Dynamic control of endogenous retroviruses during development

Virology

Volumn 411, Issue 2, 2011, Pages 273-287

  Rowe, Helen M ^a   Trono, Didier ^a  

^a EPFL   (Switzerland)

Author keywords

Cytosine methylation; Development; Endogenous retrovirus (ERV); Histone methylation; Intracisternal A particle (IAP); KRAB associated protein 1 (KAP1); Kr ppel associated box domain zinc finger protein (KRAB ZFP); Long interspersed nuclear element (LINE); Retroelement

Indexed keywords

CYCLINE; DNA METHYLTRANSFERASE; HISTONE METHYLTRANSFERASE; KRUPPEL ASSOCIATED BOX DOMAIN ZINC FINGER PROTEIN; NUCLEAR PROTEIN; NUCLEAR PROTEIN 95; PROTEIN METHYLTRANSFERASE; TELOMERASE; UNCLASSIFIED DRUG; ZINC FINGER PROTEIN;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; BINDING SITE; CELL DIFFERENTIATION; CHROMATIN IMMUNOPRECIPITATION; DEACETYLATION; DEMETHYLATION; DNA METHYLATION; DNA SYNTHESIS; EMBRYO DEVELOPMENT; ENDODERM; ENDOGENOUS RETROVIRUS; GENE DISRUPTION; GENE EXPRESSION; GENE OVEREXPRESSION; GENE SILENCING; GENETIC POLYMORPHISM; GENOME; GENOME IMPRINTING; HETEROCHROMATIN; HOMOLOGOUS RECOMBINATION; HUMAN; METHYLATION; MOLECULAR DYNAMICS; MOSAICISM; NONHUMAN; PHYLOGENY; POINT MUTATION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CLEAVAGE; PROTEIN DOMAIN; PROTEIN LOCALIZATION; PROTEIN PHOSPHORYLATION; RETROPOSON; REVIEW; SEQUENCE HOMOLOGY; SYNCYTIOTROPHOBLAST; UBIQUITINATION;

EMBRYONIC DEVELOPMENT; ENDOGENOUS RETROVIRUSES; FETAL DEVELOPMENT; FETUS; GENE EXPRESSION REGULATION, VIRAL; HUMANS;

INTRACISTERNAL A-PARTICLES;

EID: 79952100303     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2010.12.007     Document Type: Review

References (256)

1. Achour M., Jacq X., Ronde P., Alhosin M., Charlot C., Chataigneau T., Jeanblanc M., Macaluso M., Giordano A., Hughes A.D., Schini-Kerth V.B., Bronner C. The interaction of the SRA domain of ICBP90 with a novel domain of DNMT1 is involved in the regulation of VEGF gene expression. Oncogene 2008, 27(15):2187-2197.
2. Akgun E., Ziegler M., Grez M. Determinants of retrovirus gene expression in embryonal carcinoma cells. J. Virol. 1991, 65(1):382-388.
3. Aravin A., Gaidatzis D., Pfeffer S., Lagos-Quintana M., Landgraf P., Iovino N., Morris P., Brownstein M.J., Kuramochi-Miyagawa S., Nakano T., Chien M., Russo J.J., Ju J., Sheridan R., Sander C., Zavolan M., Tuschl T. A novel class of small RNAs bind to MILI protein in mouse testes. Nature 2006, 442(7099):203-207.
4. Aravin A.A., Bourc'his D. Small RNA guides for de novo DNA methylation in mammalian germ cells. Genes Dev. 2008, 22(8):970-975.
5. Aravin A.A., Hannon G.J., Brennecke J. The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science 2007, 318(5851):761-764.
6. Aravin A.A., Naumova N.M., Tulin A.V., Vagin V.V., Rozovsky Y.M., Gvozdev V.A. Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Curr. Biol. 2001, 11(13):1017-1027.
7. Aravin A.A., Sachidanandam R., Bourc'his D., Schaefer C., Pezic D., Toth K.F., Bestor T., Hannon G.J. A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol. Cell 2008, 31(6):785-799.
8. Aravin A.A., Sachidanandam R., Girard A., Fejes-Toth K., Hannon G.J. Developmentally regulated piRNA clusters implicate MILI in transposon control. Science 2007, 316(5825):744-747.
9. Ayyanathan K., Lechner M.S., Bell P., Maul G.G., Schultz D.C., Yamada Y., Tanaka K., Torigoe K., Rauscher F.J. Regulated recruitment of HP1 to a euchromatic gene induces mitotically heritable, epigenetic gene silencing: a mammalian cell culture model of gene variegation. Genes Dev. 2003, 17(15):1855-1869.
10. Balada E., Ordi-Ros J., Vilardell-Tarres M. Molecular mechanisms mediated by human endogenous retroviruses (HERVs) in autoimmunity. Rev. Med. Virol. 2009, 19(5):273-286.
11. Bannert N., Kurth R. Retroelements and the human genome: new perspectives on an old relation. Proc. Natl Acad. Sci. USA 2004, 101(Suppl 2):14572-14579.
12. Bannister A.J., Zegerman P., Partridge J.F., Miska E.A., Thomas J.O., Allshire R.C., Kouzarides T. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 2001, 410(6824):120-124.
13. Barklis E., Mulligan R.C., Jaenisch R. Chromosomal position or virus mutation permits retrovirus expression in embryonal carcinoma cells. Cell 1986, 47(3):391-399.
14. Beck C.R., Collier P., Macfarlane C., Malig M., Kidd J.M., Eichler E.E., Badge R.M., Moran J.V. LINE-1 retrotransposition activity in human genomes. Cell 2010, 141(7):1159-1170.
15. Beckstead R.B., Ner S.S., Hales K.G., Grigliatti T.A., Baker B.S., Bellen H.J. Bonus, a Drosophila TIF1 homolog, is a chromatin-associated protein that acts as a modifier of position-effect variegation. Genetics 2005, 169(2):783-794.
16. Belshaw R., Dawson A.L., Woolven-Allen J., Redding J., Burt A., Tristem M. Genomewide screening reveals high levels of insertional polymorphism in the human endogenous retrovirus family HERV-K(HML2): implications for present-day activity. J. Virol. 2005, 79(19):12507-12514.
17. Best S., Le Tissier P., Towers G., Stoye J.P. Positional cloning of the mouse retrovirus restriction gene Fv1. Nature 1996, 382(6594):826-829.
18. Bestor T., Laudano A., Mattaliano R., Ingram V. Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells. The carboxyl-terminal domain of the mammalian enzymes is related to bacterial restriction methyltransferases. J. Mol. Biol. 1988, 203(4):971-983.
19. Bestor T.H. Cloning of a mammalian DNA methyltransferase. Gene 1988, 74(1):9-12.
20. Bhutani N., Brady J.J., Damian M., Sacco A., Corbel S.Y., Blau H.M. Reprogramming towards pluripotency requires AID-dependent DNA demethylation. Nature 2010, 463(7284):1042-1047.
21. Bilodeau S., Kagey M.H., Frampton G.M., Rahl P.B., Young R.A. SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state. Genes Dev. 2009, 23(21):2484-2489.
22. Birtle Z., Ponting C.P. Meisetz and the birth of the KRAB motif. Bioinformatics 2006, 22(23):2841-2845.
23. Blaise S., de Parseval N., Benit L., Heidmann T. Genomewide screening for fusogenic human endogenous retrovirus envelopes identifies syncytin 2, a gene conserved on primate evolution. Proc. Natl Acad. Sci. USA 2003, 100(22):13013-13018.
24. Blaise S., de Parseval N., Heidmann T. Functional characterization of two newly identified Human Endogenous Retrovirus coding envelope genes. Retrovirology 2005, 2:19.
25. Blomberg J., Benachenhou F., Blikstad V., Sperber G., Mayer J. Classification and nomenclature of endogenous retroviral sequences (ERVs): problems and recommendations. Gene 2009, 448(2):115-123.
26. Blond J.L., Lavillette D., Cheynet V., Bouton O., Oriol G., Chapel-Fernandes S., Mandrand B., Mallet F., Cosset F.L. An envelope glycoprotein of the human endogenous retrovirus HERV-W is expressed in the human placenta and fuses cells expressing the type D mammalian retrovirus receptor. J. Virol. 2000, 74(7):3321-3329.
27. Bostick M., Kim J.K., Esteve P.O., Clark A., Pradhan S., Jacobsen S.E. UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science 2007, 317(5845):1760-1764.
28. Bourc'his D., Voinnet O. A small-RNA perspective on gametogenesis, fertilization, and early zygotic development. Science 2010, 330(6004):617-622.
29. Brady T., Lee Y.N., Ronen K., Malani N., Berry C.C., Bieniasz P.D., Bushman F.D. Integration target site selection by a resurrected human endogenous retrovirus. Genes Dev. 2009, 23(5):633-642.
30. Brennecke J., Aravin A.A., Stark A., Dus M., Kellis M., Sachidanandam R., Hannon G.J. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 2007, 128(6):1089-1103.
31. Brower-Toland B., Findley S.D., Jiang L., Liu L., Yin H., Dus M., Zhou P., Elgin S.C., Lin H. Drosophila PIWI associates with chromatin and interacts directly with HP1a. Genes Dev. 2007, 21(18):2300-2311.
32. Brunmeir R., Lagger S., Simboeck E., Sawicka A., Egger G., Hagelkruys A., Zhang Y., Matthias P., Miller W.J., Seiser C. Epigenetic regulation of a murine retrotransposon by a dual histone modification mark. PLoS Genet. 2010, 6(4):e1000927.
33. Cammas F., Herzog M., Lerouge T., Chambon P., Losson R. Association of the transcriptional corepressor TIF1beta with heterochromatin protein 1 (HP1): an essential role for progression through differentiation. Genes Dev. 2004, 18(17):2147-2160.
34. Cammas F., Mark M., Dolle P., Dierich A., Chambon P., Losson R. Mice lacking the transcriptional corepressor TIF1beta are defective in early postimplantation development. Development 2000, 127(13):2955-2963.
35. Carlson L.L., Page A.W., Bestor T.H. Properties and localization of DNA methyltransferase in preimplantation mouse embryos: implications for genomic imprinting. Genes Dev. 1992, 6(12B):2536-2541.
36. Carmell M.A., Girard A., van de Kant H.J., Bourc'his D., Bestor T.H., de Rooij D.G., Hannon G.J. MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Dev. Cell 2007, 12(4):503-514.
37. Cedar H., Bergman Y. Linking DNA methylation and histone modification: patterns and paradigms. Nat. Rev. Genet. 2009, 10(5):295-304.
38. Chang P.C., Fitzgerald L.D., Van Geelen A., Izumiya Y., Ellison T.J., Wang D.H., Ann D.K., Luciw P.A., Kung H.J. Kruppel-associated box domain-associated protein-1 as a latency regulator for Kaposi's sarcoma-associated herpesvirus and its modulation by the viral protein kinase. Cancer Res. 2009, 69(14):5681-5689.
39. Chedin F., Lieber M.R., Hsieh C.L. The DNA methyltransferase-like protein DNMT3L stimulates de novo methylation by Dnmt3a. Proc. Natl Acad. Sci. USA 2002, 99(26):16916-16921.
40. Chen W.Y., Townes T.M. Molecular mechanism for silencing virally transduced genes involves histone deacetylation and chromatin condensation. Proc. Natl Acad. Sci. USA 2000, 97(1):377-382.
41. Chiu Y.L., Greene W.C. The APOBEC3 cytidine deaminases: an innate defensive network opposing exogenous retroviruses and endogenous retroelements. Annu. Rev. Immunol. 2008, 26:317-353.
42. Chow J.C., Ciaudo C., Fazzari M.J., Mise N., Servant N., Glass J.L., Attreed M., Avner P., Wutz A., Barillot E., Greally J.M., Voinnet O., Heard E. LINE-1 activity in facultative heterochromatin formation during X chromosome inactivation. Cell 2010, 141(6):956-969.
43. Colicelli J., Goff S.P. Isolation of a recombinant murine leukemia virus utilizing a new primer tRNA. J. Virol. 1986, 57(1):37-45.
44. Coufal N.G., Garcia-Perez J.L., Peng G.E., Yeo G.W., Mu Y., Lovci M.T., Morell M., O'Shea K.S., Moran J.V., Gage F.H. L1 retrotransposition in human neural progenitor cells. Nature 2009, 460(7259):1127-1131.
45. 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):1448-1454.
46. de Parseval N., Lazar V., Casella J.F., Benit L., Heidmann T. Survey of human genes of retroviral origin: identification and transcriptome of the genes with coding capacity for complete envelope proteins. J. Virol. 2003, 77(19):10414-10422.
47. Dekker J. Gene regulation in the third dimension. Science 2008, 319(5871):1793-1794.
48. Deng W., Lin H. Miwi, a murine homolog of piwi, encodes a cytoplasmic protein essential for spermatogenesis. Dev. Cell 2002, 2(6):819-830.
49. Dennis K., Fan T., Geiman T., Yan Q., Muegge K. Lsh, a member of the SNF2 family, is required for genome-wide methylation. Genes Dev. 2001, 15(22):2940-2944.
50. 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):534-539.
51. Dodge J.E., Kang Y.K., Beppu H., Lei H., Li E. Histone H3-K9 methyltransferase ESET is essential for early development. Mol. Cell. Biol. 2004, 24(6):2478-2486.
52. Dong K.B., Maksakova I.A., Mohn F., Leung D., Appanah R., Lee S., Yang H.W., Lam L.L., Mager D.L., Schubeler D., Tachibana M., Shinkai Y., Lorincz M.C. DNA methylation in ES cells requires the lysine methyltransferase G9a but not its catalytic activity. EMBO J. 2008, 27(20):2691-2701.
53. Duhl D.M., Vrieling H., Miller K.A., Wolff G.L., Barsh G.S. Neomorphic agouti mutations in obese yellow mice. Nat. Genet. 1994, 8(1):59-65.
54. Dupressoir A., Vernochet C., Bawa O., Harper F., Pierron G., Opolon P., Heidmann T. Syncytin-A knockout mice demonstrate the critical role in placentation of a fusogenic, endogenous retrovirus-derived, envelope gene. Proc. Natl Acad. Sci. USA 2009, 106(29):12127-12132.
55. Emerson R.O., Thomas J.H. Adaptive evolution in zinc finger transcription factors. PLoS Genet. 2009, 5(1):e1000325.
56. Epsztejn-Litman S., Feldman N., Abu-Remaileh M., Shufaro Y., Gerson A., Ueda J., Deplus R., Fuks F., Shinkai Y., Cedar H., Bergman Y. De novo DNA methylation promoted by G9a prevents reprogramming of embryonically silenced genes. Nat. Struct. Mol. Biol. 2008, 15(11):1176-1183.
57. Esnault C., Heidmann O., Delebecque F., Dewannieux M., Ribet D., Hance A.J., Heidmann T., Schwartz O. APOBEC3G cytidine deaminase inhibits retrotransposition of endogenous retroviruses. Nature 2005, 433(7024):430-433.
58. Feldman N., Gerson A., Fang J., Li E., Zhang Y., Shinkai Y., Cedar H., Bergman Y. G9a-mediated irreversible epigenetic inactivation of Oct-3/4 during early embryogenesis. Nat. Cell Biol. 2006, 8(2):188-194.
59. Feng S., Cokus S.J., Zhang X., Chen P.Y., Bostick M., Goll M.G., Hetzel J., Jain J., Strauss S.H., Halpern M.E., Ukomadu C., Sadler K.C., Pradhan S., Pellegrini M., Jacobsen S.E. Conservation and divergence of methylation patterning in plants and animals. Proc. Natl Acad. Sci. USA 2010, 107(19):8689-8694.
60. Feng S., Jacobsen S.E., Reik W. Epigenetic reprogramming in plant and animal development. Science 2010, 330(6004):622-627.
61. Ferguson-Smith A.C., Greally J.M. Epigenetics: perceptive enzymes. Nature 2007, 449(7159):148-149.
62. Feuer G., Taketo M., Hanecak R.C., Fan H. Two blocks in Moloney murine leukemia virus expression in undifferentiated F9 embryonal carcinoma cells as determined by transient expression assays. J. Virol. 1989, 63(5):2317-2324.
63. Filion G.J., van Bemmel J.G., Braunschweig U., Talhout W., Kind J., Ward L.D., Brugman W., de Castro I.J., Kerkhoven R.M., Bussemaker H.J., van Steensel B. Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell 2010, 143(2):212-224.
64. Fraser P., Bickmore W. Nuclear organization of the genome and the potential for gene regulation. Nature 2007, 447(7143):413-417.
65. Freitag M., Selker E.U. Controlling DNA methylation: many roads to one modification. Curr. Opin. Genet. Dev. 2005, 15(2):191-199.
66. Friedli M., Nikolaev S., Lyle R., Arcangeli M., Duboule D., Spitz F., Antonarakis S.E. Characterization of mouse Dactylaplasia mutations: a model for human ectrodactyly SHFM3. Mamm. Genome 2008, 19(4):272-278.
67. Fuks F., Hurd P.J., Deplus R., Kouzarides T. The DNA methyltransferases associate with HP1 and the SUV39H1 histone methyltransferase. Nucleic Acids Res. 2003, 31(9):2305-2312.
68. Gao X., Hou Y., Ebina H., Levin H.L., Voytas D.F. Chromodomains direct integration of retrotransposons to heterochromatin. Genome Res. 2008, 18(3):359-369.
69. Garcia-Perez J.L., Marchetto M.C., Muotri A.R., Coufal N.G., Gage F.H., O'Shea K.S., Moran J.V. LINE-1 retrotransposition in human embryonic stem cells. Hum. Mol. Genet. 2007, 16(13):1569-1577.
70. Garcia-Perez J.L., Morell M., Scheys J.O., Kulpa D.A., Morell S., Carter C.C., Hammer G.D., Collins K.L., O'Shea K.S., Menendez P., Moran J.V. Epigenetic silencing of engineered L1 retrotransposition events in human embryonic carcinoma cells. Nature 2010, 466(7307):769-773.
71. Gasior S.L., Roy-Engel A.M., Deininger P.L. ERCC1/XPF limits L1 retrotransposition. DNA Repair (Amst) 2008, 7(6):983-989.
72. Gaudet F., Rideout W.M., 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):1640-1648.
73. Gautsch J.W., Wilson M.C. Delayed de novo methylation in teratocarcinoma suggests additional tissue-specific mechanisms for controlling gene expression. Nature 1983, 301(5895):32-37.
74. Gifford R., Tristem M. The evolution, distribution and diversity of endogenous retroviruses. Virus Genes 2003, 26(3):291-315.
75. Gifford R.J., Katzourakis A., Tristem M., Pybus O.G., Winters M., Shafer R.W. A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution. Proc. Natl Acad. Sci. USA 2008, 105(51):20362-20367.
76. Gilbert C., Maxfield D.G., Goodman S.M., Feschotte C. Parallel germline infiltration of a lentivirus in two Malagasy lemurs. PLoS Genet. 2009, 5(3):e1000425.
77. Girard A., Sachidanandam R., Hannon G.J., Carmell M.A. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 2006, 442(7099):199-202.
78. Glass J.L., Fazzari M.J., Ferguson-Smith A.C., Greally J.M. CG dinucleotide periodicities recognized by the DNMT3a-DNMT3L complex are distinctive at retroelements and imprinted domains. Mamm. Genome 2009, 20(9-10):633-643.
79. Golding M.C., Zhang L., Mann M.R. Multiple epigenetic modifiers induce aggressive viral extinction in extraembryonic endoderm stem cells. Cell Stem Cell 2010, 6(5):457-467.
80. Goll M.G., Kirpekar F., Maggert K.A., Yoder J.A., Hsieh C.L., Zhang X., Golic K.G., Jacobsen S.E., Bestor T.H. Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2. Science 2006, 311(5759):395-398.
81. Goodier J.L., Kazazian H.H. Retrotransposons revisited: the restraint and rehabilitation of parasites. Cell 2008, 135(1):23-35.
82. Groner A.C., Meylan S., Ciuffi A., Zangger N., Ambrosini G., Denervaud N., Bucher P., Trono D. KRAB-zinc finger proteins and KAP1 can mediate long-range transcriptional repression through heterochromatin spreading. PLoS Genet. 2010, 6(3):e1000869.
83. Gunawardane L.S., Saito K., Nishida K.M., Miyoshi K., Kawamura Y., Nagami T., Siomi H., Siomi M.C. A slicer-mediated mechanism for repeat-associated siRNA 5' end formation in Drosophila. Science 2007, 315(5818):1587-1590.
84. Haas D.L., Lutzko C., Logan A.C., Cho G.J., Skelton D., Jin Yu X., Pepper K.A., Kohn D.B. The Moloney murine leukemia virus repressor binding site represses expression in murine and human hematopoietic stem cells. J. Virol. 2003, 77(17):9439-9450.
85. Hajkova P., Erhardt S., Lane N., Haaf T., El-Maarri O., Reik W., Walter J., Surani M.A. Epigenetic reprogramming in mouse primordial germ cells. Mech. Dev. 2002, 117(1-2):15-23.
86. Hamilton A.T., Huntley S., Tran-Gyamfi M., Baggott D.M., Gordon L., Stubbs L. Evolutionary expansion and divergence in the ZNF91 subfamily of primate-specific zinc finger genes. Genome Res. 2006, 16(5):584-594.
87. Hanna J.H., Saha K., Jaenisch R. Pluripotency and cellular reprogramming: facts, hypotheses, unresolved issues. Cell 2010, 143(4):508-525.
88. Hirasawa R., Chiba H., Kaneda M., Tajima S., Li E., Jaenisch R., Sasaki H. Maternal and zygotic Dnmt1 are necessary and sufficient for the maintenance of DNA methylation imprints during preimplantation development. Genes Dev. 2008, 22(12):1607-1616.
89. Howlett S.K., Reik W. Methylation levels of maternal and paternal genomes during preimplantation development. Development 1991, 113(1):119-127.
90. Huang J., Fan T., Yan Q., Zhu H., Fox S., Issaq H.J., Best L., Gangi L., Munroe D., Muegge K. Lsh, an epigenetic guardian of repetitive elements. Nucleic Acids Res. 2004, 32(17):5019-5028.
91. Huntley S., Baggott D.M., Hamilton A.T., Tran-Gyamfi M., Yang S., Kim J., Gordon L., Branscomb E., Stubbs L. A comprehensive catalog of human KRAB-associated zinc finger genes: insights into the evolutionary history of a large family of transcriptional repressors. Genome Res. 2006, 16(5):669-677.
92. Huthoff H., Towers G.J. Restriction of retroviral replication by APOBEC3G/F and TRIM5alpha. Trends Microbiol. 2008, 16(12):612-619.
93. Ivanov A.V., Peng H., Yurchenko V., Yap K.L., Negorev D.G., Schultz D.C., Psulkowski E., Fredericks W.J., White D.E., Maul G.G., Sadofsky M.J., Zhou M.M., Rauscher F.J. PHD domain-mediated E3 ligase activity directs intramolecular sumoylation of an adjacent bromodomain required for gene silencing. Mol. Cell 2007, 28(5):823-837.
94. Jackson J.P., Lindroth A.M., Cao X., Jacobsen S.E. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 2002, 416(6880):556-560.
95. Jacob Y., Stroud H., Leblanc C., Feng S., Zhuo L., Caro E., Hassel C., Gutierrez C., Michaels S.D., Jacobsen S.E. Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases. Nature 2010, 466(7309):987-991.
96. Jahner D., Stuhlmann H., Stewart C.L., Harbers K., Lohler J., Simon I., Jaenisch R. De novo methylation and expression of retroviral genomes during mouse embryogenesis. Nature 1982, 298(5875):623-628.
97. Jern P., Coffin J.M. Effects of retroviruses on host genome function. Annu. Rev. Genet. 2008, 42:709-732.
98. Jia D., Jurkowska R.Z., Zhang X., Jeltsch A., Cheng X. Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature 2007, 449(7159):248-251.
99. Jones P.L., Veenstra G.J., Wade P.A., Vermaak D., Kass S.U., Landsberger N., Strouboulis J., Wolffe A.P. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat. Genet. 1998, 19(2):187-191.
100. Jurka J. Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 2000, 16(9):418-420.
101. Jurka J., Kapitonov V.V., Pavlicek A., Klonowski P., Kohany O., Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 2005, 110(1-4):462-467.
102. Kaiser S.M., Malik H.S., Emerman M. Restriction of an extinct retrovirus by the human TRIM5alpha antiviral protein. Science 2007, 316(5832):1756-1758.
103. Kaneda M., Okano M., Hata K., Sado T., Tsujimoto N., Li E., Sasaki H. Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting. Nature 2004, 429(6994):900-903.
104. Kano H., Godoy I., Courtney C., Vetter M.R., Gerton G.L., Ostertag E.M., Kazazian H.H. L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism. Genes Dev. 2009, 23(11):1303-1312.
105. Kano H., Kurahashi H., Toda T. Genetically regulated epigenetic transcriptional activation of retrotransposon insertion confers mouse dactylaplasia phenotype. Proc. Natl Acad. Sci. USA 2007, 104(48):19034-19039.
106. Kato Y., Kaneda M., Hata K., Kumaki K., Hisano M., Kohara Y., Okano M., Li E., Nozaki M., Sasaki H. 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):2272-2280.
107. Katzourakis A., Gifford R.J., Tristem M., Gilbert M.T., Pybus O.G. Macroevolution of complex retroviruses. Science 2009, 325(5947):1512.
108. Katzourakis A., Tristem M., Pybus O.G., Gifford R.J. Discovery and analysis of the first endogenous lentivirus. Proc. Natl Acad. Sci. USA 2007, 104(15):6261-6265.
109. Keckesova Z., Ylinen L.M., Towers G.J., Gifford R.J., Katzourakis A. Identification of a RELIK orthologue in the European hare (Lepus europaeus) reveals a minimum age of 12 million years for the lagomorph lentiviruses. Virology 2009, 384(1):7-11.
110. Kempler G., Freitag B., Berwin B., Nanassy O., Barklis E. Characterization of the Moloney murine leukemia virus stem cell-specific repressor binding site. Virology 1993, 193(2):690-699.
111. Kidwell M.G. Transposable elements and the evolution of genome size in eukaryotes. Genetica 2002, 115(1):49-63.
112. Kigami D., Minami N., Takayama H., Imai H. MuERV-L is one of the earliest transcribed genes in mouse one-cell embryos. Biol. Reprod. 2003, 68(2):651-654.
113. Kim F.J., Battini J.L., Manel N., Sitbon M. Emergence of vertebrate retroviruses and envelope capture. Virology 2004, 318(1):183-191.
114. Kim J.K., Esteve P.O., Jacobsen S.E., Pradhan S. UHRF1 binds G9a and participates in p21 transcriptional regulation in mammalian cells. Nucleic Acids Res. 2009, 37(2):493-505.
115. Kourmouli N., Jeppesen P., Mahadevhaiah S., Burgoyne P., Wu R., Gilbert D.M., Bongiorni S., Prantera G., Fanti L., Pimpinelli S., Shi W., Fundele R., Singh P.B. Heterochromatin and tri-methylated lysine 20 of histone H4 in animals. J. Cell Sci. 2004, 117(Pt 12):2491-2501.
116. Kunarso G., Chia N.Y., Jeyakani J., Hwang C., Lu X., Chan Y.S., Ng H.H., Bourque G. Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat. Genet. 2010, 42(7):631-634.
117. Kuramochi-Miyagawa S., Watanabe T., Gotoh K., Totoki Y., Toyoda A., Ikawa M., Asada N., Kojima K., Yamaguchi Y., Ijiri T.W., Hata K., Li E., Matsuda Y., Kimura T., Okabe M., Sakaki Y., Sasaki H., Nakano T. DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes. Genes Dev. 2008, 22(7):908-917.
118. Kurth R., Bannert N. Beneficial and detrimental effects of human endogenous retroviruses. Int. J. Cancer 2010, 126(2):306-314.
119. Lachner M., O'Carroll D., Rea S., Mechtler K., Jenuwein T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 2001, 410(6824):116-120.
120. Lander E.S., et al. Initial sequencing and analysis of the human genome. Nature 2001, 409(6822):860-921.
121. Lane N., Dean W., Erhardt S., Hajkova P., Surani A., Walter J., Reik W. Resistance of IAPs to methylation reprogramming may provide a mechanism for epigenetic inheritance in the mouse. Genesis 2003, 35(2):88-93.
122. Law J.A., Jacobsen S.E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 2010, 11(3):204-220.
123. Lee J., Inoue K., Ono R., Ogonuki N., Kohda T., Kaneko-Ishino T., Ogura A., Ishino F. Erasing genomic imprinting memory in mouse clone embryos produced from day 11.5 primordial germ cells. Development 2002, 129(8):1807-1817.
124. Leeb M., Pasini D., Novatchkova M., Jaritz M., Helin K., Wutz A. Polycomb complexes act redundantly to repress genomic repeats and genes. Genes Dev. 2010, 24(3):265-276.
125. Lees-Murdock D.J., De Felici M., Walsh C.P. Methylation dynamics of repetitive DNA elements in the mouse germ cell lineage. Genomics 2003, 82(2):230-237.
126. Lehnertz B., Ueda Y., Derijck A.A., Braunschweig U., Perez-Burgos L., Kubicek S., Chen T., Li E., Jenuwein T., Peters A.H. Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr. Biol. 2003, 13(14):1192-1200.
127. Li H., Rauch T., Chen Z.X., Szabo P.E., Riggs A.D., Pfeifer G.P. The histone methyltransferase SETDB1 and the DNA methyltransferase DNMT3A interact directly and localize to promoters silenced in cancer cells. J. Biol. Chem. 2006, 281(28):19489-19500.
128. Li X., Ito M., Zhou F., Youngson N., Zuo X., Leder P., Ferguson-Smith A.C. A maternal-zygotic effect gene, Zfp57, maintains both maternal and paternal imprints. Dev. Cell 2008, 15(4):547-557.
129. Li X., Lee Y.K., Jeng J.C., Yen Y., Schultz D.C., Shih H.M., Ann D.K. Role for KAP1 serine 824 phosphorylation and sumoylation/desumoylation switch in regulating KAP1-mediated transcriptional repression. J. Biol. Chem. 2007, 282(50):36177-36189.
130. Li X., Lin H.H., Chen H., Xu X., Shih H.M., Ann D.K. SUMOylation of the transcriptional co-repressor KAP1 is regulated by the serine and threonine phosphatase PP1. Sci. Signal. 2010, 3(119):ra32.
131. Linney E., Davis B., Overhauser J., Chao E., Fan H. Non-function of a Moloney murine leukaemia virus regulatory sequence in F9 embryonal carcinoma cells. Nature 1984, 308(5958):470-472.
132. Lister R., Pelizzola M., Dowen R.H., Hawkins R.D., Hon G., Tonti-Filippini J., Nery J.R., Lee L., Ye Z., Ngo Q.M., Edsall L., Antosiewicz-Bourget J., Stewart R., Ruotti V., Millar A.H., Thomson J.A., Ren B., Ecker J.R. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009, 462(7271):315-322.
133. Litman G.W., Rast J.P., Fugmann S.D. The origins of vertebrate adaptive immunity. Nat. Rev. Immunol. 2010, 10(8):543-553.
134. Loebel D.A., Tsoi B., Wong N., O'Rourke M.P., Tam P.P. Restricted expression of ETn-related sequences during post-implantation mouse development. Gene Expr. Patterns 2004, 4(4):467-471.
135. Loh T.P., Sievert L.L., Scott R.W. Proviral sequences that restrict retroviral expression in mouse embryonal carcinoma cells. Mol. Cell. Biol. 1987, 7(10):3775-3784.
136. Loh T.P., Sievert L.L., Scott R.W. Evidence for a stem cell-specific repressor of Moloney murine leukemia virus expression in embryonal carcinoma cells. Mol. Cell. Biol. 1990, 10(8):4045-4057.
137. Lorincz M.C., Schubeler D., Goeke S.C., Walters M., Groudine M., Martin D.I. Dynamic analysis of proviral induction and de novo methylation: implications for a histone deacetylase-independent, methylation density-dependent mechanism of transcriptional repression. Mol. Cell. Biol. 2000, 20(3):842-850.
138. Lueders K.K., Kuff E.L. Sequences associated with intracisternal A particles are reiterated in the mouse genome. Cell 1977, 12(4):963-972.
139. Macfarlane C., Simmonds P. Allelic variation of HERV-K(HML-2) endogenous retroviral elements in human populations. J. Mol. Evol. 2004, 59(5):642-656.
140. Macia A., Munoz-Lopez M., Cortes J.L., Hastings R.K., Morell S., Lucena-Aguilar G., Marchal J.A., Badge R.M., Garcia-Perez J.L. Epigenetic control of retrotransposon expression in human embryonic stem cells. Mol. Cell. Biol. 2011, 3(2):300-316.
141. Mackay D.J., Callaway J.L., Marks S.M., White H.E., Acerini C.L., Boonen S.E., Dayanikli P., Firth H.V., Goodship J.A., Haemers A.P., Hahnemann J.M., Kordonouri O., Masoud A.F., Oestergaard E., Storr J., Ellard S., Hattersley A.T., Robinson D.O., Temple I.K. Hypomethylation of multiple imprinted loci in individuals with transient neonatal diabetes is associated with mutations in ZFP57. Nat. Genet. 2008, 40(8):949-951.
142. Maksakova I.A., Romanish M.T., Gagnier L., Dunn C.A., van de Lagemaat L.N., Mager D.L. Retroviral elements and their hosts: insertional mutagenesis in the mouse germ line. PLoS Genet. 2006, 2(1):e2.
143. Malik H.S., Henikoff S., Eickbush T.H. Poised for contagion: evolutionary origins of the infectious abilities of invertebrate retroviruses. Genome Res. 2000, 10(9):1307-1318.
144. Manel N., Hogstad B., Wang Y., Levy D.E., Unutmaz D., Littman D.R. A cryptic sensor for HIV-1 activates antiviral innate immunity in dendritic cells. Nature 2010, 467(7312):214-217.
145. Martens J.H., O'Sullivan R.J., Braunschweig U., Opravil S., Radolf M., Steinlein P., Jenuwein T. The profile of repeat-associated histone lysine methylation states in the mouse epigenome. EMBO J. 2005, 24(4):800-812.
146. Matsui T., Leung D., Miyashita H., Maksakova I.A., Miyachi H., Kimura H., Tachibana M., Lorincz M.C., Shinkai Y. Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET. Nature 2010, 464(7290):927-931.
147. Medstrand P., van de Lagemaat L.N., Mager D.L. Retroelement distributions in the human genome: variations associated with age and proximity to genes. Genome Res. 2002, 12(10):1483-1495.
148. Meilinger D., Fellinger K., Bultmann S., Rothbauer U., Bonapace I.M., Klinkert W.E., Spada F., Leonhardt H. Np95 interacts with de novo DNA methyltransferases, Dnmt3a and Dnmt3b, and mediates epigenetic silencing of the viral CMV promoter in embryonic stem cells. EMBO Rep. 2009, 10(11):1259-1264.
149. Meissner A., Mikkelsen T.S., Gu H., Wernig M., Hanna J., Sivachenko A., Zhang X., Bernstein B.E., Nusbaum C., Jaffe D.B., Gnirke A., Jaenisch R., Lander E.S. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 2008, 454(7205):766-770.
150. Meylan S., Trono D. Innate immunity against retroviral pathogens: from an ambiguous genetic self to novel therapeutic approaches. Swiss Med. Wkly 2009, 139(49-50):706-711.
151. Michaud E.J., van Vugt M.J., Bultman S.J., Sweet H.O., Davisson M.T., Woychik R.P. Differential expression of a new dominant agouti allele (Aiapy) is correlated with methylation state and is influenced by parental lineage. Genes Dev. 1994, 8(12):1463-1472.
152. Mikkelsen T.S., Ku M., Jaffe D.B., Issac B., Lieberman E., Giannoukos G., Alvarez P., Brockman W., Kim T.K., Koche R.P., Lee W., Mendenhall E., O'Donovan A., Presser A., Russ C., Xie X., Meissner A., Wernig M., Jaenisch R., Nusbaum C., Lander E.S., Bernstein B.E. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007, 448(7153):553-560.
153. Modin C., Lund A.H., Schmitz A., Duch M., Pedersen F.S. Alleviation of murine leukemia virus repression in embryonic carcinoma cells by genetically engineered primer binding sites and artificial tRNA primers. Virology 2000, 278(2):368-379.
154. Mohn F., Weber M., Rebhan M., Roloff T.C., Richter J., Stadler M.B., Bibel M., Schubeler D. Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Mol. Cell 2008, 30(6):755-766.
155. Morgan H.D., Santos F., Green K., Dean W., Reik W. Epigenetic reprogramming in mammals. Hum. Mol. Genet. 2005, 14(Spec No 1):R47-R58.
156. Morgan H.D., Sutherland H.G., Martin D.I., Whitelaw E. Epigenetic inheritance at the agouti locus in the mouse. Nat. Genet. 1999, 23(3):314-318.
157. Moyes D., Griffiths D.J., Venables P.J. Insertional polymorphisms: a new lease of life for endogenous retroviruses in human disease. Trends Genet. 2007, 23(7):326-333.
158. Muotri A.R., Chu V.T., Marchetto M.C., Deng W., Moran J.V., Gage F.H. Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. Nature 2005, 435(7044):903-910.
159. Muotri A.R., Marchetto M.C., Coufal N.G., Oefner R., Yeo G., Nakashima K., Gage F.H. L1 retrotransposition in neurons is modulated by MeCP2. Nature 2010, 468(7322):443-446.
160. Nakamura T., Arai Y., Umehara H., Masuhara M., Kimura T., Taniguchi H., Sekimoto T., Ikawa M., Yoneda Y., Okabe M., Tanaka S., Shiota K., Nakano T. PGC7/Stella protects against DNA demethylation in early embryogenesis. Nat. Cell Biol. 2007, 9(1):64-71.
161. Nan X., Ng H.H., Johnson C.A., Laherty C.D., Turner B.M., Eisenman R.N., Bird A. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 1998, 393(6683):386-389.
162. Niwa O., Yokota Y., Ishida H., Sugahara T. Independent mechanisms involved in suppression of the Moloney leukemia virus genome during differentiation of murine teratocarcinoma cells. Cell 1983, 32(4):1105-1113.
163. O'Geen H., Squazzo S.L., Iyengar S., Blahnik K., Rinn J.L., Chang H.Y., Green R., Farnham P.J. Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs. PLoS Genet. 2007, 3(6):e89.
164. Okano M., Bell D.W., Haber D.A., Li E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 1999, 99(3):247-257.
165. Okano M., Xie S., Li E. Dnmt2 is not required for de novo and maintenance methylation of viral DNA in embryonic stem cells. Nucleic Acids Res. 1998, 26(11):2536-2540.
166. Okita K., Ichisaka T., Yamanaka S. Generation of germline-competent induced pluripotent stem cells. Nature 2007, 448(7151):313-317.
167. Okitsu C.Y., Hsieh C.L. DNA methylation dictates histone H3K4 methylation. Mol. Cell. Biol. 2007, 27(7):2746-2757.
168. Ollinger R., Childs A.J., Burgess H.M., Speed R.M., Lundegaard P.R., Reynolds N., Gray N.K., Cooke H.J., Adams I.R. Deletion of the pluripotency-associated Tex19.1 gene causes activation of endogenous retroviruses and defective spermatogenesis in mice. PLoS Genet. 2008, 4(9):e1000199.
169. Ono M., Kawakami M., Ushikubo H. Stimulation of expression of the human endogenous retrovirus genome by female steroid hormones in human breast cancer cell line T47D. J. Virol. 1987, 61(6):2059-2062.
170. Ooi S.K., Qiu C., Bernstein E., Li K., Jia D., Yang Z., Erdjument-Bromage H., Tempst P., Lin S.P., Allis C.D., Cheng X., Bestor T.H. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 2007, 448(7154):714-717.
171. Oswald J., Engemann S., Lane N., Mayer W., Olek A., Fundele R., Dean W., Reik W., Walter J. Active demethylation of the paternal genome in the mouse zygote. Curr. Biol. 2000, 10(8):475-478.
172. Pannell D., Osborne C.S., Yao S., Sukonnik T., Pasceri P., Karaiskakis A., Okano M., Li E., Lipshitz H.D., Ellis J. Retrovirus vector silencing is de novo methylase independent and marked by a repressive histone code. EMBO J. 2000, 19(21):5884-5894.
173. Payer B., Saitou M., Barton S.C., Thresher R., Dixon J.P., Zahn D., Colledge W.H., Carlton M.B., Nakano T., Surani M.A. Stella is a maternal effect gene required for normal early development in mice. Curr. Biol. 2003, 13(23):2110-2117.
174. Peaston A.E., Evsikov A.V., Graber J.H., de Vries W.N., Holbrook A.E., Solter D., Knowles B.B. Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev. Cell 2004, 7(4):597-606.
175. Peters A.H., O'Carroll D., Scherthan H., Mechtler K., Sauer S., Schofer C., Weipoltshammer K., Pagani M., Lachner M., Kohlmaier A., Opravil S., Doyle M., Sibilia M., Jenuwein T. Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability. Cell 2001, 107(3):323-337.
176. Petersen R., Kempler G., Barklis E. A stem cell-specific silencer in the primer-binding site of a retrovirus. Mol. Cell. Biol. 1991, 11(3):1214-1221.
177. Piko L., Hammons M.D., Taylor K.D. Amounts, synthesis, and some properties of intracisternal A particle-related RNA in early mouse embryos. Proc. Natl Acad. Sci. USA 1984, 81(2):488-492.
178. Poznanski A.A., Calarco P.G. The expression of intracisternal A particle genes in the preimplantation mouse embryo. Dev. Biol. 1991, 143(2):271-281.
179. Rakyan V.K., Chong S., Champ M.E., Cuthbert P.C., Morgan H.D., Luu K.V., Whitelaw E. Transgenerational inheritance of epigenetic states at the murine Axin(Fu) allele occurs after maternal and paternal transmission. Proc. Natl Acad. Sci. USA 2003, 100(5):2538-2543.
180. Ramirez M.A., Pericuesta E., Fernandez-Gonzalez R., Moreira P., Pintado B., Gutierrez-Adan A. Transcriptional and post-transcriptional regulation of retrotransposons IAP and MuERV-L affect pluripotency of mice ES cells. Reprod. Biol. Endocrinol. 2006, 4:55.
181. Ramsahoye B.H., Biniszkiewicz D., Lyko F., Clark V., Bird A.P., Jaenisch R. Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc. Natl Acad. Sci. USA 2000, 97(10):5237-5242.
182. Reese K.J., Lin S., Verona R.I., Schultz R.M., Bartolomei M.S. Maintenance of paternal methylation and repression of the imprinted H19 gene requires MBD3. PLoS Genet. 2007, 3(8):e137.
183. Reik W. Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 2007, 447(7143):425-432.
184. Reiss D., Mager D.L. Stochastic epigenetic silencing of retrotransposons: does stability come with age?. Gene 2007, 390(1-2):130-135.
185. Ribet D., Dewannieux M., Heidmann T. An active murine transposon family pair: retrotransposition of "master" MusD copies and ETn trans-mobilization. Genome Res. 2004, 14(11):2261-2267.
186. Ribet D., Harper F., Dupressoir A., Dewannieux M., Pierron G., Heidmann T. An infectious progenitor for the murine IAP retrotransposon: emergence of an intracellular genetic parasite from an ancient retrovirus. Genome Res. 2008, 18(4):597-609.
187. Riclet R., Chendeb M., Vonesch J.L., Koczan D., Thiesen H.J., Losson R., Cammas F. Disruption of the interaction between transcriptional intermediary factor 1{beta} and heterochromatin protein 1 leads to a switch from DNA hyper- to hypomethylation and H3K9 to H3K27 trimethylation on the MEST promoter correlating with gene reactivation. Mol. Biol. Cell 2009, 20(1):296-305.
188. Rowe H.M., Jakobsson J., Mesnard D., Rougemont J., Reynard S., Aktas T., Maillard P.V., Layard-Liesching H., Verp S., Marquis J., Spitz F., Constam D.B., Trono D. KAP1 controls endogenous retroviruses in embryonic stem cells. Nature 2010, 463(7278):237-240.
189. Sado T., Okano M., Li E., Sasaki H. De novo DNA methylation is dispensable for the initiation and propagation of X chromosome inactivation. Development 2004, 131(5):975-982.
190. SanMiguel P., Tikhonov A., Jin Y.K., Motchoulskaia N., Zakharov D., Melake-Berhan A., Springer P.S., Edwards K.J., Lee M., Avramova Z., Bennetzen J.L. Nested retrotransposons in the intergenic regions of the maize genome. Science 1996, 274(5288):765-768.
191. Satou A., Taira T., Iguchi-Ariga S.M., Ariga H. A novel transrepression pathway of c-Myc. Recruitment of a transcriptional corepressor complex to c-Myc by MM-1, a c-Myc-binding protein. J. Biol. Chem. 2001, 276(49):46562-46567.
192. Schiavetti F., Thonnard J., Colau D., Boon T., Coulie P.G. A human endogenous retroviral sequence encoding an antigen recognized on melanoma by cytolytic T lymphocytes. Cancer Res. 2002, 62(19):5510-5516.
193. Schon U., Diem O., Leitner L., Gunzburg W.H., Mager D.L., Salmons B., Leib-Mosch C. Human endogenous retroviral long terminal repeat sequences as cell type-specific promoters in retroviral vectors. J. Virol. 2009, 83(23):12643-12650.
194. Schotta G., Lachner M., Sarma K., Ebert A., Sengupta R., Reuter G., Reinberg D., Jenuwein T. A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin. Genes Dev. 2004, 18(11):1251-1262.
195. Schroder A.R., Shinn P., Chen H., Berry C., Ecker J.R., Bushman F. HIV-1 integration in the human genome favors active genes and local hotspots. Cell 2002, 110(4):521-529.
196. Schubeler D., Lorincz M.C., Cimbora D.M., Telling A., Feng Y.Q., Bouhassira E.E., Groudine M. Genomic targeting of methylated DNA: influence of methylation on transcription, replication, chromatin structure, and histone acetylation. Mol. Cell. Biol. 2000, 20(24):9103-9112.
197. Schultz D.C., Ayyanathan K., Negorev D., Maul G.G., Rauscher F.J. SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins. Genes Dev. 2002, 16(8):919-932.
198. Schultz D.C., Friedman J.R., Rauscher F.J. Targeting histone deacetylase complexes via KRAB-zinc finger proteins: the PHD and bromodomains of KAP-1 form a cooperative unit that recruits a novel isoform of the Mi-2alpha subunit of NuRD. Genes Dev. 2001, 15(4):428-443.
199. Seifarth W., Frank O., Zeilfelder U., Spiess B., Greenwood A.D., Hehlmann R., Leib-Mosch C. Comprehensive analysis of human endogenous retrovirus transcriptional activity in human tissues with a retrovirus-specific microarray. J. Virol. 2005, 79(1):341-352.
200. Sharif J., Muto M., Takebayashi S., Suetake I., Iwamatsu A., Endo T.A., Shinga J., Mizutani-Koseki Y., Toyoda T., Okamura K., Tajima S., Mitsuya K., Okano M., Koseki H. The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. Nature 2007, 450(7171):908-912.
201. Shi Y., Lan F., Matson C., Mulligan P., Whetstine J.R., Cole P.A., Casero R.A. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 2004, 119(7):941-953.
202. Singh S., Kaye S., Gore M.E., McClure M.O., Bunker C.B. The role of human endogenous retroviruses in melanoma. Br. J. Dermatol. 2009, 161(6):1225-1231.
203. Song S.U., Gerasimova T., Kurkulos M., Boeke J.D., Corces V.G. An env-like protein encoded by a Drosophila retroelement: evidence that gypsy is an infectious retrovirus. Genes Dev. 1994, 8(17):2046-2057.
204. Soper S.F., van der Heijden G.W., Hardiman T.C., Goodheart M., Martin S.L., de Boer P., Bortvin A. Mouse maelstrom, a component of nuage, is essential for spermatogenesis and transposon repression in meiosis. Dev. Cell 2008, 15(2):285-297.
205. Sripathy S.P., Stevens J., Schultz D.C. The KAP1 corepressor functions to coordinate the assembly of de novo HP1-demarcated microenvironments of heterochromatin required for KRAB zinc finger protein-mediated transcriptional repression. Mol. Cell. Biol. 2006, 26(22):8623-8638.
206. Stetson D.B., Ko J.S., Heidmann T., Medzhitov R. Trex1 prevents cell-intrinsic initiation of autoimmunity. Cell 2008, 134(4):587-598.
207. Su A.I., Wiltshire T., Batalov S., Lapp H., Ching K.A., Block D., Zhang J., Soden R., Hayakawa M., Kreiman G., Cooke M.P., Walker J.R., Hogenesch J.B. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl Acad. Sci. USA 2004, 101(16):6062-6067.
208. Suetake I., Shinozaki F., Miyagawa J., Takeshima H., Tajima S. DNMT3L stimulates the DNA methylation activity of Dnmt3a and Dnmt3b through a direct interaction. J. Biol. Chem. 2004, 279(26):27816-27823.
209. Svoboda P., Stein P., Anger M., Bernstein E., Hannon G.J., Schultz R.M. RNAi and expression of retrotransposons MuERV-L and IAP in preimplantation mouse embryos. Dev. Biol. 2004, 269(1):276-285.
210. Tachibana M., Matsumura Y., Fukuda M., Kimura H., Shinkai Y. G9a/GLP complexes independently mediate H3K9 and DNA methylation to silence transcription. EMBO J. 2008, 27(20):2681-2690.
211. Tachibana M., Sugimoto K., Nozaki M., Ueda J., Ohta T., Ohki M., Fukuda M., Takeda N., Niida H., Kato H., Shinkai Y. G9a histone methyltransferase plays a dominant role in euchromatic histone H3 lysine 9 methylation and is essential for early embryogenesis. Genes Dev. 2002, 16(14):1779-1791.
212. Tachibana M., Ueda J., Fukuda M., Takeda N., Ohta T., Iwanari H., Sakihama T., Kodama T., Hamakubo T., Shinkai Y. Histone methyltransferases G9a and GLP form heteromeric complexes and are both crucial for methylation of euchromatin at H3-K9. Genes Dev. 2005, 19(7):815-826.
213. Tadepally H.D., Burger G., Aubry M. Evolution of C2H2-zinc finger genes and subfamilies in mammals: species-specific duplication and loss of clusters, genes and effector domains. BMC Evol. Biol. 2008, 8:176.
214. Takabatake T., Ishihara H., Ohmachi Y., Tanaka I., Nakamura M.M., Fujikawa K., Hirouchi T., Kakinuma S., Shimada Y., Oghiso Y., Tanaka K. Microarray-based global mapping of integration sites for the retrotransposon, intracisternal A-particle, in the mouse genome. Nucleic Acids Res. 2008, 36(10):e59.
215. Takahashi K., Sugi Y., Hosono A., Kaminogawa S. Epigenetic regulation of TLR4 gene expression in intestinal epithelial cells for the maintenance of intestinal homeostasis. J. Immunol. 2009, 183(10):6522-6529.
216. Takahashi K., Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 2006, 126(4):663-676.
217. Tam O.H., Aravin A.A., Stein P., Girard A., Murchison E.P., Cheloufi S., Hodges E., Anger M., Sachidanandam R., Schultz R.M., Hannon G.J. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 2008, 453(7194):534-538.
218. Teich N.M., Weiss R.A., Martin G.R., Lowy D.R. Virus infection of murine teratocarcinoma stem cell lines. Cell 1977, 12(4):973-982.
219. Terranova R., Yokobayashi S., Stadler M.B., Otte A.P., van Lohuizen M., Orkin S.H., Peters A.H. Polycomb group proteins Ezh2 and Rnf2 direct genomic contraction and imprinted repression in early mouse embryos. Dev. Cell 2008, 15(5):668-679.
220. Towbin B.D., Meister P., Gasser S.M. The nuclear envelope - a scaffold for silencing?. Curr. Opin. Genet. Dev. 2009, 19(2):180-186.
221. Tran R.K., Henikoff J.G., Zilberman D., Ditt R.F., Jacobsen S.E., Henikoff S. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Curr. Biol. 2005, 15(2):154-159.
222. Trono D., Van Lint C., Rouzioux C., Verdin E., Barre-Sinoussi F., Chun T.W., Chomont N. HIV persistence and the prospect of long-term drug-free remissions for HIV-infected individuals. Science 2010, 329(5988):174-180.
223. Tsukiyama T., Niwa O., Yokoro K. Mechanism of suppression of the long terminal repeat of Moloney leukemia virus in mouse embryonal carcinoma cells. Mol. Cell. Biol. 1989, 9(11):4670-4676.
224. Tsumura A., Hayakawa T., Kumaki Y., Takebayashi S., Sakaue M., Matsuoka C., Shimotohno K., Ishikawa F., Li E., Ueda H.R., Nakayama J., Okano M. Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b. Genes Cells 2006, 11(7):805-814.
225. Turelli P., Trono D. Editing at the crossroad of innate and adaptive immunity. Science 2005, 307(5712):1061-1065.
226. Turner G., Barbulescu M., Su M., Jensen-Seaman M.I., Kidd K.K., Lenz J. Insertional polymorphisms of full-length endogenous retroviruses in humans. Curr. Biol. 2001, 11(19):1531-1535.
227. Underhill C., Qutob M.S., Yee S.P., Torchia J. A novel nuclear receptor corepressor complex, N-CoR, contains components of the mammalian SWI/SNF complex and the corepressor KAP-1. J. Biol. Chem. 2000, 275(51):40463-40470.
228. Urrutia R. KRAB-containing zinc-finger repressor proteins. Genome Biol. 2003, 4(10):231.
229. van de Lagemaat L.N., Landry J.R., Mager D.L., Medstrand P. Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions. Trends Genet. 2003, 19(10):530-536.
230. van Steensel B., Delrow J., Henikoff S. Chromatin profiling using targeted DNA adenine methyltransferase. Nat. Genet. 2001, 27(3):304-308.
231. Venter J.C., et al. The sequence of the human genome. Science 2001, 291(5507):1304-1351.
232. Vernet M., Cebrian J. Cis-acting elements that mediate the negative regulation of Moloney murine leukemia virus in mouse early embryos. J. Virol. 1996, 70(8):5630-5633.
233. Walsh C.P., Chaillet J.R., Bestor T.H. Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat. Genet. 1998, 20(2):116-117.
234. Watanabe T., Totoki Y., Toyoda A., Kaneda M., Kuramochi-Miyagawa S., Obata Y., Chiba H., Kohara Y., Kono T., Nakano T., Surani M.A., Sakaki Y., Sasaki H. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 2008, 453(7194):539-543.
235. Waterston R.H., et al. Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420(6915):520-562.
236. Weber M., Hellmann I., Stadler M.B., Ramos L., Paabo S., Rebhan M., Schubeler D. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet. 2007, 39(4):457-466.
237. Wen B., Wu H., Shinkai Y., Irizarry R.A., Feinberg A.P. Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. Nat. Genet. 2009, 41(2):246-250.
238. Wernig M., Meissner A., Foreman R., Brambrink T., Ku M., Hochedlinger K., Bernstein B.E., Jaenisch R. In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature 2007, 448(7151):318-324.
239. Wiznerowicz M., Jakobsson J., Szulc J., Liao S., Quazzola A., Beermann F., Aebischer P., Trono D. The Kruppel-associated box repressor domain can trigger de novo promoter methylation during mouse early embryogenesis. J. Biol. Chem. 2007, 282(47):34535-34541.
240. Wolf D., Cammas F., Losson R., Goff S.P. Primer binding site-dependent restriction of murine leukemia virus requires HP1 binding by TRIM28. J. Virol. 2008, 82(9):4675-4679.
241. Wolf D., Goff S.P. TRIM28 mediates primer binding site-targeted silencing of murine leukemia virus in embryonic cells. Cell 2007, 131(1):46-57.
242. Wolf D., Goff S.P. Host restriction factors blocking retroviral replication. Annu. Rev. Genet. 2008, 42:143-163.
243. Wolf D., Goff S.P. Embryonic stem cells use ZFP809 to silence retroviral DNAs. Nature 2009, 458(7242):1201-1204.
244. Wolf D., Hug K., Goff S.P. TRIM28 mediates primer binding site-targeted silencing of Lys1, 2 tRNA-utilizing retroviruses in embryonic cells. Proc. Natl Acad. Sci. USA 2008, 105(34):12521-12526.
245. Wu S.C., Zhang Y. Active DNA demethylation: many roads lead to Rome. Nat. Rev. Mol. Cell Biol. 2010, 11(9):607-620.
246. Yamauchi M., Freitag B., Khan C., Berwin B., Barklis E. Stem cell factor binding to retrovirus primer binding site silencers. J. Virol. 1995, 69(2):1142-1149.
247. Yan Q., Huang J., Fan T., Zhu H., Muegge K. Lsh, a modulator of CpG methylation, is crucial for normal histone methylation. EMBO J. 2003, 22(19):5154-5162.
248. Yang N., Kazazian H.H. L1 retrotransposition is suppressed by endogenously encoded small interfering RNAs in human cultured cells. Nat. Struct. Mol. Biol. 2006, 13(9):763-771.
249. Yoder J.A., Walsh C.P., Bestor T.H. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 1997, 13(8):335-340.
250. Yoshimura T., Toyoda S., Kuramochi-Miyagawa S., Miyazaki T., Miyazaki S., Tashiro F., Yamato E., Nakano T., Miyazaki J. 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):216-227.
251. You A., Tong J.K., Grozinger C.M., Schreiber S.L. CoREST is an integral component of the CoREST-human histone deacetylase complex. Proc. Natl Acad. Sci. USA 2001, 98(4):1454-1458.
252. Yuan P., Han J., Guo G., Orlov Y.L., Huss M., Loh Y.H., Yaw L.P., Robson P., Lim B., Ng H.H. Eset partners with Oct4 to restrict extraembryonic trophoblast lineage potential in embryonic stem cells. Genes Dev. 2009, 23(21):2507-2520.
253. Zeng L., Yap K.L., Ivanov A.V., Wang X., Mujtaba S., Plotnikova O., Rauscher F.J., Zhou M.M. Structural insights into human KAP1 PHD finger-bromodomain and its role in gene silencing. Nat. Struct. Mol. Biol. 2008, 15(6):626-633.
254. Zhang Y., Maksakova I.A., Gagnier L., van de Lagemaat L.N., Mager D.L. Genome-wide assessments reveal extremely high levels of polymorphism of two active families of mouse endogenous retroviral elements. PLoS Genet. 2008, 4(2):e1000007.
255. Zhu H., Geiman T.M., Xi S., Jiang Q., Schmidtmann A., Chen T., Li E., Muegge K. Lsh is involved in de novo methylation of DNA. EMBO J. 2006, 25(2):335-345.
256. Ziv Y., Bielopolski D., Galanty Y., Lukas C., Taya Y., Schultz D.C., Lukas J., Bekker-Jensen S., Bartek J., Shiloh Y. Chromatin relaxation in response to DNA double-strand breaks is modulated by a novel ATM- and KAP-1 dependent pathway. Nat. Cell Biol. 2006, 8(8):870-876.