The Zinc-Finger Antiviral Protein ZAP Inhibits LINE and Alu Retrotransposition
Long INterspersed Element-1 (LINE-1 or L1) is the only active autonomous retrotransposon in the human genome. L1s comprise ~17% of human DNA and it is estimated that an average human genome has ~80–100 active L1s. L1 moves throughout the genome via a “copy-and-paste” mechanism known as retrotransposition. L1 retrotransposition is known to cause mutations; thus, it stands to reason that the host cell has evolved mechanisms to protect the cell from unabated retrotransposition. Here, we demonstrate that the zinc-finger antiviral protein (ZAP) inhibits the retrotransposition of human L1 and Alu retrotransposons, as well as related retrotransposons from mice and zebrafish. Biochemical and genetic data suggest that ZAP interacts with L1 RNA. Fluorescent microscopy demonstrates that ZAP associates with L1 in cytoplasmic foci that co-localize with stress granule proteins. Mechanistic analyses suggest that ZAP reduces the expression of full-length L1 RNA and the L1-encoded proteins, thereby providing mechanistic insight for how ZAP may restricts retrotransposition. Importantly, these data suggest that ZAP initially may have evolved to combat endogenous retrotransposons and subsequently was co-opted as a viral restriction factor.
Vyšlo v časopise:
The Zinc-Finger Antiviral Protein ZAP Inhibits LINE and Alu Retrotransposition. PLoS Genet 11(5): e32767. doi:10.1371/journal.pgen.1005121
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1005121
Souhrn
Long INterspersed Element-1 (LINE-1 or L1) is the only active autonomous retrotransposon in the human genome. L1s comprise ~17% of human DNA and it is estimated that an average human genome has ~80–100 active L1s. L1 moves throughout the genome via a “copy-and-paste” mechanism known as retrotransposition. L1 retrotransposition is known to cause mutations; thus, it stands to reason that the host cell has evolved mechanisms to protect the cell from unabated retrotransposition. Here, we demonstrate that the zinc-finger antiviral protein (ZAP) inhibits the retrotransposition of human L1 and Alu retrotransposons, as well as related retrotransposons from mice and zebrafish. Biochemical and genetic data suggest that ZAP interacts with L1 RNA. Fluorescent microscopy demonstrates that ZAP associates with L1 in cytoplasmic foci that co-localize with stress granule proteins. Mechanistic analyses suggest that ZAP reduces the expression of full-length L1 RNA and the L1-encoded proteins, thereby providing mechanistic insight for how ZAP may restricts retrotransposition. Importantly, these data suggest that ZAP initially may have evolved to combat endogenous retrotransposons and subsequently was co-opted as a viral restriction factor.
Zdroje
1. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860–921. 11237011
2. Beck CR, Garcia-Perez JL, Badge RM, Moran JV (2011) LINE-1 elements in structural variation and disease. Annu Rev Genomics Hum Genet 12: 187–215. doi: 10.1146/annurev-genom-082509-141802 21801021
3. Grimaldi G, Skowronski J, Singer MF (1984) Defining the beginning and end of KpnI family segments. Embo J 3: 1753–1759. 6090124
4. Brouha B, Schustak J, Badge RM, Lutz-Prigge S, Farley AH, et al. (2003) Hot L1s account for the bulk of retrotransposition in the human population. Proc Natl Acad Sci U S A 100: 5280–5285. 12682288
5. Sassaman DM, Dombroski BA, Moran JV, Kimberland ML, Naas TP, et al. (1997) Many human L1 elements are capable of retrotransposition. Nat Genet 16: 37–43. 9140393
6. Beck CR, Collier P, Macfarlane C, Malig M, Kidd JM, et al. (2010) LINE-1 retrotransposition activity in human genomes. Cell 141: 1159–1170. doi: 10.1016/j.cell.2010.05.021 20602998
7. Cordaux R, Batzer MA (2009) The impact of retrotransposons on human genome evolution. Nat Rev Genet 10: 691–703. doi: 10.1038/nrg2640 19763152
8. Kazazian HH Jr., Wong C, Youssoufian H, Scott AF, Phillips DG, et al. (1988) Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man. Nature 332: 164–166. 2831458
9. Holmes SE, Dombroski BA, Krebs CM, Boehm CD, Kazazian HH Jr. (1994) A new retrotransposable human L1 element from the LRE2 locus on chromosome 1q produces a chimaeric insertion. Nat Genet 7: 143–148. 7920631
10. Miki Y, Nishisho I, Horii A, Miyoshi Y, Utsunomiya J, et al. (1992) Disruption of the APC Gene by a Retrotransposal Insertion of L1 Sequence in a Colon Cancer. Cancer Research 52: 643–645. 1310068
11. Shukla R, Upton KR, Munoz-Lopez M, Gerhardt DJ, Fisher ME, et al. (2013) Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell 153: 101–111. doi: 10.1016/j.cell.2013.02.032 23540693
12. Hancks DC, Kazazian HH Jr. (2012) Active human retrotransposons: variation and disease. Curr Opin Genet Dev 22: 191–203. doi: 10.1016/j.gde.2012.02.006 22406018
13. Swergold GD (1990) Identification, characterization, and cell specificity of a human LINE-1 promoter. Mol Cell Biol 10: 6718–6729. 1701022
14. Athanikar JN, Badge RM, Moran JV (2004) A YY1-binding site is required for accurate human LINE-1 transcription initiation. Nucleic Acids Res 32: 3846–3855. 15272086
15. Becker KG, Swergold GD, Ozato K, Thayer RE (1993) Binding of the ubiquitous nuclear transcription factor YY1 to a cis regulatory sequence in the human LINE-1 transposable element. Hum Mol Genet 2: 1697–1702. 8268924
16. Scott AF, Schmeckpeper BJ, Abdelrazik M, Comey CT, O'Hara B, et al. (1987) Origin of the human L1 elements: proposed progenitor genes deduced from a consensus DNA sequence. Genomics 1: 113–125. 3692483
17. Dombroski BA, Mathias SL, Nanthakumar E, Scott AF, Kazazian HH Jr. (1991) Isolation of an active human transposable element. Science 254: 1805–1808. 1662412
18. Martin SL (1991) Ribonucleoprotein particles with LINE-1 RNA in mouse embryonal carcinoma cells. Mol Cell Biol 11: 4804–4807. 1715025
19. Hohjoh H, Singer MF (1996) Cytoplasmic ribonucleoprotein complexes containing human LINE-1 protein and RNA. Embo J 15: 630–639. 8599946
20. Hohjoh H, Singer MF (1997) Sequence-specific single-strand RNA binding protein encoded by the human LINE-1 retrotransposon. Embo J 16: 6034–6043. 9312060
21. Holmes SE, Singer MF, Swergold GD (1992) Studies on p40, the leucine zipper motif-containing protein encoded by the first open reading frame of an active human LINE-1 transposable element. J Biol Chem 267: 19765–19768. 1328181
22. Khazina E, Weichenrieder O (2009) Non-LTR retrotransposons encode noncanonical RRM domains in their first open reading frame. Proceedings of the National Academy of Sciences 106: 731–736. doi: 10.1073/pnas.0809964106 19139409
23. Martin SL, Bushman FD (2001) Nucleic acid chaperone activity of the ORF1 protein from the mouse LINE-1 retrotransposon. Mol Cell Biol 21: 467–475. 11134335
24. Ergun S, Buschmann C, Heukeshoven J, Dammann K, Schnieders F, et al. (2004) Cell type-specific expression of LINE-1 open reading frames 1 and 2 in fetal and adult human tissues. J Biol Chem 279: 27753–27763. 15056671
25. Goodier JL, Mandal PK, Zhang L, Kazazian HH Jr. (2010) Discrete subcellular partitioning of human retrotransposon RNAs despite a common mechanism of genome insertion. Hum Mol Genet 19: 1712–1725. doi: 10.1093/hmg/ddq048 20147320
26. Doucet AJ, Hulme AE, Sahinovic E, Kulpa DA, Moldovan JB, et al. (2010) Characterization of LINE-1 ribonucleoprotein particles. PLoS Genet 6: pii: e1001150. doi: 10.1371/journal.ppat.1001150 20976200
27. Feng Q, Moran JV, Kazazian HH Jr., Boeke JD (1996) Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87: 905–916. 8945517
28. Dombroski BA, Feng Q, Mathias SL, Sassaman DM, Scott AF, et al. (1994) An in vivo assay for the reverse transcriptase of human retrotransposon L1 in Saccharomyces cerevisiae. Mol Cell Biol 14: 4485–4492. 7516468
29. Mathias SL, Scott AF, Kazazian HH Jr., Boeke JD, Gabriel A (1991) Reverse transcriptase encoded by a human transposable element. Science 254: 1808–1810. 1722352
30. Moran JV, Holmes SE, Naas TP, DeBerardinis RJ, Boeke JD, et al. (1996) High frequency retrotransposition in cultured mammalian cells. Cell 87: 917–927. 8945518
31. Leibold DM, Swergold GD, Singer MF, Thayer RE, Dombroski BA, et al. (1990) Translation of LINE-1 DNA elements in vitro and in human cells. Proc Natl Acad Sci U S A 87: 6990–6994. 1698287
32. McMillan JP, Singer MF (1993) Translation of the human LINE-1 element, L1Hs. Proc Natl Acad Sci U S A 90: 11533–11537. 8265584
33. Alisch RS, Garcia-Perez JL, Muotri AR, Gage FH, Moran JV (2006) Unconventional translation of mammalian LINE-1 retrotransposons. Genes Dev 20: 210–224. 16418485
34. Dmitriev SE, Andreev DE, Terenin IM, Olovnikov IA, Prassolov VS, et al. (2007) Efficient translation initiation directed by the 900-nucleotide-long and GC-rich 5' untranslated region of the human retrotransposon LINE-1 mRNA is strictly cap dependent rather than internal ribosome entry site mediated. Mol Cell Biol 27: 4685–4697. 17470553
35. Wei W, Gilbert N, Ooi SL, Lawler JF, Ostertag EM, et al. (2001) Human L1 retrotransposition: cis preference versus trans complementation. Mol Cell Biol 21: 1429–1439. 11158327
36. Esnault C, Maestre J, Heidmann T (2000) Human LINE retrotransposons generate processed pseudogenes. Nat Genet 24: 363–367. 10742098
37. Kulpa DA, Moran JV (2005) Ribonucleoprotein particle formation is necessary but not sufficient for LINE-1 retrotransposition. Hum Mol Genet 14: 3237–3248. 16183655
38. Kulpa DA, Moran JV (2006) Cis-preferential LINE-1 reverse transcriptase activity in ribonucleoprotein particles. Nat Struct Mol Biol 13: 655–660. 16783376
39. Kubo S, Seleme Mdel C, Soifer HS, Perez JL, Moran JV, et al. (2006) L1 retrotransposition in nondividing and primary human somatic cells. Proc Natl Acad Sci U S A 103: 8036–8041. 16698926
40. Shi X, Seluanov A, Gorbunova V (2007) Cell divisions are required for L1 retrotransposition. Mol Cell Biol 27: 1264–1270. 17145770
41. Xie Y, Mates L, Ivics Z, Izsvak Z, Martin SL, et al. (2013) Cell division promotes efficient retrotransposition in a stable L1 reporter cell line. Mob DNA 4: 10. doi: 10.1186/1759-8753-4-10 23497436
42. Luan DD, Korman MH, Jakubczak JL, Eickbush TH (1993) Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell 72: 595–605. 7679954
43. Cost GJ, Feng Q, Jacquier A, Boeke JD (2002) Human L1 element target-primed reverse transcription in vitro. Embo J 21: 5899–5910. 12411507
44. Cost GJ, Boeke JD (1998) Targeting of human retrotransposon integration is directed by the specificity of the L1 endonuclease for regions of unusual DNA structure. Biochemistry 37: 18081–18093. 9922177
45. Morrish TA, Gilbert N, Myers JS, Vincent BJ, Stamato TD, et al. (2002) DNA repair mediated by endonuclease-independent LINE-1 retrotransposition. Nat Genet 31: 159–165. 12006980
46. Suzuki J, Yamaguchi K, Kajikawa M, Ichiyanagi K, Adachi N, et al. (2009) Genetic evidence that the non-homologous end-joining repair pathway is involved in LINE retrotransposition. PLoS Genet 5: e1000461. doi: 10.1371/journal.pgen.1000461 19390601
47. Taylor MS, Lacava J, Mita P, Molloy KR, Huang CR, et al. (2013) Affinity Proteomics Reveals Human Host Factors Implicated in Discrete Stages of LINE-1 Retrotransposition. Cell 155: 1034–1048. doi: 10.1016/j.cell.2013.10.021 24267889
48. Gilbert N, Lutz S, Morrish TA, Moran JV (2005) Multiple fates of l1 retrotransposition intermediates in cultured human cells. Mol Cell Biol 25: 7780–7795. 16107723
49. Dewannieux M, Esnault C, Heidmann T (2003) LINE-mediated retrotransposition of marked Alu sequences. Nat Genet 35: 41–48. 12897783
50. Ostertag EM, Goodier JL, Zhang Y, Kazazian HH Jr. (2003) SVA elements are nonautonomous retrotransposons that cause disease in humans. Am J Hum Genet 73: 1444–1451. 14628287
51. Hancks DC, Goodier JL, Mandal PK, Cheung LE, Kazazian HH Jr. (2011) Retrotransposition of marked SVA elements by human L1s in cultured cells. Hum Mol Genet 20: 3386–3400. doi: 10.1093/hmg/ddr245 21636526
52. Raiz J, Damert A, Chira S, Held U, Klawitter S, et al. (2012) The non-autonomous retrotransposon SVA is trans-mobilized by the human LINE-1 protein machinery. Nucleic Acids Res 40: 1666–1683. doi: 10.1093/nar/gkr863 22053090
53. Buzdin A, Ustyugova S, Gogvadze E, Vinogradova T, Lebedev Y, et al. (2002) A new family of chimeric retrotranscripts formed by a full copy of U6 small nuclear RNA fused to the 3' terminus of l1. Genomics 80: 402–406. 12376094
54. Garcia-Perez JL, Doucet AJ, Bucheton A, Moran JV, Gilbert N (2007) Distinct mechanisms for trans-mediated mobilization of cellular RNAs by the LINE-1 reverse transcriptase. Genome Res 17: 602–611. 17416749
55. Weber MJ (2006) Mammalian Small Nucleolar RNAs Are Mobile Genetic Elements. PLoS Genet 2: e205. 17154719
56. Levin HL, Moran JV (2011) Dynamic interactions between transposable elements and their hosts. Nature reviews Genetics 12: 615–627. doi: 10.1038/nrg3030 21850042
57. Yoder JA, Walsh CP, Bestor TH (1997) Cytosine methylation and the ecology of intragenomic parasites. Trends Genet 13: 335–340. 9260521
58. Bourc'his D, Bestor TH (2004) Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431: 96–99. 15318244
59. Siomi MC, Sato K, Pezic D, Aravin AA (2011) PIWI-interacting small RNAs: the vanguard of genome defence. Nat Rev Mol Cell Biol 12: 246–258. doi: 10.1038/nrm3089 21427766
60. Aravin AA, Sachidanandam R, Girard A, Fejes-Toth K, Hannon GJ (2007) Developmentally regulated piRNA clusters implicate MILI in transposon control. Science 316: 744–747. 17446352
61. Richardson SR, Narvaiza I, Planegger RA, Weitzman MD, Moran JV (2014) APOBEC3A deaminates transiently exposed single-strand DNA during LINE-1 retrotransposition. Elife 3: e02008. doi: 10.7554/eLife.02008 24843014
62. Schumann GG (2007) APOBEC3 proteins: major players in intracellular defence against LINE-1-mediated retrotransposition. Biochem Soc Trans 35: 637–642. 17511669
63. Stetson DB, Ko JS, Heidmann T, Medzhitov R (2008) Trex1 prevents cell-intrinsic initiation of autoimmunity. Cell 134: 587–598. doi: 10.1016/j.cell.2008.06.032 18724932
64. Arjan-Odedra S, Swanson CM, Sherer NM, Wolinsky SM, Malim MH (2012) Endogenous MOV10 inhibits the retrotransposition of endogenous retroelements but not the replication of exogenous retroviruses. Retrovirology 9: 53. doi: 10.1186/1742-4690-9-53 22727223
65. Goodier JL, Cheung LE, Kazazian HH Jr. (2012) MOV10 RNA helicase is a potent inhibitor of retrotransposition in cells. PLoS Genet 8: e1002941. doi: 10.1371/journal.pgen.1002941 23093941
66. Li X, Zhang J, Jia R, Cheng V, Xu X, et al. (2013) The MOV10 helicase inhibits LINE-1 mobility. J Biol Chem 288: 21148–21160. doi: 10.1074/jbc.M113.465856 23754279
67. Peddigari S, Li PW- L, Rabe JL, Martin SL (2013) hnRNPL and nucleolin bind LINE-1 RNA and function as host factors to modulate retrotransposition. Nucleic Acids Research 41: 575–585. doi: 10.1093/nar/gks1075 23161687
68. Zhao K, Du J, Han X, Goodier JL, Li P, et al. (2013) Modulation of LINE-1 and Alu/SVA retrotransposition by Aicardi-Goutieres syndrome-related SAMHD1. Cell Rep 4: 1108–1115. doi: 10.1016/j.celrep.2013.08.019 24035396
69. Zhang A, Dong B, Doucet AJ, Moldovan JB, Moran JV, et al. (2014) RNase L restricts the mobility of engineered retrotransposons in cultured human cells. Nucleic Acids Res 42: 3803–3820. doi: 10.1093/nar/gkt1308 24371271
70. deHaro D, Kines KJ, Sokolowski M, Dauchy RT, Streva VA, et al. (2014) Regulation of L1 expression and retrotransposition by melatonin and its receptor: implications for cancer risk associated with light exposure at night. Nucleic Acids Research 42: 7694–7707. doi: 10.1093/nar/gku503 24914052
71. Wei W, Morrish TA, Alisch RS, Moran JV (2000) A transient assay reveals that cultured human cells can accommodate multiple LINE-1 retrotransposition events. Anal Biochem 284: 435–438. 10964437
72. Gao G, Guo X, Goff SP (2002) Inhibition of retroviral RNA production by ZAP, a CCCH-type zinc finger protein. Science 297: 1703–1706. 12215647
73. Burdick R, Smith JL, Chaipan C, Friew Y, Chen J, et al. (2010) P body-associated protein Mov10 inhibits HIV-1 replication at multiple stages. J Virol 84: 10241–10253. doi: 10.1128/JVI.00585-10 20668078
74. Leeds P, Peltz SW, Jacobson A, Culbertson MR (1991) The product of the yeast UPF1 gene is required for rapid turnover of mRNAs containing a premature translational termination codon. Genes Dev 5: 2303–2314. 1748286
75. Hui J, Stangl K, Lane WS, Bindereif A (2003) HnRNP L stimulates splicing of the eNOS gene by binding to variable-length CA repeats. Nat Struct Biol 10: 33–37. 12447348
76. Kernan MJ, Kuroda MI, Kreber R, Baker BS, Ganetzky B (1991) napts, a mutation affecting sodium channel activity in Drosophila, is an allele of mle, a regulator of X chromosome transcription. Cell 66: 949–959. 1653649
77. Kuroda MI, Kernan MJ, Kreber R, Ganetzky B, Baker BS (1991) The maleless protein associates with the X chromosome to regulate dosage compensation in Drosophila. Cell 66: 935–947. 1653648
78. Bergemann AD, Ma ZW, Johnson EM (1992) Sequence of cDNA comprising the human pur gene and sequence-specific single-stranded-DNA-binding properties of the encoded protein. Mol Cell Biol 12: 5673–5682. 1448097
79. Grana X, De Luca A, Sang N, Fu Y, Claudio PP, et al. (1994) PITALRE, a nuclear CDC2-related protein kinase that phosphorylates the retinoblastoma protein in vitro. Proc Natl Acad Sci U S A 91: 3834–3838. 8170997
80. Kao PN, Chen L, Brock G, Ng J, Kenny J, et al. (1994) Cloning and expression of cyclosporin A- and FK506-sensitive nuclear factor of activated T-cells: NF45 and NF90. J Biol Chem 269: 20691–20699. 7519613
81. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25–29. 10802651
82. Castello A, Fischer B, Eichelbaum K, Horos R, Beckmann BM, et al. (2012) Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 149: 1393–1406. doi: 10.1016/j.cell.2012.04.031 22658674
83. Baltz AG, Munschauer M, Schwanhausser B, Vasile A, Murakawa Y, et al. (2012) The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol Cell 46: 674–690. doi: 10.1016/j.molcel.2012.05.021 22681889
84. Mandal PK, Ewing AD, Hancks DC, Kazazian HH Jr. (2013) Enrichment of processed pseudogene transcripts in L1-ribonucleoprotein particles. Hum Mol Genet 22: 3730–3748. doi: 10.1093/hmg/ddt225 23696454
85. Kopera HC, Moldovan JB, Morrish TA, Garcia-Perez JL, Moran JV (2011) Similarities between long interspersed element-1 (LINE-1) reverse transcriptase and telomerase. Proc Natl Acad Sci U S A.
86. Muckenfuss H, Hamdorf M, Held U, Perkovic M, Lower J, et al. (2006) APOBEC3 proteins inhibit human LINE-1 retrotransposition. J Biol Chem 281: 22161–22172. 16735504
87. Bogerd HP, Wiegand HL, Hulme AE, Garcia-Perez JL, O'Shea KS, et al. (2006) Cellular inhibitors of long interspersed element 1 and Alu retrotransposition. Proc Natl Acad Sci U S A 103: 8780–8785. 16728505
88. Chen H, Lilley CE, Yu Q, Lee DV, Chou J, et al. (2006) APOBEC3A is a potent inhibitor of adeno-associated virus and retrotransposons. Curr Biol 16: 480–485. 16527742
89. Goodier JL, Cheung LE, Kazazian HH Jr. (2013) Mapping the LINE1 ORF1 protein interactome reveals associated inhibitors of human retrotransposition. Nucleic Acids Res 41: 7401–19. doi: 10.1093/nar/gkt512 23749060
90. Kerns JA, Emerman M, Malik HS (2008) Positive selection and increased antiviral activity associated with the PARP-containing isoform of human zinc-finger antiviral protein. PLoS Genet 4: e21. doi: 10.1371/journal.pgen.0040021 18225958
91. Chen S, Xu Y, Zhang K, Wang X, Sun J, et al. (2012) Structure of N-terminal domain of ZAP indicates how a zinc-finger protein recognizes complex RNA. Nat Struct Mol Biol 19: 430–435. doi: 10.1038/nsmb.2243 22407013
92. Guo X, Carroll J- WN, MacDonald MR, Goff SP, Gao G (2004) The Zinc Finger Antiviral Protein Directly Binds to Specific Viral mRNAs through the CCCH Zinc Finger Motifs. Journal of Virology 78: 12781–12787. 15542630
93. Ullu E, Tschudi C (1984) Alu sequences are processed 7SL RNA genes. Nature 312: 171–172. 6209580
94. Goodier JL, Ostertag EM, Du K, Kazazian HH Jr. (2001) A novel active L1 retrotransposon subfamily in the mouse. Genome Res 11: 1677–1685. 11591644
95. Sugano T, Kajikawa M, Okada N (2006) Isolation and characterization of retrotransposition-competent LINEs from zebrafish. Gene 365: 74–82. 16356661
96. Han JS, Boeke JD (2004) A highly active synthetic mammalian retrotransposon. Nature 429: 314–318. 15152256
97. Ostertag EM, Prak ET, DeBerardinis RJ, Moran JV, Kazazian HH Jr. (2000) Determination of L1 retrotransposition kinetics in cultured cells. Nucleic Acids Res 28: 1418–1423. 10684937
98. Martin SL, Cruceanu M, Branciforte D, Wai-Lun Li P, Kwok SC, et al. (2005) LINE-1 retrotransposition requires the nucleic acid chaperone activity of the ORF1 protein. J Mol Biol 348: 549–561. 15826653
99. Belancio VP, Roy-Engel AM, Deininger P (2008) The impact of multiple splice sites in human L1 elements. Gene 411: 38–45. doi: 10.1016/j.gene.2007.12.022 18261861
100. Belancio VP, Hedges DJ, Deininger P (2006) LINE-1 RNA splicing and influences on mammalian gene expression. Nucleic Acids Research 34: 1512–1521. 16554555
101. Perepelitsa-Belancio V, Deininger P (2003) RNA truncation by premature polyadenylation attenuates human mobile element activity. Nat Genet 35: 363–366. 14625551
102. Hohjoh H, Singer MF (1997) Ribonuclease and high salt sensitivity of the ribonucleoprotein complex formed by the human LINE-1 retrotransposon. J Mol Biol 271: 7–12. 9300051
103. Wissing S, Montano M, Garcia-Perez JL, Moran JV, Greene WC (2011) Endogenous APOBEC3B Restricts LINE-1 Retrotransposition in Transformed Cells and Human Embryonic Stem Cells. Journal of Biological Chemistry 286: 36427–36437. doi: 10.1074/jbc.M111.251058 21878639
104. Goodier JL, Zhang L, Vetter MR, Kazazian HH Jr. (2007) 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 27: 6469–6483. 17562864
105. Liu L, Chen G, Ji X, Gao G (2004) ZAP is a CRM1-dependent nucleocytoplasmic shuttling protein. Biochemical and biophysical research communications 321: 517–523. 15358138
106. Garcia-Perez JL, Morell M, Scheys JO, Kulpa DA, Morell S, et al. (2010) Epigenetic silencing of engineered L1 retrotransposition events in human embryonic carcinoma cells. Nature 466: 769–773. doi: 10.1038/nature09209 20686575
107. Zeuthen J, Norgaard JO, Avner P, Fellous M, Wartiovaara J, et al. (1980) Characterization of a human ovarian teratocarcinoma-derived cell line. Int J Cancer 25: 19–32. 6931103
108. Leung AK, Vyas S, Rood JE, Bhutkar A, Sharp PA, et al. (2011) Poly(ADP-ribose) regulates stress responses and microRNA activity in the cytoplasm. Mol Cell 42: 489–499. doi: 10.1016/j.molcel.2011.04.015 21596313
109. Guo X, Ma J, Sun J, Gao G (2007) The zinc-finger antiviral protein recruits the RNA processing exosome to degrade the target mRNA. Proc Natl Acad Sci U S A 104: 151–156. 17185417
110. Belancio VP, Roy-Engel AM, Pochampally RR, Deininger P (2010) Somatic expression of LINE-1 elements in human tissues. Nucleic Acids Res 38: 3909–3922. doi: 10.1093/nar/gkq132 20215437
111. Zhu Y, Chen G, Lv F, Wang X, Ji X, et al. (2011) Zinc-finger antiviral protein inhibits HIV-1 infection by selectively targeting multiply spliced viral mRNAs for degradation. Proc Natl Acad Sci U S A 108: 15834–15839. doi: 10.1073/pnas.1101676108 21876179
112. Bick MJ, Carroll JW, Gao G, Goff SP, Rice CM, et al. (2003) Expression of the zinc-finger antiviral protein inhibits alphavirus replication. J Virol 77: 11555–11562. 14557641
113. Zhu Y, Wang X, Goff SP, Gao G (2012) Translational repression precedes and is required for ZAP-mediated mRNA decay. EMBO J 31: 4236–4246. doi: 10.1038/emboj.2012.271 23023399
114. Chen G, Guo X, Lv F, Xu Y, Gao G (2008) p72 DEAD box RNA helicase is required for optimal function of the zinc-finger antiviral protein. Proc Natl Acad Sci U S A 105: 4352–4357. doi: 10.1073/pnas.0712276105 18334637
115. Buchan JR, Parker R (2009) Eukaryotic Stress Granules: The Ins and Outs of Translation. Molecular Cell 36: 932–941. doi: 10.1016/j.molcel.2009.11.020 20064460
116. Reineke LC, Lloyd RE (2013) Diversion of stress granules and P-bodies during viral infection. Virology 436: 255–267. doi: 10.1016/j.virol.2012.11.017 23290869
117. Bick MJ, Carroll J-WN, Gao G, Goff SP, Rice CM, et al. (2003) Expression of the Zinc-Finger Antiviral Protein Inhibits Alphavirus Replication. Journal of Virology 77: 11555–11562. 14557641
118. Muller S, Moller P, Bick MJ, Wurr S, Becker S, et al. (2007) Inhibition of filovirus replication by the zinc finger antiviral protein. J Virol 81: 2391–2400. 17182693
119. Mao R, Nie H, Cai D, Zhang J, Liu H, et al. (2013) Inhibition of hepatitis B virus replication by the host zinc finger antiviral protein. PLoS Pathog 9: e1003494. doi: 10.1371/journal.ppat.1003494 23853601
120. Burton FH, Loeb DD, Voliva CF, Martin SL, Edgell MH, et al. (1986) Conservation throughout mammalia and extensive protein-encoding capacity of the highly repeated DNA long interspersed sequence one. J Mol Biol 187: 291–304. 3009828
121. Smit AF, Toth G, Riggs AD, Jurka J (1995) Ancestral, mammalian-wide subfamilies of LINE-1 repetitive sequences. J Mol Biol 246: 401–417. 7877164
122. Yang L, Brunsfeld J, Scott L, Wichman H (2014) Reviving the dead: history and reactivation of an extinct l1. PLoS Genet 10: e1004395. doi: 10.1371/journal.pgen.1004395 24968166
123. Sawyer SL, Emerman M, Malik HS (2004) Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G. PLoS Biol 2: E275. 15269786
124. Sawyer SL, Wu LI, Emerman M, Malik HS (2005) Positive selection of primate TRIM5alpha identifies a critical species-specific retroviral restriction domain. Proc Natl Acad Sci U S A 102: 2832–2837. 15689398
125. Sawyer SL, Malik HS (2006) Positive selection of yeast nonhomologous end-joining genes and a retrotransposon conflict hypothesis. Proc Natl Acad Sci U S A 103: 17614–17619. 17101967
126. Hulme AE, Bogerd HP, Cullen BR, Moran JV (2007) Selective inhibition of Alu retrotransposition by APOBEC3G. Gene 390: 199–205. 17079095
127. Dombroski BA, Scott AF, Kazazian HH Jr. (1993) Two additional potential retrotransposons isolated from a human L1 subfamily that contains an active retrotransposable element. Proc Natl Acad Sci U S A 90: 6513–6517. 8393568
128. Freeman JD, Goodchild NL, Mager DL (1994) A modified indicator gene for selection of retrotransposition events in mammalian cells. Biotechniques 17: 46, 48–49, 52. 7946311
129. Wallace MR, Andersen LB, Saulino AM, Gregory PE, Glover TW, et al. (1991) A de novo Alu insertion results in neurofibromatosis type 1. Nature 353: 864–866. 1719426
130. Esnault C, Casella JF, Heidmann T (2002) A Tetrahymena thermophila ribozyme-based indicator gene to detect transposition of marked retroelements in mammalian cells. Nucleic Acids Res 30: e49. 12034850
131. Bogerd HP, Wiegand HL, Doehle BP, Lueders KK, Cullen BR (2006) APOBEC3A and APOBEC3B are potent inhibitors of LTR-retrotransposon function in human cells. Nucleic Acids Res 34: 89–95. 16407327
132. Liu J, Valencia-Sanchez MA, Hannon GJ, Parker R (2005) MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies. Nat Cell Biol 7: 719–723. 15937477
133. Tourriere H, Chebli K, Zekri L, Courselaud B, Blanchard JM, et al. (2003) The RasGAP-associated endoribonuclease G3BP assembles stress granules. J Cell Biol 160: 823–831. 12642610
134. Shevchenko A, Wilm M, Vorm O, Mann M (1996) Mass Spectrometric Sequencing of Proteins from Silver-Stained Polyacrylamide Gels. Analytical Chemistry 68: 850–858. 8779443
135. Licklider LJ, Thoreen CC, Peng J, Gygi SP (2002) Automation of Nanoscale Microcapillary Liquid Chromatography,àíTandem Mass Spectrometry with a Vented Column. Analytical Chemistry 74: 3076–3083. 12141667
136. Rauch A, Bellew M, Eng J, Fitzgibbon M, Holzman T, et al. (2005) Computational Proteomics Analysis System (CPAS): An Extensible, Open-Source Analytic System for Evaluating and Publishing Proteomic Data and High Throughput Biological Experiments. Journal of Proteome Research 5: 112–121.
137. Craig R, Beavis RC (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20: 1466–1467. 14976030
138. Nesvizhskii AI, Keller A, Kolker E, Aebersold R (2003) A Statistical Model for Identifying Proteins by Tandem Mass Spectrometry. Analytical Chemistry 75: 4646–4658. 14632076
139. Keller A, Nesvizhskii AI, Kolker E, Aebersold R (2002) Empirical Statistical Model To Estimate the Accuracy of Peptide Identifications Made by MS/MS and Database Search. Analytical Chemistry 74: 5383–5392. 12403597
140. Schneider CA, Rasband WS, Eliceiri KW (2012) NIH Image to ImageJ: 25 years of image analysis. Nat Methods 9: 671–675. 22930834
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2015 Číslo 5
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