Chapter 5 : Transposable Elements as Sources of Genomic Variation

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This chapter provides a general description of the types of genetic variation caused by transposable elements in animals and plants, and examines this variation within an evolutionary framework. It focuses on the variation induced by transposable elements in their host organisms. The host variation associated with transposable elements can result from several interconnected aspects of transposable element activity. Estimates of the frequencies of new transposable element-induced mutations have been made under laboratory conditions and varied over an enormous range. The partial or complete sterility associated with several systems of hybrid dysgenesis in provides an interesting aspect of variation associated with transposable element activity. Heterochromatin proteins can recognize and silence transposable elements, some of which target heterochromatin for insertion. Thus, the evolution of heterochromatin could have led to a self-perpetuating expansion of domains rich in transposable elements. Two mechanisms are considered most likely to be responsible for transposable element-induced karyotypic changes. The best known mechanism is ectopic recombination, in which homologous recombination occurs between multiple copies of a transposable element present in a genome. A second mechanism for inducing genomic rearrangements is alternative transposition of class II elements in bacteria, plants, and animals. Some features of both transposable elements and hosts suggest coadaptations to mitigate the reduction of fitness expected from unfettered transposition, and to provide a wide range of new variations on which natural selection can act.

Citation: Kidwell M, Lisch D. 2002. Transposable Elements as Sources of Genomic Variation, p 59-90. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch5
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Image of Figure 1
Figure 1

transposon insertion into an intron causes ectopic expression of the gene in maize. In the presence of the transposase, function of a putative leaf-specific repressor in the intron is blocked. In the absence of transposase, the repressor functions normally and expression in the leaf is blocked. Thus, in this case, the transposase becomes part of a regulatory pathway in plant development. Adapted from ( ) with permission from the publisher.

Citation: Kidwell M, Lisch D. 2002. Transposable Elements as Sources of Genomic Variation, p 59-90. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch5
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Image of Figure 2
Figure 2

Insertions of a element into the first intron of the locus in have opposite effects depending on the orientation of the transposon. In one orientation the result of an insertion is a recessive homeotic conversion of sex organs to sterile perianth organs because of loss of expression in the inner two whorls of the flower. Insertion in the opposite orientation leads to a semidominant conversion of sterile organs into sex organs caused by ectopic expression of plena in the outer two whorls of the flower and vegetative organs for promoting sex organ development within the context of the flower. Adapted from ( ) with permission from the publisher.

Citation: Kidwell M, Lisch D. 2002. Transposable Elements as Sources of Genomic Variation, p 59-90. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch5
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Figure 3

A histogram showing total genome sizes and the percentage of those sizes occupied by transposable elements (TEs) for eight species: barley ( species) ( ), maize () ( ), human () ( ), rice () ( ), fruit fly () ( ), vetch () ( ), worm () ( ), and yeast () ( ). Genome sizes for each of these species except barley and maize are taken from http://www.cbs.dtu.dk/databases/DOGS/.

Citation: Kidwell M, Lisch D. 2002. Transposable Elements as Sources of Genomic Variation, p 59-90. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch5
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Figure 4

Preferential insertion of elements near the 5′ end of transcription units. The insertion sites of 56 different mutagenic elements are shown. Each insertion site is plotted with respect to a simplified standard gene containing one intron before, and one intron after, the AUG initiation site. Reprinted from the ( ) with permission from the publisher.

Citation: Kidwell M, Lisch D. 2002. Transposable Elements as Sources of Genomic Variation, p 59-90. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch5
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Figure 5

A Y chromosome inversion generated by recombination between LINE elements in hominids. At the top is depicted a schematic representation of a prototypical, full-length human LINE element showing the location of two long open reading frames (ORFs) and the polyadenylated tail. Below that is shown a model of an inversion between two LINE elements drawn out of register. Reprinted from ( ) with permission from the publisher.

Citation: Kidwell M, Lisch D. 2002. Transposable Elements as Sources of Genomic Variation, p 59-90. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch5
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Figure 6

Association of a retrovirus-related element with androgen regulation of the sex-limited protein () gene in mouse. Adapted from ( ) with permission from the publisher.

Citation: Kidwell M, Lisch D. 2002. Transposable Elements as Sources of Genomic Variation, p 59-90. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch5
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Figure 7

A gypsy insertion blocks a subset of upstream enhancers of the yellow gene in The gypsy transposon carries a chromatin insulator which binds to the protein product of () (circle). Because this insulator acts in a polar fashion, when the element is inserted between the promoter and the enhancers specific for wing and body expression, the yellow gene only expresses in the mouth, whose enhancer remains unaffected. Adapted from ( ) with permission from the publisher.

Citation: Kidwell M, Lisch D. 2002. Transposable Elements as Sources of Genomic Variation, p 59-90. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch5
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Figure 8

Promoter scrambling in plants. The original insertion of a transposon into the TATA box of the gene caused a tissue-specific change in expression. Subsequent excision and promoter “scrambling” caused additional changes in tissue specificity. Reprinted from the ( ) with permission from the publisher.

Citation: Kidwell M, Lisch D. 2002. Transposable Elements as Sources of Genomic Variation, p 59-90. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch5
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1. Agrawal, A.,, Q. M. Eastman,, and D. G. Schatz. 1998. Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 394: 744 751.
2. Ananiev, E. V.,, R. L. Phillips,, and H. W. Rines. 1998. Chromosome- specific molecular organization of maize ( Zea mays L.) centromeric regions. Proc. Natl. Acad. Sci. USA 95: 13073 13078.
3. Ananiev, E. V.,, R. L. Phillips,, and H. W. Rines. 1998. Complex structure of knob DNA on maize chromosome 9. Retrotransposon invasion into heterochromatin. Genetics 149: 2025 2037.
4. Anderson, R.,, R. J. Britten,, and E. H. Davidson. 1994. Repeated sequence target sites for maternal DNA-binding proteins in genes activated in early sea urchin development. Dev. Biol. 163: 11 18.
5. Anholt, R. R.,, R. F. Lyman,, and T. F. Mackay. 1996. Effects of single P-element insertions on olfactory behavior in Drosophila melanogaster. Genetics 143: 293 301.
6. Ashburner, M. 1992. Drosophila, a Laboratory Handbook. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
7. Bailey, J. A.,, L. Carrel,, A. Chakravarti,, and E. E. Eichler. 2000. 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.
8. Banks, J. A.,, P. Masson,, and N. Fedoroff. 1988. Molecular mechanisms in the developmental regulation of the maize Suppressor-mutator transposable element. Genes Dev. 2: 1364 1380.
9. Baran, G.,, C. Echt,, T. Bureau,, and S. Wessler. 1992. Molecular analysis of the maize wx-B3 allele indicates that precise excision of the transposable Ac element is rare. Genetics 130: 377 384.
10. Barlow, D. P. 1993. Methylation and imprinting: from host defense to gene regulation? Science 260: 309 310.
11. Barry, A. E.,, E. V. Howman,, M. R. Cancilla,, R. Saffery,, and K. H. Choo. 1999. Sequence analysis of an 80 kb human neocentromere. Hum. Mol. Genet. 8: 217 227.
12. Baum, M.,, and L. Clarke. 2000. Fission yeast homologs of human CENP-B have redundant functions affecting cell growth and chromosome segregation. Mol. Cell. Biol. 20: 2852 2864.
13. Beebe, S. J.,, P. Salomonsky,, T. Jahnsen,, and Y. Li. 1992. The Cgamma subunit is a unique isozyme of the cAMP-dependent protein kinase. J. Biol. Chem. 267: 25505 25512.
14. Bellen, H.,, C. J. O’Kane,, C. Wilson,, U. Grossniklaus,, R. K. Pearson,, and W. J. Gehring. 1989. P-element-mediated enhancer detection: a versatile method to study development in Drosophila. Genes Dev. 3: 1288 1300.
15. Bennetzen, J. L. 2000. Transposable element contributions to plant gene and genome evolution. Plant Mol. Biol. 42: 251 269.
16. Best, S.,, P. Le Tissier,, G. Towers,, and J. P. Stoye. 1996. Positional cloning of the mouse retrovirus restriction gene Fv1. Nature 382: 826 829.
17. Biemont, C.,, A. Tsitrone,, C. Vieira,, and C. Hoogland. 1997. Transposable element distribution in Drosophila. Genetics 147: 1997 1999.
18. Biessmann, H.,, and J. M. Mason. 1997. Telomere maintenance without telomerase. Chromosoma 106: 63 69.
19. Bird, A. 1997. Does DNA methylation control transposition of selfish elements in the germline? Trends Genet. 13: 469 472.
20. Black, D. M.,, M. S. Jackson,, M. G. Kidwell,, and G. A. Dover. 1987. KP elements repress P-induced hybrid dysgenesis in Drosophila melanogaster. EMBO J. 6: 4125 4135.
21. Blackman, R.,, R. Grimaila,, M. Koehler,, and W. Gelbart. 1987. Mobilization of hobo elements residing within the decapentaplegic gene complex: suggestion of a new hybrid dysgenesis system in Drosophila melanogaster. Cell 49: 497 505.
22. Boyd, M. T.,, C. M. Bax,, B. E. Bax,, D. L. Bloxam,, and R. A. Weiss. 1993. The human endogenous retrovirus ERV-3 is upregulated in differentiating placental trophoblast cells. Virology 196: 905 909.
23. Bradley, D.,, R. Carpenter,, H. Sommer,, N. Hartley,, and E. Coen. 1993. Complementary floral homeotic phenotypes result from opposite orientations of a transposon at the plena locus of Antirrhinum. Cell 72: 85 95.
24. Bregliano, J. C.,, and M. G. Kidwell,. 1983. Hybrid dysgenesis determinants, p. 363 410. In J. A. Shapiro (ed.), Mobile Genetic Elements. Academic Press, New York, N.Y.
25. Britten, R. J. 1996. Cases of ancient mobile element DNA insertions that now affect gene regulation. Mol. Phylogenet. Evol. 5: 13 17.
26. Britten, R. J. 1996. DNA sequence insertion and evolutionary variation in gene regulation. Proc. Natl. Acad. Sci. USA 93: 9374 9377.
27. Britten, R. J. 1997. Mobile elements inserted in the distant past have taken on important functions. Gene 205: 177 182.
28. Britten, R. J.,, and E. H. Davidson. 1971. Repetitive and non-repetitive DNA sequences and a speculation on the origin of evolutionary novelty. Q. Rev. Biol. 46: 111 138.
29. Brosius, J. 1999. Genomes were forged by massive bombardments with retroelements and retrosequences. Genetica 107: 209 238.
30. Brosius, J. 1999. RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 238: 115 134.
31. Brosius, J.,, and S. J. Gould. 1992. On “genomenclature”: a comprehensive (and respectful) taxonomy for pseudogenes and other “junk DNA.” Proc. Natl. Acad. Sci. USA 89: 10706 10710.
32. Brosius, J.,, and H. Tiedge. 1995. Reverse transcriptase: mediator of genomic plasticity. Virus Genes 11: 163 179.
33. Bureau, T. E.,, P. C. Ronald,, and S. R. Wessler. 1996. A computer-based systematic survey reveals the predominance of small inverted-repeat elements in wild-type rice genes. Proc. Natl. Acad. Sci. USA 93: 8524 8529.
34. Bureau, T. E.,, S. E. White,, and S. R. Wessler. 1994. Transduction of a cellular gene by a plant retroelement. Cell 77: 479 480.
35. Burwinkel, B.,, and M. W. Kilimann. 1998. Unequal homologous recombination between LINE-1 elements as a mutational mechanism in human genetic disease. J. Mol. Biol. 277: 513 517.
36. Caceres, M.,, J. M. Ranz,, A. Barbadilla,, M. Long,, and A. Ruiz. 1999. Generation of a widespread Drosophila inversion by a transposable element. Science 285: 415 418.
37. Cambareri, E. B.,, R. Aisner,, and J. Carbon. 1998. Structure of the chromosome VII centromere region in Neurospora crassa: degenerate transposons and simple repeats. Mol. Cell. Biol. 18: 5465 5477.
38. Charlesworth, B.,, C. H. Langley,, and P. D. Sniegowski. 1997. Transposable element distributions in Drosophila. Genetics 147: 1993 1995.
39. Charlesworth, B.,, P. Sniegowski,, and W. Stephan. 1994. The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371: 215 220.
40. Choo, K. H. 2000. Centromerization. Trends Cell Biol. 10: 182 188.
41. Chu, W. M.,, R. Ballard,, B. W. Carpick,, B. R. Williams,, and C. W. Schmid. 1998. Potential Alu function: regulation of the activity of double-stranded RNA-activated kinase PKR. Mol. Cell. Biol. 18: 58 68.
42. Cianciolo, G. J.,, T. D. Copeland,, S. Oroszlan,, and R. Snyderman. 1985. Inhibition of lymphocyte proliferation by a synthetic peptide homologous to retroviral envelope proteins. Science 230: 453 455.
43. Civardi, L.,, Y. Xia,, K. J. Edwards,, P. S. Schnable,, and B. J. Nikolau. 1994. The relationship between genetic and physical distances in the cloned a1-sh2 interval of the Zea mays L. genome. Proc. Natl. Acad. Sci. USA 91: 8268 8272.
44. Clarke, L.,, H. Amstutz,, B. Fishel,, and J. Carbon. 1986. Analysis of centromeric DNA in the fission yeast Schizosaccharomyces pombe. Proc. Natl. Acad. Sci. USA 83: 8253 8257.
45. Clegg, M. T.,, and M. L. Durbin. 2000. Flower color variation: a model for the experimental study of evolution. Proc. Natl. Acad. Sci. USA 97: 7016 7023.
46. Cogoni, C.,, and G. Macino. 1999. Gene silencing in Neurospora crassa requires a protein homologous to RNA-dependent RNA polymerase. Nature 399: 166 169.
47. Colot, V.,, V. Haedens,, and J. L. Rossignol. 1998. Extensive, nonrandom diversity of excision footprints generated by Ds-like transposon Ascot-1 suggests new parallels with V(D)J recombination. Mol. Cell. Biol. 18: 4337 4346.
48. Consortium, A. S. 2000. The complete sequence of a heterochromatic island from a higher eukaryote. The Cold Spring Harbor Laboratory: Washington University Genome Sequencing Center, and PE Biosystems Arabidopsis Sequencing Consortium. Cell 100: 377 386.
49. Copenhaver, G. P.,, and D. Preuss. 1999. Centromeres in the genomic era: unraveling paradoxes. Curr. Opin. Plant Biol. 2: 104 108.
50. Corces, V. G.,, and P. K. Geyer. 1991. Interactions of retrotransposons with the host genome. Trends Genet. 7: 86 90.
51. Cottarel, G.,, J. H. Shero,, P. Hieter,, and J. H. Hegemann. 1989. A 125-base-pair CEN6 DNA fragment is sufficient for complete meiotic and mitotic centromere functions in Saccharomyces cerevisiae. Mol. Cell. Biol. 9: 3342 3349.
52. Craig, N. L. 1997. Target site selection in transposition. Annu. Rev. Biochem. 66: 437 474.
53. Cresse, A. D.,, S. H. Hulbert,, W. E. Brown,, J. R. Lucas,, and J. L. Bennetzen. 1995. Mu1-related transposable elements of maize preferentially insert into low copy number DNA. Genetics 140: 315 324.
54. Currie, D. B.,, T. F. Mackay,, and L. Partridge. 1998. Pervasive effects of P element mutagenesis on body size in Drosophila melanogaster. Genet. Res. 72: 19 24.
55. Cuypers, H.,, S. Dash,, P. A. Peterson,, H. Saedler,, and A. Gierl. 1988. The defective En-I102 element encodes a product reducing the mutability of the En-Spm system of Zea mays. EMBO J. 7: 2953 2960.
56. Daboussi, M. J. 1997. Fungal transposable elements and genome evolution. Genetica 100: 253 260.
57. Daniels, S. B.,, A. Chovnick,, and M. G. Kidwell. 1989. Hybrid dysgenesis in Drosophila simulans lines transformed with autonomous P elements. Genetics 121: 281 291.
58. Daniels, S. B.,, M. McCarron,, C. Love,, and A. Chovnick. 1985. Dysgenesis-induced instability of rosy locus transformation in Drosophila melanogaster: analysis of excision events and the selective recovery of control element deletions. Genetics 109: 95 117.
59. Deininger, P. L.,, and M. A. Batzer. 1999. Alu repeats and human disease. Mol. Genet. Metab. 67: 183 193.
60. Dimitri, P.,, B. Arca,, L. Berghella,, and E. Mei. 1997. High genetic instability of heterochromatin after transposition of the LINE-like I factor in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 94: 8052 8057.
61. Dobie, K.,, M. Mehtali,, M. McClenaghan,, and R. Lathe. 1997. Variegated gene expression in mice. Trends Genet. 13: 127 130.
62. Dominguez, A.,, and J. Albornoz. 1996. Rates of movement of transposable elements in Drosophila melanogaster. Mol. Gen. Genet. 251: 130 138.
63. Dominguez, A.,, and J. Albornoz. 1999. Structural instability of 297 element in Drosophila melanogaster. Genetica 105: 239 248.
64. Dong, F.,, J. T. Miller,, S. A. Jackson,, G. L. Wang,, P. C. Ronald,, and J. Jiang. 1998. Rice ( Oryza sativa) centromeric regions consist of complex DNA. Proc. Natl. Acad. Sci. USA 95: 8135 8140.
65. Donlin, M. J.,, D. Lisch,, and M. Freeling. 1995. Tissue-specific accumulation of MURB, a protein encoded by MuDR, the autonomous regulator of the Mutator transposable element family. Plant Cell 7: 1989 2000.
66. Doolittle, R. F.,, D. F. Feng,, M. S. Johnson,, and M. A. Mc- Clure. 1989. Origins and evolutionary relationships of retroviruses. Q. Rev. Biol. 64: 1 30.
67. Dorer, D. R.,, and S. Henikoff. 1994. Expansions of transgene repeats cause heterochromatin formation and gene silencing in Drosophila. Cell 77: 993 1002.
68. Doseff, A.,, R. Martienssen,, and V. Sundaresan. 1991. Somatic excision of the Mu1 transposable element of maize. Nucleic Acids Res. 19: 579 584.
69. Dupressoir, A.,, and T. Heidmann. 1996. Germ line-specific expression of intracisternal A-particle retrotransposons in transgenic mice. Mol. Cell. Biol. 16: 4495 4503.
70. Earnshaw, W. C.,, K. F. Sullivan,, P. S. Machlin,, C. A. Cooke,, D. A. Kaiser,, T. D. Pollard,, N. F. Rothfield,, and D. W. Cleveland. 1987. Molecular cloning of cDNA for CENP-B, the major human centromere autoantigen. J. Cell Biol. 104: 817 829.
71. Eberl, D. F.,, B. J. Duyf,, and A. J. Hilliker. 1993. The role of heterochromatin in the expression of a heterochromatic gene, the rolled locus of Drosophila melanogaster. Genetics 134: 277 292.
72. Eden, S.,, T. Hashimshony,, I. Keshet,, H. Cedar,, and A. W. Thorne. 1998. DNA methylation models histone acetylation. Nature 394: 842.
73. Eichler, E. E.,, M. L. Budarf,, M. Rocchi,, L. L. Deaven,, N. A. Doggett,, A. Baldini,, D. L. Nelson,, and H. W. Mohrenweiser. 1997. Interchromosomal duplications of the adrenoleukodystrophy locus: a phenomenon of pericentromeric plasticity. Hum. Mol. Genet. 6: 991 1002.
74. Engels, W. R., 1989. P elements in Drosophila, p. 437 484. In D. E. Berg, and M. M. Howe (ed.), Mobile DNA. American Society for Microbiology, Washington, D.C.
75. Engels, W. R., 1996. P elements in Drosophila, p. 103 123. In H. Saedler, and A. Gierl (ed.), Transposable Elements. Springer-Verlag, Berlin, Germany.
76. Engels, W. R.,, D. M. Johnson-Schlitz,, W. B. Eggleston,, and J. Sved. 1990. High-frequency P element loss in Drosophila is homolog dependent. Cell 62: 515 525.
77. Engels, W. R.,, and C. R. Preston. 1984. Formation of chromosome rearrangements by P factors in Drosophila. Genetics 107: 657 678.
78. Esnault, C.,, J. Maestre,, and T. Heidmann. 2000. Human LINE retrotransposons generate processed pseudogenes. Nat. Genet. 24: 363 367.
79. Evgen’ev, M. B.,, H. Zelentsova,, H. Poluectova,, G. T. Lyozin,, V. Veleikodvorskaja,, K. I. Pyatkov,, L. Zhivotovski,, and M. G. Kidwell. 2000. Mobile elements and chromosomal evolution in the virilis group of Drosophila. Proc. Natl. Acad. Sci. USA 97: 11337 11342.
80. Fanti, L.,, D. R. Dorer,, M. Berloco,, S. Henikoff,, and S. Pimpinelli. 1998. Heterochromatin protein 1 binds transgene arrays. Chromosoma 107: 286 292.
81. Farkas, G.,, J. Gausz,, M. Galloni,, G. Reuter,, H. Gyurkovics,, and F. Karch. 1994. The Trithorax-like gene encodes the Drosophila GAGA factor. Nature 371: 806 808.
82. Fedoroff, N., 1989. Maize transposable elements, p. 375 411. In D. E. Berg, and M. M. Howe (ed.), Mobile DNA. American Society for Microbiology, Washington, D.C.
83. Fedoroff, N.,, S. Wessler,, and M. Shure. 1983. Isolation of the transposable maize controlling elements Ac and Ds. Cell 35: 235 242.
84. Feschotte, C.,, and C. Mouches. 2000. Evidence that a family of miniature inverted-repeat transposable elements (MITEs) from the Arabidopsis thaliana genome has arisen from a pogo-like DNA transposon. Mol. Biol. Evol. 17: 730 737.
85. Fincham, J. R. S.,, and G. R. K. Sastry. 1974. Controlling elements in maize. Annu. Rev. Genet. 8: 15 50.
86. Finnegan, D. J., 1992. Transposable elements, p. 1096 1107. In D. L. Lindsley, and G. Zimm (ed.), The Genome of Drosophila melanogaster. Academic Press, New York, N.Y.
87. Finnegan, E. J.,, W. J. Peacock,, and E. S. Dennis. 1996. Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proc. Natl. Acad. Sci. USA 93: 8449 8454.
87a.. Fire, A.,, S. Xu,, M. K. Montgomery,, S. A. Kostas,, S. E. Driver,, and C. C. Mello. 1998. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806 811.
88. Firtel, R. A., 1989. Mobile elements in the cellular slime mold Dictyostelium discoideum, p. 557 566. In D. E. Berg, and M. M. Howe (ed.), Mobile DNA. American Society for Microbiology, Washington, D.C.
89. Fishel, B.,, H. Amstutz,, M. Baum,, J. Carbon,, and L. Clarke. 1988. Structural organization and functional analysis of centromeric DNA in the fission yeast Schizosaccharomyces pombe. Mol. Cell. Biol. 8: 754 763.
90. Foss, K. B.,, B. Landmark,, B. S. Skalhegg,, K. Tasken,, E. Jellum,, V. Hansson,, and T. Jahnsen. 1994. Characterization of in-vitro-translated human regulatory and catalytic subunits of cAMP-dependent protein kinases. Eur. J. Biochem. 220: 217 223.
91. Fowler, K. J.,, D. F. Hudson,, L. A. Salamonsen,, S. R. Edmondson,, E. Earle,, M. C. Sibson,, and K. H. Choo. 2000. Uterine dysfunction and genetic modifiers in centromere protein B-deficient mice. Genome Res. 10: 30 41.
92. Fridell, R. A.,, A. M. Pret,, and L. L. Searles. 1990. A retrotransposon 412 insertion within an exon of the Drosophila melanogaster vermilion gene is spliced from the precursor RNA. Genes Dev. 4: 559 566.
92a.. Fugmann, S. D.,, A. I. Lee,, P. E. Shockett,, I. J. Villey,, and D. G. Schatz. 2000. The RAG proteins and V(D)J recombination: complexes, ends, and transposition. Annu. Rev. Immunol. 18: 495 527.
93. Garber, K.,, I. Bilic,, O. Pusch,, J. Tohme,, A. Bachmair,, D. Schweizer,, and V. Jantsch. 1999. The Tpv2 family of retro transposons of Phaseolus vulgaris: structure, integration characteristics, and use for genotype classification. Plant Mol. Biol. 39: 797 807.
94. Golovkina, T. V.,, A. Chervonsky,, J. P. Dudley,, and S. R. Ross. 1992. Transgenic mouse mammary tumor virus super-antigen expression prevents viral infection. Cell 69: 637 645.
95. 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.
96. Gottschling, D. E.,, O. M. Aparicio,, B. L. Billington,, and V. A. Zakian. 1990. Position effect at S. cerevisiae telomeres: reversible repression of Pol II transcription. Cell 63: 751 762.
97. Gray, Y. H. 2000. It takes two transposons to tango: transposable- element-mediated chromosomal rearrangements. Trends Genet. 16: 461 468.
98. Greene, B.,, R. Walko,, and S. Hake. 1994. Mutator insertions in an intron of the maize knotted1 gene result in dominant suppressible mutations. Genetics 138: 1275 1285.
99. Gregory, T. R.,, and P. D. Hebert. 1999. The modulation of DNA content: proximate causes and ultimate consequences. Genome Res. 9: 317 324.
100. Guo, S.,, and K. J. Kemphues. 1995. par-1, a gene required for establishing polarity in C. elegans embryos, encodes a putative Ser/Thr kinase that is asymmetrically distributed. Cell 81: 611 620.
101. Hambor, J. E.,, J. Mennone,, M. E. Coon,, J. H. Hanke,, and P. Kavathas. 1993. Identification and characterization of an Alu-containing, T-cell-specific enhancer located in the last intron of the human CD8 alpha gene. Mol. Cell. Biol. 13: 7056 7070.
102. Harendza, C. J.,, and L. F. Johnson. 1990. Polyadenylylation signal of the mouse thymidylate synthase gene was created by insertion of an L1 repetitive element downstream of the open reading frame. Proc. Natl. Acad. Sci. USA 87: 2531 2535.
103. Harper, L. C.,, and W. Z. Cande. Mapping a new frontier; development of integrated cytogenetic maps in plants. Func. Integr. Genomics, in press.
104. Henikoff, S.,, E. A. Greene,, S. Pietrokovski,, P. Bork,, T. K. Attwood,, and L. Hood. 1997. Gene families: the taxonomy of protein paralogs and chimeras. Science 278: 609 614.
105. Henikoff, S.,, and M. A. Matzke. 1997. Exploring and explaining epigenetic effects. Trends Genet. 13: 293 295.
106. Higashiyama, T.,, Y. Noutoshi,, M. Fujie,, and T. Yamada. 1997. Zepp, a LINE-like retrotransposon accumulated in the Chlorella telomeric region. EMBO J. 16: 3715 3723.
107. Hilliker, A. J.,, R. Appels,, and A. Schalet. 1980. The genetic analysis of D. melanogaster heterochromatin. Cell 21: 607 619.
108. 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.
109. Hirochika, H.,, H. Okamoto,, and T. Kakutani. 2000. Silencing of retrotransposons in Arabidopsis and reactivation by the ddm1 mutation. Plant Cell 12: 357 369.
110. Holmes, S. E.,, B. A. Dombroski,, C. M. Krebs,, C. D. Boehm,, and H. H. Kazazian, Jr. 1994. A new retrotransposable human L1 element from the LRE2 locus on chromosome 1q produces a chimaeric insertion. Nat. Genet. 7: 143 148.
111. Hunter, C. P. 2000. Gene silencing: shrinking the black box of RNAi. Curr. Biol. 10: 137 140.
112. Ivanova, A. V.,, M. J. Bonaduce,, S. V. Ivanov,, and A. J. Klar. 1998. The chromo and SET domains of the Clr4 protein are essential for silencing in fission yeast. Nat. Genet. 19: 192 195.
113. Iwasa, Y. 1998. The conflict theory of genomic imprinting: how much can be explained? Curr. Top. Dev. Biol. 40: 255 293.
114. Jacobsen, S. E.,, H. Sakai,, E. J. Finnegan,, X. Cao,, and E. M. Meyerowitz. 2000. Ectopic hypermethylation of flower-specific genes in Arabidopsis. Curr. Biol. 10: 179 186.
115. Jakubczak, J. L.,, W. D. Burke,, and T. H. Eickbush. 1991. Retrotransposable elements R1 and R2 interrupt the rRNA genes of most insects. Proc. Natl. Acad. Sci. USA 88: 3295 3299.
116. Jakubczak, J. L.,, Y. Xiong,, and T. H. Eickbush. 1990. Type I (R1) and type II (R2) ribosomal DNA insertions of Drosophila melanogaster are retrotransposable elements closely related to those of Bombyx mori. J. Mol. Biol. 212: 37 52.
117. Jensen, S.,, L. Cavarec,, M. P. Gassama,, and T. Heidmann. 1995. Defective I elements introduced into Drosophila as transgenes can regulate reactivity and prevent I-R hybrid dysgenesis. Mol. Gen. Genet. 248: 381 390.
118. Jiang, J.,, S. Nasuda,, F. Dong,, C. W. Scherrer,, S. S. Woo,, R. A. Wing,, B. S. Gill,, and D. C. Ward. 1996. A conserved repetitive DNA element located in the centromeres of cereal chromosomes. Proc. Natl. Acad. Sci. USA 93: 14210 14213.
119. Joblonka, E.,, and M. J. Lamb. 1995. Epigenetic Inheritance and Evolution. Oxford Univ. Press, Oxford, UK.
120. John, B., 1988. The biology of heterochromatin, p. 1 128. In R. S. Verma (ed.), Heterochromatin, Molecular and Structural Aspects. Cambridge University Press, Cambridge, UK.
121. Jones, P. A. 1985. Altering gene expression with 5-azacytidine. Cell 40: 485 486.
122. Jordan, I. K.,, and J. F. McDonald. 1998. Evidence for the role of recombination in the regulatory evolution of Saccharomyces cerevisiae Ty elements. J. Mol. Evol. 47: 14 20.
123. Jurka, J.,, and V. V. Kapitonov. 1999. Sectorial mutagenesis by transposable elements. Genetica 107: 239 248.
124. Kakutani, T.,, J. A. Jeddeloh,, S. K. Flowers,, K. Munakata,, and E. J. Richards. 1996. Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proc. Natl. Acad. Sci. USA 93: 12406 12411.
125. Kalendar, R.,, J. Tanskanen,, S. Immonen,, E. Nevo,, and A. H. Schulman. 2000. Genome evolution of wild barley ( Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc. Natl. Acad. Sci. USA 97: 6603 6607.
126. Karpen, G. H.,, and R. C. Allshire. 1997. The case for epigenetic effects on centromere identity and function. Trends Genet. 13: 489 496.
127. Kazazian, H. H., Jr. 1999. An estimated frequency of endogenous insertional mutations in humans. Nat. Genet. 22: 130.
128. Kazazian, H. H., Jr.,, and J. V. Moran. 1998. The impact of L1 retrotransposons on the human genome. Nat. Genet. 19: 19 24.
129. Kazazian, H. H., Jr.,, C. Wong,, H. Youssoufian,, A. F. Scott,, D. G. Phillips,, and S. E. Antonarakis. 1988. Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man. Nature 332: 164 166.
130. Ke, N.,, P. A. Irwin,, and D. F. Voytas. 1997. The pheromone response pathway activates transcription of Ty5 retrotransposons located within silent chromatin of Saccharomyces cerevisiae. EMBO J. 16: 6272 6280.
131. Ketting, R. F.,, T. H. Haverkamp,, H. G. van Luenen,, and R. H. Plasterk. 1999. Mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner syndrome helicase and RNaseD. Cell 99: 133 141.
132. Kidwell, M. G.,, J. F. Kidwell,, and J. A. Sved. 1977. Hybrid dysgenesis in Drosophila melanogaster: a syndrome of aberrant traits including mutation, sterility & male recombination. Genetics 36: 813 833.
133. Kidwell, M. G.,, and D. Lisch. 1997. Transposable elements as sources of variation in animals and plants. Proc. Natl. Acad. Sci. USA 94: 7704 7711.
134. Kidwell, M. G.,, and D. R. Lisch. 2000. Transposable elements and host genome evolution. Trends Ecol. Evol. 15: 95 99.
135. Kim, J. M.,, S. Vanguri,, J. D. Boeke,, A. Gabriel,, and D. F. Voytas. 1998. Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res. 8: 464 478.
136. Kimura, R. H.,, P. V. Choudary,, and C. W. Schmid. 1999. Silk worm Bm1 SINE RNA increases following cellular insults. Nucleic Acids Res. 27: 3380 3387.
137. King, M. C.,, and A. C. Wilson. 1975. Evolution at two levels in humans and chimpanzees. Science 188: 107 116.
138. Kipling, D.,, and P. E. Warburton. 1997. Centromeres, CENPB and Tigger too. Trends Genet. 13: 141 145.
139. Kirschner, M.,, and J. Gerhart. 1998. Evolvability. Proc. Natl. Acad. Sci. USA 95: 8420 8427.
140. Klobutcher, L. A.,, and G. Herrick. 1995. Consensus inverted terminal repeat sequence of Paramecium IESs: resemblance to termini of Tc1-related and Euplotes Tec transposons. Nucleic Acids Res. 23: 2006 2013.
141. Klobutcher, L. A.,, and G. Herrick. 1997. Developmental genome reorganization in ciliated protozoa: the transposon link. Proc. Nucleic Acid Res. Mol. Biol. 56: 1 62.
142. Kloeckener-Gruissem, B.,, and M. Freeling. 1995. Transposon- induced promoter scrambling: a mechanism for the evolution of new alleles. Proc. Natl. Acad. Sci. USA 92: 1836 1840.
143. Kloeckener-Gruissem, B.,, J. M. Vogel,, and M. Freeling. 1992. The TATA box promoter region of maize Adh1 affects its organ-specific expression. EMBO J. 11: 157 166.
144. Kobayashi, S.,, T. Hirano,, M. Kakinuma,, and T. Uede. 1993. Transcriptional repression and differential splicing of FAS mRNA by early transposon (ETn) insertion in autoimmune LPR mice. Biochem. Biophys. Res. Commun. 191: 617 624.
145. Kumar, A.,, and J. L. Bennetzen. 1999. Plant retrotransposons. Annu. Rev. Genet. 33: 479 532.
146. Lahn, B. T.,, and D. C. Page. 1999. Four evolutionary strata on the human X chromosome. Science 286: 964 967.
147. Lahn, B. T.,, and D. C. Page. 1999. Retroposition of autosomal mRNA yielded testis-specific gene family on human Y chromosome. Nat. Genet. 21: 429 433.
148. Lai, C.,, and T. F. Mackay. 1993. Mapping and characterization of P-element-induced mutations at quantitative trait loci in Drosophila melanogaster. Genet. Res. 61: 177 193.
149. Langley, C. H.,, E. Montgomery,, R. Hudson,, N. Kaplan,, and B. Charlesworth. 1988. On the role of unequal exchange on the containment of transposable element copy number. Genet. Res. 52: 223 235.
150. Le, Q. H.,, S. Wright,, Z. Yu,, and T. Bureau. 2000. Transposon diversity in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 97: 7376 7381.
151. Lee, C. C.,, Y. M. Mul,, and D. C. Rio. 1996. The Drosophila P-element KP repressor protein dimerizes and interacts with multiple sites on P-element DNA. Mol. Cell. Biol. 16: 5616 5622.
152. Lee, J. K.,, J. A. Huberman,, and J. Hurwitz. 1997. Purification and characterization of a CENP-B homologue protein that binds to the centromeric K-type repeat DNA of Schizosaccharomyces pombe. Proc. Natl. Acad. Sci. USA 94: 8427 8432.
153. 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.
154. Lewis, S. M.,, and G. E. Wu. 1997. The origins of V(D)J recombination. Cell 88: 159 162.
155. Li, E.,, C. Beard,, and R. Jaenisch. 1993. Role for DNA methylation in genomic imprinting. Nature 366: 362 365.
156. Li, E.,, T. H. Bestor,, and R. Jaenisch. 1992. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69: 915 926.
157. Li, W.-H. 1997. Molecular Evolution. Sinauer Associates Inc., Sunderland, Mass.
158. Li, X.,, and M. Noll. 1994. Evolution of distinct developmental functions of three Drosophila genes by acquisition of different cis-regulatory regions. Nature 367: 83 87.
159. Liao, G. C.,, E. J. Rehm,, and G. M. Rubin. 2000. Insertion site preferences of the P transposable element in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 97: 3347 3351.
160. Lim, J. K.,, and M. J. Simmons. 1994. Gross chromosome rearrangements mediated by transposable elements in Drosophila melanogaster. Bioessays 16: 269 275.
161. 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,, J. C. Venter, et al. 1999. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 402: 761 768.
162. Lister, C.,, D. Jackson,, and C. Martin. 1993. Transposon-induced inversion in Antirrhinum modifies nivea gene expression to give a novel flower color pattern under the control of cycloidearadialis. Plant Cell 5: 1541 1553.
163. Liu, W. M.,, W. M. Chu,, P. V. Choudary,, and C. W. Schmid. 1995. Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts. Nucleic Acids Res. 23: 1758 1765.
164. Lower, R.,, J. Lower,, and R. Kurth. 1996. The viruses in all of us: characteristics and biological significance of human endogenous retrovirus sequences. Proc. Natl. Acad. Sci. USA 93: 5177 5184.
165. Lozovskaya, E. R.,, V. S. Scheinker,, and M. B. Evgen’ev. 1990. A hybrid dysgenesis syndrome in Drosophila virilis. Genetics 126: 619 623.
166. Lu, B. Y.,, P. C. R. Emtage,, B. J. Duyf,, A. J. Hilliker,, and J. C. Eissenberg. 2000. Heterochromatin protein 1 is required for the normal expression of two heterochromatin genes in Drosophila. Genetics 155: 699 708.
167. Lyman, R. F.,, F. Lawrence,, S. V. Nuzhdin,, and T. F. Mackay. 1996. Effects of single P-element insertions on bristle number and viability in Drosophila melanogaster. Genetics 143: 277 292.
168. Lyon, M. F. 2000. LINE-1 elements and X chromosome inactivation: a function for “junk” DNA? Proc. Natl. Acad. Sci. USA 97: 6248 6249.
169. Lyon, M. F. 1998. X-chromosome inactivation: a repeat hypothesis. Cytogenet. Cell Genet. 80: 133 137.
170. Mackay, T. F.,, R. F. Lyman,, and M. S. Jackson. 1992. Effects of P element insertions on quantitative traits in Drosophila melanogaster. Genetics 130: 315 332.
171. Mackay, T. F. C. 1986. Transposable element-induced fitness mutations in Drosophila melanogaster. Genet. Res. 48: 77 87.
172. Mackay, T. F. C. 1987. Transposable element-induced polygenic mutations in Drosophila melanogaster. Genet. Res. 49: 225 233.
173. Marillonnet, S.,, and S. R. Wessler. 1997. Retrotransposon insertion into the maize waxy gene results in tissue-specific RNA processing. Plant Cell 9: 967 978.
174. Martienssen, R. A., 1996. Epigenetic silencing of Mu transposable elements in maize, p. 593 608. In V. E. A. Russo,, R. A. Martienssen,, and A. D. Riggs (ed.), Epigenetic Mechanisms of Gene Regulation. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
175. Mathiopoulos, K. D.,, A. della Torre,, V. Predazzi,, V. Petrarca,, and M. Coluzzi. 1998. Cloning of inversion breakpoints in the Anopheles gambiae complex traces a transposable element at the inversion junction. Proc. Natl. Acad. Sci. USA 95: 12444 12449.
176. Matzke, M. A.,, and A. J. Matzke. 1998. Epigenetic silencing of plant transgenes as a consequence of diverse cellular defense responses. Cell. Mol. Life Sci. 54: 94 103.
177. Matzke, M. A.,, M. F. Mette,, W. Aufsatz,, J. Jakowitsch,, and A. J. Matzke. 1999. Host defenses to parasitic sequences and the evolution of epigenetic control mechanisms. Genetica 107: 271 287.
178. McClintock, B. 1951. Chromosome organization and genic expression. Cold Spring Harbor Symp. Quant. Biol. 16: 13 47.
179. McClintock, B. 1978. Mechanisms that rapidly reorganize the genome. Stadler Symp. 10: 25 47.
180. McDonald, J. F. 1998. Transposable elements, gene silencing and macroevolution. Trends Ecol. Evol. 13: 94 95.
181. McDonald, J. F.,, L. V. Matyunina,, S. Wilson,, I. K. Jordan,, N. J. Bowen,, and W. J. Miller. 1997. LTR retrotransposons and the evolution of eukaryotic enhancers. Genetica 100: 3 13.
182. McNaughton, J. C.,, G. Hughes,, W. A. Jones,, P. A. Stockwell,, H. J. Klamut,, and G. B. Petersen. 1997. The evolution of an intron: analysis of a long, deletion-prone intron in the human dystrophin gene. Genomics 40: 294 304.
183. Miki, Y.,, I. Nishisho,, A. Horii,, Y. Miyoshi,, J. Utsunomiya,, K. W. Kinzler,, B. Vogelstein,, and Y. Nakamura. 1992. Disruption of the APC gene by a retrotransposal insertion of L1 sequence in a colon cancer. Cancer Res. 52: 643 645.
184. Miller, W. J.,, S. Hagemann,, E. Reiter,, and W. Pinsker. 1992. P-element homologous sequences are tandemly repeated in the genome of Drosophila guanche. Proc. Natl. Acad. Sci. USA 89: 4018 4022.
185. Miller, W. J.,, J. F. McDonald,, D. Nouaud,, and D. Anxolabehere. 1999. Molecular domestication: more than a sporadic episode in evolution. Genetica 107: 197 207.
186. Miller, W. J.,, J. F. McDonald,, and W. Pinsker. 1997. Molecular domestication of mobile elements. Genetica 100: 261 270.
187. Misra, S.,, and D. C. Rio. 1990. Cytotype control of Drosophila P element transposition: the 66 kd protein is a repressor of transposase activity. Cell 62: 269 284.
188. Moran, J. V.,, R. J. DeBerardinis,, and H. H. Kazazian, Jr. 1999. Exon shuffling by L1 retrotransposition. Science 283: 1530 1534.
189. Mourrain, P.,, C. Beclin,, T. Elmayan,, F. Feuerbach,, C. Godon,, J. B. Morel,, D. Jouette,, A. M. Lacombe,, S. Nikic,, N. Picault,, K. Remoue,, M. Sanial,, T. A. Vo,, and H. Vaucheret. 2000. Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell 101: 533 542.
190. Mustajoki, S.,, H. Ahola,, P. Mustajoki,, and R. Kauppinen. 1999. Insertion of Alu element responsible for acute intermittent porphyria. Hum. Mutat. 13: 431 438.
191. Napoli, C.,, C. Lemieux,, and R. Jorgensen. 1990. Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans. Plant Cell 2: 279 289.
192. Ng, H. H.,, P. Jeppesen,, and A. Bird. 2000. Active repression of methylated genes by the chromosomal protein MBD1. Mol. Cell. Biol. 20: 1394 1406.
193. Nihrane, A.,, I. Lebedeva,, M. S. Lyu,, K. Fujita,, and J. Silver. 1997. Secretion of a murine retroviral Env associated with resistance to infection. J. Gen. Virol. 78: 785 793.
194. Nimmo, E. R.,, G. Cranston,, and R. C. Allshire. 1994. Telomere- associated chromosome breakage in fission yeast results in variegated expression of adjacent genes. EMBO J. 13: 3801 3811.
195. Nouaud, D.,, and D. Anxolabéhère. 1997. P element domestication: a stationary truncated P element may encode a 66- kDa repressor-like protein in the Drosophila montium species subgroup. Mol. Biol. Evol. 14: 1132 1144.
196. Nouaud, D.,, B. Boeda,, L. Levy,, and D. Anxolabéhère. 1999. A P element has induced intron formation in Drosophila. Mol. Biol. Evol. 16: 1503 1510.
197. Nuzhdin, S. V.,, and T. F. Mackay. 1994. Direct determination of retrotransposon transposition rates in Drosophila melanogaster. Genet. Res. 63: 139 144.
198. Nuzhdin, S. V.,, E. G. Pasyukova,, and T. F. Mackay. 1997. Accumulation of transposable elements in laboratory lines of Drosophila melanogaster. Genetica 100: 167 175.
199. Oettinger, M. A.,, D. G. Schatz,, C. Gorka,, and D. Baltimore. 1990. RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination. Science 248: 1517 1523.
200. Okazaki, S.,, H. Ishikawa,, and H. Fujiwara. 1995. Structural analysis of TRAS1, a novel family of telomeric repeat-associated retrotransposons in the silkworm, Bombyx mori. Mol. Cell. Biol. 15: 4545 4552.
201. Panning, B.,, and R. Jaenisch. 1998. RNA and the epigenetic regulation of X chromosome inactivation. Cell 93: 305 308.
202. Pardue, M. L.,, O. N. Danilevskaya,, K. Lowenhaupt,, F. Slot,, and K. L. Traverse. 1996. Drosophila telomeres: new views on chromosome evolution. Trends Genet. 12: 48 52.
203. Pardue, M. L.,, and P. G. DeBaryshe. 1999. Drosophila telomeres: two transposable elements with important roles in chromosomes. Genetics 107: 189 196.
204. Pearce, S. R.,, U. Pich,, G. Harrison,, A. J. Flavell,, J. S. Heslop- Harrison,, I. Schubert,, and A. Kumar. 1996. The Ty1-copia group retrotransposons of Allium cepa are distributed throughout the chromosomes but are enriched in the terminal heterochromatin. Chromosome Res. 4: 357 364.
205. 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.
206. Pimpinelli, S.,, M. Berloco,, L. Fanti,, P. Dimitri,, S. Bonaccorsi,, E. Marchetti,, R. Caizzi,, C. Caggese,, and M. Gatti. 1995. Transposable elements are stable structural components of Drosophila melanogaster heterochromatin. Proc. Natl. Acad. Sci. USA 92: 3804 3808.
207. Prescott, D. M. 1994. The DNA of ciliated protozoa. Microbiol. Rev. 58: 233 267.
207a.. Pryciak, P. M.,, and H. E. Varmus. 1992. Fv-1 restriction and its effects on murine leukemia virus integration in vivo and in vitro. J. Virol. 66: 5959 5966.
208. Rasmussen, H. B.,, and J. Clausen. 1998. Large number of polymorphic nucleotides and a termination codon in the env gene of the endogenous human retrovirus ERV3. Dis. Markers 14: 127 133.
209. Reik, W.,, and E. R. Maher. 1997. Imprinting in clusters: lessons from Beckwith-Wiedemann syndrome. Trends Genet. 13: 330 334.
210. Reinton, N.,, T. B. Haugen,, S. Orstavik,, B. S. Skalhegg,, V. Hansson,, T. Jahnsen,, and K. Tasken. 1998. The gene encoding the C gamma catalytic subunit of cAMP-dependent protein kinase is a transcribed retroposon. Genomics 49: 290 297.
211. Reiter, L. T.,, T. Liehr,, B. Rautenstrauss,, H. M. Robertson,, and J. R. Lupski. 1999. Localization of mariner DNA transposons in the human genome by PRINS. Genome Res. 9: 839 843.
212. Rhounim, L.,, J. L. Rossignol,, and G. Faugeron. 1992. Epimutation of repeated genes in Ascobolus immersus. EMBO J. 11: 4451 4457.
213. Robertson, D. S. 1978. Characterization of a mutator system in maize. Mutat. Res. 51: 21 28.
214. Rubin, G. M.,, M. G. Kidwell,, and P. M. Bingham. 1982. The molecular basis of P-M hybrid dysgenesis: the nature of induced mutations. Cell 29: 987 994.
215. Rushforth, A. M.,, and P. Anderson. 1996. Splicing removes the Caenorhabditis elegans transposon Tc1 from most mutant pre-mRNAs. Mol. Cell. Biol. 16: 422 429.
216. Sankaranarayanan, K., 1988. Mobile genetic elements, spontaneous mutations, amd the assessment of genetic radiation hazards in man. In M. E. Lambert,, J. F. McDonald,, and I. B. Weinstein (ed.), Eukaryotic Transposable Elements as Mutagenic Agents. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
217. 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.
218. Schiefelbein, J. W.,, D. B. Furtek,, H. K. Dooner,, and O. E. Nelson, Jr. 1988. Two mutations in a maize bronze-1 allele caused by transposable elements of the Ac-Ds family alter the quantity and quality of the gene product. Genetics 120: 767 777.
219. Schmid, C. W. 1998. Does SINE evolution preclude Alu function? Nucleic Acids Res. 26: 4541 4550.
220. Schwartz, A.,, D. C. Chan,, L. G. Brown,, R. Alagappan,, D. Pettay,, C. Disteche,, B. McGillivray,, A. de la Chapelle,, and D. C. Page. 1998. Reconstructing hominid Y evolution: X-homologous block, created by X-Y transposition, was disrupted by Yp inversion through LINE-LINE recombination. Hum. Mol. Genet. 7: 1 11.
221. Seegmiller, A.,, and G. Herrick. 1998. A short internal eliminated sequence with central conserved sequences interrupting the LA-MSC gene of the 81 locus in the hypotrichous ciliates Oxytricha fallax and O. trifallax. J. Eukaryot. Microbiol. 45: 55 58.
222. Seegmiller, A.,, K. R. Williams,, R. L. Hammersmith,, T. G. Doak,, D. Witherspoon,, T. Messick,, L. L. Storjohann,, and G. Herrick. 1996. Internal eliminated sequences interrupting the Oxytricha 81 locus: allelic divergence, conservation, conversions, and possible transposon origins. Mol. Biol. Evol. 13: 1351 1362.
223. Selinger, D. A.,, and V. L. Chandler. 1999. Major recent and independent changes in levels and patterns of expression have occurred at the b gene, a regulatory locus in maize. Proc. Natl. Acad. Sci. USA 96: 15007 15012.
224. Selker, E. U. 1997. Epigenetic phenomena in filamentous fungi: useful paradigms or repeat-induced confusion? Trends Genet. 13: 296 301.
225. Selker, E. U. 1998. Trichostatin A causes selective loss of DNA methylation in Neurospora. Proc. Natl. Acad. Sci. USA 95: 9430 9435.
226. Shapiro, J. A. 1999. Transposable elements as the key to a 21st century view of evolution. Genetica 107: 171 179.
227. Siebel, C. W.,, A. Admon,, and D. C. Rio. 1995. Soma-specific expression and cloning of PSI, a negative regulator of P element pre-mRNA splicing. Genes Dev. 9: 269 283.
228. Siebel, C. W.,, L. D. Fresco,, and D. C. Rio. 1992. The mechanism of somatic inhibition of Drosophila P-element pre-mRNA splicing: multiprotein complexes at an exon pseudo- 5′ splice site control U1 snRNP binding. Genes Dev. 6: 1386 1401.
229. Sijen, T.,, and J. M. Kooter. 2000. Post-transcriptional gene-silencing: RNAs on the attack or on the defense? Bioessays 22: 520 531.
230. Singer, M. F.,, V. Krek,, J. P. McMillan,, G. D. Swergold,, and R. E. Thayer. 1993. LINE-1: a human transposable element. Gene 135: 183 188.
231. Skryabin, B. V.,, J. Kremerskothen,, D. Vassilacopoulou,, T. R. Disotell,, V. V. Kapitonov,, J. Jurka,, and J. Brosius. 1998. The BC200 RNA gene and its neural expression are conserved in Anthropoidea (primates). J. Mol. Evol. 47: 677 685.
232. Smardon, A.,, J. M. Spoerke,, S. C. Stacey,, M. E. Klein,, N. Mackin,, and E. M. Maine. 2000. EGO-1 is related to RNA-directed RNA polymerase and functions in germ-line development and RNA interference in C. elegans. Curr. Biol. 10: 169 178.
233. Smit, A. F. 1999. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr. Opin. Genet. Dev. 9: 657 663.
234. Spanopoulou, E.,, F. Zaitseva,, F. H. Wang,, S. Santagata,, D. Baltimore,, and G. Panayotou. 1996. The homeodomain region of Rag-1 reveals the parallel mechanisms of bacterial and V(D)J recombination. Cell 87: 263 276.
235. Spradling, A. C.,, D. M. Stern,, I. Kiss,, J. Roote,, T. Laverty,, and G. M. Rubin. 1995. Gene disruptions using P transposable elements: an integral component of the Drosophila genome project. Proc. Natl. Acad. Sci. USA 92: 10824 10830.
236. Stavenhagen, J. B.,, and D. M. Robins. 1988. An ancient provirus has imposed androgen regulation on the adjacent mouse sex-limited protein gene. Cell 55: 247 254.
237. Steinemann, M.,, and S. Steinemann. 1998. Enigma of Y chromosome degeneration: neo- Y and neo- X chromosomes of Drosophila miranda a model for sex chromosome evolution. Genetica 103: 409 420.
238. Sun, X.,, J. Wahlstrom,, and G. Karpen. 1997. Molecular structure of a functional Drosophila centromere. Cell 91: 1007 1019.
239. Surzycki, S. A.,, and W. R. Belknap. 2000. Repetitive-DNA elements are similarly distributed on Caenorhabditis elegans autosomes. Proc. Natl. Acad. Sci. USA 97: 245 949.
240. Tabara, H.,, M. Sarkissian,, W. G. Kelly,, J. Fleenor,, A. Grishok,, L. Timmons,, A. Fire,, and C. C. Mello. 1999. The rde- 1 gene, RNA interference, and transposon silencing in C. elegans. Cell 99: 123 132.
241. Takahashi, H.,, S. Okazaki,, and H. Fujiwara. 1997. A new family of site-specific retrotransposons, SART1, is inserted into telomeric repeats of the silkworm, Bombyx mori. Nucleic Acids Res. 25: 1578 1584.
242. Takahashi, S.,, Y. Inagaki,, H. Satoh,, A. Hoshino,, and S. Iida. 1999. Capture of a genomic HMG domain sequence by the En/Spm-related transposable element Tpn1 in the Japanese morning glory. Mol. Gen. Genet. 261: 447 451.
243. Talbert, L. E.,, and V. L. Chandler. 1988. Characterization of a highly conserved sequence related to mutator transposable elements in maize. Mol. Biol. Evol. 5: 519 529.
244. Tarchini, R.,, P. Biddle,, R. Wineland,, S. Tingey,, and A. Rafal ski. 2000. The complete sequence of 340 kb of DNA around the rice Adh1-adh2 region reveals interrupted colinearity with maize chromosome 4. Plant Cell 12: 381 391.
245. Taruscio, D.,, and L. Manuelidis. 1991. Integration site preferences of endogenous retroviruses. Chromosoma 101: 141 156.
246. Tate, P. H.,, and A. P. Bird. 1993. Effects of DNA methylation on DNA-binding proteins and gene expression. Curr. Opin. Genet. Dev. 3: 226 231.
247. 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-LTR retrotransposon. J. Mol. Evol. 45: 145 153.
248. Timmons, L.,, and A. Fire. 1998. Specific interference by ingested dsRNA. Nature 395: 854.
249. Torti, C.,, L. M. Gomulski,, D. Moralli,, E. Raimondi,, H. M. Robertson,, P. Capy,, G. Gasperi,, and A. R. Malacrida. 2000. Evolution of different subfamilies of mariner elements within the medfly genome inferred from abundance and chromosomal distribution Chromosoma 108: 523 532.
250. Trelogan, S. A.,, and S. L. Martin. 1995. Tightly regulated, developmentally specific expression of the first open reading frame from LINE-1 during mouse embryogenesis. Proc. Natl. Acad. Sci. USA 92: 1520 1524.
251. Tschiersch, B.,, A. Hofmann,, V. Krauss,, R. Dorn,, G. Korge,, and G. Reuter. 1994. The protein encoded by the Drosophila position-effect variegation suppressor gene Su(var)3 -9 combines domains of antagonistic regulators of homeotic gene complexes. EMBO J. 13: 3822 3831.
252. Tu, Z. 1997. Three novel families of miniature inverted-repeat transposable elements are associated with genes of the yellow fever mosquito, Aedes aegypti. Proc. Natl. Acad. Sci. USA 94: 7475 7480.
252a.. Tu, Z. 2001. Eight novel families of miniature inverted repeat transposable elements in the African malaria mosquito, Anopheles gambiae. Proc. Natl. Acad. Sci. USA 98: 1699 1704.
253. Tyler-Smith, C.,, R. J. Oakey,, Z. Larin,, R. B. Fisher,, M. Crocker,, N. A. Affara,, M. A. Ferguson-Smith,, M. Muenke,, O. Zuffardi,, and M. A. Jobling. 1993. Localization of DNA sequences required for human centromere function through an analysis of rearranged Y chromosomes. Nat. Genet. 5: 368 375.
254. van der Krol, A. R.,, L. A. Mur,, M. Beld,, J. N. Mol,, and A. R. Stuitje. 1990. Flavonoid genes in petunia: addition of a limited number of gene copies may lead to a suppression of gene expression. Plant Cell 2: 291 299.
255. Venables, P. J.,, S. M. Brookes,, D. Griffiths,, R. A. Weiss,, and M. T. Boyd. 1995. Abundance of an endogenous retroviral envelope protein in placental trophoblasts suggests a biological function. Virology 211: 589 592.
256. Vicient, C. M.,, A. Suoniemi,, K. Anamthawat-Jonsson,, J. Tanskanen,, A. Beharav,, E. Nevo,, and A. H. Schulman. 1999. Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum. Plant Cell 11: 1769 1784.
257. Vielle-Calzada, J. P.,, J. Thomas,, C. Spillane,, A. Coluccio,, M. A. Hoeppner,, and U. Grossniklaus. 1999. Maintenance of genomic imprinting at the Arabidopsis medea locus requires zygotic DDM1 activity. Genes Dev. 13: 2971 2982.
258. Walker, E. L. 1998. Paramutation of the r1 locus of maize is associated with increased cytosine methylation. Genetics 148: 1973 1981.
259. Walsh, C. P.,, J. R. Chaillet,, and T. H. Bestor. 1998. Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat. Genet. 20: 116 117.
259a.. Wargelius, A.,, S. Ellingsen,, and A. Fjose. 1999. Doublestranded RNA induces specific developmental defects in zebrafish embryos. Biochem. Biophys. Res. Commun. 263: 156 161.
260. Waterhouse, P. M.,, M. W. Graham,, and M. B. Wang. 1998. Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA. Proc. Natl. Acad. Sci. USA 95: 13959 13964.
261. Waterston, R.,, and J. Sulston. 1995. The genome of Caenorhabditis elegans. Proc. Natl. Acad. Sci. USA 92: 10836 10840.
262. Weiler, K. S.,, and B. T. Wakimoto. 1995. Heterochromatin and gene expression in Drosophila. Annu. Rev. Genet. 29: 577 605.
263. Wendel, J. F.,, and S. R. Wessler. 2000. Retrotransposon-mediated genome evolution on a local ecological scale. Proc. Natl. Acad. Sci. USA 97: 6250 6252.
264. Wessler, S. R. 1988. Phenotypic diversity mediated by the maize transposable elements Ac and Spm. Science 242: 399 405.
265. Wessler, S. R. 1996. Turned on by stress. Plant retrotransposons. Curr. Biol. 6: 959 961.
266. Wessler, S. R.,, T. E. Bureau,, and S. E. White. 1995. LTR retrotransposons and MITEs: important players in the evolution of plant genomes. Curr. Opin. Genet. Dev. 5: 814 821.
267. Wichman, H. A.,, R. A. Van den Bussche,, M. J. Hamilton,, and R. J. Baker. 1992. Transposable elements and the evolution of genome organization in mammals. Genetica 86: 287 293.