Impact of transposable elements on the human genome

References

• Britten R J, Kohne D E. Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms. Science 1968; 161: 529–40
   PubMed Web of Science ®Google Scholar
• Kim J M, Vanguri S, Boeke J D, Gabriel A, Voytas D F. Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res 1998; 8: 464–78
   PubMedGoogle Scholar
• SanMiguel P, Tikhonov A, Jin Y K, Motchoulskaia N, Zakharov D, Melake-Berhan A, et al. Nested retrotransposons in the intergenic regions of the maize genome. Science 1996; 274: 765–8
   PubMed Web of Science ®Google Scholar
• Smit A FA. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev 1999; 9: 657–63
   PubMed Web of Science ®Google Scholar
• Dawkins R. The extended phenotype. Oxford University Press, OxfordUK 1982
   Google Scholar
• Dawkins R. The selfish gene. Oxford University Press, OxfordUK 1976
   Google Scholar
• Hall B G. Mobile elements as activators of cryptic genes. E. coli. Genetica 2000, in press
   Google Scholar
• Grandbastien M A. Activation of plant retrotransposons under stress conditions. Trends Plants Sci 1998; 3: 181–7
   Web of Science ®Google Scholar
• McClintock B. The significance of responses of the genome to challenge. Science 1984; 226: 792–801
   PubMed Web of Science ®Google Scholar
• Deininger P L, Batzer M A. Alu repeats and human disease. Mol Genet Metab 1999; 67: 183–93
   PubMed Web of Science ®Google Scholar
• Smit A F, Riggs A D. Tiggers and other DNA transposon fossils in the human genome. Proc Natl Acad Sci USA 1996; 93: 1443–8
   PubMed Web of Science ®Google Scholar
• Temin H M. Origin of retroviruses from cellular moveable genetic elements. Cell 1980; 21: 599–600
   PubMedGoogle Scholar
• Xiong Y, Eickbush T H. Origin and evolution of retro-elements based upon their reverse transcriptase sequences. EMBO J 1990; 9: 3353–62
   PubMed Web of Science ®Google Scholar
• Lerat E, Brunet F, Bazin C, Capy P. Is the evolution of transposable elements modular. Genetica 2000, in press
   Google Scholar
• Friedlander A, Patarca R. Endogenous proviruses. Crit Rev Oncog 1999; 10: 129–59
   Google Scholar
• Kazazian H H, Jr. An estimated frequency of endogenous insertional mutations in humans. Nut Genet 1999; 22: 130
   PubMed Web of Science ®Google Scholar
• Mustajoki S, Ahola H, Mustajoki P, Kauppinen R. Insertion of Alu element responsible for acute intermittent porphyria. Hum Mutat 1999; 13: 431–8
   Google Scholar
• Miki Y. Retrotransposal integration of mobile genetic elements in human diseases. J Hum Genet 1998; 43: 77–84
   Google Scholar
• Kobayashi K, Nakahori Y, Miyake M, Matsumura K, Kondo-Ida E, Nomura Y, et al. An ancient retrotransposal insertion causes Fukuyama-type congenital muscular dystrophy. Nature 1998; 394: 388–91
   PubMed Web of Science ®Google Scholar
• Labuda D, Zietkiewick E, Mitchell G A. Alu element as a source of genomic variation: deleterious effects and evolutionary novelties. The impact of short interspersed elements (SINEs) on the host genome, R J Maraia. RG Landes Company, Springer, Austin, TX 1995; 1–24
   Google Scholar
• Vervoort R, Gitzelmann R, Lissens W, Liebaers I A. mutation (IVS8+0.6kbdelTC) creating a new donor splice site activates a cryptic exon in an Alu-element in intron 8 of the human β-glucuronidase gene. Hum Genet 1998; 103: 686–93
   PubMed Web of Science ®Google Scholar
• den Hollander A I, ten Brink J B, deKok Y J, van Soest S, van den Born L I, van Driel M A, et al. Mutations in a human homologue of drosophila crumbs cause retinitis pigmentosa (RP12). Nut Genet 1999; 23: 217–21
   PubMed Web of Science ®Google Scholar
• Seidl C, Donner H, Petershofen E, Usadel K H, Seifried E, Kaltwasser J P, et al. An endogenous retroviral long terminal repeat at the HLA-DQB1 gene locus confers susceptibility to rheumatoid arthritis. Hum Immunol 1999; 60: 63–8
   PubMed Web of Science ®Google Scholar
• Segal Y, Peissel B, Renieri A, deMarchi M, Ballabio A, Pei Y, et al. LINE-1 elements at the sites of molecular rearrangements in Alport syndrome-diffuse leiomyomatosis. Am J Hum Genet 1999; 64: 62–9
   PubMedGoogle Scholar
• Montagna M, Santacatterina M, Tom A, Menin C, Zullato D, Chieco-Bianchi L, et al. Identification of a 3 kb Alu-mediated BRCA1 gene rearrangement in two breast/ovarian cancer families. Oncogene 1999; 18: 4160–5
   PubMed Web of Science ®Google Scholar
• Reiter L T, Murakami T, Koeuth T, Pentao L, Muzny D M, Gibbs R A, et al. A recombination hot spot responsible for two inherited peripheral neuropathies is located near a mariner transposon-like element. Nat Genet 1996; 12: 288–97
   PubMed Web of Science ®Google Scholar
• Kumatori A, Faizunnessa N N, Suzuki S, Moriuchi T, Kurozumi H, Nakamura M. Nonhomologous recombination between the cytochrome b558 heavy chain gene (CYBB) and LINE-1 causes an X-linked chronic granulomatous disease. Genomics 1998; 53: 123–8
   Google Scholar
• Jeffs A R, Benjes S M, Smith T L, Sowerby S J, Moms C M. The BCR gene recombines preferentially with Alu elements in complex BCR-ABL translocation of chronic myeloid leukaemia. Hum Mol Genet 1998; 7: 767–76
   PubMed Web of Science ®Google Scholar
• Obata K, Hiraga H, Nojima T, Yoshida M C, Abe S. Molecular characterization of the genomic breakpoint junction in a t(11;22) translocation in Ewing sarcoma. Genes Chromosomes Cancer 1999; 25: 6–15
   PubMed Web of Science ®Google Scholar
• Centra M, Memeo E, d'Apolito M, Savino M, Ianzano L, Notarangelo A, et al. Fine-exon-intron structure of the Fanconi anemia group A (FAA) gene and characterization of two genomic deletions. Genomics 1998; 51: 463–7
   Google Scholar
• Rosenberg N, Yatuv R, Orion Y, Zivelin A, Dardik R, Peretz H, et al. Glanzmann thrombasthenia caused by an 11.2-kb deletion in the glycoprotein IIIa (beta3) is a second mutation in Iraqi Jews that stemmed from a distinct founder. Blood 1997; 89: 3654–62
   PubMedGoogle Scholar
• Rothberg P G, Ponnuru S, Baker D, Bradley J F, Freeman A I, Cibis G W, et al. A deletion polymorphism due to Alu-Alu recombination in intron 2 of the retinoblastoma gene: association with human gliomas. Mol Carcinog 1997; 19: 69–73
   Google Scholar
• Huie M L, Shanske A L, Kasper J S, Marion R W, Hirschhorn R A. large Alu-mediated deletion, identified by PCR, as the molecular basis for glycogen storage disease type II (GSDII). Hum Genet 1999; 104: 94–8
   Google Scholar
• Burwinkel B, Kilimann M W. Unequal homologous recombination between LINE-1 elements as a mutational mechanism in human genetic disease. J Mol Biol 1998; 277: 513–7
   PubMedGoogle Scholar
• Luzi P, Rafi M A, Wenger D A. Characterization of the large deletion in the GALC gene found in patients with Krabbe disease. Hum Mol Genet 1995; 4: 2335–8
   Google Scholar
• Magewu A N, Jones P A. Ubiquitous and tenacious methylation of the CpG site in codon 248 of the p53 gene may explain its frequent appearance as a mutational hot spot in human cancer. Mol Cell Biol 1994; 14: 4225–32
   PubMed Web of Science ®Google Scholar
• Graff J R, Herman J G, Myöhänen S, Baylin S B, Vertino P M. Mapping patterns of CpG island methylation in normal and neoplastic cells implicates both upstream and downstream regions in de novo methylation. J Biol Chem 1997; 272: 22322–9
   PubMed Web of Science ®Google Scholar
• Arnaud P, Goubely C, Pélissier T, Deragon J M. SINE retroposons can be used in vivo as nucleation centers for de novo methylation. Mol Cell Biol 2000, in press
   Google Scholar
• Romig H, Ruff J, Fackelmeyer F, Patil M, Richter A. Characterization of two intronic nuclear matrix attachment regions in the human DNA topoisomerase I gene. Eur J Biochem 1994; 221: 411–9
   PubMedGoogle Scholar
• Bruni R, Argentini C, D'Ugo E, Ciccaglione A, Rapicetta M. Recurrence of WHV integration in the b3n locus in woodchuck hepatocellular carcinoma. Virology 1995; 214: 229–34
   Google Scholar
• Schmid C W. Does SINE evolution preclude Alu function. Nucl Acids Res 1998; 26: 4541–50
   PubMed Web of Science ®Google Scholar
• Kuo K W, Sheu H M, Huang Y S, Leung W C. Expression of transposon LINE-1 is relatively human-specific and function of the transcripts may be proliferation-essential. Biochem Biophys Res Commun 1998; 253: 566–70
   Google Scholar
• Asch H L, Eliacin E, Fanning T G, Connolly J L, Bratthauer G, Asch B. Comparative expression of the LINE p40 protein in human breast carcinomas and normal breast tissues. Oncol Res 1996; 8: 239–47
   PubMedGoogle Scholar
• Florl A R, Löwer R, Schmitz-Dräger B J, Schulz W A. DNA methylation and expression of LINE-1 and HERV-K provirus sequences in urothelial and renal cell carcinomas. Br J Cancer 1999; 80: 1312–21
   PubMed Web of Science ®Google Scholar
• Larsson E, Andersson G. Beneficial role of human endogenous retroviruses: facts and hypotheses. Scand J Immunol 1998; 48: 329–38
   PubMedGoogle Scholar
• Xie H, Brines M L, de Lanerolle N C. Transcripts of the transposon mariner are present in epileptic brain. Epilepsy Res 1998; 32: 140–53
   Google Scholar
• Fujino T, Navaratnam N, Scott J. Human apolipoprotein B RNA editing deaminase gene (APOBEC1). Genomics 1998; 47: 266–75
   PubMed Web of Science ®Google Scholar
• Brittens R J. Mobile elements inserted in the distant past have taken on important functions. Gene 1997; 205: 177–82
   Google Scholar
• Brosius J, Tiedge H. Reverse transcriptase: mediator of genomic plasticity. Virus Genes 1996; 11: 163–79
   Google Scholar
• Long Q, Bengra C, Li C, Kutlar F, Tuan D. A long terminal repeat of the human endogenous retrovirus ERV-9 is located in the 5′ boundary area of the human β-globin locus control region. Genomics 1998; 54: 542–55
   PubMedGoogle Scholar
• Mager D L, Hunter D G, Schemer M, Freeman J D. Endogenous retroviruses provide the primary polyadenylation signal for two new human genes. Genomics 1999; 59: 255–63
   Google Scholar
• Gu J J, Spychala J, Mitchell B S. Regulation of the human inosine monophosphate dehydrogenase type I gene. Utilization of alternative promoters. J Biol Chem 1997; 272: 4458–66
   PubMed Web of Science ®Google Scholar
• Lowe D, Henning D, Reddy R. An RNA polymerase III transcription unit located in the upstream control regions of the human proliferating-cell nucleolar protein p120 is transcribed in vitro and in vivo. Eur J Biochem 1999; 266: 112–22
   Google Scholar
• Kazakov V I, Tomilin N V. Increased concentration of some transcription factor binding sites in human retroposons of the Alu family. Genetica 1996; 97: 15–22
   Google Scholar
• Babich V, Aksenov N, Alexeenko V, Oei S L, Buchlow G, Tomilin N. Association of some potential hormone response elements in human genes with the alu family repeats. Gene 1999; 239: 341–9
   Google Scholar
• Monte S M, Ghanbari K, Frey W H, Beheshti I, Averback P, Hauser S L, et al. Characterization of the AD7C-NTP cDNA expression in Alzheimer's disease and mesurement of a 41-kD protein in cerebrospinal fluid. J Clin Invest 1997; 100: 3093–104
   Google Scholar
• Tulko J, Korotkov E V, Phoenix D A. MIRs are present in coding regions of human genes. DNA Seq 1997; 8: 31–8
   PubMed Web of Science ®Google Scholar
• Platzer M, Roman G, Bauer D, Uziel T, Savitsky K, Bar-Shira A, et al. Ataxia-telangiectasia locus: sequence analysis of 184 kb of human genomic DNA containing the entire ATM gene. Genome Res 1997; 7: 592–605
   Google Scholar
• Berquin I M, Ahram M, Sloane B F. Exon 2 of human cathepsin B derives from an Alu element. FEBS Lett 1997; 419: 121–3
   Google Scholar
• Mullersman J E, Pfeffer L M. An Alu cassette in the cytoplasmic domain of an interferon receptor subunit. J Interferon Cytokine Res 1995; 15: 815–7
   Google Scholar
• Donohue S J, Roseboom P H, Illnerova H, Weller J L, Klein D C. Human hydroxyindole-O—methyltransferase: presence of LINE-1 fragment in a cDNA clone and pineal mRNA. DNA Cell Biol 1993; 12: 715–27
   Google Scholar
• Hakim I, Amariglio N, Grossman Z, Simoni-Brok F, Ohno S, Rechavi G. The genome of the THE I transposable repetitive elements is composed of a basic motif homologous to an ancestral immunoglobulin gene sequence. Proc Natl Acad Sci USA 1994; 91: 7967–9
   Google Scholar
• Gerber A, O'Connel M A, Keller W. Two forms of human double-stranded RNA-specific editase 1 (hRED1) generated by the insertion of an Alu cassette. RNA 1997; 3: 453–63
   PubMed Web of Science ®Google Scholar
• Banki K, Halladay D, Perl A. Cloning and expression of the human gene for transaldolase. A novel highly repetitive element constitutes an integral part of the coding sequence. J Biol Chem 1994; 269: 2847–51
   Google Scholar
• Makalowski W, Mitchell G A, Labuda D. Alu sequences in the coding regions of mRNA: a source of protein variability. Trends Genet 1994; 10: 188–93
   PubMed Web of Science ®Google Scholar
• Yulug I G, Yulug A, Fisher E MC. The frequency and position of Alu repeats in cDNAs, as determined by database searching. Genomics 1995; 27: 544–8
   PubMed Web of Science ®Google Scholar
• Vidal F, Mougneau E, Glaichenhaus N, Vaigot P, Darmon M, Cuzin F. Coordinated posttranscriptional control of gene expression by modular elements including Alu-like repetitive sequences. Proc Natl Acad Sci USA 1993; 90: 208–12
   Google Scholar
• Merritt C M, Easteal S, Board P G. Evolution of human al-acid glycoprotein genes and surrounding Alu repeats. Genomics 1990; 6: 659–65
   Google Scholar
• Dulai K S, von Dornum M, Mollon J D, Hunt D M. The evolution of trichromatic color vision by opsin gene duplication in new world and old world primates. Genome Res 1999; 9: 629–38
   Google Scholar
• Kulski J K, Gaudieri S, Bellgard M, Balmer L, Giles K, Inoko H, et al. The evolution of MCH diversity by segmental duplication and transposition of retroelements. J Mol Evol 1997; 45: 599–609
   Google Scholar
• Gaudieri S, Leelayuwat C, Townend D C, Kulski J K, Dawkmgs R L. Genomic characterization of the region between HLA-B and TNF: implication for the evolution of multicopy gene families. J Mol Evol 1997; 44: S147–54
   Google Scholar
• Kulski J K, Gaudieri S, Martin A, Dawking R L. Coevolution of PERB11 and HLA class I genes with HERV-16 and retroelements by extended genomic duplication. J Mol Evol 1999; 49: 84–97
   Google Scholar
• Moran J V, DeBerardinis R J, Kazazian H H. Exon shuffling by LINE-1 retrotransposition. Science 1999; 283: 1530–4
   PubMed Web of Science ®Google Scholar
• Laurent A M, Puechberty J, Roizès G. Hypothesis: for the worst and for the best, LINE-1Hs retrotransposons actively participate in the evolution of the human centromeric alphoid sequences. Chrom Res 1999; 7: 305–17
   Google Scholar
• Choo K H. Centromere DNA dynamics: latent centromeres and neocentromere formation. Am J Hum Genet 1997; 61: 1225–33
   PubMedGoogle Scholar
• Marçais B, Bellis M, Gerard A, Pages M, Boublik Y, Roizès G. Structural organization and polymorphism of the alpha satellite DNA sequences of chromosome 13 and 21 as revealed by pulse field electrophoresis. Hum Genet 1991; 86: 311–6
   Google Scholar
• Laurent A M, Puechberty J, Prades C, Gimenez S, Roizès G. Site-specific retrotransposition of LINE-1 elements within human alphoid satellite sequences. Genomics 1997; 46: 127–32
   Google Scholar
• Puechberty J, Laurent A M, Gimenez S, Billault A, Brun-Laurent M A, Calenda A, et al. Genetic and physical analyses of the centromeric and pericentromeric regions of human chromosome 5: recombination across ken. Genomics 1999; 56: 274–87
   Google Scholar
• Kipling D, Warburton P E. Centromeres, CENP-B and Tigger too. Trends Genet 1997; 13: 141–4
   PubMedGoogle Scholar
• Cook J M, Tristem M. SINEs of a times-transposable element as clade markers for their hosts. Trends Ecol Evol 1997; 12: 295–7
   Google Scholar
• Hillis D M. SINEs of the perfect character. Proc Natl Acad Sci U S A 1999; 96: 9979–81
   Google Scholar
• Jurka J. Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc Natl Acad Sci USA 1997; 94: 1872–7
   PubMed Web of Science ®Google Scholar
• Feng Q, Moran J V, Kazazian H H, Boeke J D. Human LINE-1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 1996; 87: 905–16
   PubMed Web of Science ®Google Scholar
• Batzer M A, Stoneking M, Alegria-Hartman M, Bazan H, Kass D H, Shaikh T H, et al. African origin of human-specific polymorphic Alu insertions. Proc Natl Acad Sci U S A 1994; 91: 12288–92
   PubMed Web of Science ®Google Scholar
• Novick G E, Novick C C, Yunis J, Yunis E, Antunez de Mayolo P, Scheer W D, et al. Polymorphic Alu insertions and the Asian origin of Native American populations. Hum Biol 1998; 70: 23–39
   PubMed Web of Science ®Google Scholar
• Hamdi H, Nishio H, Zielinski R, Dugaiczyk A. Origin and phylogenetic distribution of Alu DNA repeats: irreversible events in the evolution of primates. J Mol Biol 1999; 289: 861–71
   Google Scholar
• Johnson W E, Coffin J M. Constructing primate phylogenies from ancient retrovirus sequences. Proc Natl Acad Sci U S A 1999; 96: 10254–60
   PubMed Web of Science ®Google Scholar
• Verneau O, Catzeflis F, Furano A. Determining and dating recent rodent speciation events by using LINE-1 retrotransposons. Proc Natl Acad Sci USA 1998; 95: 11284–9
   Google Scholar
• Zietkiewicz E, Labuda M, Sinnett D, Glorieux F H, Labuda D. Linkage mapping by simultaneous screening of multiple polymorphic loci using Alu oligonucleotide-directed PCR. Proc Natl Acad Sci USA 1992; 89: 8448–51
   Google Scholar