Restricting retrotransposons: A review

Mobile DNA

Volumn 7, Issue 1, 2016, Pages

  Goodier, John L ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Alu; Autoimmunity; Epigenetics; LINE 1; Methylation; Restriction; Retrovirus; RNAi; SINE; SVA

Indexed keywords

ACTIVATION INDUCED CYTIDINE DEAMINASE; ADENOSINE DEAMINASE ACTING ON RNA PROTEIN; APOLIPOPROTEIN B MESSENGER RNA EDITING ENZYME CATALYTIC POLYPEPTIDE; CELL PROTEIN; DNA METHYLTRANSFERASE 1; DNA METHYLTRANSFERASE 3A; DNA METHYLTRANSFERASE 3B; EXONUCLEASE; HYDROLASE; KRAB ASSOCIATED PROTEIN 1; MARF1 PROTEIN; MOLONEY LEUKEMIA VIRUS 10 HOMOLOG PROTEIN; NICOTINAMIDE ADENINE DINUCLEOTIDE ADENOSINE DIPHOSPHATE RIBOSYLTRANSFERASE; PIWI INTERACTING RNA; POLYA BINDING PROTEIN C1; REPRESSOR PROTEIN; RIBONUCLEASE L; RNA HELICASE; RNA INDUCED SILENCING COMPLEX; SAM DOMAIN AND HD DOMAIN 1 PROTEIN; TEX19.1 PROTEIN; THREE PRIME REPAIR EXONUCLEASE 1; UNCLASSIFIED DRUG; ZINC FINGER CCCH TYPE ANTIVIRAL 1 PROTEIN;

AICARDI GOUTIERES SYNDROME; DNA METHYLATION; EMBRYO DEVELOPMENT; ENDOGENOUS RETROVIRUS; GENE MUTATION; HISTONE MODIFICATION; HUMAN; HUMAN GENOME; INDUCED PLURIPOTENT STEM CELL; LONG TERMINAL REPEAT; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; RETROPOSON; REVIEW; RNA INTERFERENCE; TUMOR GROWTH; TUMOR SUPPRESSOR GENE; VIRUS REPLICATION;

EID: 84982112297     PISSN: None     EISSN: 17598753     Source Type: Journal    
DOI: 10.1186/s13100-016-0070-z     Document Type: Review

References (521)

1. McClintock B. The origin and behavior of mutable loci in maize. Proc Natl Acad Sci. 1950;36(6):344-55.
2. Kazazian HH. Mobile DNA: Finding Treasure in Junk. New Jersey: FT Press, Upper Saddle River; 2011.
3. Goodier JL, Kazazian HH. Retrotransposons revisited: the restraint and rehabilitation of parasites. Cell. 2008;135(1):23-35.
4. Mitra R, Li X, Kapusta A, Mayhew D, Mitra RD, Feschotte C, et al. Functional characterization of piggyBat from the bat Myotis lucifugus unveils an active mammalian DNA transposon. Proc Natl Acad Sci. 2013;110(1):234-9.
5. Stocking C, Kozak CA. Endogenous retroviruses. Cell Mol Life Sci. 2008;65(21):3383-98.
6. Stoye JP. Studies of endogenous retroviruses reveal a continuing evolutionary saga. Nat Rev Microbiol. 2012.
7. Mager DL, Stoye JP. Mammalian Endogenous Retroviruses. Mobile DNA III: Washington, DC: American Society for Microbiology; 2015. p. 1079-100.
8. Zhang Y, Maksakova IA, Gagnier L, van de Lagemaat LN, Mager DL. Genome-Wide assessments reveal extremely high levels of polymorphism of two active families of mouse endogenous retroviral elements. PLoS Genet. 2008;4(2):e1000007.
9. Jenkins NA, Copeland NG. High frequency germline acquisition of ecotropic MuLV proviruses in SWR/J-RF/J hybrid mice. Cell. 1985;43(3):811-9.
10. Dewannieux M, Harper F, Richaud A, Letzelter C, Ribet D, Pierron G, et al. Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements. Genome Res. 2006;16(12):1548-56.
11. Young GR, Eksmond U, Salcedo R, Alexopoulou L, Stoye JP, Kassiotis G. Resurrection of endogenous retroviruses in antibody-deficient mice. Nature. 2012;491(7426):774-8.
12. Contreras-Galindo R, Kaplan MH, Dube D, Gonzalez-Hernandez MJ, Chan S, Meng F, et al. Human Endogenous Retrovirus Type K (HERV-K) Particles Package and Transmit HERV-K-Related Sequences. J Virol. 2015;89(14):7187-201.
13. Marchi E, Kanapin A, Magiorkinis G, Belshaw R. Unfixed endogenous retroviral insertions in the human population. J Virol. 2014;88(17):9529-37.
14. Naveira H, Bello X, Abal-Fabeiro JL, Maside X. Evidence for the persistence of an active endogenous retrovirus (ERVE) in humans. Genetica. 2014;142(5):451-60.
15. Wildschutte JH, Williams ZH, Montesion M, Subramanian RP, Kidd JM, Coffin JM. Discovery of unfixed endogenous retrovirus insertions in diverse human populations. Proc Natl Acad Sci. 2016;113(16):E2326-34.
16. Thompson PJ, Macfarlan TS, Lorincz MC. Long Terminal Repeats: From Parasitic Elements to Building Blocks of the Transcriptional Regulatory Repertoire. Mol Cell. 2016;62(5):766-76.
17. Malik HS, Burke WD, Eickbush TH. The age and evolution of non-LTR retrotransposable elements. Mol Biol Evol. 1999;16(6):793-805.
18. Kapitonov VV, Tempel S, Jurka J. Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences. Gene. 2009;448(2):207-13.
19. Boissinot S, Furano AV. Adaptive evolution in LINE-1 retrotransposons. Mol Biol Evol. 2001;18(12):2186-94.
20. Khan H, Smit A, Boissinot S. Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. Genome Res. 2006;16(1):78-87.
21. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409(6822):860-921.
22. Zhang Z, Harrison PM, Liu Y, Gerstein M. Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res. 2003;13(12):2541-58.
23. Ade C, Roy-Engel AM, Deininger PL. Alu elements: an intrinsic source of human genome instability. Curr Opin Virol. 2013;3(6):639-45.
24. Ono M, Kawakami M, Takezawa T. A novel human nonviral retroposon derived from an endogenous retrovirus. Nucleic Acids Res. 1987;15(21):8725-37.
25. Shen L, Wu LC, Sanlioglu S, Chen R, Mendoza AR, Dangel AW, et al. Structure and genetics of the partially duplicated gene RP located immediately upstream of the complement C4A and the C4B genes in the HLA class III region. Molecular cloning, exon-intron structure, composite retroposon, and breakpoint of gene duplication. J Biol Chem. 1994;269(11):8466-76.
26. Ostertag EM, Goodier JL, Zhang Y, Kazazian HH. SVA elements are nonautonomous retrotransposons that cause disease in humans. Am J Hum Genet. 2003;73(6):1444-51.
27. Bennett EA, Coleman LE, Tsui C, Pittard WS, Devine SE. Natural genetic variation caused by transposable elements in humans. Genetics. 2004;168(2):933-51.
28. Wang H, Xing J, Grover D, Hedges DJ, Han K, Walker JA, et al. SVA elements: a hominid-specific retroposon family. J Mol Biol. 2005;354(4):994-1007.
29. Damert A, Raiz J, Horn AV, Lower J, Wang H, Xing J, et al. 5'-Transducing SVA retrotransposon groups spread efficiently throughout the human genome. Genome Res. 2009;19(11):1992-2008.
30. Hancks DC, Kazazian Jr HH. SVA retrotransposons: Evolution and genetic instability. Semin Cancer Biol. 2010;20(4):234-45.
31. Friedli M, Trono D. The developmental control of transposable elements and the evolution of higher species. Annu Rev Cell Dev Biol. 2015;31(1):429-51.
32. Bantysh O, Buzdin A. Novel family of human transposable elements formed due to fusion of the first exon of gene MAST2 with retrotransposon SVA. Biochem Mosc. 2009;74(12):1393-9.
33. Hancks DC, Ewing AD, Chen JE, Tokunaga K, Kazazian HH. Exon-trapping mediated by the human retrotransposon SVA. Genome Res. 2009;19(11):1983-91.
34. Carbone L, Harris RA, Mootnick AR, Milosavljevic A, Martin DIK, Rocchi M, et al. Centromere remodeling in hoolock leuconedys (Hylobatidae) by a new transposable element unique to the gibbons. Genome Biol Evol. 2012;4(7):648-58.
35. Hara T, Hirai Y, Baicharoen S, Hayakawa T, Hirai H, Koga A. A novel composite retrotransposon derived from or generated independently of the SVA (SINE/VNTR/Alu) transposon has undergone proliferation in gibbon genomes. Genes Genet Syst. 2012;87(3):181-90.
36. Ianc B, Ochis C, Persch R, Popescu O, Damert A. Hominoid composite non-LTR retrotransposons - variety, assembly, evolution, and structural determinants of mobilization. Mol Biol Evol. 2014;31(11):2847-64.
37. Brouha B, Schustak J, Badge RM, Lutz-Prigge S, Farley AH, Moran JV, et al. Hot L1s account for the bulk of retrotransposition in the human population. Proc Natl Acad Sci. 2003;100(9):5280-5.
38. Beck CR, Collier P, Macfarlane C, Malig M, Kidd JM, Eichler EE, et al. LINE-1 retrotransposition activity in human genomes. Cell. 2010;141(7):1159-70.
39. del Carmen SM, Vetter MR, Cordaux R, Bastone L, Batzer MA, Kazazian HH. Extensive individual variation in L1 retrotransposition capability contributes to human genetic diversity. Proc Natl Acad Sci. 2006;103(17):6611-6.
40. Cordaux R, Hedges DJ, Herke SW, Batzer MA. Estimating the retrotransposition rate of human Alu elements. Gene. 2006;373:134-7.
41. Hancks DC, Kazazian HH. Active human retrotransposons: variation and disease. Curr Opin Genet Dev. 2012;22(3):191-203.
42. Hancks DC, Kazazian HH. Roles for retrotransposon insertions in human disease. Mob DNA. 2016;7(1):1.
43. Luan DD, Korman MH, Jakubczak JL, Eickbush TH. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: A mechanism for non-LTR retrotransposition. Cell. 1993;72(4):595-605.
44. Speek M. Antisense promoter of human L1 retrotransposon drives transcription of adjacent cellular genes. Mol Cell Biol. 2001;21(6):1973-85.
45. Denli Ahmet M, Narvaiza I, Kerman Bilal E, Pena M, Benner C, Marchetto Maria CN, et al. Primate-specific ORF0 contributes to retrotransposon-mediated diversity. Cell. 2015;163(3):583-93.
46. Adey NB, Schichman SA, Graham DK, Peterson SN, Edgell MH, Hutchison C. Rodent L1 evolution has been driven by a single dominant lineage that has repeatedly acquired new transcriptional regulatory sequences. Mol Biol Evol. 1994;11(5):778-89.
47. Martin SL. The ORF1 protein encoded by LINE-1: structure and function during L1 retrotransposition. J Biomed Biotechnol. 2006;2006:1-6.
48. Martin SL. Nucleic acid chaperone properties of ORF1p from the non-LTR retrotransposon, LINE-1. RNA Biol. 2010;7(6):706-11.
49. Martin SL, Branciforte D. Synchronous expression of LINE-1 RNA and protein in mouse embryonal carcinoma cells. Mol Cell Biol. 1993;13(9):5383-92.
50. Hohjoh H, Singer MF. Ribonuclease and high salt sensitivity of the ribonucleoprotein complex formed by the human LINE-1 retrotransposon. J Mol Biol. 1997;271(1):7-12.
51. Goodier JL, Zhang L, Vetter MR, Kazazian HH. LINE-1 ORF1 protein localizes in stress granules with other RNA-binding proteins, including components of RNA interference RNA-induced silencing complex. Mol Cell Biol. 2007;27(18):6469-83.
52. Guo H, Chitiprolu M, Gagnon D, Meng L, Perez-Iratxeta C, Lagace D, et al. Autophagy supports genomic stability by degrading retrotransposon RNA. Nat Commun. 2014;5:5276.
53. Anderson P, Kedersha N. RNA granules. J Cell Biol. 2006;172(6):803-8.
54. Voronina E, Seydoux G, Sassone-Corsi P, Nagamori I. RNA granules in germ cells. Cold Spring Harb Perspect Biol. 2011;3(12):a002774-a.
55. Goodier JL, Ostertag EM, Engleka K, Seleme M, Kazazian HH. A potential role for the nucleolus in L1 retrotransposition. Hum Mol Genet. 2004;13(10):1041-8.
56. Goodier JL, Cheung LE, Kazazian HH. Mapping the LINE1 ORF1 protein interactome reveals associated inhibitors of human retrotransposition. Nucleic Acids Res. 2013;41(15):7401-19.
57. Rodić N, Sharma R, Sharma R, Zampella J, Dai L, Taylor MS, et al. Long interspersed element-1 protein expression is a hallmark of many human cancers. Am J Pathol. 2014;184(5):1280-6.
58. Doucet AJ, Hulme AE, Sahinovic E, Kulpa DA, Moldovan JB, Kopera HC, et al. Characterization of LINE-1 ribonucleoprotein particles. PLoS Genet. 2010;6(10):e1001150.
59. Goodier JL, Mandal PK, Zhang L, Kazazian HH. Discrete subcellular partitioning of human retrotransposon RNAs despite a common mechanism of genome insertion. Hum Mol Genet. 2010;19(9):1712-25.
60. De Luca C, Guadagni F, Sinibaldi-Vallebona P, Sentinelli S, Gallucci M, Hoffmann A, et al. Enhanced expression of LINE-1-encoded ORF2 protein in early stages of colon and prostate transformation. Oncotarget. 2015;7(4):4048-61.
61. Belancio VP, Hedges DJ, Deininger P. Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health. Genome Res. 2008;18(3):343-58.
62. Zamudio N, Bourc'his D. Transposable elements in the mammalian germline: a comfortable niche or a deadly trap? Heredity. 2010;105(1):92-104.
63. Beck CR, Garcia-Perez JL, Badge RM, Moran JV. LINE-1 elements in structural variation and disease. Annu Rev Genomics Hum Genet. 2011;12(1):187-215.
64. Burns KH, Boeke JD. Human transposon tectonics. Cell. 2012;149(4):740-52.
65. Huang CR, Burns KH, Boeke JD. Active transposition in genomes. Annu Rev Genet. 2012;46:651-75.
66. Richardson SR, Moran JV, Kopera HC, Doucet AJ, Moldovan JB, Garcia-Perez JL. The Influence of LINE-1 and SINE Retrotransposons on Mammalian Genomes. Mobile DNA III: Washington, DC: American Society for Microbiology; 2015. p. 1165-208.
67. Mita P, Boeke JD. How retrotransposons shape genome regulation. Curr Opin Genet Dev. 2016;37:90-100.
68. Morrish TA, Gilbert N, Myers JS, Vincent BJ, Stamato TD, Taccioli GE, et al. DNA repair mediated by endonuclease-independent LINE-1 retrotransposition. Nat Genet. 2002;31(2):159-65.
69. Belgnaoui SM, Gosden RG, Semmes OJ, Haoudi A. Human LINE-1 retrotransposon induces DNA damage and apoptosis in cancer cells. Cancer Cell Int. 2006;6(1):1.
70. Sinibaldi-Vallebona P, Lavia P, Garaci E, Spadafora C. A role for endogenous reverse transcriptase in tumorigenesis and as a target in differentiating cancer therapy. Genes Chromosom Cancer. 2006;45(1):1-10.
71. Hedges DJ, Deininger PL. Inviting instability: Transposable elements, double-strand breaks, and the maintenance of genome integrity. Mutat Res. 2007;616(1-2):46-59.
72. Morrish TA, Garcia-Perez JL, Stamato TD, Taccioli GE, Sekiguchi J, Moran JV. Endonuclease-independent LINE-1 retrotransposition at mammalian telomeres. Nature. 2007;446(7132):208-12.
73. Xiong Y, Eickbush TH. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 1990;9(10):3353.
74. Doolittle RF, Feng DF. Tracing the origin of retroviruses. Curr Top Microbiol Immunol. 1992;176:195-211.
75. Malik HS. Poised for contagion: evolutionary origins of the infectious abilities of invertebrate retroviruses. Genome Res. 2000;10(9):1307-18.
76. Malik HS, Eickbush TH. Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses. Genome Res. 2001;11(7):1187-97.
77. Maxwell PH, Curcio MJ. Host factors that control long terminal repeat retrotransposons in Saccharomyces cerevisiae: implications for regulation of mammalian retroviruses. Eukaryotic Cell. 2007;6(7):1069-80.
78. Beauregard A, Curcio MJ, Belfort M. The take and give between retrotransposable elements and their hosts. Annu Rev Genet. 2008;42(1):587-617.
79. Siomi MC, Saito K, Siomi H. How selfish retrotransposons are silenced in Drosophila germline and somatic cells. FEBS Lett. 2008;582(17):2473-8.
80. Eickbush TH, Eickbush DG. Integration, Regulation, and Long-Term Stability of R2 Retrotransposons. Mobile DNA III: American Society for Microbiology; 2015. p. 1127-46.
81. Rangwala SH, Kazazian HH. The L1 retrotransposition assay: a retrospective and toolkit. Methods. 2009;49(3):219-26.
82. Kopera HC, Larson PA, Moldovan JB, Richardson SR, Liu Y, Moran JV. LINE-1 Cultured Cell Retrotransposition Assay. Methods Mol Biol. 2016;1400:139-56.
83. Boeke JD, Garfinkel DJ, Styles CA, Fink GR. Ty elements transpose through an RNA intermediate. Cell. 1985;40(3):491-500.
84. Heidmann T, Heidmann O, Nicolas JF. An indicator gene to demonstrate intracellular transposition of defective retroviruses. Proc Natl Acad Sci. 1988;85(7):2219-23.
85. Freeman J, Goodchild N, Mager D. A modified indicator gene for selection of retrotransposition events in mammalian cells. Biotechniques. 1994;17(1):46-52.
86. Moran JV, Holmes SE, Naas TP, DeBerardinis RJ, Boeke JD, Kazazian HH. High frequency retrotransposition in cultured mammalian cells. Cell. 1996;87(5):917-27.
87. Ostertag EM, Prak E, DeBerardinis R, Moran JV, Kazazian HH. Determination of L1 retrotransposition kinetics in cultured cells. Nucleic Acids Res. 2000;28(6):1418-23.
88. Xie Y, Rosser JM, Thompson TL, Boeke JD, An W. Characterization of L1 retrotransposition with high-throughput dual-luciferase assays. Nucleic Acids Res. 2011;39(3):e16-e.
89. Terasaki N, Goodier JL, Cheung LE, Wang YJ, Kajikawa M, Kazazian HH, et al. In vitro screening for compounds that enhance human L1 mobilization. PLoS ONE. 2013;8(9):e74629.
90. Esnault C, Casella J-F, Heidmann T. A Tetrahymena thermophila ribozyme-based indicator gene to detect transposition of marked retroelements in mammalian cells. Nucleic Acids Res. 2002;30(11):e49-e.
91. Dewannieux M, Esnault C, Heidmann T. LINE-mediated retrotransposition of marked Alu sequences. Nat Genet. 2003;35(1):41-8.
92. Dewannieux M, Dupressoir A, Harper F, Pierron G, Heidmann T. Identification of autonomous IAP LTR retrotransposons mobile in mammalian cells. Nat Genet. 2004;36(5):534-9.
93. Dewannieux M, Heidmann T. L1-mediated retrotransposition of murine B1 and B2 SINEs recapitulated in cultured cells. J Mol Biol. 2005;349(2):241-7.
94. Hancks DC, Goodier JL, Mandal PK, Cheung LE, Kazazian HH. Retrotransposition of marked SVA elements by human L1s in cultured cells. Hum Mol Genet. 2011;20(17):3386-400.
95. Raiz J, Damert A, Chira S, Held U, Klawitter S, Hamdorf M, et al. The non-autonomous retrotransposon SVA is trans-mobilized by the human LINE-1 protein machinery. Nucleic Acids Res. 2012;40(4):1666-83.
96. Bock A, Schumann GG. The Engineered SVA Trans-mobilization Assay. Methods Mol Biol. 2016;1400:203-22.
97. Ewing AD. Transposable element detection from whole genome sequence data. Mobile DNA. 2015;6(1).
98. Ostertag EM, Kazazian HH. Twin priming: a proposed mechanism for the creation of inversions in L1 retrotransposition. Genome Res. 2001;11(12):2059-65.
99. Han JS, Szak ST, Boeke JD. Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature. 2004;429(6989):268-74.
100. Minakami R, Kurose K, Etoh K, Furuhata Y, Hattori M, Sakaki Y. Identification of an internal cis-element essential for the human Li transcription and a nuclear factor (s) binding to the element. Nucleic Acids Res. 1992;20(12):3139-45.
101. Becker KG, Swergold G, Ozato K, Thayer RE. Binding of the ubiquitous nuclear transcription factor YY1 to a cis regulatory sequence in the human LINE-1 transposable element. Hum Mol Genet. 1993;2(10):1697-702.
102. Yang Z, Boffelli D, Boonmark N, Schwartz K, Lawn R. Apolipoprotein(a) gene enhancer resides within a LINE element. J Biol Chem. 1998;273(2):891-7.
103. Tchénio T, Casella J, Heidmann T. Members of the SRY family regulate the human LINE retrotransposons. Nucleic Acids Res. 2000;28(2):411-5.
104. Yang N, Kazazian HH. An important role for RUNX3 in human L1 transcription and retrotransposition. Nucleic Acids Res. 2003;31(16):4929-40.
105. Athanikar JN, Badge RM, Moran JV. A YY1-binding site is required for accurate human LINE-1 transcription initiation. Nucleic Acids Res. 2004;32(13):3846-55.
106. Muotri AR, Chu VT, Marchetto MCN, Deng W, Moran JV, Gage FH. Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. Nature. 2005;435(7044):903-10.
107. Laperriere D, Wang TT, White JH, Mader S. Widespread Alu repeat-driven expansion of consensus DR2 retinoic acid response elements during primate evolution. BMC Genomics. 2007;8:23.
108. Bourque G, Leong B, Vega VB, Chen X, Lee YL, Srinivasan KG, et al. Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res. 2008;18(11):1752-62.
109. Román AC, Benitez DA, Carvajal-Gonzalez JM, Fernandez-Salguero PM. Genome-wide B1 retrotransposon binds the transcription factors dioxin receptor and Slug and regulates gene expression in vivo. Proc Natl Acad Sci. 2008;105(5):1632-7.
110. Harris C, Dewan A, Zupnick A, Normart R, Gabriel A, Prives C, et al. p53 responsive elements in human retrotransposons. Oncogene. 2009;28(44):3857-65.
111. Kuwabara T, Hsieh J, Muotri A, Yeo G, Warashina M, Lie DC, et al. Wnt-mediated activation of NeuroD1 and retro-elements during adult neurogenesis. Nat Neurosci. 2009;12(9):1097-105.
112. Montoya-Durango DE, Liu Y, Teneng I, Kalbfleisch T, Lacy ME, Steffen MC, et al. Epigenetic control of mammalian LINE-1 retrotransposon by retinoblastoma proteins. Mutat Res/Fundam Mol Mech Mutagen. 2009;665(1-2):20-8.
113. Lee S-H, Cho S-Y, Shannon MF, Fan J, Rangasamy D. The impact of CpG island on defining transcriptional activation of the mouse L1 retrotransposable elements. PLoS ONE. 2010;5(6):e11353.
114. Román AC, González-Rico FJ, Moltó E, Hernando H, Neto A, Vicente-Garcia C, et al. Dioxin receptor and SLUG transcription factors regulate the insulator activity of B1 SINE retrotransposons via an RNA polymerase switch. Genome Res. 2011;21(3):422-32.
115. Hu Q, Tanasa B, Trabucchi M, Li W, Zhang J, Ohgi KA, et al. DICER- and AGO3-dependent generation of retinoic acid-induced DR2 Alu RNAs regulates human stem cell proliferation. Nat Struct Mol Biol. 2012;19(11):1168-75.
116. Schmidt D, Schwalie PC, Wilson MD, Ballester B, Gonçalves Â, Kutter C, et al. Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell. 2012;148(1):335-48.
117. Belancio VP, Hedges DJ, Deininger P. LINE-1 RNA splicing and influences on mammalian gene expression. Nucleic Acids Res. 2006;34(5):1512-21.
118. Belancio VP, Roy-Engel AM, Deininger P. The impact of multiple splice sites in human L1 elements. Gene. 2008;411(1-2):38-45.
119. Sorek R, Ast G, Graur D. Alu-containing exons are alternatively spliced. Genome Res. 2002;12(7):1060-7.
120. Lev-Maor G, Sorek R, Shomron N, Ast G. The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons. Science. 2003;300(5623):1288-91.
121. Sela N, Mersch B, Gal-Mark N, Lev-Maor G, Hotz-Wagenblatt A, Ast G. Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome. Genome Biol. 2007;8(6):R127.
122. Shen S, Lin L, Cai JJ, Jiang P, Kenkel EJ, Stroik MR, et al. Widespread establishment and regulatory impact of Alu exons in human genes. Proc Natl Acad Sci. 2011;108(7):2837-42.
123. Zarnack K, König J, Tajnik M, Martincorena I, Eustermann S, Stévant I, et al. Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell. 2013;152(3):453-66.
124. Holmes SE, Dombroski BA, Krebs CM, Boehm CD, Kazazian HH. A new retrotransposable human L1 element from the LRE2 locus on chromosome 1q produces a chimaeric insertion. Nat Genet. 1994;7(2):143-8.
125. Moran JV, DeBerardinis R, Kazazian HH. Exon shuffling by L1 retrotransposition. Science. 1999;283(5407):1530-4.
126. Pickeral OK, Makalowski W, Boguski M, Boeke JD. Frequent human genomic DNA transduction driven by LINE-1 retrotransposition. Genome Res. 2000;10(4):411-5.
127. Goodier JL, Ostertag EM, Kazazian HH. Transduction of 3'-flanking sequences is common in L1 retrotransposition. Hum Mol Genet. 2000;9(4):653-7.
128. Perepelitsa-Belancio V, Deininger P. RNA truncation by premature polyadenylation attenuates human mobile element activity. Nat Genet. 2003;35(4):363-6.
129. Hohjoh H, Singer MF. Cytoplasmic ribonucleoprotein complexes containing human LINE-1 protein and RNA. EMBO J. 1996;15(3):630.
130. Cook PR, Jones CE, Furano AV. Phosphorylation of ORF1p is required for L1 retrotransposition. Proc Natl Acad Sci. 2015;112(14):4298-303.
131. Sheehy AM, Gaddis NC, Choi JD, Malim MH. Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein. Nature. 2002;418(6898):646-50.
132. Harris RS, Liddament MT. Retroviral restriction by APOBEC proteins. Nat Rev Immunol. 2004;4(11):868-77.
133. Vieira VC, Soares MA. The role of cytidine deaminases on innate immune responses against human viral infections. BioMed Res Int. 2013;2013:1-18.
134. Willems L, Gillet NA. APOBEC3 Interference during Replication of Viral Genomes. Viruses. 2015;7(6):2999-3018.
135. Holmes RK, Malim MH, Bishop KN. APOBEC-mediated viral restriction: not simply editing? Trends Biochem Sci. 2007;32(3):118-28.
136. Kinomoto M, Kanno T, Shimura M, Ishizaka Y, Kojima A, Kurata T, et al. All APOBEC3 family proteins differentially inhibit LINE-1 retrotransposition. Nucleic Acids Res. 2007;35(9):2955-64.
137. Schumann G. APOBEC3 proteins: major players in intracellular defence against LINE-1-mediated retrotransposition. Biochem Soc Trans. 2007;35(3):637-42.
138. Chiu Y-L, Greene WC. The APOBEC3 cytidine deaminases: an innate defensive network opposing exogenous retroviruses and endogenous retroelements. Annu Rev Immunol. 2008;26(1):317-53.
139. Koito A, Ikeda T. Intrinsic restriction activity by AID/APOBEC family of enzymes against the mobility of retroelements. Mobile Genetic Elements. 2011;1(3):197-202.
140. Arias JF, Koyama T, Kinomoto M, Tokunaga K. Retroelements versus APOBEC3 family members: No great escape from the magnificent seven. Front Microbio. 2012;3:275.
141. Koito A, Ikeda T. Intrinsic immunity against retrotransposons by APOBEC cytidine deaminases. Front Microbio. 2013;4:28.
142. MacDuff DA, Demorest ZL, Harris RS. AID can restrict L1 retrotransposition suggesting a dual role in innate and adaptive immunity. Nucleic Acids Res. 2009;37(6):1854-67.
143. Ikeda T, Abd El Galil KH, Tokunaga K, Maeda K, Sata T, Sakaguchi N, et al. Intrinsic restriction activity by apolipoprotein B mRNA editing enzyme APOBEC1 against the mobility of autonomous retrotransposons. Nucleic Acids Res. 2011;39(13):5538-54.
144. Metzner M, Jäck HM, Wabl M. LINE-1 retroelements complexed and inhibited by activation induced cytidine deaminase. PLoS ONE. 2012;7(11):e49358.
145. Lindič N, Budič M, Petan T, Knisbacher BA, Levanon EY, Lovšin N. Differential inhibition of LINE1 and LINE2 retrotransposition by vertebrate AID/APOBEC proteins. Retrovirology. 2013;10(1):156.
146. Popp C, Dean W, Feng S, Cokus SJ, Andrews S, Pellegrini M, et al. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature. 2010;463(7284):1101-5.
147. Khatua AK, Taylor HE, Hildreth JEK, Popik W. Inhibition of LINE-1 and Alu retrotransposition by exosomes encapsidating APOBEC3G and APOBEC3F. Virology. 2010;400(1):68-75.
148. Balaj L, Lessard R, Dai L, Cho Y-J, Pomeroy SL, Breakefield XO, et al. Tumour microvesicles contain retrotransposon elements and amplified oncogene sequences. Nat Commun. 2011;2:180.
149. Stenglein MD, Harris RS. APOBEC3B and APOBEC3F Inhibit L1 Retrotransposition by a DNA Deamination-independent Mechanism. J Biol Chem. 2006;281(25):16837-41.
150. Esnault C, Priet S, Ribet D, Heidmann O, Heidmann T. Restriction by APOBEC3 proteins of endogenous retroviruses with an extracellular life cycle: ex vivo effects and in vivo "traces" on the murine IAPE and human HERV-K elements. Retrovirology. 2008;5(1):75.
151. Anwar F, Davenport MP, Ebrahimi D. Footprint of APOBEC3 on the genome of human retroelements. J Virol. 2013;87(14):8195-204.
152. Bogerd HP, Wiegand HL, Hulme AE, Garcia-Perez JL, O'Shea KS, Moran JV, et al. Cellular inhibitors of long interspersed element 1 and Alu retrotransposition. Proc Natl Acad Sci. 2006;103(23):8780-5.
153. Chiu YL, Witkowska HE, Hall SC, Santiago M, Soros VB, Esnault C, et al. High-molecular-mass APOBEC3G complexes restrict Alu retrotransposition. Proc Natl Acad Sci. 2006;103(42):15588-93.
154. Kozak SL, Marin M, Rose KM, Bystrom C, Kabat D. The Anti-HIV-1 editing enzyme APOBEC3G binds HIV-1 RNA and messenger RNAs that shuttle between polysomes and stress granules. J Biol Chem. 2006;281(39):29105-19.
155. Wichroski MJ, Robb GB, Rana TM. Human retroviral host restriction factors APOBEC3G and APOBEC3F localize to mRNA processing bodies. PLoS Pathog. 2006;2(5):e41.
156. Gallois-Montbrun S, Kramer B, Swanson CM, Byers H, Lynham S, Ward M, et al. Antiviral protein APOBEC3G localizes to ribonucleoprotein complexes found in P bodies and stress granules. J Virol. 2007;81(5):2165-78.
157. Lu C, Contreras X, Peterlin BM. P bodies inhibit retrotransposition of endogenous intracisternal A particles. J Virol. 2011;85(13):6244-51.
158. Horn AV, Klawitter S, Held U, Berger A, Vasudevan AAJ, Bock A, et al. Human LINE-1 restriction by APOBEC3C is deaminase independent and mediated by an ORF1p interaction that affects LINE reverse transcriptase activity. Nucleic Acids Res. 2014;42(1):396-416.
159. Carmi S, Church GM, Levanon EY. Large-scale DNA editing of retrotransposons accelerates mammalian genome evolution. Nat Commun. 2011;2:519.
160. Richardson SR, Narvaiza I, Planegger RA, Weitzman MD, Moran JV. APOBEC3A deaminates transiently exposed single-strand DNA during LINE-1 retrotransposition. eLife. 2014;3:e02008.
161. Kulpa DA, Moran JV. Cis-preferential LINE-1 reverse transcriptase activity in ribonucleoprotein particles. Nat Struct Mol Biol. 2006;13(7):655-60.
162. Goldstone DC, Ennis-Adeniran V, Hedden JJ, Groom HCT, Rice GI, Christodoulou E, et al. HIV-1 restriction factor SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase. Nature. 2011;480(7377):379-82.
163. Lahouassa H, Daddacha W, Hofmann H, Ayinde D, Logue EC, Dragin L, et al. SAMHD1 restricts the replication of human immunodeficiency virus type 1 by depleting the intracellular pool of deoxynucleoside triphosphates. Nat Immunol. 2012;13(3):223-8.
164. Baldauf H-M, Pan X, Erikson E, Schmidt S, Daddacha W, Burggraf M, et al. SAMHD1 restricts HIV-1 infection in resting CD4+ T cells. Nat Med. 2012;18(11):1682-9.
165. Gramberg T, Kahle T, Bloch N, Wittmann S, Müllers E, Daddacha W, et al. Restriction of diverse retroviruses by SAMHD1. Retrovirology. 2013;10(1):26.
166. Kim ET, White TE, Brandariz-Núñez A, Diaz-Griffero F, Weitzman MD. SAMHD1 restricts herpes simplex virus 1 in macrophages by limiting DNA replication. J Virol. 2013;87(23):12949-56.
167. Rice GI, Bond J, Asipu A, Brunette RL, Manfield IW, Carr IM, et al. Mutations involved in Aicardi-Goutieres syndrome implicate SAMHD1 as regulator of the innate immune response. Nat Genet. 2009;41(7):829-32.
168. Zhao K, Du J, Han X, Goodier John L, Li P, Zhou X, et al. Modulation of LINE-1 and Alu/SVA retrotransposition by Aicardi-Goutières syndrome-related SAMHD1. Cell Rep. 2013;4(6):1108-15.
169. White TE, Brandariz-Nuñez A, Valle-Casuso JC, Knowlton C, Kim B, Sawyer SL, et al. Effects of human SAMHD1 polymorphisms on HIV-1 susceptibility. Virology. 2014;460-461:34-44.
170. Upton K, Gerhardt D, Jesuadian J, Richardson S, Sánchez-Luque F, Bodea G, et al. Ubiquitous L1 mosaicism in hippocampal neurons. Cell. 2015;161(2):228-39.
171. Hu S, Li J, Xu F, Mei S, Le Duff Y, Yin L, et al. SAMHD1 Inhibits LINE-1 Retrotransposition by Promoting Stress Granule Formation. PLoS Genet. 2015;11(7):e1005367.
172. Zhu C, Gao W, Zhao K, Qin X, Zhang Y, Peng X et al. Structural insight into dGTP-dependent activation of tetrameric SAMHD1 deoxynucleoside triphosphate triphosphohydrolase. Nature Communications. 2013;4.
173. Ryoo J, Choi J, Oh C, Kim S, Seo M, Kim S-Y, et al. The ribonuclease activity of SAMHD1 is required for HIV-1 restriction. Nat Med. 2014;20(8):936-41.
174. Beliakova-Bethell N, Terry LJ, Bilanchone V, DaSilva R, Nagashima K, Wente SR, et al. Ty3 nuclear entry is initiated by viruslike particle docking on GLFG nucleoporins. J Virol. 2009;83(22):11914-25.
175. Checkley MA, Nagashima K, Lockett SJ, Nyswaner KM, Garfinkel DJ. P-Body components are required for Ty1 retrotransposition during assembly of retrotransposition-competent virus-like particles. Mol Cell Biol. 2010;30(2):382-98.
176. Bilanchone V, Clemens K, Kaake R, Dawson AR, Matheos D, Nagashima K, et al. Ty3 Retrotransposon Hijacks Mating Yeast RNA Processing Bodies to Infect New Genomes. PLoS Genet. 2015;11(9):e1005528.
177. O'Donnell KA, Boeke JD. Mighty Piwis defend the germline against genome intruders. Cell. 2007;129(1):37-44.
178. Obbard DJ, Gordon KHJ, Buck AH, Jiggins FM. The evolution of RNAi as a defence against viruses and transposable elements. Philos Trans R Soc Lond B Biol Sci. 2009;364(1513):99-115.
179. Siomi MC, Sato K, Pezic D, Aravin AA. PIWI-interacting small RNAs: the vanguard of genome defence. Nat Rev Mol Cell Biol. 2011;12(4):246-58.
180. Castañeda J, Genzor P, Bortvin A. piRNAs, transposon silencing, and germline genome integrity. Mutat Res/Fundam Mol Mech Mutagen. 2011;714(1-2):95-104.
181. Bao J, Yan W. Male germline control of transposable elements. Biol Reprod. 2012;86(5):162.
182. Guo M, Wu Y. Fighting an old war with a new weapon - silencing transposons by Piwi-interacting RNA. IUBMB Life. 2013;65(9):739-47.
183. Yang F, Wang PJ. Multiple LINEs of retrotransposon silencing mechanisms in the mammalian germline. Seminars in Cell & Developmental Biology. 2016;pii: S1084-9521(16)30066-0.
184. Smalheiser N, Torvik V. Mammalian microRNAs derived from genomic repeats. Trends Genet. 2005;21(6):322-6.
185. Tam OH, Aravin AA, Stein P, Girard A, Murchison EP, Cheloufi S, et al. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature. 2008;453(7194):534-8.
186. Watanabe T, Totoki Y, Toyoda A, Kaneda M, Kuramochi-Miyagawa S, Obata Y, et al. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature. 2008;453(7194):539-43.
187. Oey HM, Youngson NA, Whitelaw E. The characterisation of piRNA-related 19mers in the mouse. BMC Genomics. 2011;12(1):315.
188. Lukic S, Chen K. Human piRNAs are under selection in Africans and repress transposable elements. Mol Biol Evol. 2011;28(11):3061-7.
189. Roberts JT, Cardin SE, Borchert GM. Burgeoning evidence indicates that microRNAs were initially formed from transposable element sequences. Mobile Genetic Elements. 2014;4(3):e29255.
190. Soifer HS, Zaragoza A, Peyvan M, Behlke M, Rossi J. A potential role for RNA interference in controlling the activity of the human LINE-1 retrotransposon. Nucleic Acids Res. 2005;33(3):846-56.
191. Chen L, Dahlstrom JE, Lee S-H, Rangasamy D. Naturally occurring endo-siRNA silences LINE-1 retrotransposons in human cells through DNA methylation. Epigenetics. 2012;7(7):758-71.
192. Hamdorf M, Idica A, Zisoulis DG, Gamelin L, Martin C, Sanders KJ, et al. miR-128 represses L1 retrotransposition by binding directly to L1 RNA. Nat Struct Mol Biol. 2015;22(10):824-31.
193. Murchison EP, Stein P, Xuan Z, Pan H, Zhang MQ, Schultz RM, et al. Critical roles for Dicer in the female germline. Genes Dev. 2007;21(6):682-93.
194. Yang N, Kazazian HH. L1 retrotransposition is suppressed by endogenously encoded small interfering RNAs in human cultured cells. Nat Struct Mol Biol. 2006;13(9):763-71.
195. Kanellopoulou C, Muljo S, Kung A, Ganesan S, Drapkin R, Jenuwein T, et al. Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev. 2005;19(4):489-501.
196. Macias S, Plass M, Stajuda A, Michlewski G, Eyras E, Cáceres JF. DGCR8 HITS-CLIP reveals novel functions for the Microprocessor. Nat Struct Mol Biol. 2012;19(8):760-6.
197. Heras SR, Macias S, Plass M, Fernandez N, Cano D, Eyras E, et al. The Microprocessor controls the activity of mammalian retrotransposons. Nat Struct Mol Biol. 2013;20(10):1173-81.
198. Heras SR, Macias S, Cáceres JF, Garcia-Perez JL. Control of mammalian retrotransposons by cellular RNA processing activities. Mobile Genetic Elements. 2014;4(2):e28439.
199. Gunawardane LS, Saito K, Nishida KM, Miyoshi K, Kawamura Y, Nagami T, et al. A slicer-mediated mechanism for repeat-associated siRNA 5'end formation in Drosophila. Science. 2007;315(5818):1587-90.
200. Aravin AA, Sachidanandam R, Girard A, Fejes-Toth K, Hannon GJ. Developmentally regulated piRNA clusters implicate MILI in transposon control. Science. 2007;316(5825):744-7.
201. Aravin AA, Sachidanandam R, Bourc'his D, Schaefer C, Pezic D, Toth KF, et al. A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol Cell. 2008;31(6):785-99.
202. Kuramochi-Miyagawa S, Watanabe T, Gotoh K, Totoki Y, Toyoda A, Ikawa M, et al. DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes. Genes Dev. 2008;22(7):908-17.
203. Carmell MA, Girard A, van de Kant HJG, Bourc'his D, Bestor TH, de Rooij DG, et al. MIWI2 Is essential for spermatogenesis and repression of transposons in the mouse male germline. Dev Cell. 2007;12(4):503-14.
204. Soper SF, van der Heijden GW, Hardiman TC, Goodheart M, Martin SL, de Boer P, et al. Mouse maelstrom, a component of nuage, is essential for spermatogenesis and transposon repression in meiosis. Dev Cell. 2008;15(2):285-97.
205. Xu M, You Y, Hunsicker P, Hori T, Small C, Griswold MD, et al. Mice deficient for a small cluster of Piwi-interacting RNAs implicate Piwi-interacting RNAs in transposon control. Biol Reprod. 2008;79(1):51-7.
206. Ma L, Buchold GM, Greenbaum MP, Roy A, Burns KH, Zhu H, et al. GASZ is essential for male meiosis and suppression of retrotransposon expression in the male germline. PLoS Genet. 2009;5(9):e1000635.
207. Reuter M, Chuma S, Tanaka T, Franz T, Stark A, Pillai RS. Loss of the Mili-interacting Tudor domain-containing protein-1 activates transposons and alters the Mili-associated small RNA profile. Nat Struct Mol Biol. 2009;16(6):639-46.
208. Shoji M, Tanaka T, Hosokawa M, Reuter M, Stark A, Kato Y, et al. The TDRD9-MIWI2 complex is essential for piRNA-mediated retrotransposon silencing in the mouse male germline. Dev Cell. 2009;17(6):775-87.
209. Yoshimura T, Toyoda S, Kuramochi-Miyagawa S, Miyazaki T, Miyazaki S, Tashiro F, et al. Gtsf1/Cue110, a gene encoding a protein with two copies of a CHHC Zn-finger motif, is involved in spermatogenesis and retrotransposon suppression in murine testes. Dev Biol. 2009;335(1):216-27.
210. Kuramochi-Miyagawa S, Watanabe T, Gotoh K, Takamatsu K, Chuma S, Kojima-Kita K, et al. MVH in piRNA processing and gene silencing of retrotransposons. Genes Dev. 2010;24(9):887-92.
211. De Fazio S, Bartonicek N, Di Giacomo M, Abreu-Goodger C, Sankar A, Funaya C, et al. The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements. Nature. 2011;480(7376):259-63.
212. Reuter M, Berninger P, Chuma S, Shah H, Hosokawa M, Funaya C, et al. Miwi catalysis is required for piRNA amplification-independent LINE1 transposon silencing. Nature. 2011;480(7376):264-7.
213. Watanabe T, Chuma S, Yamamoto Y, Kuramochi-Miyagawa S, Totoki Y, Toyoda A, et al. MITOPLD is a mitochondrial protein essential for nuage formation and piRNA biogenesis in the mouse germline. Dev Cell. 2011;20(3):364-75.
214. Yabuta Y, Ohta H, Abe T, Kurimoto K, Chuma S, Saitou M. TDRD5 is required for retrotransposon silencing, chromatoid body assembly, and spermiogenesis in mice. J Cell Biol. 2011;192(5):781-95.
215. Xiol J, Cora E, Koglgruber R, Chuma S, Subramanian S, Hosokawa M, et al. A role for Fkbp6 and the chaperone machinery in piRNA amplification and transposon silencing. Mol Cell. 2012;47(6):970-9.
216. Di Giacomo M, Comazzetto S, Saini H, De Fazio S, Carrieri C, Morgan M, et al. Multiple epigenetic mechanisms and the piRNA pathway enforce LINE1 silencing during adult spermatogenesis. Mol Cell. 2013;50(4):601-8.
217. Lim AK, Lorthongpanich C, Chew TG, Tan CWG, Shue YT, Balu S, et al. The nuage mediates retrotransposon silencing in mouse primordial ovarian follicles. Development. 2013;140(18):3819-25.
218. Pandey RR, Tokuzawa Y, Yang Z, Hayashi E, Ichisaka T, Kajita S, et al. Tudor domain containing 12 (TDRD12) is essential for secondary PIWI interacting RNA biogenesis in mice. Proc Natl Acad Sci. 2013;110(41):16492-7.
219. Saxe JP, Chen M, Zhao H, Lin H. Tdrkh is essential for spermatogenesis and participates in primary piRNA biogenesis in the germline. EMBO J. 2013;32(13):1869-85.
220. Ichiyanagi T, Ichiyanagi K, Ogawa A, Kuramochi-Miyagawa S, Nakano T, Chuma S, et al. HSP90 plays an important role in piRNA biogenesis and retrotransposon repression in mouse. Nucleic Acids Res. 2014;42(19):11903-11.
221. Lim SL, Qu ZP, Kortschak RD, Lawrence DM, Geoghegan J, Hempfling A-L, et al. HENMT1 and piRNA stability are required for adult male germ cell transposon repression and to define the spermatogenic program in the mouse. PLoS Genet. 2015;11(10):e1005620.
222. Zamudio N, Barau J, Teissandier A, Walter M, Borsos M, Servant N, et al. DNA methylation restrains transposons from adopting a chromatin signature permissive for meiotic recombination. Genes Dev. 2015;29(12):1256-70.
223. Yang Z, Chen K-M, Pandey Radha R, Homolka D, Reuter M, Janeiro BK, et al. PIWI Slicing and EXD1 Drive Biogenesis of Nuclear piRNAs from Cytosolic Targets of the Mouse piRNA Pathway. Mol Cell. 2016;61(1):138-52.
224. Jaenisch R, Jähner D, Nobis P, Simon I, Löhler J, Harbers K, et al. Chromosomal position and activation of retroviral genomes inserted into the germ line of mice. Cell. 1981;24(2):519-29.
225. Mooslehner K, Müller U, Karls U, Hamann L, Harbers K. Structure and expression of a gene encoding a putative GTP-binding protein identified by provirus integration in a transgenic mouse strain. Mol Cell Biol. 1991;11(2):886-93.
226. Dalmay T, Horsefield R, Braunstein TH, Baulcombe DC. SDE3 encodes an RNA helicase required for post-transcriptional gene silencing in Arabidopsis. EMBO J. 2001;20(8):2069-77.
227. Cook HA, Koppetsch BS, Wu J, Theurkauf WE. The Drosophila SDE3 homolog armitage is required for oskar mRNA silencing and embryonic axis specification. Cell. 2004;116(6):817-29.
228. Meister G, Landthaler M, Peters L, Chen PY, Urlaub H, Lührmann R, et al. Identification of novel argonaute-associated proteins. Curr Biol. 2005;15(23):2149-55.
229. Furtak V, Mulky A, Rawlings SA, Kozhaya L, Lee K, KewalRamani VN, et al. Perturbation of the P-Body component Mov10 inhibits HIV-1 infectivity. PLoS ONE. 2010;5(2):e9081.
230. Wang X, Han Y, Dang Y, Fu W, Zhou T, Ptak RG, et al. Moloney leukemia virus 10 (MOV10) protein inhibits retrovirus replication. J Biol Chem. 2010;285(19):14346-55.
231. Burdick R, Smith JL, Chaipan C, Friew Y, Chen J, Venkatachari NJ, et al. P body-associated protein Mov10 inhibits HIV-1 replication at multiple stages. J Virol. 2010;84(19):10241-53.
232. Arjan-Odedra S, Swanson CM, Sherer NM, Wolinsky SM, Malim MH. Endogenous MOV10 inhibits the retrotransposition of endogenous retroelements but not the replication of exogenous retroviruses. Retrovirology. 2012;9(1):53.
233. Huang F, Zhang J, Zhang Y, Geng G, Liang J, Li Y, et al. RNA helicase MOV10 functions as a co-factor of HIV-1 Rev to facilitate Rev/RRE-dependent nuclear export of viral mRNAs. Virology. 2015;486:15-26.
234. Goodier JL, Cheung LE, Kazazian HH. MOV10 RNA helicase is a potent inhibitor of retrotransposition in cells. PLoS Genet. 2012;8(10):e1002941.
235. Gregersen L, Schueler M, Munschauer M, Mastrobuoni G, Chen W, Kempa S, et al. MOV10 Is a 5′ to 3′ RNA helicase contributing to UPF1 mRNA target degradation by translocation along 3′ UTRs. Mol Cell. 2014;54(4):573-85.
236. Moldovan JB, Moran JV. The Zinc-Finger Antiviral Protein ZAP Inhibits LINE and Alu Retrotransposition. PLoS Genet. 2015;11(5):e1005121.
237. Li X, Zhang J, Jia R, Cheng V, Xu X, Qiao W, et al. The MOV10 helicase inhibits LINE-1 mobility. J Biol Chem. 2013;288(29):21148-60.
238. Lu C, Luo Z, Jager S, Krogan NJ, Peterlin BM. Moloney leukemia virus type 10 inhibits reverse transcription and retrotransposition of intracisternal A particles. J Virol. 2012;86(19):10517-23.
239. Taylor MS, LaCava J, Mita P, Molloy K, Huang CR, Li D, et al. Affinity proteomics reveals human host factors implicated in discrete stages of LINE-1 retrotransposition. Cell. 2013;155(5):1034-48.
240. Moldovan JB. Identification of cellular host factors that associate with LINE-1 ORF1p and the effect of the Zinc Finger Antiviral Protein ZAP on LINE-1 retrotransposition [Ph.D. Thesis]: University of Michigan; 2015.
241. Zheng K, Wang PJ. Blockade of pachytene piRNA biogenesis reveals a novel requirement for maintaining post-meiotic germline genome integrity. PLoS Genet. 2012;8(11):e1003038.
242. Vourekas A, Zheng K, Fu Q, Maragkakis M, Alexiou P, Ma J, et al. The RNA helicase MOV10L1 binds piRNA precursors to initiate piRNA processing. Genes Dev. 2015;29(6):617-29.
243. Zhu X, Zhi E, Li Z. MOV10L1 in piRNA processing and gene silencing of retrotransposons during spermatogenesis. Reproduction. 2015;149(5):R229-35.
244. Frost RJ, Hamra FK, Richardson JA, Qi X, Bassel-Duby R, Olson EN. MOV10L1 is necessary for protection of spermatocytes against retrotransposons by Piwi-interacting RNAs. Proc Natl Acad Sci. 2010;107(26):11847-52.
245. Zheng K, Xiol J, Reuter M, Eckardt S, Leu NA, McLaughlin KJ, et al. Mouse MOV10L1 associates with Piwi proteins and is an essential component of the Piwi-interacting RNA (piRNA) pathway. Proc Natl Acad Sci. 2010;107(26):11841-6.
246. Hayakawa S, Shiratori S, Yamato H, Kameyama T, Kitatsuji C, Kashigi F, et al. ZAPS is a potent stimulator of signaling mediated by the RNA helicase RIG-I during antiviral responses. Nat Immunol. 2011;12(1):37-44.
247. Guo X, Carroll JWN, MacDonald MR, Goff SP, Gao G. The zinc finger antiviral protein directly binds to specific viral mRNAs through the CCCH zinc finger motifs. J Virol. 2004;78(23):12781-7.
248. Guo X, Ma J, Sun J, Gao G. The zinc-finger antiviral protein recruits the RNA processing exosome to degrade the target mRNA. Proc Natl Acad Sci. 2007;104(1):151-6.
249. Lee H, Komano J, Saitoh Y, Yamaoka S, Kozaki T, Misawa T, et al. Zinc-finger antiviral protein mediates retinoic acid inducible gene I-like receptor-independent antiviral response to murine leukemia virus. Proc Natl Acad Sci. 2013;110(30):12379-84.
250. Goodier JL, Pereira GC, Cheung LE, Rose RJ, Kazazian HH. The Broad-Spectrum Antiviral Protein ZAP Restricts Human Retrotransposition. PLoS Genet. 2015;11(5):e1005252.
251. Bick MJ, Carroll JW, Gao G, Goff SP, Rice CM, MacDonald MR. Expression of the zinc-finger antiviral protein inhibits alphavirus replication. J Virol. 2003;77(21):11555-62.
252. Zhu Y, Chen G, Lv F, Wang X, Ji X, Xu Y, et al. Zinc-finger antiviral protein inhibits HIV-1 infection by selectively targeting multiply spliced viral mRNAs for degradation. Proc Natl Acad Sci. 2011;108(38):15834-9.
253. Silverman RH. Viral Encounters with 2',5'-Oligoadenylate Synthetase and RNase L during the Interferon Antiviral Response. J Virol. 2007;81(23):12720-9.
254. Zhang A, Dong B, Doucet AJ, Moldovan JB, Moran JV, Silverman RH. RNase L restricts the mobility of engineered retrotransposons in cultured human cells. Nucleic Acids Res. 2014;42(6):3803-20.
255. Yan N, Regalado-Magdos AD, Stiggelbout B, Lee-Kirsch MA, Lieberman J. The cytosolic exonuclease TREX1 inhibits the innate immune response to human immunodeficiency virus type 1. Nat Immunol. 2010;11(11):1005-13.
256. Hasan M, Yan N. Safeguard against DNA sensing: the role of TREX1 in HIV-1 infection and autoimmune diseases. Front Microbiol. 2014;5:193.
257. Stetson DB, Ko JS, Heidmann T, Medzhitov R. Trex1 prevents cell-intrinsic initiation of autoimmunity. Cell. 2008;134(4):587-98.
258. deHaro D, Kines KJ, Sokolowski M, Dauchy RT, Streva VA, Hill SM, et al. Regulation of L1 expression and retrotransposition by melatonin and its receptor: implications for cancer risk associated with light exposure at night. Nucleic Acids Res. 2014;42(12):7694-707.
259. Dai L, Taylor MS, O'Donnell KA, Boeke JD. Poly(A) binding protein C1 is essential for efficient L1 retrotransposition and affects L1 RNP formation. Mol Cell Biol. 2012;32(21):4323-36.
260. Li P, Li J, Timmerman S, Krushel L, Martin S. The dicistronic RNA from the mouse LINE-1 retrotransposon contains an internal ribosome entry site upstream of each ORF: implications for retrotransposition. Nucleic Acids Res. 2006;34(3):853-64.
261. Peddigari S, Li PW-L, Rabe JL, Martin SL. hnRNPL and nucleolin bind LINE-1 RNA and function as host factors to modulate retrotransposition. Nucleic Acids Res. 2013;41(1):575-85.
262. Kuntz S, Kieffer E, Bianchetti L, Lamoureux N, Fuhrmann G, Viville S. Tex19, a Mammalian-Specific Protein with a Restricted Expression in Pluripotent Stem Cells and Germ Line. Stem Cells. 2008;26(3):734-44.
263. Ollinger R, Childs AJ, Burgess HM, Speed RM, Lundegaard PR, Reynolds N, et al. Deletion of the pluripotency-associated Tex19.1 gene causes activation of endogenous retroviruses and defective spermatogenesis in mice. PLoS Genet. 2008;4(9):e1000199.
264. Reichmann J, Reddington JP, Best D, Read D, Ollinger R, Meehan RR, et al. The genome-defence gene Tex19.1 suppresses LINE-1 retrotransposons in the placenta and prevents intra-uterine growth retardation in mice. Hum Mol Genet. 2013;22(9):1791-806.
265. Tarabay Y, Kieffer E, Teletin M, Celebi C, Van Montfoort A, Zamudio N, et al. The mammalian-specific Tex19.1 gene plays an essential role in spermatogenesis and placenta-supported development. Hum Reprod. 2013;28(8):2201-14.
266. Su Y-Q, Sugiura K, Sun F, Pendola JK, Cox GA, Handel MA, et al. MARF1 regulates essential oogenic processes in mice. Science. 2012;335(6075):1496-9.
267. Su Y-Q, Sun F, Handel MA, Schimenti JC, Eppig JJ. Meiosis arrest female 1 (MARF1) has nuage-like function in mammalian oocytes. Proc Natl Acad Sci. 2012;109(46):18653-60.
268. Bloch DB, Li P, Bloch EG, Berenson DF, Galdos RL, Arora P, et al. LMKB/MARF1 localizes to mRNA processing bodies, interacts with Ge-1, and regulates IFI44L gene expression. PLoS ONE. 2014;9(4):e94784.
269. Suzuki K, Morimoto M, Kondo C, Ohsumi Y. Selective autophagy regulates insertional mutagenesis by the Ty1 retrotransposon in Saccharomyces cerevisiae. Dev Cell. 2011;21(2):358-65.
270. Samuel CE. Adenosine deaminases acting on RNA (ADARs) are both antiviral and proviral. Virology. 2011;411(2):180-93.
271. Athanasiadis A, Rich A, Maas S. Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PLoS Biol. 2004;2(12):e391.
272. Blow M, Futreal P, Wooster R, Stratton M. A survey of RNA editing in human brain. Genome Res. 2004;14(12):2379-87.
273. Kim D, Kim T, Walsh T, Kobayashi Y, Matise T, Buyske S, et al. Widespread RNA editing of embedded Alu elements in the human transcriptome. Genome Res. 2004;14(9):1719-25.
274. Levanon EY, Eisenberg E, Yelin R, Nemzer S, Hallegger M, Shemesh R, et al. Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat Biotechnol. 2004;22(8):1001-5.
275. Eisenberg E, Nemzer S, Kinar Y, Sorek R, Rechavi G, Levanon EY. Is abundant A-to-I RNA editing primate-specific? Trends Genet. 2005;21(2):77-81.
276. Nishikura K. Editor meets silencer: crosstalk between RNA editing and RNA interference. Nat Rev Mol Cell Biol. 2006;7(12):919-31.
277. Nishikura K. A-to-I editing of coding and non-coding RNAs by ADARs. NatRev Mol Cell Biol. 2016;17(2):83-96.
278. Crichton JH, Dunican DS, MacLennan M, Meehan RR, Adams IR. Defending the genome from the enemy within: mechanisms of retrotransposon suppression in the mouse germline. Cell Mol Life Sci. 2014;71(9):1581-605.
279. Schlesinger S, Goff SP. Retroviral transcriptional regulation and embryonic stem cells: war and peace. Mol Cell Biol. 2015;35(5):770-7.
280. Zhang H, Zhu JK. RNA-directed DNA methylation. Curr Opin Plant Biol. 2011;14(2):142-7.
281. Gebert D, Rosenkranz D. RNA-based regulation of transposon expression. Wiley Interdiscip Rev: RNA. 2015;6(6):687-708.
282. Hutnick LK, Huang X, Loo T-C, Ma Z, Fan G. Repression of retrotransposal elements in mouse embryonic stem cells is primarily mediated by a DNA methylation-independent mechanism. J Biol Chem. 2010;285(27):21082-91.
283. Arand J, Spieler D, Karius T, Branco MR, Meilinger D, Meissner A, et al. In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases. PLoS Genet. 2012;8(6):e1002750.
284. Leung DC, Lorincz MC. Silencing of endogenous retroviruses: when and why do histone marks predominate? Trends Biochem Sci. 2012;37(4):127-33.
285. Kondo Y, Issa JP. Enrichment for histone H3 lysine 9 methylation at Alu repeats in human cells. J Biol Chem. 2003;278(30):27658-62.
286. Martens JH, O'Sullivan RJ, Braunschweig U, Opravil S, Radolf M, Steinlein P, et al. The profile of repeat-associated histone lysine methylation states in the mouse epigenome. EMBO J. 2005;24(4):800-12.
287. Hunter RG, Murakami G, Dewell S, Seligsohn M, Baker ME, Datson NA, et al. Acute stress and hippocampal histone H3 lysine 9 trimethylation, a retrotransposon silencing response. Proc Natl Acad Sci. 2012;109(43):17657-62.
288. Bulut-Karslioglu A, De La Rosa-Velázquez IA, Ramirez F, Barenboim M, Onishi-Seebacher M, Arand J, et al. Suv39h-dependent H3K9me3 marks intact retrotransposons and silences LINE elements in mouse embryonic stem cells. Mol Cell. 2014;55(2):277-90.
289. Di Giacomo M, Comazzetto S, Sampath SC, Sampath SC, O'Carroll D. G9a co-suppresses LINE1 elements in spermatogonia. Epigenetics Chromatin. 2014;7(1):24.
290. Dong KB, Maksakova IA, Mohn F, Leung D, Appanah R, Lee S, et al. DNA methylation in ES cells requires the lysine methyltransferase G9a but not its catalytic activity. EMBO J. 2008;27(20):2691-701.
291. Varshney D, Vavrova-Anderson J, Oler AJ, Cowling VH, Cairns BR, White RJ. SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation. Nat Commun. 2015;6:6569.
292. Liu S, Brind'Amour J, Karimi MM, Shirane K, Bogutz A, Lefebvre L, et al. Setdb1 is required for germline development and silencing of H3K9me3-marked endogenous retroviruses in primordial germ cells. Genes Dev. 2014;28(18):2041-55.
293. Huda A, Mariño-Ramírez L, Jordan IK. Epigenetic histone modifications of human transposable elements: genome defense versus exaptation. Mob DNA. 2010;1(1):2.
294. Rangasamy D. Distinctive patterns of epigenetic marks are associated with promoter regions of mouse LINE-1 and LTR retrotransposons. Mob DNA. 2013;4(1):27.
295. Su M, Han D, Boyd-Kirkup J, Yu X, Han J-DJ. Evolution of Alu elements toward enhancers. Cell Rep. 2014;7(2):376-85.
296. Fadloun A, Le Gras S, Jost B, Ziegler-Birling C, Takahashi H, Gorab E, et al. Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA. Nat Struct Mol Biol. 2013;20(3):332-8.
297. Hatanaka Y, Inoue K, Oikawa M, Kamimura S, Ogonuki N, Kodama EN, et al. Histone chaperone CAF-1 mediates repressive histone modifications to protect preimplantation mouse embryos from endogenous retrotransposons. Proc Natl Acad Sci. 2015;112(47):14641-6.
298. Montoya-Durango DE, Ramos KA, Bojang P, Ruiz L, Ramos IN, Ramos KS. LINE-1 silencing by retinoblastoma proteins is effected through the nucleosomal and remodeling deacetylase multiprotein complex. BMC Cancer. 2016;16(1):1.
299. Hagan CR, Rudin CM. DNA cleavage and Trp53 differentially affect SINE transcription. Genes Chromosomes Cancer. 2007;46(3):248-60.
300. Wylie A, Jones AE, D'Brot A, Lu W-J, Kurtz P, Moran JV, et al. p53 genes function to restrain mobile elements. Genes Dev. 2015;30(1):64-77.
301. Iyengar S, Farnham PJ. KAP1 protein: an enigmatic master regulator of the genome. J Biol Chem. 2011;286(30):26267-76.
302. Cheng C-T. KAPtain in charge of multiple missions: Emerging roles of KAP1. World J Biol Chem. 2014;5(3):308.
303. Wolf D, Goff SP. TRIM28 mediates primer binding site-targeted silencing of murine leukemia virus in embryonic cells. Cell. 2007;131(1):46-57.
304. Wolf D, Goff SP. Embryonic stem cells use ZFP809 to silence retroviral DNAs. Nature. 2009;458(7242):1201-4.
305. Rowe HM, Jakobsson J, Mesnard D, Rougemont J, Reynard S, Aktas T, et al. KAP1 controls endogenous retroviruses in embryonic stem cells. Nature. 2010;463(7278):237-40.
306. Rowe HM, Friedli M, Offner S, Verp S, Mesnard D, Marquis J, et al. De novo DNA methylation of endogenous retroviruses is shaped by KRAB-ZFPs/KAP1 and ESET. Development. 2013;140(3):519-29.
307. Turelli P, Castro-Diaz N, Marzetta F, Kapopoulou A, Raclot C, Duc J, et al. Interplay of TRIM28 and DNA methylation in controlling human endogenous retroelements. Genome Res. 2014;24(8):1260-70.
308. Wolf G, Greenberg D, Macfarlan TS. Spotting the enemy within: Targeted silencing of foreign DNA in mammalian genomes by the Krüppel-associated box zinc finger protein family. Mobile DNA. 2015;6(1).
309. Matsui T, Leung D, Miyashita H, Maksakova IA, Miyachi H, Kimura H, et al. Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET. Nature. 2010;464(7290):927-31.
310. Karimi M, Goyal P, Maksakova Irina A, Bilenky M, Leung D, Tang Jie X, et al. DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs. Cell Stem Cell. 2011;8(6):676-87.
311. Maksakova IA, Thompson PJ, Goyal P, Jones SJM, Singh PB, Karimi MM, et al. Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells. Epigenetics Chromatin. 2013;6(1):15.
312. Collins PL, Kyle KE, Egawa T, Shinkai Y, Oltz EM. The histone methyltransferase SETDB1 represses endogenous and exogenous retroviruses in B lymphocytes. Proc Natl Acad Sci. 2015;112(27):8367-72.
313. Castro-Diaz N, Ecco G, Coluccio A, Kapopoulou A, Yazdanpanah B, Friedli M, et al. Evolutionally dynamic L1 regulation in embryonic stem cells. Genes Dev. 2014;28(13):1397-409.
314. Tan X, Xu X, Elkenani M, Smorag L, Zechner U, Nolte J, et al. Zfp819, a novel KRAB-zinc finger protein, interacts with KAP1 and functions in genomic integrity maintenance of mouse embryonic stem cells. Stem Cell Res. 2013;11(3):1045-59.
315. Jacobs FM, Greenberg D, Nguyen N, Haeussler M, Ewing AD, Katzman S, et al. An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons. Nature. 2014;516(7530):242-5.
316. Castro-Diaz N, Friedli M, Trono D. Drawing a fine line on endogenous retroelement activity. Mobile Genetic Elements. 2015;5(1):1-6.
317. Puszyk W, Down T, Grimwade D, Chomienne C, Oakey RJ, Solomon E, et al. The epigenetic regulator PLZF represses L1 retrotransposition in germ and progenitor cells. EMBO J. 2013;32(13):1941-52.
318. Rollins RA, Haghighi F, Edwards JR, Das R, Zhang MQ, Ju J, et al. Large-scale structure of genomic methylation patterns. Genome Res. 2006;16(2):157-63.
319. Xie H, Wang M, Bonaldo MF, Smith C, Rajaram V, Goldman S, et al. High-throughput sequence-based epigenomic analysis of Alu repeats in human cerebellum. Nucleic Acids Res. 2009;37(13):4331-40.
320. Crowther P, Doherty J, Linsenmeyer M, Williamson M, Woodcock D. Revised genomic consensus for the hypermethylated CpG island region of the human L1 transposon and integration sites of full length L1 elements from recombinant clones made using methylation-tolerant host strains. Nucleic Acids Res. 1991;19(9):2395-401.
321. Thayer RE, Singer MF, Fanning TG. Undermethylation of specific LINE-1 sequences in human cells producing a LINE-1 -encoded protein. Gene. 1993;133(2):273-7.
322. Hata K, Sakaki Y. Identification of critical CpG sites for repression of L1 transcription by DNA methylation. Gene. 1997;189(2):227-34.
323. Woodcock DM, Lawler CB, Linsenmeyer ME, Doherty JP, Warren WD. Asymmetric methylation in the hypermethylated CpG promoter region of the human L1 retrotransposon. J Biol Chem. 1997;272(12):7810-6.
324. Yoder JA, Walsh CP, Bestor TH. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 1997;13(8):335-40.
325. Garcia-Perez JL, Morell M, Scheys JO, Kulpa DA, Morell S, Carter CC, et al. Epigenetic silencing of engineered L1 retrotransposition events in human embryonic carcinoma cells. Nature. 2010;466(7307):769-73.
326. Graff JR, Herman JG, Myohanen S, Baylin SB, Vertino PM. Mapping patterns of CpG island methylation in normal and neoplastic cells implicates both upstream and downstream regions in de Novo methylation. J Biol Chem. 1997;272(35):22322-9.
327. Rebollo R, Karimi MM, Bilenky M, Gagnier L, Miceli-Royer K, Zhang Y, et al. Retrotransposon-induced heterochromatin spreading in the mouse revealed by insertional polymorphisms. PLoS Genet. 2011;7(9):e1002301.
328. Zhang Y, Shu J, Si J, Shen L, Estecio MRH, Issa JPJ. Repetitive elements and enforced transcriptional repression co-operate to enhance DNA methylation spreading into a promoter CpG-island. Nucleic Acids Res. 2012;40(15):7257-68.
329. Pezic D, Manakov SA, Sachidanandam R, Aravin AA. piRNA pathway targets active LINE1 elements to establish the repressive H3K9me3 mark in germ cells. Genes Dev. 2014;28(13):1410-28.
330. Grandi FC, Rosser JM, Newkirk SJ, Yin J, Jiang X, Xing Z, et al. Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites. Genome Res. 2015;25(8):1135-46.
331. Sanford JP, Clark HJ, Chapman VM, Rossant J. Differences in DNA methylation during oogenesis and spermatogenesis and their persistence during early embryogenesis in the mouse. Genes Dev. 1987;1(10):1039-46.
332. Howlett SK, Reik W. Methylation levels of maternal and paternal genomes during preimplantation development. Development. 1991;113(1):119-27.
333. Hajkova P, Erhardt S, Lane N, Haaf T, El-Maarri O, Reik W, et al. Epigenetic reprogramming in mouse primordial germ cells. Mech Dev. 2002;117(1-2):15-23.
334. Lane N, Dean W, Erhardt S, Hajkova P, Surani A, Walter J, et al. Resistance of IAPs to methylation reprogramming may provide a mechanism for epigenetic inheritance in the mouse. Genesis. 2003;35(2):88-93.
335. Seki Y, Yamaji M, Yabuta Y, Sano M, Shigeta M, Matsui Y, et al. Cellular dynamics associated with the genome-wide epigenetic reprogramming in migrating primordial germ cells in mice. Development. 2007;134(14):2627-38.
336. Saitou M, Kagiwada S, Kurimoto K. Epigenetic reprogramming in mouse pre-implantation development and primordial germ cells. Development. 2012;139(1):15-31.
337. Seisenberger S, Andrews S, Krueger F, Arand J, Walter J, Santos F, et al. The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells. Mol Cell. 2012;48(6):849-62.
338. Molaro A, Falciatori I, Hodges E, Aravin AA, Marran K, Rafii S, et al. Two waves of de novo methylation during mouse germ cell development. Genes Dev. 2014;28(14):1544-9.
339. Walsh CP, Chaillet JR, Bestor TH. Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat Genet. 1998;20(2):116-7.
340. Liang G, Chan MF, Tomigahara Y, Tsai YC, Gonzales FA, Li E, et al. Cooperativity between DNA methyltransferases in the maintenance methylation of repetitive elements. Mol Cell Biol. 2002;22(2):480-91.
341. Gaudet F, Rideout WM, Meissner A, Dausman J, Leonhardt H, Jaenisch R. Dnmt1 expression in pre- and postimplantation embryogenesis and the maintenance of IAP silencing. Mol Cell Biol. 2004;24(4):1640-8.
342. Kato Y, Kaneda M, Hata K, Kumaki K, Hisano M, Kohara Y, et al. Role of the Dnmt3 family in de novo methylation of imprinted and repetitive sequences during male germ cell development in the mouse. Hum Mol Genet. 2007;16(19):2272-80.
343. Takebayashi S, Tamura T, Matsuoka C, Okano M. Major and essential role for the DNA Methylation mark in mouse embryogenesis and stable association of DNMT1 with newly replicated regions. Mol Cell Biol. 2007;27(23):8243-58.
344. Li Z, Dai H, Martos SN, Xu B, Gao Y, Li T et al. Distinct roles of DNMT1-dependent and DNMT1-independent methylation patterns in the genome of mouse embryonic stem cells. Genome Biol. 2015;16(1):115.
345. Bourc'his D, Bestor TH. Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature. 2004;431(7004):96-9.
346. Myant K, Stancheva I. LSH cooperates with DNA methyltransferases to repress transcription. Mol Cell Biol. 2008;28(1):215-26.
347. Huang J, Fan T, Yan Q, Zhu H, Fox S, Issaq H, et al. Lsh, an epigenetic guardian of repetitive elements. Nucleic Acids Res. 2004;32(17):5019-28.
348. De La Fuente R, Baumann C, Fan T, Schmidtmann A, Dobrinski I, Muegge K. Lsh is required for meiotic chromosome synapsis and retrotransposon silencing in female germ cells. Nat Cell Biol. 2006;8(12):1448-54.
349. Dunican DS, Cruickshanks HA, Suzuki M, Semple CA, Davey T, Arceci RJ, et al. Lsh regulates LTR retrotransposon repression independently of Dnmt3b function. Genome Biol. 2013;14:R146.
350. Bostick M, Kim JK, Esteve PO, Clark A, Pradhan S, Jacobsen SE. UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science. 2007;317(5845):1760-4.
351. Sharif J, Muto M, Takebayashi S-i, Suetake I, Iwamatsu A, Endo TA, et al. The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. Nature. 2007;450(7171):908-12.
352. Pastor WA, Stroud H, Nee K, Liu W, Pezic D, Manakov S et al. MORC1 represses transposable elements in the mouse male germline. Nature Communications. 2014;5:5795.
353. Moissiard G, Cokus SJ, Cary J, Feng S, Billi AC, Stroud H, et al. MORC family ATPases required for heterochromatin condensation and gene silencing. Science. 2012;336(6087):1448-51.
354. Fuks F, Hurd P, Deplus R, Kouzarides T. The DNA methyltransferases associate with HP1 and the SUV39H1 histone methyltransferase. Nucleic Acids Res. 2003;31(9):2305-12.
355. Yu F, Zingler N, Schumann GG, Stratling WH. Methyl-CpG-binding protein 2 represses LINE-1 expression and retrotransposition but not Alu transcription. Nucleic Acids Res. 2001;29(21):4493-501.
356. Muotri AR, Marchetto MCN, Coufal NG, Oefner R, Yeo G, Nakashima K, et al. L1 retrotransposition in neurons is modulated by MeCP2. Nature. 2010;468(7322):443-6.
357. Skene PJ, Illingworth RS, Webb S, Kerr AR, James KD, Turner DJ, et al. Neuronal MeCP2 is expressed at near histone-octamer levels and globally alters the chromatin state. Mol Cell. 2010;37(4):457-68.
358. Sampey GC, Guendel I, Das R, Jaworski E, Klase Z, Narayanan A, et al. Transcriptional Gene Silencing (TGS) via the RNAi Machinery in HIV-1 Infections. Biology. 2012;1(3):339-69.
359. Aravin AA, Bourc'his D. Small RNA guides for de novo DNA methylation in mammalian germ cells. Genes Dev. 2008;22(8):970-5.
360. Sienski G, Dönertas D, Brennecke J. Transcriptional silencing of transposons by Piwi and maelstrom and its impact on chromatin state and gene expression. Cell. 2012;151(5):964-80.
361. Sienski G, Batki J, Senti K-A, Dönertas D, Tirian L, Meixner K, et al. Silencio/CG9754 connects the Piwi-piRNA complex to the cellular heterochromatin machinery. Genes Dev. 2015;29(21):2258-71.
362. Macfarlan TS, Gifford WD, Agarwal S, Driscoll S, Lettieri K, Wang J, et al. Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1A. Genes Dev. 2011;25(6):594-607.
363. Ancelin K, Syx L, Borensztein M, Ranisavljevic N, Vassilev I, Briseño-Roa L et al. Maternal LSD1/KDM1A is an essential regulator of chromatin and transcription landscapes during zygotic genome activation. eLife. 2016:e08851.
364. Branco MR, Ficz G, Reik W. Uncovering the role of 5-hydroxymethylcytosine in the epigenome. Nat Rev Genet. 2012;13(1):7-13.
365. Ficz G, Branco MR, Seisenberger S, Santos F, Krueger F, Hore TA, et al. Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature. 2011;473(7347):398-402.
366. Wu TP, Wang T, Seetin MG, Lai Y, Zhu S, Lin K, et al. DNA methylation on N6-adenine in mammalian embryonic stem cells. Nature. 2016;532(7599):329-33.
367. Suzuki J, Yamaguchi K, Kajikawa M, Ichiyanagi K, Adachi N, Koyama H, et al. Genetic evidence that the non-homologous end-joining repair pathway is involved in LINE retrotransposition. PLoS Genet. 2009;5(4):e1000461.
368. Gasior SL, Roy-Engel AM, Deininger PL. ERCC1/XPF limits L1 retrotransposition. DNA Repair. 2008;7(6):983-9.
369. Gasior SL, Wakeman TP, Xu B, Deininger PL. The human LINE-1 retrotransposon creates DNA double-strand breaks. J Mol Biol. 2006;357(5):1383-93.
370. Wallace NA, Gasior SL, Faber ZJ, Howie HL, Deininger PL, Galloway DA. HPV 5 and 8 E6 expression reduces ATM protein levels and attenuates LINE-1 retrotransposition. Virology. 2013;443(1):69-79.
371. Coufal NG, Garcia-Perez JL, Peng GE, Marchetto MCN, Muotri AR, Mu Y, et al. Ataxia telangiectasia mutated (ATM) modulates long interspersed element-1 (L1) retrotransposition in human neural stem cells. Proc Natl Acad Sci. 2011;108(51):20382-7.
372. Thomas CA, Paquola AC, Muotri AR. LINE-1 retrotransposition in the nervous system. Annu Rev Cell Dev Biol. 2012;28:555-73.
373. Liu H-S, Jan M-S, Chou C-K, Chen P-H, Ke N-J. Is green fluorescent protein toxic to the living cells? Biochem Biophys Res Commun. 1999;260(3):712-7.
374. Zimmerly S, Guo H, Perlman PS, Lambowitz AM. Group II intron mobility occurs by target DNA-primed reverse transcription. Cell. 1995;82(4):545-54.
375. Eickbush DG, Luan DD, Eickbush TH. Integration of Bombyx mori R2 sequences into the 28S ribosomal RNA genes of Drosophila melanogaster. Mol Cell Biol. 2000;20(1):213-23.
376. Cost GJ, Feng Q, Jacquier A, Boeke JD. Human L1 element target-primed reverse transcription in vitro. EMBO J. 2002;21(21):5899-910.
377. Dawkins R, Krebs JR. Arms races between and within species. Proc R Soc B Biol Sci. 1979;205(1161):489-511.
378. Kerns JA, Emerman M, Malik HS. Positive selection and increased antiviral activity associated with the PARP-containing isoform of human zinc-finger antiviral protein. PLoS Genet. 2008;4(1):e21.
379. McLaughlin RN, Gable JT, Wittkopp C, Emerman M, Malik HS. Conservation and innovation of APOBEC3A restriction functions during primate evolution. Mol Biol Evol. 2016;33(8):1889-901.
380. Rowe HM, Trono D. Dynamic control of endogenous retroviruses during development. Virology. 2011;411(2):273-87.
381. Najafabadi HS, Mnaimneh S, Schmitges FW, Garton M, Lam KN, Yang A, et al. C2H2 zinc finger proteins greatly expand the human regulatory lexicon. Nat Biotechnol. 2015;33(5):555-62.
382. Närvä E, Rahkonen N, Emani MR, Lund R, Pursiheimo J-P, Nästi J, et al. RNA-binding protein L1TD1 interacts with LIN28 via RNA and is required for human embryonic stem cell self-renewal and cancer cell proliferation. Stem Cells. 2012;30(3):452-60.
383. Iwabuchi KA, Yamakawa T, Sato Y, Ichisaka T, Takahashi K, Okita K, et al. ECAT11/L1td1 is enriched in ESCs and rapidly activated during iPSCGeneration, but it is dispensable for the maintenance and induction of pluripotency. PLoS ONE. 2011;6(5):e20461.
384. McLaughlin RN, Young JM, Yang L, Neme R, Wichman HA, Malik HS. Positive selection and multiple losses of the LINE-1-derived L1TD1 gene in mammals suggest a dual role in genome defense and pluripotency. PLoS Genet. 2014;10(9):e1004531.
385. Kuhn A, Ong YM, Cheng C-Y, Wong TY, Quake SR, Burkholder WF. Linkage disequilibrium and signatures of positive selection around LINE-1 retrotransposons in the human genome. Proc Natl Acad Sci. 2014;111(22):8131-6.
386. Furano AV. The biological properties and evolutionary dynamics of mammalian LINE-1 retrotransposons. Prog Nucleic Acid Res Mol Biol. 2000;64:255-94.
387. Goodier JL, Ostertag EM, Du K, Kazazian HH. A novel active L1 retrotransposon subfamily in the mouse. Genome Res. 2001;11(10):1677-85.
388. Furano A, Duvernell D, Boissinot S. L1 (LINE-1) retrotransposon diversity differs dramatically between mammals and fish. Trends Genet. 2004;20(1):9-14.
389. Sookdeo A, Hepp CM, McClure MA, Boissinot S. Revisiting the evolution of mouse LINE-1 in the genomic era. Mob DNA. 2013;4(1):1.
390. Strebel K. HIV accessory proteins versus host restriction factors. Current Opinion in Virology. 2013;3(6):692-9.
391. Collins DR, Collins KL. HIV-1 accessory proteins adapt cellular adaptors to facilitate immune evasion. PLoS Pathog. 2014;10(1):e1003851.
392. Simon V, Bloch N, Landau NR. Intrinsic host restrictions to HIV-1 and mechanisms of viral escape. Nat Immunol. 2015;16(6):546-53.
393. Jones RB, Song H, Xu Y, Garrison KE, Buzdin AA, Anwar N, et al. LINE-1 retrotransposable element DNA accumulates in HIV-1-infected cells. J Virol. 2013;87(24):13307-20.
394. Romani B, Cohen ÉA. Lentivirus Vpr and Vpx accessory proteins usurp the cullin4-DDB1 (DCAF1) E3 ubiquitin ligase. Current Opinion in Virology. 2012;2(6):755-63.
395. Iijima K, Okudaira N, Tamura M, Doi A, Saito Y, Shimura M, et al. Viral protein R of human immunodeficiency virus type-1 induces retrotransposition of long interspersed element-1. Retrovirology. 2013;10(1):83.
396. Doi A, Iijima K, Kano S, Ishizaka Y. Viral protein R of HIV type-1 induces retrotransposition and upregulates glutamate synthesis by the signal transducer and activator of transcription 1 signaling pathway. Microbiol Immunol. 2015;59(7):398-409.
397. Coufal NG, Garcia-Perez JL, Peng GE, Yeo GW, Mu Y, Lovci MT, et al. L1 retrotransposition in human neural progenitor cells. Nature. 2009;460(7259):1127-31.
398. Bundo M, Toyoshima M, Okada Y, Akamatsu W, Ueda J, Nemoto-Miyauchi T, et al. Increased L1 retrotransposition in the neuronal genome in schizophrenia. Neuron. 2014;81(2):306-13.
399. White TB, McCoy AM, Streva VA, Fenrich J, Deininger PL. A droplet digital PCR detection method for rare L1 insertions in tumors. Mob DNA. 2014;5(1):30.
400. Goodier JL. Retrotransposition in tumors and brains. Mob DNA. 2014;5(1):11.
401. Sciamanna I, Gualtieri A, Cossetti C, Osimo EF, Ferracin M, Macchia G, et al. A tumor-promoting mechanism mediated by retrotransposon-encoded reverse transcriptase is active in human transformed cell lines. Oncotarget. 2013;4(12):2271-87.
402. Dhellin O, Maestre J, Heidmann T. Functional differences between the human LINE retrotransposon and retroviral reverse transcriptases for invivo mRNA reverse transcription. EMBO J. 1997;16(21):6590-602.
403. Shimizu A, Nakatani Y, Nakamura T, Jinno-Oue A, Ishikawa O, Boeke JD, et al. Characterisation of cytoplasmic DNA complementary to non-retroviral RNA viruses in human cells. Sci Rep. 2014;4:5074.
404. Fujimoto S, Tsuda T, Toda M, Yamagishi H. Transposon-like sequences in extrachromosomal circular DNA from mouse thymocytes. Proc Natl Acad Sci. 1985;82(7):2072-6.
405. Jones RS, Potter SS. L1 sequences in HeLa extrachromosomal circular DNA: evidence for circularization by homologous recombination. Proc Natl Acad Sci. 1985;82(7):1989-93.
406. Yamagishi H. Role of mammalian circular DNA in cellular differentiation. Bioessays. 1986;4(5):218-21.
407. Han JS, Shao S. Circular retrotransposition products generated by a LINE retrotransposon. Nucleic Acids Res. 2012;40(21):10866-77.
408. Cohen S, Regev A, Lavi S. Small polydispersed circular DNA (spcDNA) in human cells: association with genomic instability. Oncogene. 1997;14(8):977-85.
409. Schmidt H, Taubert H, Lange H, Kriese K, Schmitt WD, Hoffmann S, et al. Small polydispersed circular DNA contains strains of mobile genetic elements and occurs more frequently in permanent cell lines of malignant tumors than in normal lymphocytes. Oncol Rep. 2009;22(2):393-400.
410. Deininger P, Belancio VP. Detection of LINE-1 RNAs by Northern Blot. Methods Mol Biol. 2016;1400:223-36.
411. An W, Han JS, Wheelan SJ, Davis ES, Coombes CE, Ye P, et al. Active retrotransposition by a synthetic L1 element in mice. Proc Natl Acad Sci. 2006;103(49):18662-7.
412. van den Hurk JA, Meij IC, del Carmen SM, Kano H, Nikopoulos K, Hoefsloot LH, et al. L1 retrotransposition can occur early in human embryonic development. Hum Mol Genet. 2007;16(13):1587-92.
413. Kano H, Godoy I, Courtney C, Vetter MR, Gerton GL, Ostertag EM, et al. L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism. Genes Dev. 2009;23(11):1303-12.
414. Baillie JK, Barnett MW, Upton KR, Gerhardt DJ, Richmond TA, De Sapio F, et al. Somatic retrotransposition alters the genetic landscape of the human brain. Nature. 2011;479(7374):534-7.
415. Evrony G, Cai X, Lee E, Hills LB, Elhosary PC, Lehmann Hillel S, et al. Single-Neuron Sequencing Analysis of L1 Retrotransposition and Somatic Mutation in the Human Brain. Cell. 2012;151(3):483-96.
416. Evrony G, Lee E, Mehta Bhaven K, Benjamini Y, Johnson Robert M, Cai X, et al. Cell Lineage Analysis in Human Brain Using Endogenous Retroelements. Neuron. 2015;85(1):49-59.
417. Reilly MT, Faulkner GJ, Dubnau J, Ponomarev I, Gage FH. The role of transposable elements in health and diseases of the central nervous system. J Neurosci. 2013;33(45):17577-86.
418. Erwin JA, Marchetto MC, Gage FH. Mobile DNA elements in the generation of diversity and complexity in the brain. Nat Rev Neurosci. 2014;15(8):497-506.
419. Richardson SR, Morell S, Faulkner GJ. L1 retrotransposons and somatic mosaicism in the brain. Annu Rev Genet. 2014;48:1-27.
420. Hazen JL, Faust GG, Rodriguez AR, Ferguson WC, Shumilina S, Clark RA, et al. The Complete Genome Sequences, Unique Mutational Spectra, and Developmental Potency of Adult Neurons Revealed by Cloning. Neuron. 2016;89(6):1223-36.
421. Evrony GD, Lee E, Park PJ, Walsh CA. Resolving rates of mutation in the brain using single-neuron genomics. eLife. 2016;5:e12966.
422. Singer T, McConnell MJ, Marchetto MC, Coufal NG, Gage FH. LINE-1 retrotransposons: mediators of somatic variation in neuronal genomes? Trends Neurosci. 2010;33(8):345-54.
423. Iskow RC, McCabe MT, Mills RE, Torene S, Pittard WS, Neuwald AF, et al. Natural Mutagenesis of Human Genomes by Endogenous Retrotransposons. Cell. 2010;141(7):1253-61.
424. Lee E, Iskow R, Yang L, Gokcumen O, Haseley P, Luquette LJ, et al. Landscape of Somatic Retrotransposition in Human Cancers. Science. 2012;337(6097):967-71.
425. Helman E, Lawrence MS, Stewart C, Sougnez C, Getz G, Meyerson M. Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing. Genome Res. 2014;24(7):1053-63.
426. Shen Y, Chow J, Wang Z, Fan G. Abnormal CpG island methylation occurs during in vitro differentiation of human embryonic stem cells. Hum Mol Genet. 2006;15(17):2623-35.
427. Garcia-Perez JL, Marchetto MC, Muotri AR, Coufal NG, Gage FH, O'Shea KS, et al. LINE-1 retrotransposition in human embryonic stem cells. Hum Mol Genet. 2007;16(13):1569-77.
428. Macia A, Muñoz-Lopez M, Cortes JL, Hastings RK, Morell S, Lucena-Aguilar G, et al. Epigenetic control of retrotransposon expression in human embryonic stem cells. Mol Cell Biol. 2011;31(2):300-16.
429. Wissing S, Montano M, Garcia-Perez JL, Moran JV, Greene WC. Endogenous APOBEC3B restricts LINE-1 retrotransposition in transformed cells and human embryonic stem cells. J Biol Chem. 2011;286(42):36427-37.
430. Lee S-H, Rangasamy D. LINE-1 based insertional mutagenesis screens to identify genes involved in embryonic stem cell differentiation. J Stem Cell Res Ther. 2012;2:117.
431. Wissing S, Muñoz-Lopez M, Macia A, Yang Z, Montano M, Collins W, et al. Reprogramming somatic cells into iPS cells activates LINE-1 retroelement mobility. Hum Mol Genet. 2012;21(1):208-18.
432. Marchetto MC, Narvaiza I, Denli AM, Benner C, Lazzarini TA, Nathanson JL, et al. Differential L1 regulation in pluripotent stem cells of humans and apes. Nature. 2013;503(7477):525-9.
433. Friedli M, Turelli P, Kapopoulou A, Rauwel B, Castro-Díaz N, Rowe HM, et al. Loss of transcriptional control over endogenous retroelements during reprogramming to pluripotency. Genome Res. 2014;24(8):1251-9.
434. Macia A, Blanco-Jimenez E, García-Pérez JL. Retrotransposons in pluripotent cells: Impact and new roles in cellular plasticity. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. 2015;1849(4):417-26.
435. Gerdes P, Richardson SR, Mager DL, Faulkner GJ. Transposable elements in the mammalian embryo: pioneers surviving through stealth and service. Genome Biol. 2016;17(1):1.
436. Arokium H, Kamata M, Kim S, Kim N, Liang M, Presson AP, et al. Deep sequencing reveals low incidence of endogenous LINE-1 retrotransposition in human induced pluripotent stem cells. PLoS ONE. 2014;9(10):e108682.
437. Klawitter S, Fuchs NV, Upton KR, Muñoz-Lopez M, Shukla R, Wang J, et al. Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells. Nat Commun. 2016;7:10286.
438. Shukla R, Upton Kyle R, Muñoz-Lopez M, Gerhardt Daniel J, Fisher Malcolm E, Nguyen T, et al. Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell. 2013;153(1):101-11.
439. Doucet-O'Hare TT, Rodić N, Sharma R, Darbari I, Abril G, Choi JA, et al. LINE-1 expression and retrotransposition in Barrett's esophagus and esophageal carcinoma. Proc Natl Acad Sci. 2015;112(35):E4894-900.
440. Ewing AD, Gacita A, Wood LD, Ma F, Xing D, Kim M-S, et al. Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution. Genome Res. 2015;25(10):1536-45.
441. Doucet-O'Hare TT, Sharma R, Rodić N, Anders RA, Burns KH, Kazazian HH. Somatically acquired LINE-1 insertions in normal esophagus undergo clonal expansion in esophageal squamous cell carcinoma. Hum Mutat. 2016. doi: 10.1002/humu.23027.
442. Ewing AD, Ballinger TJ, Earl D, Harris CC, Ding L, Wilson RK, et al. Retrotransposition of gene transcripts leads to structural variation in mammalian genomes. Genome Biol. 2013;14(3):R22.
443. Tubio JM, Li Y, Ju YS, Martincorena I, Cooke SL, et al. Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes. Science. 2014;345(6196):1251343.
444. Rodić N, Steranka JP, Makohon-Moore A, Moyer A, Shen P, Sharma R, et al. Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma. Nat Med. 2015;21(9):1060-4.
445. Solyom S, Ewing AD, Rahrmann EP, Doucet T, Nelson HH, Burns MB, et al. Extensive somatic L1 retrotransposition in colorectal tumors. Genome Res. 2012;22(12):2328-38.
446. Belancio VP, Roy-Engel AM, Deininger PL. All y'all need to know 'bout retroelements in cancer. Seminars in Cancer Biology. 2010;20(4):200-10.
447. Carreira PE, Richardson SR, Faulkner GJ. L1 retrotransposons, cancer stem cells and oncogenesis. FEBS J. 2014;281(1):63-73.
448. Kemp JR, Longworth MS. Crossing the LINE toward genomic instability: LINE-1 retrotransposition in cancer. Front Chem. 2015;3:68.
449. Miki Y, Nishisho I, Horii A, Miyoshi Y, Utsunomiya J, Kinzler KW, et al. Disruption of the APC gene by a retrotransposal insertion of L1 sequence in a colon cancer. Cancer Res. 1992;52(3):643-5.
450. Scott EC, Gardner EJ, Masood A, Chuang NT, Vertino PM, Devine SE. A hot L1 retrotransposon evades somatic repression and initiates human colorectal cancer. Genome Res. 2016;26(6):745-55.
451. Burns MB, Temiz NA, Harris RS. Evidence for APOBEC3B mutagenesis in multiple human cancers. Nat Genet. 2013;45(9):977-83.
452. Roberts SA, Lawrence MS, Klimczak LJ, Grimm SA, Fargo D, Stojanov P, et al. An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers. Nat Genet. 2013;45(9):970-6.
453. Henderson S, Fenton T. APOBEC3 genes: retroviral restriction factors to cancer drivers. Trends Mol Med. 2015;21(5):274-84.
454. Rebhandl S, Huemer M, Greil R, Geisberger R. AID/APOBEC deaminases and cancer. Oncoscience. 2015;2:320.
455. Asch H, Eliacin E, Fanning T, Connolly J, Bratthauer G, Asch B. Comparative expression of the LINE-1 p40 protein in human breast carcinomas and normal breast tissues. Oncol Res. 1996;8(6):239.
456. Harris CR, Normart R, Yang Q, Stevenson E, Haffty BG, Ganesan S, et al. Association of nuclear localization of a Long Interspersed Nuclear Element-1 Protein in breast tumors with poor prognostic outcomes. Genes Cancer. 2010;1(2):115-24.
457. Chen L, Dahlstrom JE, Chandra A, Board P, Rangasamy D. Prognostic value of LINE-1 retrotransposon expression and its subcellular localization in breast cancer. Breast Cancer Res Treat. 2012;136(1):129-42.
458. Gualtieri A, Andreola F, Sciamanna I, Sinibaldi Vallebona P, Serafino A, Spadafora C. Increased expression and copy number amplification of LINE-1 and SINE B1 retrotransposable elements in murine mammary carcinoma progression. Oncotarget. 2013;4((11):1882-93.
459. Alves G, Tatro A, Fanning T. Differential methylation of human LINE-1 retrotransposons in malignant cells. Gene. 1996;176(1-2):39-44.
460. Kitkumthorn N, Mutirangura A. Long interspersed nuclear element-1 hypomethylation in cancer: biology and clinical applications. Clinical Epigenetics. 2011;2(2):315-30.
461. Haoudi A, Semmes OJ, Mason JM, Cannon RE. Retrotransposition-Competent Human LINE-1 Induces Apoptosis in Cancer Cells With Intact p53. J Biomed Biotechnol. 2004;2004(4):185-94.
462. Farkash EA, Prak ETL. DNA damage and L1 retrotransposition. J Biomed Biotechnol. 2006;2006:1-8.
463. Malki S, van der Heijden GW, O'Donnell Kathryn A, Martin Sandra L, Bortvin A. A role for retrotransposon LINE-1 in fetal oocyte attrition in mice. Dev Cell. 2014;29(5):521-33.
464. Chuma S. LINE-1 of evidence for fetal oocyte attrition by retrotransposon. Dev Cell. 2014;29(5):501-2.
465. St. Laurent G, Hammell N, McCaffrey TA. A LINE-1 component to human aging: Do LINE elements exact a longevity cost for evolutionary advantage? Mech Ageing Dev. 2010;131(5):299-305.
466. Wood JG, Helfand SL. Chromatin structure and transposable elements in organismal aging. Front Genet. 2013;4.
467. Sedivy JM, Kreiling JA, Neretti N, Cecco MD, Criscione SW, Hofmann JW, et al. Death by transposition - the enemy within? BioEssays. 2013;35(12):1035-43.
468. Belancio VP, Blask DE, Deininger P, Hill SM, Jazwinski SM. The aging clock and circadian control of metabolism and genome stability. Front Genet. 2015;5.
469. Maxwell PH. What might retrotransposons teach us about aging? Curr Genet. 2015.
470. Li W, Prazak L, Chatterjee N, Grüninger S, Krug L, Theodorou D, et al. Activation of transposable elements during aging and neuronal decline in Drosophila. Nat Neurosci. 2013;16(5):529-31.
471. De Cecco M, Criscione SW, Peckham EJ, Hillenmeyer S, Hamm EA, Manivannan J, et al. Genomes of replicatively senescent cells undergo global epigenetic changes leading to gene silencing and activation of transposable elements. Aging Cell. 2013;12(2):247-56.
472. De Cecco M, Criscione SW, Peterson AL, Neretti N, Sedivy JM, Kreiling JA. Transposable elements become active and mobile in the genomes of aging mammalian somatic tissues. Aging. 2013;5(12):867-83.
473. Van Meter M, Kashyap M, Rezazadeh S, Geneva AJ, Morello TD, Seluanov A, et al. SIRT6 represses LINE1 retrotransposons by ribosylating KAP1 but this repression fails with stress and age. Nat Commun. 2014;5:5011.
474. Flockerzi A, Ruggieri A, Frank O, Sauter M, Maldener E, Kopper B, et al. Expression patterns of transcribed human endogenous retrovirus HERV-K (HML-2) loci in human tissues and the need for a HERV Transcriptome Project. BMC Genomics. 2008;9(1):354.
475. Perron H, Hamdani N, Faucard R, Lajnef M, Jamain S, Daban-Huard C, et al. Molecular characteristics of Human Endogenous Retrovirus type-W in schizophrenia and bipolar disorder. Transl Psychiatry. 2012;2(12):e201.
476. Schmitt K, Reichrath J, Roesch A, Meese E, Mayer J. Transcriptional profiling of human endogenous retrovirus group HERV-K (HML-2) loci in melanoma. Genome Biol Evol. 2013;5(2):307-28.
477. Schmitt K, Richter C, Backes C, Meese E, Ruprecht K, Mayer J. Comprehensive analysis of human endogenous retrovirus group HERV-W locus transcription in multiple sclerosis brain lesions by high-throughput amplicon sequencing. J Virol. 2013;87(24):13837-52.
478. Douville RN, Nath A. Human endogenous retroviruses and the nervous system. Handb Clin Neurol. 2014;123:465-85.
479. Perl A, Fernandez D, Telarico T, Phillips PE. Endogenous retroviral pathogenesis in lupus. Curr Opin Rheumatol. 2010;22(5):483-92.
480. Lee Y-J, Jeong B-H, Choi E-K, Kim Y-S. Involvement of endogenous retroviruses in prion diseases. Pathogens. 2013;2(3):533-43.
481. Katoh I, Kurata S. Association of endogenous retroviruses and long terminal repeats with human disorders. Front Oncol. 2013;3:234.
482. Volkman HE, Stetson DB. The enemy within: endogenous retroelements and autoimmune disease. Nat Immunol. 2014;15(5):415-22.
483. Kassiotis G. Endogenous retroviruses and the development of cancer. J Immunol. 2014;192(4):1343-9.
484. Suntsova M, Garazha A, Ivanova A, Kaminsky D, Zhavoronkov A, Buzdin A. Molecular functions of human endogenous retroviruses in health and disease. Cell Mol Life Sci. 2015;72(19):3653-75.
485. Li W, Lee MH, Henderson L, Tyagi R, Bachani M, Steiner J, et al. Human endogenous retrovirus-K contributes to motor neuron disease. Sci Transl Med. 2015;7(307):307ra153.
486. Antony JM, DesLauriers AM, Bhat RK, Ellestad KK, Power C. Human endogenous retroviruses and multiple sclerosis: Innocent bystanders or disease determinants? Biochim Biophys Acta. 2011;1812(2):162-76.
487. Kiesel P, Gibson TJ, Ciesielczyk B, Bodemer M, Kaup F-J, Bodemer W, et al. Transcription of Alu DNA elements in blood cells of sporadic Creutzfeldt-Jakob disease (sCJD). Prion. 2010;4(2):87-93.
488. Kaneko H, Dridi S, Tarallo V, Gelfand BD, Fowler BJ, Cho WG, et al. DICER1 deficit induces Alu RNA toxicity in age-related macular degeneration. Nature. 2011;471(7338):325-30.
489. Tarallo V, Hirano Y, Gelfand Bradley D, Dridi S, Kerur N, Kim Y, et al. DICER1 loss and Alu RNA induce age-related macular degeneration via the NLRP3 inflammasome and MyD88. Cell. 2012;149(4):847-59.
490. Hung T, Pratt GA, Sundararaman B, Townsend MJ, Chaivorapol C, Bhangale T, et al. The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression. Science. 2015;350(6259):455-9.
491. Yu Q, Carbone CJ, Katlinskaya YV, Zheng H, Zheng K, Luo M, et al. Type I Interferon controls propagation of Long Interspersed Element-1. J Biol Chem. 2015;290(16):10191-9.
492. Crow YJ, Chase DS, Lowenstein Schmidt J, Szynkiewicz M, Forte GM, Gornall HL, et al. Characterization of human disease phenotypes associated with mutations in TREX1, RNASEH2A, RNASEH2B, RNASEH2C, SAMHD1, ADAR, and IFIH1. Am J Med Genet. 2015;167(2):296-312.
493. Crow YJ, Manel N. Aicardi-Goutières syndrome and the type I interferonopathies. Nat Rev Immunol. 2015;15(7):429-40.
494. Lee-Kirsch MA, Gong M, Chowdhury D, Senenko L, Engel K, Lee Y-A, et al. Mutations in the gene encoding the 3′-5′ DNA exonuclease TREX1 are associated with systemic lupus erythematosus. Nat Genet. 2007;39(9):1065-7.
495. Rice G, Newman WG, Dean J, Patrick T, Parmar R, Flintoff K, et al. Heterozygous mutations in TREX1 cause familial chilblain lupus and dominant Aicardi-Goutières syndrome. Am J Hum Genet. 2007;80(4):811-5.
496. Crow YJ, Rehwinkel J. Aicardi-Goutieres syndrome and related phenotypes: linking nucleic acid metabolism with autoimmunity. Hum Mol Genet. 2009;18(R2):R130-6.
497. Morita M, Stamp G, Robins P, Dulic A, Rosewell I, Hrivnak G, et al. Gene-targeted mice lacking the Trex1 (DNase III) 3'- > 5' DNA exonuclease develop inflammatory myocarditis. Mol Cell Biol. 2004;24(15):6719-27.
498. Ahn J, Ruiz P, Barber GN. Intrinsic self-DNA triggers inflammatory disease dependent on STING. J Immunol. 2014;193(9):4634-42.
499. Beck-Engeser GB, Eilat D, Wabl M. An autoimmune disease prevented by anti-retroviral drugs. Retrovirology. 2011;8(1):91.
500. Mills RE, Bennett EA, Iskow RC, Luttig CT, Tsui C, Pittard WS, et al. Recently mobilized transposons in the human and chimpanzee genomes. Am J Hum Genet. 2006;78(4):671-9.
501. Sciamanna I, Landriscina M, Pittoggi C, Quirino M, Mearelli C, Beraldi R, et al. Inhibition of endogenous reverse transcriptase antagonizes human tumor growth. Oncogene. 2005;24(24):3923-31.
502. Douville R, Liu J, Rothstein J, Nath A. Identification of active loci of a human endogenous retrovirus in neurons of patients with amyotrophic lateral sclerosis. Ann Neurol. 2011;69(1):141-51.
503. Patnala R, Lee S-H, Dahlstrom JE, Ohms S, Chen L, Dheen ST, et al. Inhibition of LINE-1 retrotransposon-encoded reverse transcriptase modulates the expression of cell differentiation genes in breast cancer cells. Breast Cancer Res Treat. 2014;143(2):239-53.
504. Sciamanna I, Gualtieri A, Piazza PV, Spadafora C. Regulatory roles of LINE-1-encoded reverse transcriptase in cancer onset and progression. Oncotarget. 2014;5(18):8039-51.
505. Rangasamy D, Lenka N, Ohms S, Dahlstrom J, Blackburn A, Board P. Activation of LINE-1 Retrotransposon Increases the Risk of Epithelial-Mesenchymal Transition and Metastasis in Epithelial Cancer. Curr Mol Med. 2015;15(7):588-97.
506. Ishizaka Y, Okudaira N, Tamura M, Iijima K, Shimura M, Goto M, et al. Modes of retrotransposition of long interspersed element-1 by environmental factors. Front Microbiol. 2012;3:191.
507. Mourier T, Nielsen LP, Hansen AJ, Willerslev E. Transposable elements in cancer as a by-product of stress-induced evolvability. Front Genet. 2014;5:156. eCollection 2014.
508. Okudaira N, Ishizaka Y, Nishio H. Retrotransposition of long interspersed element 1 induced by methamphetamine or cocaine. J Biol Chem. 2014;289(37):25476-85.
509. Hunter RG, Gagnidze K, McEwen BS, Pfaff DW. Stress and the dynamic genome: Steroids, epigenetics, and the transposome. Proc Natl Acad Sci. 2015;112(22):6828-33.
510. Miousse IR, Chalbot M-CG, Lumen A, Ferguson A, Kavouras IG, Koturbash I. Response of transposable elements to environmental stressors. Mutat Res/Rev Mutat Res. 2015;765:19-39.
511. Morales ME, Servant G, Ade C, Roy-Engel AM. Altering genomic integrity: heavy metal exposure promotes transposable element-mediated damage. Biol Trace Elem Res. 2015;166(1):24-33.
512. Moszczynska A, Flack A, Qiu P, Muotri AR, Killinger BA. Neurotoxic Methamphetamine Doses Increase LINE-1 Expression in the Neurogenic Zones of the Adult Rat Brain. Sci Rep. 2015;5:14356.
513. Behrendt R, Roers A. Mouse models for Aicardi-Goutières syndrome provide clues to the molecular pathogenesis of systemic autoimmunity. Clin Experiment Immunol. 2014;175(1):9-16.
514. Blankson JN, Siliciano JD, Siliciano RF. Finding a cure for human immunodeficiency virus-1 infection. Infect Dis Clin N Am. 2014;28(4):633-50.
515. Turelli P, Vianin S, Trono D. The innate antiretroviral factor APOBEC3G does not affect human LINE-1 retrotransposition in a cell culture assay. J Biol Chem. 2004;279(42):43371-3.
516. Bogerd HP, Wiegand HL, Doehle BP, Lueders KK, Cullen BR. APOBEC3A and APOBEC3B are potent inhibitors of LTR-retrotransposon function in human cells. Nucleic Acids Res. 2006;34(1):89-95.
517. Chen H, Lilley CE, Yu Q, Lee DV, Chou J, Narvaiza I, et al. APOBEC3A is a potent Inhibitor of adeno-associated virus and retrotransposons. Curr Biol. 2006;16(5):480-5.
518. Muckenfuss H, Hamdorf M, Held U, Perković M, Lower J, Cichutek K, et al. APOBEC3 proteins inhibit human LINE-1 retrotransposition. J Biol Chem. 2006;281(31):22161-72.
519. Hulme AE, Bogerd HP, Cullen BR, Moran JV. Selective inhibition of Alu retrotransposition by APOBEC3G. Gene. 2007;390(1):199-205.
520. Tan L, Sarkis PT, Wang T, Tian C, Yu X-F. Sole copy of Z2-type human cytidine deaminase APOBEC3H has inhibitory activity against retrotransposons and HIV-1. FASEB J. 2009;23(1):279-87.
521. Liang W, Xu J, Yuan W, Song X, Zhang J, Wei W, Yu XF, Yang Y. APOBEC3DE inhibits LINE-1 retrotransposition by interacting with ORF1p and influencing LINE reverse transcriptase activity. PLoS ONE. 2016;11(7):e0157220.