Ancient transposable elements, processed pseudogenes, and endogenous retroviruses

Genomic Disorders: The Genomic Basis of Disease

Volumn , Issue , 2006, Pages 57-72

  Pavlicek, Adam ^a   Jurka, Jerzy ^a  

^a Genetic Information Research Institute   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84891424797     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-59745-039-3_4     Document Type: Chapter

References (128)

1. Temin HM, Mizutani S. RNA-dependent DNA polymerase in virions of Rous sarcoma virus. Nature 1970;226:1211-1213.
2. Baltimore D. RNA-dependent DNA polymerase in virions of RNA tumour viruses. Nature 1970;226: 1209-1211.
3. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 2001;409:860-921.
4. Jurka J. Repbase update: a database and an electronic journal of repetitive elements. Trends Genet 2000;16:418-420.
5. Kapitonov VV, Jurka J. The esterase and PHD domains in CR1-like non-LTR retrotransposons. Mol Biol Evol 2003;20:38-46.
6. Kapitonov VV, Pavlicek A, Jurka J. Anthology of Human Repetitive DNA. In: Encyclopedia of Molecular Cell Biology and Molecular Medicine, vol. 1 (Meyers RA, ed.). Weinheim, Germany: Wiley-VCH 2004; pp 251-306.
7. 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;72:595-605.
8. Smit AF, Riggs AD. MIRs are classic, tRNA-derived SINEs that amplified before the mammalian radiation. Nucleic Acids Res 1995;23:98-102.
9. Okada N, Hamada M, Ogiwara I, Ohshima K. SINEs and LINEs share common 3' sequences: a review. Gene 1997;205:229-243.
10. Jacq C, Miller JR, Brownlee GG. A pseudogene structure in 5S DNA of Xenopus laevis. Cell 1997;12:109-120.
11. Vanin EF. Processed pseudogenes: characteristics and evolution. Annu Rev Genet 1985;19:253-272.
12. Weiner AM, Deininger PL, Efstratiadis A. Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu Rev Biochem 1986;55:631-661.
13. Jurka J. Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc Natl Acad Sci USA 1997;94:1872-1877.
14. Tchenio T, Segal-Bendirdjian E, Heidmann T. Generation of processed pseudogenes in murine cells. EMBO J 1993;12:1487-1497.
15. Maestre J, Tchenio T, Dhellin O, Heidmann T. mRNA retroposition in human cells: processed pseudogene formation. EMBO J 1995;14:6333-6338.
16. Dhellin O, Maestre J, Heidmann T. Functional differences between the human LINE retrotransposon and retroviral reverse transcriptases for in vivo mRNA reverse transcription. EMBO J 1997;16:6590-6602.
17. Esnault C, Maestre J, Heidmann T. Human LINE retrotransposons generate processed pseudogenes. Nat Genet 2000;24:363-367.
18. Wei W, Gilbert N, Ooi SL, et al. Human L1 retrotransposition: cis preference versus trans complementation. Mol Cell Biol 2001;21:1429-1439.
19. Ohshima K, Hattori M, Yada T, Gojobori T, Sakaki Y, Okada N. Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates. Genome Biol 2003;4:R74.
20. 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;13:2541-2558.
21. Pavlicek A, Jabbari K, Paces J, Paces V, Hejnar J, Bernardi G. Similar integration but different stability of Alus and LINEs in the human genome. Gene 2001;276:39-45.
22. Zhang Z, Harrison P, Gerstein M. Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Res 2002;12:1466-1482.
23. Pavlicek A, Paces J, Zika R, Hejnar J. Length distribution of long interspersed nucleotide elements (LINEs) and processed pseudogenes of human endogenous retroviruses: implications for retrotransposition and pseudogene detection. Gene 2002;300:189-194.
24. Zhang Z, Gerstein M. Identification and characterization of over 100 mitochondrial ribosomal protein pseudogenes in the human genome. Genomics 2003;81:468-480.
25. Strichman-Almashanu LZ, Bustin M, Landsman D. Retroposed copies of the HMG genes: a window to genome dynamics. Genome Res 2003;13:800-812.
26. Jamain S, Girondot M, Leroy P, et al. Transduction of the human gene FAM8A1 by endogenous retrovirus during primate evolution. Genomics 2001;78:38-45.
27. Goncalves I, Duret L, Mouchiroud D. Nature and structure of human genes that generate retropseudogenes. Genome Res 2000;10:672-678.
28. Torrents D, Suyama M, Zdobnov E, Bork P. A genome-wide survey of human pseudogenes. Genome Res 2003;13:2559-2567.
29. Harrison PM, Hegyi H, Balasubramanian S, et al. Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res 2002;12:272-280.
30. Pavlicek A, Paces J, EllederD, Hejnar J. Processed pseudogenes of human endogenous retroviruses generated by LINEs: their integration, stability, and distribution. Genome Res 2002;12:391-399.
31. Ejima Y, Yang L. Trans mobilization of genomic DNA as a mechanism for retrotransposon-mediated exon shuffling. Hum Mol Genet 2003;12:1321-1328.
32. Goodchild NL, Freeman JD, Mager DL. Spliced HERV-H endogenous retroviral sequences in human genomic DNA: evidence for amplification via retrotransposition. Virology 1995;206:164-173.
33. Costas J. Characterization of the intragenomic spread of the human endogenous retrovirus family HERV-W. Mol Biol Evol 2002;19:526-533.
34. Boeke JD. LINEs and Alus: the polyA connection. Nat Genet 1997;16:6-7.
35. Brosius J. RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 1999;238:115-134.
36. Gentles AJ, Karlin S. Why are human G-protein-coupled receptors predominantly intronless? Trends Genet 1999;15:47-49.
37. Harrison PM, Gerstein M. Studying genomes through the aeons: protein families, pseudogenes and proteome evolution. J Mol Biol 2002;318:1155-1174.
38. McCarrey JR, Kumari M, Aivaliotis MJ, et al. Analysis of the cDNA and encoded protein of the human testis-specific PGK-2 gene. Dev Genet 1996;19:321-332.
39. Fujii GH, Morimoto AM, Berson AE, Bolen JB. Transcriptional analysis of the PTEN/MMAC1 pseudogene, psiPTEN. Oncogene 1999;18:1765-1769.
40. Olsen MA, Schechter LE. Cloning, mRNA localization and evolutionary conservation of a human 5-HT7 receptor pseudogene. Gene 1999;227:63-69.
41. Reyes A, Mezzina M, Gadaleta G. Human mitochondrial transcription factor A (mtTFA): gene structure and characterization of related pseudogenes. Gene 2002;291:223-232.
42. Yano Y, Saito R, Yoshida N, et al. A new role for expressed pseudogenes as ncRNA: regulation of mRNA stability of its homologous coding gene. J Mol Med 2004;82:414-422.
43. McCarrey JR, Thomas K. Human testis-specific PGK gene lacks introns and possesses characteristics of a processed gene. Nature 1987;326:501-505.
44. Ashworth A, Skene B, Swift S, Lovell-Badge R. Zfa is an expressed retroposon derived from an alternative transcript of the Zfx gene. EMBO J 1990:9:1529-1534.
45. Dahl HH, Brown RM, Hutchison WM, Maragos C, Brown GK. A testis-specific form of the human pyruvate dehydrogenase E1 alpha subunit is coded for by an intronless gene on chromosome 4. Genomics 1990;8: 225-232.
46. Mardon G, Luoh SW, Simpson EM, Gill G, Brown LG, Page DC. Mouse Zfx protein is similar to Zfy-2: each contains an acidic activating domain and 13 zinc fingers. Mol Cell Biol 1990;10:681-688.
47. Sargent CA, Young C, Marsh S, Ferguson-Smith MA, Affara NA. The glycerol kinase gene family: structure of the Xp gene, and related intronless retroposons. Hum Mol Genet 1994;3:1317-1324.
48. Hendriksen PJ, Hoogerbrugge JW, Baarends WM, et al. Testis-specific expression of a functional retroposon encoding glucose-6-phosphate dehydrogenase in the mouse. Genomics 1997;41:350-359.
49. Sedlacek Z, Munstermann E, Dhorne-Pollet S, et al. Human and mouse XAP-5 and XAP-5-like (X5L) genes: identification of an ancient functional retroposon differentially expressed in testis. Genomics 1999;61: 125-132.
50. Elliott DJ, Venables JP, Newton CS, et al. An evolutionarily conserved germ cell-specific hnRNP is encoded by a retrotransposed gene. Hum Mol Genet 2000;9:2117-2124.
51. Dass B, McMahon KW, Jenkins NA, Gilbert DJ, Copeland NG, MacDonald CC. The gene for a variant form of the polyadenylation protein CstF-64 is on chromosome 19 and is expressed in pachytene spermatocytes in mice. J Biol Chem 2001;276:8044-8050.
52. Wang PJ, Page DC. Functional substitution for TAF(II)250 by a retroposed homolog that is expressed in human spermatogenesis. Hum Mol Genet 2002;11:2341-2346.
53. Emerson JJ, Kaessmann H, Betran E, Long M. Extensive gene traffic on the mammalian X chromosome. Science 2004;303:537-540.
54. Bradley J, Baltus A, Skaletsky H, Royce-Tolland M, Dewar K, Page DC. An X-to-autosome retrogene is required for spermatogenesis in mice. Nat Genet 2004;36:872-876.
55. Dupuy D, Duperat VG, Arveiler B. SCAN domain-containing 2 gene (SCAND2) is a novel nuclear protein derived from the zinc finger family by exon shuffling. Gene 2002;289:1-6.
56. Hirotsune S, Yoshida N, Chen A, et al. An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature 2003;423:91-96.
57. Ostertag EM, Kazazian HH Jr. Biology of mammalian L1 retrotransposons. Annu Rev Genet 2001;35: 501-538.
58. Scherrer K. Control of gene expression in animal cells: the cascade regulation hypothesis revisited. Adv Exp Med Biol 1974;44:169-219.
59. Coffin JM, Hughes SH, Varmus HE. Retroviruses. Cold Spring Harbor Laboratory Press, New York, NY, 1997.
60. Cianciolo GJ, Copeland TD, Oroszlan S, Snyderman R. Inhibition of lymphocyte proliferation by a synthetic peptide homologous to retroviral envelope proteins. Science 1985;230:453-455.
61. Sonigo P, Barker C, Hunter E, Wain-Hobson S. Nucleotide sequence of Mason-Pfizer monkey virus: an immunosuppressive D-type retrovirus. Cell 1986;45:375-385.
62. Bukreyev A, Volchkov VE, Blinov VM, Netesov SV. The GP-protein of Marburg virus contains the region similar to the 'immunosuppressive domain' of oncogenic retrovirus P15E proteins. FEBS Lett 1993;323: 183-187.
63. Benit L, Lallemand JB, Casella JF, Philippe H, Heidmann T. ERV-L elements: a family of endogenous retrovirus-like elements active throughout the evolution of mammals. J Virol 1999;73:3301-3308.
64. Yin H, Medstrand P, Kristofferson A, Dietrich U, Aman P, Blomberg J. Characterization of human MMTV-like (HML) elements similar to a sequence that was highly expressed in a human breast cancer: further definition of the HML-6 group. Virology 1999;256:22-35.
65. Magin C, Lower R, Lower J. cORF and RcRE, the Rev/Rex and RRE/RxRE homologues of the human endogenous retrovirus family HTDV/HERV-K. J Virol 1999;73:9496-9507.
66. Yang J, Bogerd HP, Peng S, Wiegand H, Truant R, Cullen BR. An ancient family of human endogenous retroviruses encodes a functional homolog of the HIV-1 Rev protein. Proc Natl Acad Sci USA 1999;96:13, 404-13, 408.
67. Martin MA, Bryan T, Rasheed S, Khan AS. Identification and cloning of endogenous retroviral sequences present in human DNA. Proc Natl Acad Sci USA 1981;78:4892-4896.
68. Paces J, Pavlicek A, Zika R, Kapitonov VV, Jurka J, Paces V. HERVd: the Human Endogenous RetroViruses Database: update. Nucleic Acids Res 2004;32:D50.
69. Wilkinson DA, Mager DL, Leong JC. Endogenous human retroviruses. In: The Retroviridae (Levy, J. A., ed.). New York, NY: Plenum Press, 1994; pp 465-535.
70. Zhang J, Temin HM. Rate and mechanism of nonhomologous recombination during a single cycle of retroviral replication. Science 1993;259:234-238.
71. Cordonnier A, Casella JF, Heidmann T. Isolation of novel human endogenous retrovirus-like elements with foamy virus-related pol sequence. J Virol 1995;69:5890-5897.
72. Charlier C, Segers K, Wagenaar D, et al. Human-ovine comparative sequencing of a 250-kb imprinted domain encompassing the callipyge (clpg) locus and identification of six imprinted transcripts: DLK1, DAT, GTL2, PEG11, antiPEG11, and MEG8. Genome Res 2001;11:850-862.
73. Ono R, Kobayashi S, Wagatsuma H, et al. A retrotransposon-derived gene, PEG10, is a novel imprinted gene located on human chromosome 7q21. Genomics 2001;73:232-237.
74. Lynch C, Tristem M. A co-opted gypsy-type LTR-retrotransposon is conserved in the genomes of humans, sheep, mice, and rats. Curr Biol 2003;13:1518-1523.
75. Dewannieux M, Dupressoir A, Harper F, Pierron G, Heidmann T. Identification of autonomous IAP LTR retrotransposons mobile in mammalian cells. Nat Genet 2004;36:534-539.
76. Cohen M, Powers M, O'Connell C, Kato N. The nucleotide sequence of the env gene from the human provirus ERV3 and isolation and characterization of an ERV3-specific cDNA. Virology 1985;147:449-458.
77. Blond JL, Beseme F, Duret L, et al. Molecular characterization and placental expression of HERV-W, a new human endogenous retrovirus family. J Virol 1999;73:1175-1185.
78. Kjellman C, Sjogren HO, Salford LG, Widegren B. HERV-F (XA34) is a full-length human endogenous retrovirus expressed in placental and fetal tissues. Gene 1999;239:99-107.
79. Lindeskog M, Mager DL, Blomberg J. Isolation of a human endogenous retroviral HERV-H element with an open env reading frame. Virology 1999;258:441-450.
80. Benit L, Dessen P, Heidmann T. Identification, phylogeny, and evolution of retroviral elements based on their envelope genes. J Virol 2001;75:11, 709-11, 719.
81. Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature 2002;420:520-562.
82. Rat Genome Sequencing Project Consortium. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 2004;428:493-521.
83. Medstrand P, Mager DL. Human-specific integrations of the HERV-K endogenous retrovirus family. J Virol 1998;72:9782-9787.
84. Barbulescu M, Turner G, Seaman MI, Deinard AS, Kidd KK, Lenz J. Many human endogenous retrovirus K (HERV-K) proviruses are unique to humans. Curr Biol 1999;9:861-868.
85. Mayer J, Sauter M, Racz A, Scherer D, Mueller-Lantzsch N, Meese E. An almost-intact human endogenous retrovirus K on human chromosome 7. Nat Genet 1999;21:257-258.
86. Turner G, Barbulescu M, Su M, Jensen-Seaman MI, Kidd KK, Lenz J. Insertional polymorphisms of full-length endogenous retroviruses in humans. Curr Biol 2001;11:1531-1535.
87. Elleder D, Pavlicek A, Paces J, Hejnar J. Preferential integration of human immunodeficiency virus type 1 into genes, cytogenetic R bands and GC-rich DNA regions: insight from the human genome sequence. FEBS Lett 2002;517:285-286.
88. Schroder AR, Shinn P, Chen H, Berry C, Ecker JR, Bushman F. HIV-1 integration in the human genome favors active genes and local hotspots. Cell 2002;110:521-529.
89. Wu X, Li Y, Crise B, Burgess SM. Transcription start regions in the human genome are favored targets for MLV integration. Science 2003;300:1749-1751.
90. Smit AF. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev 1999;9:657-663.
91. Mager DL, Goodchild NL. Homologous recombination between the LTRs of a human retrovirus-like element causes a 5-kb deletion in two siblings. Am J Hum Genet 1989;45:848-854.
92. Erlandsson R, Wilson JF, Paabo S. Sex chromosomal transposable element accumulation and male-driven substitutional evolution in humans. Mol Biol Evol 2000;17:804-812.
93. Medstrand P, van de Lagemaat LN, Mager DL. Retroelement distributions in the human genome: variations associated with age and proximity to genes. Genome Res 2002;12:1483-1495.
94. Blanco P, ShlumukovaM, Sargent CA, Jobling MA, Affara N, Hurles ME. Divergent outcomes of intrachromosomal recombination on the human Y chromosome: male infertility and recurrent polymorphism. J Med Genet 2000;37:752-758.
95. Sun C, Skaletsky H, Rozen S, et al. Deletion of azoospermia factor a (AZFa) region of human Y chromosome caused by recombination between HERV15 proviruses. Hum Mol Genet 2000;9:2291-2296.
96. Kamp C, Hirschmann P, Voss H, Huellen K, Vogt PH. Two long homologous retroviral sequence blocks in proximal Yq11 cause AZFa microdeletions as a result of intrachromosomal recombination events. Hum Mol Genet 2000;9:2563-2572.
97. Kamp C, Huellen K, Fernandes S, et al. High deletion frequency of the complete AZFa sequence in men with Sertoli-cell-only syndrome. Mol Hum Reprod 2001;7:987-994.
98. Kambhu S, Falldorf P, Lee JS. Endogenous retroviral long terminal repeats within the HLA-DQ locus. Proc Natl Acad Sci USA 1990;87:4927-4931.
99. Kulski JK, Gaudieri S, Martin A, Dawkins RL. Coevolution of PERB11 (MIC) and HLA class I genes with HERV-16 and retroelements by extended genomic duplication. J Mol Evol 1999;49:84-97.
100. Nakagawa K, Harrison LC. The potential roles of endogenous retroviruses in autoimmunity. Immunol Rev 1996;152:193-236.
101. Lower R. The pathogenic potential of endogenous retroviruses: facts and fantasies. Trends Microbiol 1999;7:350-356.
102. Nelson PN, Carnegie PR, Martin J, et al. Demystified. Human endogenous retroviruses. Mol Pathol 2003;56:11-18.
103. Perl A. Role of endogenous retroviruses in autoimmune diseases. Rheum Dis Clin North Am 2003;29:123-143.
104. Garson JA, Tuke PW, Giraud P, Paranhos-Baccala G, Perron H. Detection of virion-associated MSRV-RNA in serum of patients with multiple sclerosis. Lancet 1998;351:33.
105. Poser CM. Virion-associated MSRV-RNA in multiple sclerosis. Lancet 1998;351:755.
106. Lower R. Response from Lower. Trends Microbiol 1999;7:431-432.
107. Mager DL. Human endogenous retroviruses and pathogenicity: genomic considerations. Trends Microbiol 1999;7:431.
108. Stoye JP. The pathogenic potential of endogenous retroviruses: a sceptical view. Trends Microbiol 1999;7:430.
109. Sverdlov ED. Retroviruses and primate evolution. Bioessays 2000;22:161-171.
110. Landry JR, Mager DL, Wilhelm BT. Complex controls: the role of alternative promoters in mammalian genomes. Trends Genet 2003;19:640-648.
111. van de Lagemaat LN, Landry JR, Mager DL, Medstrand P. Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions. Trends Genet 2003;19:530-536.
112. Samuelson LC, Wiebauer K, Snow CM, Meisler MH. Retroviral and pseudogene insertion sites reveal the lineage of human salivary and pancreatic amylase genes from a single gene during primate evolution. Mol Cell Biol 1990;10:2513-2520.
113. Ting CN, Rosenberg MP, Snow CM, Samuelson LC, Meisler MH. Endogenous retroviral sequences are required for tissue-specific expression of a human salivary amylase gene. Genes Dev 1992;6:1457-1465.
114. Blond JL, Lavillette D, Cheynet V, et al. 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;74:3321-3329.
115. Mi S, Lee X, Li X, et al. Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis. Nature 2000;403:785-789.
116. 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;100:13, 013-13, 018.
117. Smit AF, Riggs AD. Tiggers and DNA transposon fossils in the human genome. Proc Natl Acad Sci USA 1996;93:1443-1448.
118. Reiter LT, Murakami T, Koeuth T, et al. A recombination hotspot responsible for two inherited peripheral neuropathies is located near a mariner transposon-like element. Nat Genet 1996;12:288-297.
119. Reiter LT, Liehr T, Rautenstrauss B, Robertson HM, Lupski J.R. Localization of mariner DNA transposons in the human genome by PRINS. Genome Res 1999;9:839-843.
120. Kapitonov VV, Jurka J. RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. PLoS Biol 2005;3:e181.
121. Kapitonov VV, Jurka J. MER53, a non-autonomous DNA transposon associated with a variety of functionally related defense genes in the human genome. DNA Seq 1998;8:277-288.
122. Jurka J, Kapitonov VV. Sectorial mutagenesis by transposable elements. Genetica 1999;107:239-248.
123. Kapitonov VV, Jurka J. Harbinger transposons and an ancient HARBI1 gene derived from a transposase. DNA Cell Biol 2004;23:311-324.
124. Lee GS, Neiditch MB, Salus SS, Roth DB. RAG proteins shepherd double-strand breaks to a specific pathway, suppressing error-prone repair, but RAG nicking initiates homologous recombination. Cell 2004;117:171-184.
125. Raghavan SC, Swanson PC, Wu X, Hsieh CL, Lieber MR. A non-B-DNA structure at the Bcl-2 major breakpoint region is cleaved by the RAG complex. Nature 2004;428:88-93.
126. Ivics Z, Hackett PB, Plasterk RH, Izsvak Z. Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells. Cell 1997;91:501-510.
127. Yant SR, Meuse L, Chiu W, Ivics Z, Izsvak Z, Kay MA. Somatic integration and long-term transgene expression in normal and haemophilic mice using a DNA transposon system. Nat Genet 2000;25:35-41.
128. Jurka J. Repeats in genomic DNA: mining and meaning. Curr Opin Struct Biol 1998;8:333-337.