Bourc’his D, Schaefer C, Pezic D, Toth KF, Bestor T, Hannon GJ (2008) A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol Cell 31:785–799. doi:10.1016/j.molcel.2008.09.003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Aravin AA, Sachidanandam R, Girard A, Fejes-Toth K, Hannon GJ (2007) Developmentally regulated piRNA clusters implicate MILI in transposon control. Science 316:744–747. doi:10.1126/science.1142612

    Article  CAS  PubMed  Google Scholar 

  • Aravin A, Gaidatzis D, Pfeffer S, Lagos-Quintana M, Landgraf P, Iovino N, Morris P, Brownstein MJ, Kuramochi-Miyagawa S, Nakano T, Chien M, Russo JJ, Ju J, Sheridan R, Sander C, Zavolan M, Tuschl T (2006) A novel class of small RNAs bind to MILI protein in mouse testes. Nature 442:203–207. doi:10.1038/nature04916

    CAS  PubMed  Google Scholar 

  • Avilion AA, Nicolis SK, Pevny LH, Perez L, Vivian N, Lovell-Badge R (2003) Multipotent cell lineages in early mouse development depend on SOX2 function. Genes Dev 17:126–140. doi:10.1101/gad.224503

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Baillie JK, Barnett MW, Upton KR, Gerhardt DJ, Richmond TA, De Sapio F, Brennan P, Rizzu P, Smith S, Fell M, Talbot RT, Gustincich S, Freeman TC, Mattick JS, Hume DA, Heutink P, Carninci P, Jeddeloh JA, Faulkner GJ (2011) Somatic retrotransposition alters the genetic landscape of the human brain. Nature 479:534–537. doi:10.1038/nature10531

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bannert N, Kurth R (2006) The evolutionary dynamics of human endogenous retroviral families. Annu Rev Genomics Hum Genet 7:149–173. doi:10.1146/annurev.genom.7.080505.115700

    Article  CAS  PubMed  Google Scholar 

  • Beck CR, Garcia-Perez JL, Badge RM, Moran JV (2011) LINE-1 elements in structural variation and disease. Annu Rev Genomics Hum Genet 12:187–215. doi:10.1146/annurev-genom-082509-141802

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Belfort M, Curcio MJ, Lue NF (2011) Telomerase and retrotransposons: reverse transcriptases that shaped genomes. Proc Natl Acad Sci U S A 108:20304–20310. doi:10.1073/pnas.1100269109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bennett EA, Keller H, Mills RE, Schmidt S, Moran JV, Weichenrieder O, Devine SE (2008) Active Alu retrotransposons in the human genome. Genome Res 18:1875–1883. doi:10.1101/gr.081737.108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Borgel J, Guibert S, Li Y, Chiba H, Schübeler D, Sasaki H, Forné T, Weber M (2010) Targets and dynamics of promoter DNA methylation during early mouse development. Nat Genet 42:1093–1100. doi:10.1038/ng.708

    Article  CAS  PubMed  Google Scholar 

  • Bourc’his D, Bestor TH (2004) Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431:96–99. doi:10.1038/nature02886

    Article  PubMed  CAS  Google Scholar 

  • Bourque G, Leong B, Vega VB, Chen X, Lee YL, Srinivasan KG, Chew J-L, Ruan Y, Wei C-L, Ng HH, Liu ET (2008) Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res 18:1752–1762. doi:10.1101/gr.080663.108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, Zucker JP, Guenther MG, Kumar RM, Murray HL, Jenner RG, Gifford DK, Melton DA, Jaenisch R, Young RA (2005) Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122:947–956. doi:10.1016/j.cell.2005.08.020

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Branciforte D, Martin SL (1994) Developmental and cell type specificity of LINE-1 expression in mouse testis: implications for transposition. Mol Cell Biol 14:2584–2592

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brûlet P, Condamine H, Jacob F (1985) Spatial distribution of transcripts of the long repeated ETn sequence during early mouse embryogenesis. Proc Natl Acad Sci U S A 82:2054–2058

    Article  PubMed  PubMed Central  Google Scholar 

  • Bulut-Karslioglu A, De La Rosa-Velázquez IA, Ramirez F, Barenboim M, Onishi-Seebacher M, Arand J, Galán C, Winter GE, Engist B, Gerle B, O’Sullivan RJ, Martens JHA, Walter J, Manke T, Lachner M, Jenuwein T (2014) Suv39h-dependent H3K9me3 marks intact retrotransposons and silences LINE elements in mouse embryonic stem cells. Mol Cell 55:277–290. doi:10.1016/j.molcel.2014.05.029

    Article  CAS  PubMed  Google Scholar 

  • Calarco JP, Borges F, Donoghue MTA, Van Ex F, Jullien PE, Lopes T, Gardner R, Berger F, Feijó JA, Becker JD, Martienssen RA (2012) Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell 151:194–205. doi:10.1016/j.cell.2012.09.001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Carmell MA, Girard A, van de Kant HJG, Bourc’his D, Bestor TH, de Rooij DG, Hannon GJ (2007) MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Dev Cell 12:503–514. doi:10.1016/j.devcel.2007.03.001

    Article  CAS  PubMed  Google Scholar 

  • 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 28:1397–1409. doi:10.1101/gad.241661.114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chinwalla AT, Cook LL, Delehaunty KD, Fewell GA, Fulton LA, Fulton RS, Graves TA, Hillier LW, Mardis ER, McPherson JD, Miner TL, Nash WE, Nelson JO, Nhan MN, Pepin KH, Pohl CS, Ponce TC, Schultz B, Thompson J, Trevaskis E, Waterston RH, Wendl MC, Wilson RK, Yang S-P, An P, Berry E, Birren B, Bloom T, Brown DG, Butler J, Daly M, David R, Deri J, Dodge S, Foley K, Gage D, Gnerre S, Holzer T, Jaffe DB, Kamal M, Karlsson EK, Kells C, Kirby A, Kulbokas EJ, Lander ES, Landers T, Leger JP, Levine R, Lindblad-Toh K, Mauceli E, Mayer JH, McCarthy M, Meldrim J, Mesirov JP, Nicol R, Nusbaum C, Seaman S, Sharpe T, Sheridan A, Singer JB, Santos R, Spencer B, Stange-Thomann N, Vinson JP, Wade CM, Wierzbowski J, Wyman D, Zody MC, Birney E, Goldman N, Kasprzyk A, Mongin E, Rust AG, Slater G, Stabenau A, Ureta-Vidal A, Whelan S, Ainscough R, Attwood J, Bailey J, Barlow K, Beck S, Burton J, Clamp M, Clee C, Coulson A, Cuff J, Curwen V, Cutts T, Davies J, Eyras E, Grafham D, Gregory S, Hubbard T, Hunt A, Jones M, Joy A, Leonard S, Lloyd C, Matthews L, McLaren S, McLay K, Meredith B, Mullikin JC, Ning Z, Oliver K, Overton-Larty E, Plumb R, Potter S, Quail M, Rogers J, Scott C, Searle S, Shownkeen R, Sims S, Wall M, West AP, Willey D, Williams S, Abril JF, Guigó R, Parra G, Agarwal P, Agarwala R, Church DM, Hlavina W, Maglott DR, Sapojnikov V, Alexandersson M, Pachter L, Antonarakis SE, Dermitzakis ET, Reymond A, Ucla C, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Hsu F, Karolchik D, Kent WJ, Roskin KM, Schwartz MS, Sugnet C, Weber RJ, Bork P, Letunic I, Suyama M, Torrents D, Zdobnov EM, Botcherby M, Brown SD, Campbell RD, Jackson I, Bray N, Couronne O, Dubchak I, Poliakov A, Rubin EM, Brent MR, Flicek P, Keibler E, Korf I, Batalov S, Bult C, Frankel WN, Carninci P, Hayashizaki Y, Kawai J, Okazaki Y, Cawley S, Kulp D, Wheeler R, Chiaromonte F, Collins FS, Felsenfeld A, Guyer M, Peterson J, Wetterstrand K, Copley RR, Mott R, Dewey C, Dickens NJ, Emes RD, Goodstadt L, Ponting CP, Winter E, Dunn DM, von Niederhausern AC, Weiss RB, Eddy SR, Johnson LS, Jones TA, Elnitski L, Kolbe DL, Eswara P, Miller W, O’Connor MJ, Schwartz S, Gibbs RA, Muzny DM, Glusman G, Smit A, Green ED, Hardison RC, Yang S, Haussler D, Hua A, Roe BA, Kucherlapati RS, Montgomery KT, Li J, Li M, Lucas S, Ma B, McCombie WR, Morgan M, Pevzner P, Tesler G, Schultz J, Smith DR, Tromp J, Worley KC, Green ED (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420:520–562. doi:10.1038/nature01262

    Article  PubMed  CAS  Google Scholar 

  • Chuong EB, Rumi MAK, Soares MJ, Baker JC (2013) Endogenous retroviruses function as species-specific enhancer elements in the placenta. Nat Genet 45:325–329. doi:10.1038/ng.2553

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cost GJ, Feng Q, Jacquier A, Boeke JD (2002) Human L1 element target-primed reverse transcription in vitro. EMBO J 21:5899–5910

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 460:1127–1131. doi:10.1038/nature08248

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Crichton JH, Dunican DS, Maclennan M, Meehan RR, Adams IR (2014) Defending the genome from the enemy within: mechanisms of retrotransposon suppression in the mouse germline. Cell Mol Life Sci 71:1581–1605. doi:10.1007/s00018-013-1468-0

    Article  CAS  PubMed  Google Scholar 

  • Cruickshanks HA, Vafadar-Isfahani N, Dunican DS, Lee A, Sproul D, Lund JN, Meehan RR, Tufarelli C (2013) Expression of a large LINE-1-driven antisense RNA is linked to epigenetic silencing of the metastasis suppressor gene TFPI-2 in cancer. Nucleic Acids Res 41:6857–6869. doi:10.1093/nar/gkt438

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Curcio MJ, Belfort M (2007) The beginning of the end: links between ancient retroelements and modern telomerases. Proc Natl Acad Sci U S A 104:9107–9108. doi:10.1073/pnas.0703224104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Davis CM, Constantinides PG, van der Riet F, van Schalkwyk L, Gevers W, Parker MI (1989) Activation and demethylation of the intracisternal A particle genes by 5-azacytidine. Cell Differ Dev 27:83–93

    Article  CAS  PubMed  Google Scholar 

  • Day DS, Luquette LJ, Park PJ, Kharchenko PV (2010) Estimating enrichment of repetitive elements from high-throughput sequence data. Genome Biol 11:R69–R69. doi:10.1186/gb-2010-11-6-r69

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • De Fazio S, Bartonicek N, Di Giacomo M, Abreu-Goodger C, Sankar A, Funaya C, Antony C, Moreira PN, Enright AJ, O’Carroll D (2011) The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements. Nature 480:259–263. doi:10.1038/nature10547

    Article  PubMed  CAS  Google Scholar 

  • De La Fuente R, Baumann C, Fan T, Schmidtmann A, Dobrinski I, Muegge K (2006) Lsh is required for meiotic chromosome synapsis and retrotransposon silencing in female germ cells. Nat Cell Biol 8:1448–1454. doi:10.1038/ncb1513

    Article  CAS  Google Scholar 

  • Denli AM, Narvaiza I, Kerman BE, Pena M, Benner C, Marchetto MCN, Diedrich JK, Aslanian A, Ma J, Moresco JJ, Moore L, Hunter T, Saghatelian A, Gage FH (2015) Primate-specific ORF0 contributes to retrotransposon-mediated diversity. Cell 163:583–593. doi:10.1016/j.cell.2015.09.025

    Article  CAS  PubMed  Google Scholar 

  • Dewannieux M, Dupressoir A, Harper F, Pierron G, Heidmann T (2004) Identification of autonomous IAP LTR retrotransposons mobile in mammalian cells. Nat Genet 36:534–539. doi:10.1038/ng1353

    Article  CAS  PubMed  Google Scholar 

  • Dewannieux M, Esnault C, Heidmann T (2003) LINE-mediated retrotransposition of marked Alu sequences. Nat Genet 35:41–48. doi:10.1038/ng1223

    Article  CAS  PubMed  Google Scholar 

  • Di Giacomo M, Comazzetto S, Saini H, De Fazio S, Carrieri C, Morgan M, Vasiliauskaite L, Benes V, Enright AJ, O’Carroll D (2013) Multiple epigenetic mechanisms and the piRNA pathway enforce LINE1 silencing during adult spermatogenesis. Mol Cell 50:601–608. doi:10.1016/j.molcel.2013.04.026

    Article  PubMed  CAS  Google Scholar 

  • Di Giacomo M, Comazzetto S, Sampath SC, Sampath SC, O’Carroll D (2014) G9a co-suppresses LINE1 elements in spermatogonia. Epigenetics Chromatin 7:24. doi:10.1186/1756-8935-7-24

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Dunican DS, Cruickshanks HA, Suzuki M, Semple CA, Davey T, Arceci RJ, Greally J, Adams IR, Meehan RR (2013) Lsh regulates LTR retrotransposon repression independently of Dnmt3b function. Genome Biol 14:R146. doi:10.1186/gb-2013-14-12-r146

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Dupressoir A, Heidmann T (1996) Germ line-specific expression of intracisternal A-particle retrotransposons in transgenic mice. Mol Cell Biol 16:4495–4503

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dupressoir A, Vernochet C, Harper F, Guégan J, Dessen P, Pierron G, Heidmann T (2011) A pair of co-opted retroviral envelope syncytin genes is required for formation of the two-layered murine placental syncytiotrophoblast. Proc Natl Acad Sci U S A 108:E1164–E1173. doi:10.1073/pnas.1112304108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ecco G, Cassano M, Kauzlaric A, Duc J, Coluccio A, Offner S, Imbeault M, Rowe HM, Turelli P, Trono D (2016) Transposable elements and their KRAB-ZFP controllers regulate gene expression in adult tissues. Dev Cell 36:611–623. doi:10.1016/j.devcel.2016.02.024

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eickbush TH (1997) Telomerase and retrotransposons: which came first? Science 277:911–912

    Article  CAS  PubMed  Google Scholar 

  • Esnault C, Maestre J, Heidmann T (2000) Human LINE retrotransposons generate processed pseudogenes. Nat Genet 24:363–367. doi:10.1038/74184

    Article  CAS  PubMed  Google Scholar 

  • Evrony GD, Cai X, Lee E, Hills LB, Elhosary PC, Lehmann HS, Parker JJ, Atabay KD, Gilmore EC, Poduri A, Park PJ, Walsh CA (2012) Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain. Cell 151:483–496. doi:10.1016/j.cell.2012.09.035

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fadloun A, Le Gras S, Jost B, Ziegler-Birling C, Takahashi H, Gorab E, Carninci P, Torres-Padilla M-E (2013) Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA. Nat Struct Mol Biol 20:332–338. doi:10.1038/nsmb.2495

    Article  CAS  PubMed  Google Scholar 

  • Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, Schroder K, Cloonan N, Steptoe AL, Lassmann T, Waki K, Hornig N, Arakawa T, Takahashi H, Kawai J, Forrest ARR, Suzuki H, Hayashizaki Y, Hume DA, Orlando V, Grimmond SM, Carninci P (2009) The regulated retrotransposon transcriptome of mammalian cells. Nat Genet 41:563–571. doi:10.1038/ng.368

    Article  CAS  PubMed  Google Scholar 

  • Feng Q, Moran JV, Kazazian HH Jr, Boeke JD (1996) Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87:905–916

    Article  CAS  PubMed  Google Scholar 

  • Flemr M, Malik R, Franke V, Nejepinska J, Sedlacek R, Vlahovicek K, Svoboda P (2013) A retrotransposon-driven dicer isoform directs endogenous small interfering RNA production in mouse oocytes. Cell 155:807–816. doi:10.1016/j.cell.2013.10.001

    Article  CAS  PubMed  Google Scholar 

  • Friedli M, Trono D (2015) The developmental control of transposable elements and the evolution of higher species. Annu Rev Cell Dev Biol 31:429–451. doi:10.1146/annurev-cellbio-100814-125514

    Article  CAS  PubMed  Google Scholar 

  • Friedman JR, Fredericks WJ, Jensen DE, Speicher DW, Huang XP, Neilson EG, Rauscher FJ (1996) KAP-1, a novel corepressor for the highly conserved KRAB repression domain. Genes Dev 10:2067–2078

    Article  CAS  PubMed  Google Scholar 

  • Fu Q, Wang PJ (2014) Mammalian piRNAs: biogenesis, function, and mysteries. Spermatogenesis 4, e27889. doi:10.4161/spmg.27889

    Article  PubMed  PubMed Central  Google Scholar 

  • Garcia-Perez JL, Morell M, Scheys JO, Kulpa DA, Morell S, Carter CC, Hammer GD, Collins KL, O’Shea KS, Menendez P, Moran JV (2010) Epigenetic silencing of engineered L1 retrotransposition events in human embryonic carcinoma cells. Nature 466:769–773. doi:10.1038/nature09209

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Georgiou I, Noutsopoulos D, Dimitriadou E, Markopoulos G, Apergi A, Lazaros L, Vaxevanoglou T, Pantos K, Syrrou M, Tzavaras T (2009) Retrotransposon RNA expression and evidence for retrotransposition events in human oocytes. Hum Mol Genet 18:1221–1228. doi:10.1093/hmg/ddp022

    Article  CAS  PubMed  Google Scholar 

  • Gimenez J, Montgiraud C, Pichon J-P, Bonnaud B, Arsac M, Ruel K, Bouton O, Mallet F (2010) Custom human endogenous retroviruses dedicated microarray identifies self-induced HERV-W family elements reactivated in testicular cancer upon methylation control. Nucleic Acids Res 38:2229–2246. doi:10.1093/nar/gkp1214

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Graham V, Khudyakov J, Ellis P, Pevny L (2003) SOX2 functions to maintain neural progenitor identity. Neuron 39:749–765

    Article  CAS  PubMed  Google Scholar 

  • Hackett JA, Reddington JP, Nestor CE, Dunican DS, Branco MR, Reichmann J, Reik W, Surani MA, Adams IR, Meehan RR (2012) Promoter DNA methylation couples genome-defence mechanisms to epigenetic reprogramming in the mouse germline. Development 139:3623–3632. doi:10.1242/dev.081661

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hajkova P, Ancelin K, Waldmann T, Lacoste N, Lange UC, Cesari F, Lee C, Almouzni G, Schneider R, Surani MA (2008) Chromatin dynamics during epigenetic reprogramming in the mouse germ line. Nature 452:877–881. doi:10.1038/nature06714

    Article  CAS  PubMed  Google Scholar 

  • Hajkova P, Erhardt S, Lane N, Haaf T, El-Maarri O, Reik W, Walter J, Surani MA (2002) Epigenetic reprogramming in mouse primordial germ cells. Mech Dev 117:15–23. doi:10.1016/S0925-4773(02)00181-8

    Article  CAS  PubMed  Google Scholar 

  • Hancks DC, Goodier JL, Mandal PK, Cheung LE, Kazazian HH (2011) Retrotransposition of marked SVA elements by human L1s in cultured cells. Hum Mol Genet 20:3386–3400. doi:10.1093/hmg/ddr245

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hancks DC, Kazazian H (2010) SVA retrotransposons: evolution and genetic instability. Semin Cancer Biol 20:234–245. doi:10.1016/j.semcancer.2010.04.001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hancks DC, Kazazian HH Jr (2012) Active human retrotransposons: variation and disease. Curr Opin Genet Dev 22:191–203. doi:10.1016/j.gde.2012.02.006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Han K, Xing J, Wang H, Hedges DJ, Garber RK, Cordaux R, Batzer MA (2005) Under the genomic radar: the stealth model of Alu amplification. Genome Res 15:655–664. doi:10.1101/gr.3492605

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hayashi K, Chuva de Sousa Lopes SM, Kaneda M, Tang F, Hajkova P, Lao K, O’Carroll D, Das PP, Tarakhovsky A, Miska EA, Surani MA (2008) MicroRNA biogenesis is required for mouse primordial germ cell development and spermatogenesis. PLoS One 3:e1738. doi:10.1371/journal.pone.0001738

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hisada K, Sánchez C, Endo TA, Endoh M, Román-Trufero M, Sharif J, Koseki H, Vidal M (2012) RYBP represses endogenous retroviruses and preimplantation- and germ line-specific genes in mouse embryonic stem cells. Mol Cell Biol 32:1139–1149. doi:10.1128/MCB.06441-11

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hogg K, Western PS (2015) Refurbishing the germline epigenome: out with the old, in with the new. Semin Cell Dev Biol 45:104–113. doi:10.1016/j.semcdb.2015.09.012

    Article  CAS  PubMed  Google Scholar 

  • Huang XA, Yin H, Sweeney S, Raha D, Snyder M, Lin H (2013) A major epigenetic programming mechanism guided by piRNAs. Dev Cell 24:502–516. doi:10.1016/j.devcel.2013.01.023

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Iwasaki YW, Siomi MC, Siomi H (2015) PIWI-interacting RNA: its biogenesis and functions. Annu Rev Biochem 84:405–433. doi:10.1146/annurev-biochem-060614-034258

    Article  CAS  PubMed  Google Scholar 

  • Jackson-Grusby L, Beard C, Possemato R, Tudor M, Fambrough D, Csankovszki G, Dausman J, Lee P, Wilson C, Lander E, Jaenisch R (2001) Loss of genomic methylation causes p53-dependent apoptosis and epigenetic deregulation. Nat Genet 27:31–39. doi:10.1038/83730

    Article  CAS  PubMed  Google Scholar 

  • 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 516:242–245. doi:10.1038/nature13760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kano H, Godoy I, Courtney C, Vetter MR, Gerton GL, Ostertag EM, Kazazian HH Jr (2009) L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism. Genes Dev 23:1303–1312. doi:10.1101/gad.1803909

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Karimi MM, Goyal P, Maksakova IA, Bilenky M, Leung D, Tang JX, Shinkai Y, Mager DL, Jones S, Hirst M, Lorincz MC (2011) DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs. Cell Stem Cell 8:676–687. doi:10.1016/j.stem.2011.04.004

    Article  CAS  PubMed  Google Scholar 

  • Khan H, Smit A, Boissinot S (2006) Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. Genome Res 16:78–87. doi:10.1101/gr.4001406

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Khazina E, Weichenrieder O (2009) Non-LTR retrotransposons encode noncanonical RRM domains in their first open reading frame. Proc Natl Acad Sci U S A 106:731–736. doi:10.1073/pnas.0809964106

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim S, Günesdogan U, Zylicz JJ, Hackett JA, Cougot D, Bao S, Lee C, Dietmann S, Allen GE, Sengupta R, Surani MA (2014) PRMT5 protects genomic integrity during global DNA demethylation in primordial germ cells and preimplantation embryos. Mol Cell 56:564–579. doi:10.1016/j.molcel.2014.10.003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Klawitter S, Fuchs NV, Upton KR, Muñoz-Lopez M, Shukla R, Wang J, Garcia-Cañadas M, Lopez-Ruiz C, Gerhardt DJ, Sebe A, Grabundzija I, Merkert S, Gerdes P, Pulgarin JA, Bock A, Held U, Witthuhn A, Haase A, Sarkadi B, Löwer J, Wolvetang EJ, Martin U, Ivics Z, Izsvák Z, Garcia-Perez JL, Faulkner GJ, Schumann GG (2016) Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells. Nat Commun 7:10286. doi:10.1038/ncomms10286

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kocer A, Reichmann J, Best D, Adams IR (2009) Germ cell sex determination in mammals. Mol Hum Reprod 15:205–213. doi:10.1093/molehr/gap008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kramerov DA, Vassetzky NS (2011) SINEs. Wiley Interdiscip Rev RNA 2:772–786. doi:10.1002/wrna.91

    Article  CAS  PubMed  Google Scholar 

  • Kulpa DA, Moran JV (2006) Cis-preferential LINE-1 reverse transcriptase activity in ribonucleoprotein particles. Nat Struct Mol Biol 13:655–660. doi:10.1038/nsmb1107

    Article  CAS  PubMed  Google Scholar 

  • Kunarso G, Chia N-Y, Jeyakani J, Hwang C, Lu X, Chan Y-S, Ng H-H, Bourque G (2010) Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat Genet 42:631–634. doi:10.1038/ng.600

    Article  CAS  PubMed  Google Scholar 

  • Kuramochi-Miyagawa S, Kimura T, Ijiri TW, Isobe T, Asada N, Fujita Y, Ikawa M, Iwai N, Okabe M, Deng W, Lin H, Matsuda Y, Nakano T (2004) Mili, a mammalian member of piwi family gene, is essential for spermatogenesis. Development 131:839–849. doi:10.1242/dev.00973

    Article  CAS  PubMed  Google Scholar 

  • Kuramochi-Miyagawa S, Kimura T, Yomogida K, Kuroiwa A, Tadokoro Y, Fujita Y, Sato M, Matsuda Y, Nakano T (2001) Two mouse piwi-related genes: miwi and mili. Mech Dev 108:121–133

    Article  CAS  PubMed  Google Scholar 

  • Kuramochi-Miyagawa S, Watanabe T, Gotoh K, Totoki Y, Toyoda A, Ikawa M, Asada N, Kojima K, Yamaguchi Y, Ijiri TW, Hata K, Li E, Matsuda Y, Kimura T, Okabe M, Sakaki Y, Sasaki H, Nakano T (2008) DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes. Genes Dev 22:908–917. doi:10.1101/gad.1640708

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowski J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J, International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921. doi:10.1038/35057062

    Article  CAS  PubMed  Google Scholar 

  • Lawson KA, Hage WJ (1994) Clonal analysis of the origin of primordial germ cells in the mouse. Ciba Found Symp 182:68–84, discussion 84–91

    CAS  PubMed  Google Scholar 

  • Leeb M, Wutz A (2007) Ring1B is crucial for the regulation of developmental control genes and PRC1 proteins but not X inactivation in embryonic cells. J Cell Biol 178:219–229. doi:10.1083/jcb.200612127

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee S-H, Cho S-Y, Shannon MF, Fan J, Rangasamy D (2010) The impact of CpG island on defining transcriptional activation of the mouse L1 retrotransposable elements. PLoS One 5, e11353. doi:10.1371/journal.pone.0011353

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Li J, Kannan M, Trivett AL, Liao H, Wu X, Akagi K, Symer DE (2014) An antisense promoter in mouse L1 retrotransposon open reading frame-1 initiates expression of diverse fusion transcripts and limits retrotransposition. Nucleic Acids Res 42:4546–4562. doi:10.1093/nar/gku091

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lim AK, Lorthongpanich C, Chew TG, Tan CWG, Shue YT, Balu S, Gounko N, Kuramochi-Miyagawa S, Matzuk MM, Chuma S, Messerschmidt DM, Solter D, Knowles BB (2013) The nuage mediates retrotransposon silencing in mouse primordial ovarian follicles. Development 140:3819–3825. doi:10.1242/dev.099184

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lu X, Sachs F, Ramsay L, Jacques P-É, Göke J, Bourque G, Ng H-H (2014) The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity. Nat Struct Mol Biol 21:423–425. doi:10.1038/nsmb.2799

    Article  CAS  PubMed  Google Scholar 

  • Lynch MD, Smith AJH, De Gobbi M, Flenley M, Hughes JR, Vernimmen D, Ayyub H, Sharpe JA, Sloane-Stanley JA, Sutherland L, Meek S, Burdon T, Gibbons RJ, Garrick D, Higgs DR (2012) An interspecies analysis reveals a key role for unmethylated CpG dinucleotides in vertebrate Polycomb complex recruitment. EMBO J 31:317–329. doi:10.1038/emboj.2011.399

    Article  CAS  PubMed  Google Scholar 

  • Macfarlan TS, Gifford WD, Driscoll S, Lettieri K, Rowe HM, Bonanomi D, Firth A, Singer O, Trono D, Pfaff SL (2012) Embryonic stem cell potency fluctuates with endogenous retrovirus activity. Nature 487:57–63. doi:10.1038/nature11244

    CAS  PubMed  PubMed Central  Google Scholar 

  • Macia A, Muñoz-Lopez M, Cortes JL, Hastings RK, Morell S, Lucena-Aguilar G, Marchal JA, Badge RM, Garcia-Perez JL (2011) Epigenetic control of retrotransposon expression in human embryonic stem cells. Mol Cell Biol 31:300–316. doi:10.1128/MCB.00561-10

    Article  CAS  PubMed  Google Scholar 

  • MacLennan M, Crichton JH, Playfoot CJ, Adams IR (2015) Oocyte development, meiosis and aneuploidy. Semin Cell Dev Biol 45:68–76. doi:10.1016/j.semcdb.2015.10.005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Magnúsdóttir E, Surani MA (2014) How to make a primordial germ cell. Development 141:245–252. doi:10.1242/dev.098269

    Article  PubMed  CAS  Google Scholar 

  • Maksakova IA, Romanish MT, Gagnier L, Dunn CA, van de Lagemaat LN, Mager DL (2006) Retroviral elements and their hosts: insertional mutagenesis in the mouse germ line. PLoS Genet 2:e2. doi:10.1371/journal.pgen.0020002

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Malki S, van der Heijden GW, O’Donnell KA, Martin SL, Bortvin A (2014) A role for retrotransposon LINE-1 in fetal oocyte attrition in mice. Dev Cell 29:521–533. doi:10.1016/j.devcel.2014.04.027

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Marchetto MCN, Narvaiza I, Denli AM, Benner C, Lazzarini TA, Nathanson JL, Paquola ACM, Desai KN, Herai RH, Weitzman MD, Yeo GW, Muotri AR, Gage FH (2013) Differential L1 regulation in pluripotent stem cells of humans and apes. Nature 503:525–529. doi:10.1038/nature12686

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Martin SL, Branciforte D (1993) Synchronous expression of LINE-1 RNA and protein in mouse embryonal carcinoma cells. Mol Cell Biol 13:5383–5392

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mathias SL, Scott AF, Kazazian HH Jr, Boeke JD, Gabriel A (1991) Reverse transcriptase encoded by a human transposable element. Science 254:1808–1810

    Article  CAS  PubMed  Google Scholar 

  • Matsui T, Leung D, Miyashita H, Maksakova IA, Miyachi H, Kimura H, Tachibana M, Lorincz MC, Shinkai Y (2010) Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET. Nature 464:927–931. doi:10.1038/nature08858

    Article  CAS  PubMed  Google Scholar 

  • McLaren A (2003) Primordial germ cells in the mouse. Dev Biol 262:1–15

    Article  CAS  PubMed  Google Scholar 

  • Mi S, Lee X, Li X, Veldman GM, Finnerty H, Racie L, LaVallie E, Tang X-Y, Edouard P, Howes S, Keith JC, McCoy JM (2000) Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis. Nature 403:785–789. doi:10.1038/35001608

    Article  CAS  PubMed  Google Scholar 

  • Molaro A, Falciatori I, Hodges E, Aravin AA, Marran K, Rafii S, McCombie WR, Smith AD, Hannon GJ (2014) Two waves of de novo methylation during mouse germ cell development. Genes Dev 28:1544–1549. doi:10.1101/gad.244350.114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Moran JV, Holmes SE, Naas TP, DeBerardinis RJ, Boeke JD, Kazazian HH Jr (1996) High frequency retrotransposition in cultured mammalian cells. Cell 87:917–927

    Article  CAS  PubMed  Google Scholar 

  • Muotri AR, Chu VT, Marchetto MCN, Deng W, Moran JV, Gage FH (2005) Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. Nature 435:903–910. doi:10.1038/nature03663

    Article  CAS  PubMed  Google Scholar 

  • Muotri AR, Marchetto MCN, Coufal NG, Gage FH (2007) The necessary junk: new functions for transposable elements. Hum Mol Genet 16:R159–R167. doi:10.1093/hmg/ddm196

    Article  CAS  PubMed  Google Scholar 

  • Nichols J, Smith A (2009) Naive and primed pluripotent states. Cell Stem Cell 4:487–492. doi:10.1016/j.stem.2009.05.015

    Article  CAS  PubMed  Google Scholar 

  • O’Donnell L (2015) Mechanisms of spermiogenesis and spermiation and how they are disturbed. Spermatogenesis 4:e979623. doi:10.4161/21565562.2014.979623

    Article  PubMed  PubMed Central  Google Scholar 

  • Ohinata Y, Payer B, O’Carroll D, Ancelin K, Ono Y, Sano M, Barton SC, Obukhanych T, Nussenzweig M, Tarakhovsky A, Saitou M, Surani MA (2005) Blimp1 is a critical determinant of the germ cell lineage in mice. Nature 436:207–213. doi:10.1038/nature03813

    Article  CAS  PubMed  Google Scholar 

  • Öllinger R, Childs AJ, Burgess HM, Speed RM, Lundegaard PR, Reynolds N, Gray NK, Cooke HJ, Adams IR (2008) Deletion of the pluripotency-associated Tex19.1 gene causes activation of endogenous retroviruses and defective spermatogenesis in mice. PLoS Genet 4:e1000199. doi:10.1371/journal.pgen.1000199

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ollinger R, Reichmann J, Adams IR (2010) Meiosis and retrotransposon silencing during germ cell development in mice. Differentiation 79:147–158. doi:10.1016/j.diff.2009.10.004

    Article  CAS  PubMed  Google Scholar 

  • Peaston AE, Evsikov AV, Graber JH, de Vries WN, Holbrook AE, Solter D, Knowles BB (2004) Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev Cell 7:597–606. doi:10.1016/j.devcel.2004.09.004

    Article  CAS  PubMed  Google Scholar 

  • Pezic D, Manakov SA, Sachidanandam R, Aravin AA (2014) piRNA pathway targets active LINE1 elements to establish the repressive H3K9me3 mark in germ cells. Genes Dev 28:1410–1428. doi:10.1101/gad.240895.114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Philippe C, Vargas-Landin DB, Doucet AJ, van Essen D, Vera-Otarola J, Kuciak M, Corbin A, Nigumann P, Cristofari G (2016) Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci. Elife 5:e13926. doi:10.7554/eLife.13926

  • Piko L, Hammons MD, Taylor KD (1984) Amounts, synthesis, and some properties of intracisternal A particle-related RNA in early mouse embryos. Proc Natl Acad Sci U S A 81:488–492

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Popp C, Dean W, Feng S, Cokus SJ, Andrews S, Pellegrini M, Jacobsen SE, Reik W (2010) Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature 463:1101–1105. doi:10.1038/nature08829

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Puech A, Dupressoir A, Loireau MP, Mattei MG, Heidmann T (1997) Characterization of two age-induced intracisternal A-particle-related transcripts in the mouse liver. Transcriptional read-through into an open reading frame with similarities to the yeast ccr4 transcription factor. J Biol Chem 272:5995–6003

    Article  CAS  PubMed  Google Scholar 

  • Raiz J, Damert A, Chira S, Held U, Klawitter S, Hamdorf M, Löwer J, Strätling WH, Löwer R, Schumann GG (2012) The non-autonomous retrotransposon SVA is trans-mobilized by the human LINE-1 protein machinery. Nucleic Acids Res 40:1666–1683. doi:10.1093/nar/gkr863

    Article  CAS  PubMed  Google Scholar 

  • Rebollo R, Romanish MT, Mager DL (2012) Transposable elements: an abundant and natural source of regulatory sequences for host genes. Annu Rev Genet 46:21–42. doi:10.1146/annurev-genet-110711-155621

    Article  CAS  PubMed  Google Scholar 

  • Reddington JP, Perricone SM, Nestor CE, Reichmann J, Youngson NA, Suzuki M, Reinhardt D, Dunican DS, Prendergast JG, Mjoseng H, Ramsahoye BH, Whitelaw E, Greally JM, Adams IR, Bickmore WA, Meehan RR (2013) Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes. Genome Biol 14:R25. doi:10.1186/gb-2013-14-3-r25

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Reichmann J, Crichton JH, Madej MJ, Taggart M, Gautier P, Garcia-Perez JL, Meehan RR, Adams IR (2012) Microarray analysis of LTR retrotransposon silencing identifies Hdac1 as a regulator of retrotransposon expression in mouse embryonic stem cells. PLoS Comput Biol 8:e1002486. doi:10.1371/journal.pcbi.1002486

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Reichmann J, Reddington JP, Best D, Read D, Öllinger R, Meehan RR, Adams IR (2013) The genome-defence gene Tex19.1 suppresses LINE-1 retrotransposons in the placenta and prevents intra-uterine growth retardation in mice. Hum Mol Genet 22:1791–1806. doi:10.1093/hmg/ddt029

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Reuter M, Berninger P, Chuma S, Shah H, Hosokawa M, Funaya C, Antony C, Sachidanandam R, Pillai RS (2011) Miwi catalysis is required for piRNA amplification-independent LINE1 transposon silencing. Nature 480:264–267. doi:10.1038/nature10672

    Article  CAS  PubMed  Google Scholar 

  • Ribet D, Dewannieux M, Heidmann T (2004) An active murine transposon family pair: retrotransposition of “master” MusD copies and ETn trans-mobilization. Genome Res 14:2261–2267. doi:10.1101/gr.2924904

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ribet D, Louvet-Vallée S, Harper F, de Parseval N, Dewannieux M, Heidmann O, Pierron G, Maro B, Heidmann T (2008) Murine endogenous retrovirus MuERV-L is the progenitor of the “orphan” epsilon viruslike particles of the early mouse embryo. J Virol 82:1622–1625. doi:10.1128/JVI.02097-07

    Article  CAS  PubMed  Google Scholar 

  • Romanish MT, Cohen CJ, Mager DL (2010) Potential mechanisms of endogenous retroviral-mediated genomic instability in human cancer. Semin Cancer Biol 20:246–253. doi:10.1016/j.semcancer.2010.05.005

    Article  CAS  PubMed  Google Scholar 

  • Roovers EF, Rosenkranz D, Mahdipour M, Han C-T, He N, Chuva de Sousa Lopes SM, van der Westerlaken LAJ, Zischler H, Butter F, Roelen BAJ, Ketting RF (2015) Piwi proteins and piRNAs in mammalian oocytes and early embryos. Cell Rep 10:2069–2082. doi:10.1016/j.celrep.2015.02.062

    Article  CAS  PubMed  Google Scholar 

  • Rossitto M, Philibert P, Poulat F, Boizet-Bonhoure B (2015) Molecular events and signalling pathways of male germ cell differentiation in mouse. Semin Cell Dev Biol 45:84–93. doi:10.1016/j.semcdb.2015.09.014

    Article  CAS  PubMed  Google Scholar 

  • Rowe HM, Friedli M, Offner S, Verp S, Mesnard D, Marquis J, Aktas T, Trono D (2013) De novo DNA methylation of endogenous retroviruses is shaped by KRAB-ZFPs/KAP1 and ESET. Development 140:519–529. doi:10.1242/dev.087585

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rowe HM, Jakobsson J, Mesnard D, Rougemont J, Reynard S, Aktas T, Maillard PV, Layard-Liesching H, Verp S, Marquis J, Spitz F, Constam DB, Trono D (2010) KAP1 controls endogenous retroviruses in embryonic stem cells. Nature 463:237–240. doi:10.1038/nature08674

    Article  CAS  PubMed  Google Scholar 

  • Seifarth W, Frank O, Zeilfelder U, Spiess B, Greenwood AD, Hehlmann R, Leib-Mösch C (2005) Comprehensive analysis of human endogenous retrovirus transcriptional activity in human tissues with a retrovirus-specific microarray. J Virol 79:341–352. doi:10.1128/JVI.79.1.341-352.2005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Seisenberger S, Andrews S, Krueger F, Arand J, Walter J, Santos F, Popp C, Thienpont B, Dean W, Reik W (2012) The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells. Mol Cell 48:849–862. doi:10.1016/j.molcel.2012.11.001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shukla R, Upton KR, Muñoz-Lopez M, Gerhardt DJ, Fisher ME, Nguyen T, Brennan PM, Baillie JK, Collino A, Ghisletti S, Sinha S, Iannelli F, Radaelli E, Dos Santos A, Rapoud D, Guettier C, Samuel D, Natoli G, Carninci P, Ciccarelli FD, Garcia-Perez JL, Faivre J, Faulkner GJ (2013) Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell 153:101–111. doi:10.1016/j.cell.2013.02.032

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Slotkin RK, Vaughn M, Borges F, Tanurdzić M, Becker JD, Feijó JA, Martienssen RA (2009) Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136:461–472. doi:10.1016/j.cell.2008.12.038

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Smallwood SA, Kelsey G (2012) De novo DNA methylation: a germ cell perspective. Trends Genet 28:33–42. doi:10.1016/j.tig.2011.09.004

    Article  CAS  PubMed  Google Scholar 

  • Solyom S, Ewing AD, Rahrmann EP, Doucet T, Nelson HH, Burns MB, Harris RS, Sigmon DF, Casella A, Erlanger B, Wheelan S, Upton KR, Shukla R, Faulkner GJ, Largaespada DA, Kazazian HH Jr (2012) Extensive somatic L1 retrotransposition in colorectal tumors. Genome Res 22:2328–2338. doi:10.1101/gr.145235.112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sookdeo A, Hepp CM, McClure MA, Boissinot S (2013) Revisiting the evolution of mouse LINE-1 in the genomic era. Mob DNA 4:3. doi:10.1186/1759-8753-4-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Soper SFC, van der Heijden GW, Hardiman TC, Goodheart M, Martin SL, de Boer P, Bortvin A (2008) Mouse maelstrom, a component of nuage, is essential for spermatogenesis and transposon repression in meiosis. Dev Cell 15:285–297. doi:10.1016/j.devcel.2008.05.015

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Speek M (2001) Antisense promoter of human L1 retrotransposon drives transcription of adjacent cellular genes. Mol Cell Biol 21:1973–1985. doi:10.1128/MCB.21.6.1973-1985.2001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sproul D, Nestor C, Culley J, Dickson JH, Dixon JM, Harrison DJ, Meehan RR, Sims AH, Ramsahoye BH (2011) Transcriptionally repressed genes become aberrantly methylated and distinguish tumors of different lineages in breast cancer. Proc Natl Acad Sci U S A 108:4364–4369. doi:10.1073/pnas.1013224108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sripathy SP, Stevens J, Schultz DC (2006) The KAP1 corepressor functions to coordinate the assembly of de novo HP1-demarcated microenvironments of heterochromatin required for KRAB zinc finger protein-mediated transcriptional repression. Mol Cell Biol 26:8623–8638. doi:10.1128/MCB.00487-06

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stein P, Rozhkov NV, Li F, Cárdenas FL, Davydenko O, Davydenk O, Vandivier LE, Gregory BD, Hannon GJ, Schultz RM (2015) Essential role for endogenous siRNAs during meiosis in mouse oocytes. PLoS Genet 11:e1005013. doi:10.1371/journal.pgen.1005013

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Su Y-Q, Sugiura K, Sun F, Pendola JK, Cox GA, Handel MA, Schimenti JC, Eppig JJ (2012a) MARF1 regulates essential oogenic processes in mice. Science 335:1496–1499. doi:10.1126/science.1214680

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Su Y-Q, Sun F, Handel MA, Schimenti JC, Eppig JJ (2012b) Meiosis arrest female 1 (MARF1) has nuage-like function in mammalian oocytes. Proc Natl Acad Sci U S A 109:18653–18660. doi:10.1073/pnas.1216904109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Swergold GD (1990) Identification, characterization, and cell specificity of a human LINE-1 promoter. Mol Cell Biol 10:6718–6729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tam OH, Aravin AA, Stein P, Girard A, Murchison EP, Cheloufi S, Hodges E, Anger M, Sachidanandam R, Schultz RM, Hannon GJ (2008) Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 453:534–538. doi:10.1038/nature06904

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Trelogan SA, Martin SL (1995) Tightly regulated, developmentally specific expression of the first open reading frame from LINE-1 during mouse embryogenesis. Proc Natl Acad Sci U S A 92:1520–1524

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Upton KR, Gerhardt DJ, Jesuadian JS, Richardson SR, Sánchez-Luque FJ, Bodea GO, Ewing AD, Salvador-Palomeque C, van der Knaap MS, Brennan PM, Vanderver A, Faulkner GJ (2015) Ubiquitous L1 mosaicism in hippocampal neurons. Cell 161:228–239. doi:10.1016/j.cell.2015.03.026

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • van den Hurk JAJM, Meij IC, Seleme M d C, Kano H, Nikopoulos K, Hoefsloot LH, Sistermans EA, de Wijs IJ, Mukhopadhyay A, Plomp AS, de Jong PTVM, Kazazian HH, Cremers FPM (2007) L1 retrotransposition can occur early in human embryonic development. Hum Mol Genet 16:1587–1592. doi:10.1093/hmg/ddm108

    Article  PubMed  CAS  Google Scholar 

  • van Valen L (1973) A new evolutionary law. Evol Theory 1:1–30

    Google Scholar 

  • Walsh CP, Chaillet JR, Bestor TH (1998) Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat Genet 20:116–117. doi:10.1038/2413

    Article  CAS  PubMed  Google Scholar 

  • Walter M, Teissandier A, Pérez-Palacios R, Bourc’his D (2016) An epigenetic switch ensures transposon repression upon dynamic loss of DNA methylation in embryonic stem cells. Elife 5:e11418. doi:10.7554/eLife.11418

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang H, Xing J, Grover D, Hedges DJ, Han K, Walker JA, Batzer MA (2005) SVA elements: a hominid-specific retroposon family. J Mol Biol 354:994–1007. doi:10.1016/j.jmb.2005.09.085

    Article  CAS  PubMed  Google Scholar 

  • Wang J, Xie G, Singh M, Ghanbarian AT, Raskó T, Szvetnik A, Cai H, Besser D, Prigione A, Fuchs NV, Schumann GG, Chen W, Lorincz MC, Ivics Z, Hurst LD, Izsvák Z (2014) Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells. Nature 516:405–409. doi:10.1038/nature13804

    Article  CAS  PubMed  Google Scholar 

  • Watanabe T, Totoki Y, Toyoda A, Kaneda M, Kuramochi-Miyagawa S, Obata Y, Chiba H, Kohara Y, Kono T, Nakano T, Surani MA, Sakaki Y, Sasaki H (2008) Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 453:539–543. doi:10.1038/nature06908

    Article  CAS  PubMed  Google Scholar 

  • Weismann A (1889) Essays upon heredity. Clarendon Press, Oxford

    Google Scholar 

  • Wei W, Gilbert N, Ooi SL, Lawler JF, Ostertag EM, Kazazian HH, Boeke JD, Moran JV (2001) Human L1 retrotransposition: cis preference versus trans complementation. Mol Cell Biol 21:1429–1439. doi:10.1128/MCB.21.4.1429-1439.2001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wildschutte JH, Williams ZH, Montesion M, Subramanian RP, Kidd JM, Coffin JM (2016) Discovery of unfixed endogenous retrovirus insertions in diverse human populations. Proc Natl Acad Sci U S A 113:E2326–E2334. doi:10.1073/pnas.1602336113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wissing S, Montano M, Garcia-Perez JL, Moran JV, Greene WC (2011) Endogenous APOBEC3B restricts LINE-1 retrotransposition in transformed cells and human embryonic stem cells. J Biol Chem 286:36427–36437. doi:10.1074/jbc.M111.251058

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wolf D, Goff SP (2009) Embryonic stem cells use ZFP809 to silence retroviral DNAs. Nature 458:1201–1204. doi:10.1038/nature07844

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wolf D, Goff SP (2007) TRIM28 mediates primer binding site-targeted silencing of murine leukemia virus in embryonic cells. Cell 131:46–57. doi:10.1016/j.cell.2007.07.026

    Article  CAS  PubMed  Google Scholar 

  • Yang Q-E, Oatley JM (2014) Spermatogonial stem cell functions in physiological and pathological conditions. Curr Top Dev Biol 107:235–267. doi:10.1016/B978-0-12-416022-4.00009-3

    Article  CAS  PubMed  Google Scholar 

  • Yotsuyanagi Y, Szöllösi D (1981) Early mouse embryo intracisternal particle: Fourth type of retrovirus-like particle associated with the mouse. J Natl Cancer Inst 67:677–685

    CAS  PubMed  Google Scholar 

  • Zamudio N, Barau J, Teissandier A, Walter M, Borsos M, Servant N, Bourc’his D (2015) DNA methylation restrains transposons from adopting a chromatin signature permissive for meiotic recombination. Genes Dev 29:1256–1270. doi:10.1101/gad.257840.114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zamudio N, Bourc’his D (2010) Transposable elements in the mammalian germline: a comfortable niche or a deadly trap? Heredity 105:92–104. doi:10.1038/hdy.2010.53

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

I thank the MRC for funding research in this area in my laboratory through an intramural programme grant from MRC Human Genetics Unit. I am extremely grateful to Chris Playfoot and Jose Luis Garcia-Perez (both MRC Human Genetics Unit, Edinburgh) for their critical comments and excellent suggestions on this chapter.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Ian R. Adams .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing AG

About this chapter

Cite this chapter

Adams, I.R. (2017). Retrotransposons and the Mammalian Germline. In: Cristofari, G. (eds) Human Retrotransposons in Health and Disease. Springer, Cham. https://doi.org/10.1007/978-3-319-48344-3_1

Download citation

Publish with us

Policies and ethics