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Chapter 47 : Mobile Elements in Animal and Plant Genomes

Authors: Prescott L. Deininger1, Astrid M. Roy-Engel1
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Affiliations: 1: Tulane Cancer Center and Department of Environmental Health Sciences, Tulane University Medical Center, 1430 Tulane Ave., New Orleans, LA 70112
Content Type: Monograph
Publication Year: 2002

Category: Microbial Genetics and Molecular Biology

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Abstract:

This chapter discusses the different classes of mobile elements seen in some of the best-characterized animal genome and plant genome. It talks about the some of the general concepts behind the colonization of genomes by mobile elements. There are basically three classes of autonomous mobile elements, all three of which can be found to various extents in different genomes of all animals and plants. These are the DNA transposons, the long terminal repeat (LTR) retrotransposons, and the non-LTR retrotransposons. DNA transposons are very common in the genome, as well as several relatively high-copy-number families of their nonautonomous relatives, miniature inverted-repeat transposable elements (MITEs). Other site-specific mobile elements are the HetA and TART elements that make up the telomeres in . Only sporadic data are available on mobile elements in reptiles, amphibians, and fish. Almost all the classes of mobile elements are present to some degree in almost all animal and plant genomes. The density of mobile elements has also been shown to extend into the centromeric region in . Not only is the impact of mobile elements on their genome a direct result of insertional mutagenesis, but there are also a series of secondary impacts on the genome including recombination and many more subtle changes that may alter the stability or evolution of an organism’s genome. Retrotransposition has also given rise to gene duplications or other useful gene modifications that allowed evolution to new function.

Citation: Deininger P, Roy-Engel A. 2002. Mobile Elements in Animal and Plant Genomes, p 1074-1092. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch47

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Mobile Elements in Animal and Plant Genomes
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Citation: Deininger P, Roy-Engel A. 2002. Mobile Elements in Animal and Plant Genomes, p 1074-1092. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch47
/content/10.1128/9781555817954.chap47.fig47-1
Figure 1.

Major classes of autonomous mobile elements in animals and plants. Schematic diagrams for the three major classes of mobile elements are shown. The DNA transposons have two or three open reading frames coding for enzymes involved in the transposition process. They are also flanked by inverted repeats (arrowheads) at the ends that act as -acting elements in the integration process. The transposition process involves direct integration through DNA intermediates. Both the LTRretrotransposons and the non-LTRretrotransposons use anRNA intermediate in the amplification process. They generally encode two open reading frames coding for RNA-binding proteins and enzymes involved in reverse transcription and endonuclease cleavage at the site of integration. The LTRretrotransposons have LTRs that contain signals for transcription of the elements and are involved in the integration process. The non-LTRretrotransposons use a promoter region found in the 5′ noncoding region of the RNA and terminate in a poly(A) tract like a typical mRNA.

10.1128/9781555817954/fig47-1_thmb.gif
10.1128/9781555817954/fig47-1.gif
Image of Figure 1.
Figure 1.

Major classes of autonomous mobile elements in animals and plants. Schematic diagrams for the three major classes of mobile elements are shown. The DNA transposons have two or three open reading frames coding for enzymes involved in the transposition process. They are also flanked by inverted repeats (arrowheads) at the ends that act as -acting elements in the integration process. The transposition process involves direct integration through DNA intermediates. Both the LTRretrotransposons and the non-LTRretrotransposons use anRNA intermediate in the amplification process. They generally encode two open reading frames coding for RNA-binding proteins and enzymes involved in reverse transcription and endonuclease cleavage at the site of integration. The LTRretrotransposons have LTRs that contain signals for transcription of the elements and are involved in the integration process. The non-LTRretrotransposons use a promoter region found in the 5′ noncoding region of the RNA and terminate in a poly(A) tract like a typical mRNA.

Citation: Deininger P, Roy-Engel A. 2002. Mobile Elements in Animal and Plant Genomes, p 1074-1092. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch47
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Figure 2.

Genomic patterns for mobile elements. The patterns show schematically some of the basic density patterns found for mobile elements in animal and plant genomes. These include elements that are distributed fairly randomly, some showing either a combined centromeric/telomeric preference, and many with a preference for the juxtacentromeric region. In more complex genomes, it is typical to see a complex series of clusters spread throughout the genome. There are also classes of mobile elements with a very high degree of specificity for very specific gene or chromosomal regions.

10.1128/9781555817954/fig47-2_thmb.gif
10.1128/9781555817954/fig47-2.gif
Image of Figure 2.
Figure 2.

Genomic patterns for mobile elements. The patterns show schematically some of the basic density patterns found for mobile elements in animal and plant genomes. These include elements that are distributed fairly randomly, some showing either a combined centromeric/telomeric preference, and many with a preference for the juxtacentromeric region. In more complex genomes, it is typical to see a complex series of clusters spread throughout the genome. There are also classes of mobile elements with a very high degree of specificity for very specific gene or chromosomal regions.

Citation: Deininger P, Roy-Engel A. 2002. Mobile Elements in Animal and Plant Genomes, p 1074-1092. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch47
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/content/10.1128/9781555817954.chap47.fig47-3
Figure 3.

Schematic of evolutionary peaks of mobile element amplification. Each of the different line types represents a theoretical amplification rate versus evolutionary time for a different mobile element. These simply show the concept that when a mobile element enters or is activated in a naïve genome, they often amplify efficiently and reach a peak amplification rate. Processes such as mobile elements regulating their own amplification, development of genomic suppression mechanisms, or simply negative selection due to the damage caused by the elements, eventually lead most elements to greatly decrease or lose all amplification capability. Because very few elements are actively removed from the genome, the modern genome will be littered with pseudogene copies of the older elements, as well as members of any active families of elements. Also, some of the highest-copy-number elements are nonautonomous and therefore only amplify in conjunction with an active, autonomous family of elements. The modern genome is littered with both the elements that amplified earlier in evolution and families of currently active elements.

10.1128/9781555817954/fig47-3_thmb.gif
10.1128/9781555817954/fig47-3.gif
Image of Figure 3.
Figure 3.

Schematic of evolutionary peaks of mobile element amplification. Each of the different line types represents a theoretical amplification rate versus evolutionary time for a different mobile element. These simply show the concept that when a mobile element enters or is activated in a naïve genome, they often amplify efficiently and reach a peak amplification rate. Processes such as mobile elements regulating their own amplification, development of genomic suppression mechanisms, or simply negative selection due to the damage caused by the elements, eventually lead most elements to greatly decrease or lose all amplification capability. Because very few elements are actively removed from the genome, the modern genome will be littered with pseudogene copies of the older elements, as well as members of any active families of elements. Also, some of the highest-copy-number elements are nonautonomous and therefore only amplify in conjunction with an active, autonomous family of elements. The modern genome is littered with both the elements that amplified earlier in evolution and families of currently active elements.

Citation: Deininger P, Roy-Engel A. 2002. Mobile Elements in Animal and Plant Genomes, p 1074-1092. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch47
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References

/content/book/10.1128/9781555817954.chap47
1. Adams, M. D.,, S. E. Celniker,, R. A. Holt,, C. A. Evans,, J. D. Gocayne,, P. G. Amanatides,, S. E. Scherer,, P. W. Li,, R. A. Hoskins,, R. F. Galle,, R. A. George,, S. E. Lewis,, S. Richards,, M. Ashburner,, S. N. Henderson,, G. G. Sutton,, J. R. Wortman,, M. D. Yandell,, Q. Zhang,, L. X. Chen,, R. C. Brandon,, Y. H. Rogers,, R. G. Blazej,, M. Champe,, B. D. Pfeiffer,, K. H. Wan,, C. Doyle,, E. G. Baxter,, G. Helt,, C. R. Nelson,, G. L. Gabor Miklos,, J. F. Abril,, A. Agbayani,, H. J. An,, C. Andrews- Pfannkoch,, D. Baldwin,, R. M. Ballew,, A. Basu,, J. Baxendale,, L. Bayraktaroglu,, E. M. Beasley,, K. Y. Beeson,, P. V. Benos,, B. P. Berman,, D. Bhandari,, S. Bolshakov,, D. Borkova,, M. R. Botchan,, J. Bouck,, P. Brokstein,, P. Brottier,, K. C. Burtis,, D. A. Busam,, H. Butler,, E. Cadieu,, A. Center,, I. Chandra,, J. M. Cherry,, S. Cawley,, C. Dahlke,, L. B. Davenport,, P. Davies,, B. de Pablos,, A. Delcher,, Z. Deng,, A. D. Mays,, I. Dew,, S. M. Dietz,, K. Dodson,, L. E. Doup,, M. Downes,, S. Dugan- Rocha,, B. C. Dunkov,, P. Dunn,, K. J. Durbin,, C. C. Evangelista,, C. Ferraz,, S. Ferriera,, W. Fleischmann,, C. Fosler,, A. E. Gabrielian,, N. S. Garg,, W. M. Gelbart,, K. Glasser,, A. Glodek,, F. Gong,, J. H. Gorrell,, Z. Gu,, P. Guan,, M. Harris,, N. L. Harris,, D. Harvey,, T. J. Heiman,, J. R. Hernandez,, J. Houck,, D. Hostin,, K. A. Houston,, T. J. Howland,, M. H. Wei,, C. Ibegwam,, M. Jalali,, F. Kalush,, G. H. Karpen,, Z. Ke,, J. A. Kennison,, K. A. Ketchum,, B. E. Kimmel,, C. D. Kodira,, C. Kraft,, S. Kravitz,, D. Kulp,, Z. Lai,, P. Lasko,, Y. Lei,, A. A. Levitsky,, J. Li,, Z. Li,, Y. Liang,, X. Lin,, X. Liu,, B. Mattei,, T. C. McIntosh,, M. P. McLeod,, D. McPherson,, G. Merkulov,, N. V. Milshina,, C. Mobarry,, J. Morris,, A. Moshrefi,, S. M. Mount,, M. Moy,, B. Murphy,, L. Murphy,, D. M. Muzny,, D. L. Nelson,, D. R. Nelson,, K. A. Nelson,, K. Nixon,, D. R. Nusskern,, J. M. Pacleb,, M. Palazzolo,, G. S. Pittman,, S. Pan,, J. Pollard,, V. Puri,, M. G. Reese,, K. Reinert,, K. Remington,, R. D. Saunders,, F. Scheeler,, H. Shen,, B. C. Shue,, I. Siden- Kiamos,, M. Simpson,, M. P. Skupski,, T. Smith,, E. Spier,, A. C. Spradling,, M. Stapleton,, R. Strong,, E. Sun,, R. Svirskas,, C. Tector,, R. Turner,, E. Venter,, A. H. Wang,, X. Wang,, Z. Y. Wang,, D. A. Wassarman,, G. M. Weinstock,, J. Weissenbach,, S. M. Williams,, T. Woodage,, K. C. Worley,, D. Wu,, S. Yang,, Q. A. Yao,, J. Ye,, R. F. Yeh,, J. S. Zaveri,, M. Zhan,, G. Zhang,, Q. Zhao,, L. Zheng,, X. H. Zheng,, F. N. Zhong,, W. Zhong,, X. Zhou,, S. Zhu,, X. Zhu,, H. O. Smith,, R. A. Gibbs,, E. W. Myers,, G. M. Rubin,, and J. C. Venter. 2000. The genome sequence of Drosophila melanogaster. Science 287: 2185– 2195.
2. Bailey, J. A.,, L. Carrel,, A. Chakravarti,, and E. E. Eichler. 2000. From the cover: molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: the Lyon repeat hypothesis. Proc. Natl. Acad. Sci. USA 97: 6634– 6639.
3. Bennetzen, J. L. 2000. Transposable element contributions to plant gene and genome evolution. Plant Mol. Biol. 42: 251– 269.
4. Biemont, C.,, and C. Terzian. 1988. Mdg-1 mobile element polymorphism in selected Drosophila melanogaster populations. Genetica 76: 7– 14.
5. Biemont, C.,, C. Vieira,, C. Hoogland,, G. Cizeron,, C. Loevenbruck,, C. Arnault,, and J. P. Carante. 1997. Maintenance of transposable element copy number in natural populations of Drosophila melanogaster and D. simulans. Genetica 100: 161– 166.
6. Biessmann, H.,, and J. M. Mason. 1997. Telomere maintenance without telomerase. Chromosoma 106: 63– 69.
7. Birchler, J. A.,, M. P. Bhadra,, and U. Bhadra. 2000. Making noise about silence: repression of repeated genes in animals. Curr. Opin. Genet. Dev. 10: 211– 216.
8. Boeke, J. D. 1997. LINEs and Alus—the polyA connection. Nat. Genet. 16: 6– 7.
9. Britten, R. J. 1995. Active gypsy/Ty3 retrotransposons or retroviruses in Caenorhabditis elegans. Proc. Natl. Acad. Sci. USA 92: 599– 601.
10. Britten, R. J. 1997. Mobile elements inserted in the distant past have taken on important functions. Gene 205: 177– 182.
11. Brosius, J.,, and H. Tiedge. 1995. Reverse transcriptase: mediator of genomic plasticity. Virus Genes 11: 163– 179.
12. Bucci, S.,, M. Ragghianti,, G. Mancino,, G. Petroni,, F. Guerrini,, and S. Giampaoli. 1999. Rana/Pol III: a family of SINElike sequences in the genomes of western Palearctic water frogs. Genome 42: 504– 511.
13. Bureau, T. E.,, S. E. White,, and S. R. Wessler. 1994. Transduction of a cellular gene by a plant retroelement. Cell 77: 479– 480.
14. Burke, W. D.,, H. S. Malik,, J. P. Jones,, and T. H. Eickbush. 1999. The domain structure and retrotransposition mechanism of R2 elements are conserved throughout arthropods. Mol. Biol. Evol. 16: 502– 511.
15. Capy, P.,, T. Langin,, Y. Bigot,, F. Brunet,, M. J. Daboussi,, G. Periquet,, J. R. David,, and D. L. Hartl. 1994. Horizontal transmission versus ancient origin: mariner in the witness box. Genetica 93: 161– 170.
16. Capy, P.,, R. Vitalis,, T. Langin,, D. Higuet,, and C. Bazin. 1996. Relationships between transposable elements based upon the integrase-transposase domains: is there a common ancestor? J. Mol. Evol. 42: 359– 368.
17. Casavant, N. C.,, L. Scott,, M. A. Cantrell,, L. E. Wiggins,, R. J. Baker,, and H. A. Wichman. 2000. The end of the LINE? Lack of recent 11 activity in a group of South American rodents. Genetics 154: 1809– 1817.
18. The C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282: 2012– 2018. (Errata, 283:35, 1999; 283:2103, 1999; 285:1493, 1999.)
19. Chang, D. Y.,, N. Sasaki-Tozawa,, L. K. Green,, and R. J. Maraia. 1995. A trinucleotide repeat-associated increase in the level of Alu RNA-binding protein occurred during the same period as the major Alu amplification that accompanied anthropoid evolution. Mol. Cell. Biol. 15: 2109– 2116.
20. Cost, G. J.,, and J. D. Boeke. 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.
21. Csink, A. K.,, and J. F. McDonald. 1990. copia expression is variable among natural populations of Drosophila. Genetics 126: 375– 385.
22. D’Andrea, A. D.,, U. Tantravahi,, M. Lalande,, M. A. Perle,, and S. A. Latt. 1983. High resolution analysis of the timing of replication of specific DNA sequences during S phase of mammalian cells. Nucleic Acids Res. 11: 4753– 4774.
23. Daniels, G.,, and P. Deininger. 1985. Repeat sequence families derived from mammalian tRNA genes. Nature 317: 819– 822.
24. Danilevskaya, O. N.,, K. Lowenhaupt,, and M. L. Pardue. 1998. Conserved subfamilies of the Drosophila HeT-A telomere- specific retrotransposon. Genetics 148: 233– 242.
25. Deininger, P. L.,, and M. A. Batzer. 1999. Alu repeats and human disease. Mol. Genet. Metab. 67: 183– 193.
26. Deininger, P.,, and M. A. Batzer. 1993. Evolution of retroposons. Evol. Biol. 27: 157– 196.
27. Deininger, P.,, and M. Batzer,. 1995. SINE master genes and population biology, p. 43– 60. In R. Maraia (ed.), The Impact of Short, Interspersed Elements (SINEs) on the Host Genome. R. G. Landes, Georgetown, Tex.
28. Deininger, P.,, M. Batzer,, I. C. Hutchison,, and M. Edgell. 1992. Master genes in mammalian repetitive DNA amplification. Trends Genet. 8: 307– 312.
29. Deininger, P.,, and G. Daniels. 1986. The recent evolution of mammalian repetitive DNA elements. Trends Genet. 2: 76– 80.
30. Dunham, I.,, N. Shimizu,, B. A. Roe,, S. Chissoe,, A. R. Hunt,, J. E. Collins,, R. Bruskiewich,, D. M. Beare,, M. Clamp,, L. J. Smink,, R. Ainscough,, J. P. Almeida,, A. Babbage,, C. Bagguley,, J. Bailey,, K. Barlow,, K. N. Bates,, O. Beasley,, C. P. Bird,, S. Blakey,, A. M. Bridgeman,, D. Buck,, J. Burgess,, W. D. Burrill,, and K. P. O’Brien. 1999. The DNA sequence of human chromosome 22. Nature 402: 489– 495. (Erratum, 404:904, 2000.)
31. Elgar, G.,, M. S. Clark,, S. Meek,, S. Smith,, S. Warner,, Y. J. Edwards,, N. Bouchireb,, A. Cottage,, G. S. Yeo,, Y. Umrania,, G. Williams,, and S. Brenner. 1999. Generation and analysis of 25 Mb of genomic DNA from the pufferfish Fugu rubripes by sequence scanning. Genome Res. 9: 960– 971.
32. Emmons, S. W.,, S. Roberts,, and K. S. Ruan. 1986. Evidence in a nematode for regulation of transposon excision by tissuespecific factors. Mol. Gen. Genet. 202: 410– 415.
33. Engels, W. R. 1992. The origin of P elements in Drosophila melanogaster. Bioessays 14: 681– 686.
34. Feng, Q.,, J. V. Moran,, H. H. Kazazian, Jr.,, and J. D. Boeke. 1996. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87: 905– 916.
35. Flavell, A. J.,, V. Jackson,, M. P. Iqbal,, I. Riach,, and S. Waddell. 1995. Ty1-copia group retrotransposon sequences in amphibia and reptilia. Mol. Gen. Genet. 246: 65– 71.
36. Garrett, J. E.,, D. S. Knutzon,, and D. Carroll. 1989. Composite transposable elements in the Xenopus laevis genome. Mol. Cell. Biol. 9: 3018– 3027.
37. Gaut, B. S.,, D. E. Le Thierry,, A. S. Peek,, and M. C. Sawkins. 2000. Maize as a model for the evolution of plant nuclear genomes. Proc. Natl. Acad. Sci. USA 97: 7008– 7015.
38. Gebow, D.,, N. Miselis,, and H. L. Liber. 2000. Homologous and nonhomologous recombination resulting in deletion: effects of p53 status, microhomology, and repetitive DNA length and orientation. Mol. Cell. Biol. 20: 4028– 4035.
39. Goldman, M. A.,, G. P. Holmquist,, M. C. Gray,, L. A. Caston,, and A. Nag. 1984. Replication timing of genes and middle repetitive sequences. Science 224: 686– 692.
40. Goodier, J. L.,, and W. S. Davidson. 1994. Tc1 transposonlike sequences are widely distributed in salmonids. J. Mol. Biol. 241: 26– 34.
41. Goodier, J. L.,, E. M. Ostertag,, and H. H. Kazazian, Jr. 2000. Transduction of 3'-flanking sequences is common in L1 retrotransposition. Hum. Mol. Genet. 9: 653– 657.
42. Hagemann, S.,, W. J. Miller,, E. Haring,, and W. Pinsker. 1998. Nested insertions of short mobile sequences in Drosophila P elements. Chromosoma 107: 6– 16.
43. Hattori, M.,, A. Fujiyama,, T. D. Taylor,, H. Watanabe,, T. Yada,, H. S. Park,, A. Toyoda,, K. Ishii,, Y. Totoki,, D. K. Choi,, E. Soeda,, M. Ohki,, T. Takagi,, Y. Sakaki,, S. Taudien,, K. Blechschmidt,, A. Polley,, U. Menzel,, J. Delabar,, K. Kumpf,, R. Lehmann,, D. Patterson,, K. Reichwald,, A. Rump,, M. Schillhabel,, and A. Schudy. 2000. The DNA sequence of human chromosome 21. The chromosome 21 mapping and sequencing consortium. Nature 405: 311– 319.
44. Heslop-Harrison, J. S.,, M. Murata,, Y. Ogura,, T. Schwarzacher,, and F. Motoyoshi. 1999. Polymorphisms and genomic organization of repetitive DNA from centromeric regions of Arabidopsis chromosomes. Plant Cell 11: 31– 42.
45. Hiom, K.,, M. Melek,, and M. Gellert. 1998. DNA transposition by the RAG1 and RAG2 proteins: a possible source of oncogenic translocations. Cell 94: 463– 470.
46. Izsvak, Z.,, Z. Ivics,, D. Garcia-Estefania,, S. C. Fahrenkrug,, and P. B. Hackett. 1996. DANA elements: a family of composite, tRNA-derived short interspersed DNA elements associated with mutational activities in zebrafish (Danio rerio). Proc. Natl. Acad. Sci. USA 93: 1077– 1081.
47. Jensen, S.,, M. P. Gassama,, and T. Heidmann. 1999. Taming of transposable elements by homology-dependent gene silencing. Nat. Genet. 21: 209– 212.
48. Johnson, W. E.,, and J. M. Coffin. 1999. Constructing primate phylogenies from ancient retrovirus sequences. Proc. Natl. Acad. Sci. USA 96: 10254– 10260.
49. Junakovic, N.,, A. Terrinoni,, C. Di Franco,, C. Vieira,, and C. Loevenbruck. 1998. Accumulation of transposable elements in the heterochromatin and on the Y chromosome of Drosophila simulans and Drosophila melanogaster. J. Mol. Evol. 46: 661– 668.
50. Jurka, J. 1997. Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc. Natl. Acad. Sci. USA 94: 1872– 1877.
51. Jurka, J. 1998. Repeats in genomic DNA: mining and meaning. Curr. Opin. Struct. Biol. 8: 333– 337.
52. Kass, D. H.,, J. Kim,, and P. L. Deininger. 1996. Sporadic amplification of ID elements in rodents. J. Mol. Evol. 42: 7– 14.
53. Kawakami, K.,, and A. Shima. 1999. Identification of the Tol2 transposase of the medaka fish Oryzias latipes that catalyzes excision of a nonautonomous Tol2 element in zebrafish Danio rerio. Gene 240: 239– 244.
54. Kazazian, H. H. J. 1998. Mobile elements and disease. Curr. Opin. Genet. Dev. 8: 343– 350.
55. Kazazian, H. H. J.,, and J. V. Moran. 1998. The impact of L1 retrotransposons on the human genome. Nat. Genet. 19: 19– 24.
56. Koga, A.,, M. Suzuki,, H. Inagaki,, Y. Bessho,, and H. Hori. 1996. Transposable element in fish. Nature 383: 30.
57. Korenberg, J. R.,, and M. C. Rykowski. 1988. Human genome organization: Alu, lines, and the molecular structure of metaphase chromosome bands. Cell 53: 391– 400.
58. Kotani, H.,, T. Hosouchi,, and H. Tsuruoka. 1999. Structural analysis and complete physical map of Arabidopsis thaliana chromosome 5 including centromeric and telomeric regions. DNA Res. 6: 381– 386.
59. Kumar, A.,, and J. L. Bennetzen. 1999. Plant retrotransposons. Annu. Rev. Genet. 33: 479– 532.
60. Labrador, M.,, M. Farre,, F. Utzet,, and A. Fontdevila. 1999. Interspecific hybridization increases transposition rates of Osvaldo. Mol. Biol. Evol. 16: 931– 937.
61. Lam, W. L.,, T. S. Lee,, and W. Gilbert. 1996. Active transposition in zebrafish. Proc. Natl. Acad. Sci. USA 93: 10870– 10875.
62.. Leeton, P. R.,, and D. R. Smyth. 1993. An abundant LINElike element amplified in the genome of Lilium speciosum. Mol. Gen. Genet. 237: 97– 104.
63. Levis, R. W.,, R. Ganesan,, K. Houtchens,, L. A. Tolar,, and F. M. Sheen. 1993. Transposons in place of telomeric repeats at a Drosophila telomere. Cell 75: 1083– 1093.
64. Lin, X.,, S. Kaul,, S. Rounsley,, T. P. Shea,, M. I. Benito,, C. D. Town,, C. Y. Fujii,, T. Mason,, C. L. Bowman,, M. Barnstead,, T. V. Feldblyum,, C. R. Buell,, K. A. Ketchum,, J. Lee,, C. M. Ronning,, H. L. Koo,, K. S. Moffat,, L. A. Cronin,, M. Shen,, G. Pai,, S. Van Aken,, L. Umayam,, L. J. Tallon,, J. E. Gill,, and J. C. Venter. 1999. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 402: 761– 768.
65. Lobachev, K. S.,, J. E. Stenger,, O. G. Kozyreva,, J. Jurka,, D. A. Gordenin,, and M. A. Resnick. 2000. Inverted Alu repeats unstable in yeast are excluded from the human genome. EMBO J. 19: 3822– 3830.
66. Lozovskaya, E. R.,, D. L. Hartl,, and D. A. Petrov. 1995. Genomic regulation of transposable elements in Drosophila. Curr. Opin. Genet. Dev. 5: 768– 773.
67. Luan, D. D.,, M. H. Korman,, J. L. Jakubczak,, and T. H. Eickbush. 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.
68. Lueders, K. K.,, and W. N. Frankel. 1994. Mapping of mouse intracisternal A-particle proviral markers in an interspecific backcross. Mamm. Genome 5: 473– 478.
69. Malik, H. S.,, and T. H. Eickbush. 1998. The RTE class of non-LTRretrotransposons is widely distributed in animals and is the origin of many SINEs. Mol. Biol. Evol. 15: 1123– 1134.
70. Marracci, S.,, R. Batistoni,, G. Pesole,, L. Citti,, and I. Nardi. 1996. Gypsy/Ty3-like elements in the genome of the terrestrial Salamander hydromantes (Amphibia, Urodela). J. Mol. Evol. 43: 584– 593.
71. Maside, X.,, S. Assimacopoulos,, and B. Charlesworth. 2000. Rates of movement of transposable elements on the second chromosome of Drosophila melanogaster. Genet. Res. 75: 275– 284.
72. Mayer, K.,, C. Schuller,, R. Wambutt,, G. Murphy,, G. Volckaert,, T. Pohl,, A. Dusterhoft,, W. Stiekema,, K. D. Entian,, N. Terryn,, B. Harris,, W. Ansorge,, P. Brandt,, L. Grivell,, M. Rieger,, M. Weichselgartner,, V. de Simone,, B. Obermaier,, R. Mache,, M. Muller,, M. Kreis,, M. Delseny,, P. Puigdomenech,, M. Watson,, W. R. McCombie, et al. 1999. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature 402: 769– 777.
73. McCarron, M.,, A. Duttaroy,, G. Doughty,, and A. Chovnick. 1994. Drosophila P element transposase induces male recombination additively and without a requirement for P element excision or insertion. Genetics 136: 1013– 1023.
74. Medstrand, P.,, and D. L. Mager. 1998. Human-specific integrations of the HERV-K endogenous retrovirus family. J. Virol. 72: 9782– 9787.
75. Mochizuki, K.,, M. Umeda,, H. Ohtsubo,, and E. Ohtsubo. 1992. Characterization of a plant SINE, p-SINE1, in rice genomes. Jpn. J. Genet. 67: 155– 166.
76. Moran, J. V.,, R. J. DeBerardinis,, and H. H. Kazazian, Jr. 1999. Exon shuffling by L1 retrotransposition. Science 283: 1530– 1534.
77. Morgan, G. T. 1995. Identification in the human genome of mobile elements spread by DNA-mediated transposition. J. Mol. Biol. 254: 1– 5.
78. Murata, S.,, N. Takasaki,, M. Saitoh,, and N. Okada. 1993. Determination of the phylogenetic relationships among Pacific salmonids by using short interspersed elements (SINEs) as temporal landmarks of evolution. Proc. Natl. Acad. Sci. USA 90: 6995– 6999.
79. Nakamura, T. M.,, and T. R. Cech. 1998. Reversing time: origin of telomerase. Cell 92: 587– 590.
80. Noma, K.,, E. Ohtsubo,, and H. Ohtsubo. 1999. Non-LTR retrotransposons (LINEs) as ubiquitous components of plant genomes. Mol. Gen. Genet. 261: 71– 79.
81. Norris, J.,, D. Fan,, C. Aleman,, J. R. Marks,, P. A. Futreal,, R. W. Wiseman,, J. D. Iglehart,, P. L. Deininger,, and D. P. McDonnell. 1995. Identification of a new subclass of Alu DNA repeats which can function as estrogen receptor-dependent transcriptional enhancers. J. Biol. Chem. 270: 22777– 22782.
82. Ohshima, K.,, M. Hamada,, Y. Terai,, and N. Okada. 1996. The 3' ends of tRNA-derived short interspersed repetitive elements are derived from the 3' ends of long interpersed repetitive elements. Mol. Cell. Biol. 16: 3756– 3764.
83. Pickeral, O. K.,, W. Makaowski,, M. S. Boguski,, and J. D. Boeke. 2000. Frequent human genomic DNA transduction driven by LINE-1 retrotransposition. Genome Res. 10: 411– 415.
84. Plasterk, R. H. 1991. The origin of footprints of the Tc1 transposon of Caenorhabditis elegans. EMBO J. 10: 1919– 1925.
85. Poulter, R.,, and M. Butler. 1998. A retrotransposon family from the pufferfish (fugu) Fugu rubripes. Gene 215: 241– 249.
86. Poulter, R.,, M. Butler,, and J. Ormandy. 1999. A LINE element from the pufferfish (fugu) Fugu rubripes which shows similarity to the CR1 family of non-LTR retrotransposons. Gene 227: 169– 179.
87. Rezsohazy, R.,, H. G. van Luenen,, R. M. Durbin,, and R. H. Plasterk. 1997. Tc7, a Tc1-hitch hiking transposon in Caenorhabditis elegans. Nucleic Acids Res. 25: 4048– 4054.
88. Rudiger, N. S.,, N. Gregersen,, and M. C. Kielland-Brandt. 1995. One short well conserved region of Alu-sequences is involved in human gene rearrangements and has homology with prokaryotic chi. Nucleic Acids Res. 23: 256– 260.
89. Ruiz, F.,, L. Vayssie,, C. Klotz,, L. Sperling,, and L. Madeddu. 1998. Homology-dependent gene silencing in Paramecium. Mol. Biol. Cell 9: 931– 943.
90. SanMiguel, P.,, B. S. Gaut,, A. Tikhonov,, Y. Nakajima,, and J. L. Bennetzen. 1998. The paleontology of intergene retrotransposons of maize. Nat. Genet. 20: 43– 45.
91. SanMiguel, P.,, A. Tikhonov,, Y. K. Jin,, N. Motchoulskaia,, D. Zakharov,, A. Melake-Berhan,, P. S. Springer,, K. J. Edwards,, M. Lee,, Z. Avramova,, and J. L. Bennetzen. 1996. Nested retrotransposons in the intergenic regions of the maize genome. Science 274: 765– 768.
92. Sassaman, D. M.,, B. A. Dombroski,, J. V. Moran,, M. L. Kimberland,, T. P. Naas,, R. J. DeBerardinis,, A. Gabriel,, G. D. Swergold,, and H. H. Kazazian, Jr. 1997. Many human L1 elements are capable of retrotransposition. Nat. Genet. 16: 37– 43.
93. Shackleford, G. M.,, C. A. MacArthur,, H. C. Kwan,, and H. E. Varmus. 1993. Mouse mammary tumor virus infection accelerates mammary carcinogenesis in Wnt-1 transgenic mice by insertional activation of int-2/Fgf-3 and hst/Fgf-4. Proc. Natl. Acad. Sci. USA 90: 740– 744.
94. Shen, M.,, M. Batzer,, and P. Deininger. 1991. Evolution of the Master Alu Gene(s). J. Mol. Evol. 33: 311– 320.
95. Slagel, V.,, E. Flemington,, V. Traina-Dorge,, H. Bradshaw,, and P. Deininger. 1987. Clustering and sub-family relationships of the Alu family in the human genome. Mol. Biol. Evol. 4: 19– 29.
96. Smit, A. F. 1993. Identification of a new, abundant superfamily of mammalian LTR-transposons. Nucleic Acids Res. 21: 1863– 1872.
97. Smit, A. F. 1996. The origin of interspersed repeats in the human genome. Curr. Opin. Genet. Dev. 6: 743– 748.
98. Smit, A. F. 1999. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr. Opin. Genet. Dev. 9: 657– 663.
99. Smit, A. F.,, G. Toth,, A. D. Riggs,, and J. Jurka. 1995. Ancestral, mammalian-wide subfamilies of LINE-1 repetitive sequences. J. Mol. Biol. 246: 401– 417.
100. Surzycki, S. A.,, and W. R. Belknap. 2000. Repetitive-DNA elements are similarly distributed on Caenorhabditis elegans autosomes. Proc. Natl. Acad. Sci. USA 97: 245– 249.
101. Takasaki, N.,, L. Park,, M. Kaeriyama,, A. J. Gharrett,, and N. Okada. 1996. Characterization of species-specifically amplified SINEs in three salmonid species—chum salmon, pink salmon, and kokanee: the local environment of the genome may be important for the generation of a dominant source gene at a newly retroposed locus. J. Mol. Evol. 42: 103– 116.
102. Tchenio, T.,, J. F. Casella,, and T. Heidmann. 2000. Members of the SRY family regulate the human LINE retrotransposons. Nucleic Acids Res. 28: 411– 415.
103. Terrinoni, A.,, C. D. Franco,, P. Dimitri,, and N. Junakovic. 1997. Intragenomic distribution and stability of transposable elements in euchromatin and heterochromatin of Drosophila melanogaster: non-LTRretrotransposon. J. Mol. Evol. 45: 145– 153.
104. Terzian, C.,, and C. Biemont. 1988. The founder effect theory: quantitative variation and mdg-1 mobile element polymorphism in experimental populations of Drosophila melanogaster. Genetica 76: 53– 63.
105. Tikhonov, A. P.,, P. J. SanMiguel,, Y. Nakajima,, N. M. Gorenstein,, J. L. Bennetzen,, and Z. Avramova. 1999. Colinearity and its exceptions in orthologous adh regions of maize and sorghum. Proc. Natl. Acad. Sci. USA 96: 7409– 7414.
106. Tudor, M.,, M. Lobocka,, M. Goodell,, J. Pettitt,, and K. O’Hare. 1992. The pogo transposable element family of Drosophila melanogaster. Mol. Gen. Genet. 232: 126– 134.
107. Turcich, M. P.,, A. Bokharririza,, D. A. Hamilton,, C. P. He,, W. Messier, et al. 1996. PREM-2, a copia-type retroelement in maize is expressed preferentially in early microspores. Sex. Plant Reprod. 9: 65– 74.
108. Unsal, K.,, and G. T. Morgan. 1995. A novel group of families of short interspersed repetitive elements (SINEs) in Xenopus: evidence of a specific target site for DNA-mediated transposition of inverted-repeat SINEs. J. Mol. Biol. 248: 812– 823.
109. Vansant, G.,, and W. F. Reynolds. 1995. The consensus sequence of a major Alu subfamily contains a functional retinoic acid response element. Proc. Natl. Acad. Sci. USA 92: 8229– 8233.
110. Varmus, H.,, and J. M. Bishop. 1986. Biochemical mechanisms of oncogene activity: proteins encoded by oncogenes. Introduction. Cancer Surv. 5: 153– 158.
111. Vieira, C.,, D. Lepetit,, S. Dumont,, and C. Biemont. 1999. Wake up of transposable elements following Drosophila simulans worldwide colonization. Mol. Biol. Evol. 16: 1251– 1255.
112. Weiner, A.,, P. Deininger,, and A. Efstratiadis. 1986. The reverse flow of genetic information: pseudogenes and transposable elements derived from nonviral cellular RNA. Annu. Rev. Biochem. 55: 631– 661.
113. Williamson, V. M.,, D. Cox,, E. T. Young,, D. W. Russell,, and M. Smith. 1983. Characterization of transposable elementassociated mutations that alter yeast alcohol dehydrogenase II expression. Mol. Cell. Biol. 3: 20– 31.
114. Wright, D. A.,, N. Ke,, J. Smalle,, B. M. Hauge,, H. M. Goodman,, and D. F. Voytas. 1996. Multiple non-LTRretrotransposons in the genome of Arabidopsis thaliana. Genetics 142: 569– 578.
115. Xiong, Y.,, and T. H. Eickbush. 1990. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9: 3353– 3362.
116. Yoder, J. A.,, C. P. Walsh,, and T. H. Bestor. 1997. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 13: 335– 340.
117. Yoshioka, Y.,, S. Matsumoto,, S. Kojima,, K. Ohshima,, N. Okada,, and Y. Machida. 1993. Molecular characterization of a short interspersed repetitive element from tobacco that exhibits sequence homology to specific tRNAs. Proc. Natl. Acad. Sci. USA 90: 6562– 6566.
118. Zelentsova, H.,, H. Poluectova,, L. Mnjoian,, G. Lyozin,, V. Veleikodvorskaja,, L. Zhivotovsky,, M. G. Kidwell,, and M. B. Evgen’ev. 1999. Distribution and evolution of mobile elements in the virilis species group of Drosophila. Chromosoma 108: 443– 456.

Tables

Mobile Elements in Animal and Plant Genomes
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Citation: Deininger P, Roy-Engel A. 2002. Mobile Elements in Animal and Plant Genomes, p 1074-1092. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch47
/content/10.1128/9781555817954.chap47.tab47-1
Table 1

Abundance of human mobile elements on chromosomes 21, 22, and X

10.1128/9781555817954/tab47-1_thmb.gif
10.1128/9781555817954/tab47-1.gif
Generic image for table
Table 1

Abundance of human mobile elements on chromosomes 21, 22, and X

Citation: Deininger P, Roy-Engel A. 2002. Mobile Elements in Animal and Plant Genomes, p 1074-1092. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch47
/content/10.1128/9781555817954.chap47.tab47-2
Table 2

Species and population variation in mobile elements

10.1128/9781555817954/tab47-2_thmb.gif
10.1128/9781555817954/tab47-2.gif
Generic image for table
Table 2

Species and population variation in mobile elements

Citation: Deininger P, Roy-Engel A. 2002. Mobile Elements in Animal and Plant Genomes, p 1074-1092. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch47

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