Transposable elements as sources of genomic variation

Mobile DNA II

Volumn , Issue , 2022, Pages 59-90

  Kidwell, Margaret G ^a   Lisch, Damon R ^b  

^a University of Arizona   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Genetic variation; Heterochromatin; Hybrid dysgenesis; Mutations; Transposable elements

Indexed keywords

EID: 85158003595     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1128/9781555817954.ch5     Document Type: Chapter

References (280)

1. Agrawal, A., Eastman Q.M., Schatz D.G. 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., Phillips R.L., Rines H.W. 1998. Chromosome-specific molecular organization of maize (Zea mays L.) centromeric regions. Proc. Natl. Acad. Sci. USA 95:13073-13078.
3. Ananiev, E. V., Phillips R.L., Rines H.W. 1998. Complex structure of knob DNA on maize chromosome 9. Retro- transposon invasion into heterochromatin. Genetics 149: 2025-2037.
4. Anderson, R., Britten R.J., Davidson E.H. 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., Lyman R.F., Mackay T.F. 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., Carrel L., Chakravarti A., Eichler E.E. 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., Masson P., Fedoroff N. 1988. Molecular mechanisms in the developmental regulation of the maize Suppressor-mutator transposable element. Genes Dev. 2: 1364-1380.
9. Baran, G., Echt C., Bureau T., Wessler S. 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., Howman E.V., Cancilla M.R., Saffery R., Choo K.H. 1999. Sequence analysis of an 80 kb human neocentromere. Hum. Mol. Genet. 8:217-227.
12. Baum, M., Clarke L. 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., Salomonsky P., Jahnsen T., Li Y. 1992. The C gamma subunit is a unique isozyme of the cAMP-dependent protein kinase. Biol J. Chem. 267:25505-25512.
14. Bellen, H., C. J. O'Kane, Wilson C., Grossniklaus U., Pearson R.K., Gehring W.J. 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, Towers G., Stoye J.P. 1996. Positional cloning of the mouse retrovirus restriction gene Fv1. Nature 382:826-829.
17. Biemont, C., Tsitrone A., Vieira C., Hoogland C. 1997. Transposable element distribution in Drosophila. Genetics 147:1997-1999.
18. Biessmann, H., Mason J.M. 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., Jackson M.S., Kidwell M.G., Dover G.A. 1987. KP elements repress P-induced hybrid dysgenesis in Drosophila melanogaster. EMBO J. 6:4125-4135.
21. Blackman, R., Grimaila R., Koehler M., Gelbart W. 1987. Mobilization of hobo elements residing within the de- capentaplegic gene complex: suggestion of a new hybrid dysgenesis system in Drosophila melanogaster. Cell49:497-505.
22. Boyd, M. T., Bax C.M., Bax B.E., Bloxam D.L., Weiss R.A. 1993. The human endogenous retrovirus ERV-3 is upregulated in differentiating placental trophoblast cells. Virology 196:905-909.
23. Bradley, D., Carpenter R., Sommer H., Hartley N., Coen E. 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., Kidwell M.G. 1983. Hybriddysgenesis 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., Davidson E.H. 1971. Repetitive and nonrepetitive DNA sequences and a speculation on the origin of evolutionary novelty. Rev Q. Biol. 46:111-138.
29. Brosius, J. 1999. Genomeswereforged bymassivebombard- ments with retroelements and retrosequences. Genetica 107: 209-238.
30. Brosius, J. 1999. RNAs from all categories generate retrose- quences that may be exapted as novel genes or regulatory elements. Gene 238:115-134.
31. Brosius, J., Gould S.J. 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., Tiedge H. 1995. Reverse transcriptase: mediator of genomic plasticity. Virus Genes 11:163-179.
33. Bureau, T. E., Ronald P.C., Wessler S.R. 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., White S.E., Wessler S.R. 1994. Transduction of a cellular gene by a plant retroelement. Cell 77: 479-480.
35. Burwinkel, B., Kilimann M.W. 1998. Unequal homologous recombination between LINE-1 elements as a mutational mechanism in human genetic disease. Mol J. Biol. 277: 513-517.
36. Caceres, M., Ranz J.M., Barbadilla A., Long M., Ruiz A. 1999. Generation of a widespread Drosophila inversion by a transposable element. Science 285:415-418.
37. Cambareri, E. B., Aisner R., Carbon J. 1998. Structureof the chromosome VII centromere region in Neurospora crassa: degenerate transposons and simple repeats. Mol. Cell. Biol. 18: 5465-5477.
38. Charlesworth, B., Langley C.H., Sniegowski P.D. 1997. Transposable element distributions in Drosophila. Genetics 147:1993-1995.
39. Charlesworth, B., Sniegowski P., Stephan W. 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., Ballard R., Carpick B.W., Williams B.R., Schmid C.W. 1998. Potential Alu function: regulation of the activity of double-stranded RNA-activated kinase Mol PKR. Cell. Biol. 18:58-68.
42. Cianciolo, G. J., Copeland T.D., Oroszlan S., Snyderman R. 1985. Inhibition of lymphocyte proliferation by a synthetic peptide homologous to retroviral envelope proteins. Science 230:453 -455.
43. Civardi, L., Xia Y., Edwards K.J., Schnable P.S., Nikolau B.J. 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., Amstutz H., Fishel B., Carbon J. 1986. Analysis of centromeric DNA in the fission yeast Schizosaccharo- myces pombe. Proc. Natl. Acad. Sci. USA 83:8253-8257.
45. Clegg, M. T., Durbin M.L. 2000. Flower color variation: a model for the experimental study of evolution. Proc. Natl. Acad. Sci. USA 97:7016-7023.
46. Cogoni, C., Macino G. 1999. Gene silencing in Neuros- pora crassa requires a protein homologous to RNA-depen- dent RNA polymerase. Nature 399:166-169.
47. Colot, V., Haedens V., Rossignol J.L. 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, PE BiosystemsArabidopsis Sequencing Consortium. Cell 100:377-386.
49. Copenhaver, G. P., Preuss D. 1999. Centromeres in the genomic era: unraveling paradoxes. Curr. Opin. Plant Biol. 2:104-108.
50. Corces, V. G., Geyer P.K. 1991. Interactions of retro- transposons with the host genome. Trends Genet. 7:86-90.
51. Cottarel, G., Shero J.H., Hieter P., Hegemann J.H. 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., Hulbert S.H., Brown W.E., Lucas J.R., Bennetzen J.L. 1995. Mu1-related transposable elements of maize preferentially insert into low copy number DNA. Genetics 140:315-324.
54. Currie, D. B., Mackay T.F., Partridge L. 1998. Pervasive effects of P element mutagenesis on body size in Drosophila melanogaster. Genet. Res. 72:19-24.
55. Cuypers, H., Dash S., Peterson P.A., Saedler H., Gierl A. 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., Chovnick A., Kidwell M.G. 1989. Hybrid dysgenesis in Drosophila simulans lines transformed with autonomous P elements. Genetics 121:281-291.
58. Daniels, S. B., M. McCarron, Love C., Chovnick A. 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., Batzer M.A. 1999. Alu repeats and human disease. Mol. Genet. Metab. 67:183-193.
60. Dimitri, P., Area B., Berghella L., Mei E. 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., Mehtali M., M. McClenaghan, Lathe R. 1997. Variegated gene expression in mice. Trends Genet. 13: 127-130.
62. Dominguez, A., Albornoz J. 1996. Rates of movement of transposable elements in Drosophila melanogaster. Mol. Gen. Genet. 251:130-138.
63. Dominguez, A., Albornoz J. 1999. Structural instability of 297 element in Drosophila melanogaster. Genetica 105: 239-248.
64. Dong, F., Miller J.T., Jackson S.A., Wang G.L., Ronald P.C., Jiang J. 1998. Rice (Oryza sativa) centromeric regions consist of complex Proc DNA. Natl. Acad. Sci. USA 95:8135-8140.
65. Donlin, M. J., Lisch D., Freeling M. 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., Feng D.F., Johnson M.S., M. A. McClure. 1989. Origins and evolutionary relationships of retroviruses. Rev Q. Biol. 64:1-30.
67. Dorer, D. R., Henikoff S. 1994. Expansions of transgene repeats cause heterochromatin formation and gene silencing in Drosophila. Cell 77:993-1002.
68. Doseff, A., Martienssen R., Sundaresan V. 1991. Somatic excision of the Mu1 transposable element of maize. Nucleic Acids Res. 19:579-584.
69. Dupressoir, A., Heidmann T. 1996. Germ line-specific expression of intracisternal A-particle retrotransposons in transgenic mice. Mol. Cell. Biol. 16:4495-4503.
70. Earnshaw, W. C., Sullivan K.F., Machlin P.S., Cooke C.A., Kaiser D.A., Pollard T.D., Rothfield N.F., Cleveland D.W. 1987. Molecular cloning of cDNA for CENP-B, the major human centromere autoantigen. J. Cell Biol. 104: 817-829.
71. Eberl, D. F., Duyf B.J., Hilliker A.J. 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., Hashimshony T., Keshet I., Cedar H., Thorne A.W. 1998. DNA methylation models histone acetylation. Nature 394:842.
73. Eichler, E. E., Budarf M.L., Rocchi M., Deaven L.L., Doggett N.A., Baldini A., Nelson D.L., Mohrenweiser H.W. 1997. Interchromosomal duplications of the adrenoleukodys- trophy 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, Eggleston W.B., Sved J. 1990. High-frequency P element loss in Drosophila is homolog dependent. Cell 62:515-525.
77. Engels, W. R., Preston C.R. 1984. Formation of chromosome rearrangements by P factors in Drosophila. Genetics 107:657-678.
78. Esnault, C., Maestre J., Heidmann T. 2000. Human LINE retrotransposons generate processed pseudogenes. Nat. Genet. 24:363-367.
79. Evgen'ev, M. B., Zelentsova H., Poluectova H., Lyozin G.T., Veleikodvorskaja V., Pyatkov K.I., Zhivotovski L., Kidwell M.G. 2000. Mobile elements and chromosomal evolution in the virilis group of Drosophila. Proc. Natl. Acad. Sci. USA 97:11337-11342.
80. Fanti, L., Dorer D.R., Berloco M., Henikoff S., Pimpinelli S. 1998. Heterochromatin protein 1 binds transgene arrays. Chromosoma 107:286-292.
81. Farkas, G., Gausz J., Galloni M., Reuter G., Gyurkovics H., Karch F. 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., Wessler S., Shure M. 1983. Isolation of the transposable maize controlling elements Ac and Ds. Cell 35:235-242.
84. Feschotte, C., Mouches C. 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., G. Sastry R.K. 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., Peacock W.J., Dennis E.S. 1996. Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proc. Natl. Acad. Sci. USA 93: 8449-8454.
88. Fire, A., Xu S., Montgomery M.K., Kostas S.A., Driver S.E., Mello C.C. 1998. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391:806-811.
89. 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.
90. Fishel, B., Amstutz H., Baum M., Carbon J., Clarke L. 1988. Structural organization and functional analysis of centromeric DNA in the fission yeast Schizosaccharomyces pombe. Mol. Cell. Biol. 8:754-763.
91. Foss, K. B., Landmark B., Skalhegg B.S., Tasken K., E. Jel- lum, Hansson V., Jahnsen T. 1994. Characterization of in-vitro-translated human regulatory and catalytic subunits of cAMP-dependent protein kinases. Eur. Biochem J. 220: 217-223.
92. Fowler, K. J., Hudson D.F., Salamonsen L.A., Edmondson S.R., Earle E., Sibson M.C., Choo K.H. 2000. Uterine dysfunction and genetic modifiers in centromere protein B- deficient mice. Genome Res. 10:30-41.
93. Fridell, R. A., Pret A.M., Searles L.L. 1990. A retro- transposon 412 insertion within an exon of the Drosophila melanogaster vermilion gene is spliced from the precursor RNA. Genes Dev. 4:559-566.
94. Fugmann, S. D., Lee A.I., Shockett P.E., Villey I.J., Schatz D.G. 2000. The RAG proteins and V(D)J recombination: complexes, ends, transposition. Annu. Rev. Immunol. 18:495-527.
95. Garber, K., Bilic I., Pusch O., Tohme J., Bachmair A., Schweizer D., Jantsch V. 1999. The Tpv2 family of retro- transposons of Phaseolus vulgaris: structure, integration characteristics, use for genotype classification. PlantMol. Biol. 39:797-807.
96. Golovkina, T. V., Chervonsky A., Dudley J.P., Ross S.R. 1992. Transgenic mouse mammary tumor virus superantigen expression prevents viral infection. Cell 69:637-645.
97. Goodier, J. L., Ostertag E.M., Kazazian H.H., Jr. 2000. Transduction of 3'-flanking sequences is common in L1 retro- transposition. Hum. Mol. Genet. 9:653-657.
98. Gottschling, D. E., Aparicio O.M., Billington B.L., Zakian V.A. 1990. Position effect at S. cerevisiae telomeres: reversible repression of Pol II transcription. Cell 63:751-762.
99. Gray, Y. H. 2000. It takes two transposons to tango: transposable-element-mediated chromosomal rearrangements. Trends Genet. 16:461-468.
100. Greene, B., Walko R., Hake S. 1994. Mutator insertions in an intron of the maize knottedl gene result in dominant suppressible mutations. Genetics 138:1275-1285.
101. Gregory, T. R., Hebert P.D. 1999. The modulation of DNA content: proximate causes and ultimate consequences. Genome Res. 9:317-324.
102. Guo, S., Kemphues K.J. 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.
103. Hambor, J. E., Mennone J., Coon M.E., Hanke J.H., Kavathas P. 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.
104. Harendza, C. J., Johnson L.F. 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.
105. Henikoff, S., Greene E.A., Pietrokovski S., Bork P., Attwood T.K., Hood L. 1997. Gene families: the taxonomy of protein paralogs and chimeras. Science 278:609-614.
106. Henikoff, S., Matzke M.A. 1997. Exploring and explaining epigenetic effects. Trends Genet. 13:293-295.
107. Higashiyama, T., Noutoshi Y., Fujie M., Yamada T. 1997. Zepp, a LINE-like retrotransposon accumulated in the Chlorella telomeric region. EMBO J. 16:3715-3723.
108. Hilliker, A. J., Appels R., Schalet A. 1980. The genetic analysis of D. melanogaster heterochromatin. Cell 21: 607-619.
109. Hiom, K., Melek M., Gellert M. 1998. DNA transposition by the RAG1 and RAG2 proteins: a possible source of oncogenic translocations. Cell 94:463-470.
110. Hirochika, H., Okamoto H., Kakutani T. 2000. Silencing of retrotransposons in Arabidopsis and reactivation by the ddml mutation. Plant Cell 12:357-369.
111. Holmes, S. E., Dombroski B.A., Krebs C.M., Boehm C.D., Kazazian H.H., Jr. 1994. A new retrotransposable human L1 element from the LRE2 locus on chromosome Iq produces a chimaeric insertion. Nat. Genet. 7:143-148.
112. Hunter, C. P. 2000. Gene silencing: shrinking the black box ofRNAi. Curr. Biol. 10:137-140.
113. Ivanova, A. V., Bonaduce M.J., Ivanov S.V., Klar A.J. 1998. The chromo and SET domains of the Clr4 protein are essential for silencing in fission yeast. Nat. Genet. 19: 192-195.
114. Iwasa, Y. 1998. The conflict theory of genomic imprinting: how much can be explained? Curr. Top. Dev. Biol. 40: 255-293.
115. Jacobsen, S. E., Sakai H., Finnegan E.J., Cao X., Meyerowitz E.M. 2000. Ectopic hypermethylation of flower- specific genes in Arabidopsis. Curr. Biol. 10:179-186.
116. Jakubczak, J. L., Burke W.D., Eickbush T.H. 1991. Retrotransposable elements R1 and R2 interrupt the rRNA genes of most insects. Proc. Natl. Acad. Sci. USA 88: 3295-3299.
117. Jakubczak, J. L., Xiong Y., Eickbush T.H. 1990. Type I (R1) and type II (R2) ribosomal DNA insertions of Drosophila melanogaster are retrotransposable elements closely related to those of Bombyx mori. Mol J. Biol. 212:37-52.
118. Jensen, S., Cavarec L., Gassama M.P., Heidmann T. 1995. Defective I elements introduced into Drosophila as transgenes can regulate reactivity and prevent I-R hybrid dysgenesis. Mol. Gen. Genet. 248:381-390.
119. Jiang, J., Nasuda S., Dong F., Scherrer C.W., Woo S.S., Wing R.A., Gill B.S., Ward D.C. 1996. A conserved repetitive DNA element located in the centromeres of cereal chromosomes. Proc. Natl. Acad. Sci. USA 93:14210-14213.
120. Joblonka, E., Lamb M.J. 1995. Epigenetic Inheritance and E-volution. Oxford Univ. Press, Oxford, UK.
121. 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.
122. Jones, P. A. 1985. Altering gene expression with 5-azacyti- dine. Cell 40:485-486.
123. Jordan, I. K., J. F. McDonald. 1998. Evidence for the role of recombination in the regulatory evolution of Saccharomyces cerevisiae Ty elements. Mol J. Evol. 47:14-20.
124. Jurka, J., Kapitonov V.V. 1999. Sectorial mutagenesis by transposable elements. Genetica 107:239-248.
125. Kakutani, T., Jeddeloh J.A., Flowers S.K., Munakata K., Richards E.J. 1996. Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proc. Natl. Acad. Sci. USA 93:12406-12411.
126. Kalendar, R., Tanskanen J., Immonen S., Nevo E., Schulman A.H. 2000. Genome evolution ofwild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc. Natl. Acad. Sci. USA 97:6603-6607.
127. Karpen, G. H., Allshire R.C. 1997. The case for epigenetic effects on centromere identity and function. Trends Genet. 13:489-496.
128. Kazazian, H. H., Jr. 1999. An estimated frequency of endogenous insertional mutations in humans. Nat. Genet. 22:130.
129. Kazazian, H. H., Jr., Moran J.V. 1998. The impact of L1 retrotransposons on the human genome. Nat. Genet. 19: 19-24.
130. Kazazian, H. H., Jr., Wong C., Youssoufian H., Scott A.F., Phillips D.G., Antonarakis S.E. 1988. Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man. Nature 332:164-166.
131. Ke, N., Irwin P.A., Voytas D.F. 1997. The pheromone response pathway activates transcription of Ty5 retrotrans- posons located within silent chromatin of Saccharomyces cer- evisiae. EMBO J. 16:6272-6280.
132. Ketting, R. F., Haverkamp T.H., H. G. van Luenen, Plasterk R.H. 1999. Mut-7 of C. elegans, required for transpo- son silencing and RNA interference, is a homolog of Werner syndrome helicase and RNaseD. Cell 99:133-141.
133. Kidwell, M. G., Kidwell J.F., Sved J.A. 1977. Hybrid dysgenesis in Drosophila melanogaster: a syndrome of aberrant traits including mutation, sterility & male recombination. Genetics 36:813-833.
134. Kidwell, M. G., Lisch D. 1997. Transposable elements as sources of variation in animals and plants. Proc. Natl. Acad. Sci. USA 94:7704-7711.
135. Kidwell, M. G., Lisch D.R. 2000. Transposable elements and host genome evolution. Trends Ecol. Evol. 15: 95-99.
136. Kim, J. M., Vanguri S., Boeke J.D., Gabriel A., Voytas D.F. 1998. Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res. 8:464-478.
137. Kimura, R. H., Choudary P.V., Schmid C.W. 1999. Silk worm Bm1 SINE RNA increases following cellular insults. Nucleic Acids Res. 27:3380-3387.
138. King, M. C., Wilson A.C. 1975. Evolution at two levels in humans and chimpanzees. Science 188:107-116.
139. Kipling, D., Warburton P.E. 1997. Centromeres, CENP- B and Tigger too. Trends Genet. 13:141-145.
140. Kirschner, M., Gerhart J. 1998. Evolvability. Proc. Natl. Acad. Sci. USA 95:8420-8427.
141. Klobutcher, L. A., Herrick G. 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.
142. Klobutcher, L. A., Herrick G. 1997. Developmental genome reorganization in ciliated protozoa: the transposon link. Proc. Nucleic Acid Res. Mol. Biol. 56:1-62.
143. Kloeckener-Gruissem, B., Freeling M. 1995. Transposon-induced promoter scrambling: a mechanism for the evolution of new alleles. Proc. Natl. Acad. Sci. USA 92: 1836-1840.
144. Kloeckener-Gruissem, B., Vogel J.M., Freeling M. 1992. The TATA box promoter region of maize Adh1 affects its organ-specific expression. EMBO J. 11:157-166.
145. Kobayashi, S., Hirano T., Kakinuma M., Uede T. 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.
146. Kumar, A., Bennetzen J.L. 1999. Plant retrotranspo- sons. Annu. Rev. Genet. 33:479-532.
147. Lahn, B. T., Page D.C. 1999. Four evolutionary strata on the human X chromosome. Science 286:964-967.
148. Lahn, B. T., Page D.C. 1999. Retroposition of autosomal mRNA yielded testis-specific gene family on human Y chromosome. Nat. Genet. 21:429-433.
149. Lai, C., Mackay T.F. 1993. Mapping and characterization of P-element-induced mutations at quantitative trait loci in Drosophila melanogaster. Genet. Res. 61:177-193.
150. Langley, C. H., Montgomery E., Hudson R., Kaplan N., Charlesworth B. 1988. On the role of unequal exchange on the containment of transposable element copy number. Genet. Res. 52:223-235.
151. Le, Q. H., Wright S., Yu Z., Bureau T. 2000. Transposon diversity in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 97:7376-7381.
152. Lee, C. C., Mul Y.M., Rio D.C. 1996. The Drosophila P-element KP repressor protein dimerizes and interacts with multiple sites on P-element Mol DNA. Cell. Biol. 16: 5616-5622.
153. Lee, J. K., Huberman J.A., Hurwitz J. 1997. Purification and characterization of a CENP-B homologue protein that binds to the centromeric K-type repeat DNA of Schizosac- charomyces pombe. Proc. Natl. Acad. Sci. USA 94: 8427-8432.
154. Levis, R. W., Ganesan R., Houtchens K., Tolar L.A., F.Sheen M. 1993. Transposons in place of telomeric repeats at a Drosophila telomere. Cell 75:1083-1093.
155. Lewis, S. M., Wu G.E. 1997. The origins of V(D)J recombination. Cell 88:159-162.
156. Li, E., Beard C., R.Jaenisch. 1993. RoleforDNAmethyl- ation in genomic imprinting. Nature 366:362-365.
157. Li, E., Bestor T.H., Jaenisch R. 1992. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69:915-926.
158. Li, W.-H. 1997. Molecular Evolution. Sinauer Associates Inc., Sunderland, Mass.
159. Li, X., Noll M. 1994. Evolution of distinct developmental functions of three Drosophila genes by acquisition of different cis-regulatory regions. Nature 367:83-87.
160. Liao, G. C., Rehm E.J., Rubin G.M. 2000. Insertion site preferences of the P transposable element in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 97:3347-3351.
161. Lim, J. K., Simmons M.J. 1994. Gross chromosome rearrangements mediated by transposable elements in Drosophila melanogaster. Bioessays 16:269-275.
162. Lin, X., Kaul S., Rounsley S., Shea T.P., Benito M.I., Town C.D., Fujii C.Y., Mason T., Bowman C.L., Barnstead M., Feldblyum T.V., Buell C.R., Ketchum K.A., Lee J., Ronning C.M., Koo H.L., Moffat K.S., Cronin L.A., Shen M., Pai G., S. Van Aken, Umayam L., Tallon L.J., Gill J.E., Venter J.C., et al. 1999. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 402:761-768.
163. Lister, C., Jackson D., Martin C. 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.
164. Liu, W. M., Chu W.M., Choudary P.V., Schmid C.W. 1995. Cell stress and translational inhibitors transiently increase the abundance of mammalian SENE transcripts. Nucleic Acids Res. 23:1758-1765.
165. Lower, R., Lower J., Kurth R. 1996. The viruses in all of us: characteristics and biological significance of human endogenous retrovirus sequences. Proc. Natl. Acad. Sci. USA 93:5177-5184.
166. Lozovskaya, E. R., Scheinker V.S., M. B. Evgen'ev. 1990. A hybrid dysgenesis syndrome in Drosophila virilis. Genetics 126:619-623.
167. Lu, B. Y., P. Emtage C.R., Duyf B.J., Hilliker A.J., Eissenberg J.C. 2000. Heterochromatin protein 1 is required for the normal expression of two heterochromatin genes in Drosophila. Genetics 155:699-708.
168. Lyman, R. F., Lawrence F., Nuzhdin S.V., Mackay T.F. 1996. Effects of single P-element insertions on bristle number and viability in Drosophila melanogaster. Genetics 143: 277-292.
169. Lyon, M. F. 2000. LINE-1 elements and X chromosome inactivation: a function for "junk" DNA? Proc. Natl. Acad. Sci. USA 97:6248-6249.
170. Lyon, M. F. 1998. X-chromosome inactivation: a repeat hypothesis. Cytogenet. Cell Genet. 80:133-137.
171. Mackay, T. F., Lyman R.F., Jackson M.S. 1992. Effects of P element insertions on quantitative traits in Drosophila melanogaster. Genetics 130:315-332.
172. Mackay, T. F. C. 1986. Transposable element-induced fitness mutations in Drosophila melanogaster. Genet. Res. 48: 77-87.
173. Mackay, T. F. C. 1987. Transposable element-induced polygenic mutations in Drosophila melanogaster. Genet. Res. 49: 225-233.
174. Marillonnet, S., Wessler S.R. 1997. Retrotransposon insertion into the maize waxy gene results in tissue-specific RNA processing. Plant Cell 9:967-978.
175. Martienssen, R. A. 1996. Epigeneticsilencingof Mu transposable elements in maize, p 593-608. In V. Russo E.A., Martienssen R.A., A.D. Riggs (ed.), Epigenetic Mechanisms of Gene Regulation. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
176. Mathiopoulos, K. D., A. dellaTorre, Predazzi V., Petrarca V., Coluzzi M. 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.
177. Matzke, M. A., Matzke A.J. 1998. Epigenetic silencing of plant transgenes as a consequence of diverse cellular defense responses. Cell. Mol. Life Sci. 54:94-103.
178. Matzke, M. A., Mette M.F., Aufsatz W., Jakowitsch J., Matzke A.J. 1999. Host defenses to parasitic sequences and the evolution of epigenetic control mechanisms. Genetica 107:271-287.
179. McClintock, B. 1951. Chromosome organization and genic expression. Cold Spring Harbor Symp. Quant. Biol. 16: 13-47.
180. McClintock, B. 1978. Mechanisms that rapidly reorganize the genome. Stadler Symp. 10:25-47.
181. McDonald, J. F. 1998. Transposable elements, gene silencing and macroevolution. Trends Ecol. Evol. 13:94-95.
182. McDonald, J. F., Matyunina L.V., Wilson S., Jordan I.K., Bowen N.J., Miller W.J. 1997. LTR retrotransposons and the evolution of eukaryotic enhancers. Genetica 100: 3-13.
183. McNaughton, J. C., Hughes G., Jones W.A., Stockwell P.A., Klamut H.J., Petersen G.B. 1997. The evolution of an intron: analysis of a long, deletion-prone intron in the human dystrophin gene. Genomics 40:294-304.
184. Miki, Y., Nishisho I., Horii A., Miyoshi Y., Utsunomiya J., Kinzler K.W., Vogelstein B., Nakamura Y. 1992. Disruption of the APC gene by a retrotransposal insertion of L1 sequence in a colon cancer. Cancer Res. 52:643-645.
185. Miller, W. J., Hagemann S., Reiter E., Pinsker W. 1992. P-element homologous sequences are tandemly repeated in the genome of Drosophila guanche. Proc. Natl. Acad. Sci. USA 89:4018-4022.
186. Miller, W. J., J. F. McDonald, Nouaud D., Anxolabehere D. 1999. Molecular domestication: more than a sporadic episode in evolution. Genetica 107:197-207.
187. Miller, W. J., J. F. McDonald, Pinsker W. 1997. Molecular domestication of mobile elements. Genetica 100: 261-270.
188. Misra, S., Rio D.C. 1990. Cytotype control of Drosophila P element transposition: the 66 kd protein is a repressor of transposase activity. Cell 62:269-284.
189. Moran, J. V., R. J. DeBerardinis, Kazazian H.H., Jr. 1999. Exon shuffling by L1 retrotransposition. Science 283: 1530-1534.
190. Mourrain, P., Beclin C., Elmayan T., Feuerbach F., Godon C., Morel J.B., Jouette D., Lacombe A.M., Nikic S., Picault N., Remoue K., Sanial M., Vo T.A., H. Vauch- eret. 2000. Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell 101:533-542.
191. Mustajoki, S., Ahola H., Mustajoki P., Kauppinen R. 1999. Insertion of Alu element responsible for acute intermittent porphyria. Hum. Mutat. 13:431-438.
192. Napoli, C., Lemieux C., Jorgensen R. 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.
193. Ng, H. H., Jeppesen P., Bird A. 2000. Active repression of methylated genes by the chromosomal protein MBD1. Mol. Cell. Biol. 20:1394-1406.
194. Nihrane, A., Lebedeva I., Lyu M.S., Fujita K., Silver J. 1997. Secretion of a murine retroviral Env associated with resistance to infection. Gen J. Virol. 78:785-793.
195. Nimmo, E. R., Cranston G., Allshire R.C. 1994. Telomere-associated chromosome breakage in fission yeast results in variegated expression of adjacent genes. EMBO J. 13:3801-3811.
196. Nouaud, D., Anxolabehere D. 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.
197. Nouaud, D., Boeda B., Levy L., Anxolabehere D. 1999. A P element has induced intron formation in Drosophila. Mol. Biol. Evol. 16:1503-1510.
198. Nuzhdin, S. V., Mackay T.F. 1994. Direct determination of retrotransposon transposition rates in Drosophila melanogaster. Genet. Res. 63:139-144.
199. Nuzhdin, S. V., Pasyukova E.G., Mackay T.F. 1997. Accumulation of transposable elements in laboratory lines of Drosophila melanogaster. Genetica 100:167-175.
200. Oettinger, M. A., Schatz D.G., Gorka C., Baltimore D. 1990. RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination. Science 248:1517-1523.
201. Okazaki, S., Ishikawa H., Fujiwara H. 1995. Structural analysis of TRAS1, a novel family of telomeric repeat-associated retrotransposons in the silkworm, Bombyx mori. Mol. Cell. Biol. 15:4545-4552.
202. Panning, B., Jaenisch R. 1998. RNA and the epigenetic regulation of X chromosome inactivation. Cell 93:305-308.
203. Pardue, M. L., Danilevskaya O.N., Lowenhaupt K., Slot F., Traverse K.L. 1996. Drosophila telomeres: new views on chromosome evolution. Trends Genet. 12:48-52.
204. Pardue, M. L., P. G. DeBaryshe. 1999. Drosophila telomeres: two transposable elements with important roles in chromosomes. Genetics 107:189-196.
205. Pearce, S. R., Pich U., Harrison G., Flavell A.J., J. S. Heslop- Harrison, Schubert I., Kumar A. 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.
206. Pickeral, O. K., Makaowski W., Boguski M.S., Boeke J.D. 2000. Frequent human genomic DNA transduction driven by LINE-1 retrotransposition. Genome Res. 10: 411-415.
207. Pimpinelli, S., Berloco M., Fanti L., Dimitri P., Bonaccorsi S., Marchetti E., Caizzi R., Caggese C., Gatti M. 1995. Transposable elements are stable structural components of Drosophila melanogaster heterochromatin. Proc. Natl. Acad. Sci. USA 92:3804-3808.
208. Prescott, D. M. 1994. The DNA of ciliated protozoa. Microbiol. Rev. 58:233 -267.
209. Pryciak, P. M., Varmus H.E. 1992. Fv-1 restriction and its effects on murine leukemia virus integration in vivo and in vitro. Virol J. 66:5959-5966.
210. Rasmussen, H. B., Clausen J. 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.
211. Reik, W., Maher E.R. 1997. Imprinting in clusters: lessons from Beckwith-Wiedemann syndrome. Trends Genet. 13:330-334.
212. Reinton, N., Haugen T.B., Orstavik S., Skalhegg B.S., Hansson V., Jahnsen T., Tasken K. 1998. The gene encoding the C gamma catalytic subunit of cAMP-dependent protein kinase is a transcribed retroposon. Genomics 49: 290-297.
213. Reiter, L. T., Liehr T., Rautenstrauss B., Robertson H.M., Lupski J.R. 1999. Localization of mariner DNA transposons in the human genome by PRINS. Genome Res. 9: 839-843.
214. Rhounim, L., Rossignol J.L., Faugeron G. 1992. Epimutation of repeated genes in Ascobolus immersus. EMBO J. 11:4451-4457.
215. Robertson, D. S. 1978. Characterization of a mutator system in maize. Mutat. Res. 51:21-28.
216. Rubin, G. M., Kidwell M.G., Bingham P.M. 1982. The molecular basis of P-M hybrid dysgenesis: the nature of induced mutations. Cell 29:987-994.
217. Rushforth, A. M., Anderson P. 1996. Splicing removes the Caenorhabditis elegans transposon Tc1 from most mutant pre-mRNAs. Mol. Cell. Biol. 16:422-429.
218. Sankaranarayanan, K. 1988. Mobile genetic elements, spontaneous mutations, amd the assessment of genetic radiation hazards in man. In Lambert M.E., J. F. McDonald, I. B. Weinstein (ed.), Eukaryotic Transposable Elements as Mutagenic Agents. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
219. San Miguel, P., Tikhonov A., Jin Y.K., Motchoulskaia N., Zakharov D., A. Melake-Berhan, Springer P.S., Edwards K.J., Lee M., Avramova Z., Bennetzen J.L. 1996. Nested retrotransposons in the intergenic regions of the maize genome. Science 274:765-768.
220. Schiefelbein, J. W., Furtek D.B., Dooner H.K., Nelson O.E., 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.
221. Schmid, C.W. 1998. DoesSINE evolutionpreclude Alu function?. Nucleic Acids Res. 26:4541-4550.
222. Schwartz, A., Chan D.C., Brown L.G., Alagappan R., Pettay D., Disteche C., B. McGillivray, A. de la Chapelle, Page D.C. 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.
223. Seegmiller, A., Herrick G. 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.Eukaryot J. Microbiol. 45: 55-58.
224. Seegmiller, A., Williams K.R., Hammersmith R.L., Doak T.G., Witherspoon D., Messick T., Storjohann L.L., Herrick G. 1996. Internal eliminated sequences interrupting the Oxytricha 81 locus: allelic divergence, conservation, conversions, possible transposon origins. Mol. Biol. Evol. 13:1351-1362.
225. Selinger, D. A., Chandler V.L. 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.
226. Selker, E. U. 1997. Epigenetic phenomena in filamentous fungi: useful paradigms or repeat-induced confusion? Trends Genet. 13:296-301.
227. Selker, E. U. 1998. Trichostatin A causes selective loss of DNA methylation in Neurospora. Proc. Natl. Acad. Sci. USA 95:9430-9435.
228. Shapiro, J. A. 1999. Transposable elements as the key to a 21st century view of evolution. Genetica 107:171-179.
229. Siebel, C. W., Admon A., Rio D.C. 1995. Soma-specific expression and cloning of PSI, a negative regulator of P element pre-mRNA splicing. Genes Dev. 9:269-283.
230. Siebel, C. W., Fresco L.D., Rio D.C. 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.
231. Sijen, T., Kooter J.M. 2000. Post-transcriptional gene- silencing: RNAs on the attack or on the defense?. Bioessays 22:520-531.
232. Singer, M. F., Krek V., J. P. McMillan, Swergold G.D., Thayer R.E. 1993. LINE-1: a human transposable element. Gene 135:183-188.
233. Skryabin, B. V., Kremerskothen J., Vassilacopoulou D., Disotell T.R., Kapitonov V.V., Jurka J., Brosius J. 1998. The BC200 RNA gene and its neural expression are conserved in Anthropoidea (primates). Mol J. Evol. 47: 677-685.
234. Smardon, A., Spoerke J.M., Stacey S.C., Klein M.E., Mackin N., Maine E.M. 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.
235. Smit, A. F. 1999. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr. Opin. Genet. Dev. 9:657-663.
236. Spanopoulou, E., Zaitseva F., Wang F.H., Santagata S., Baltimore D., Panayotou G. 1996. The homeodomain region of Rag-1 reveals the parallel mechanisms of bacterial and V(D)J recombination. Cell 87:263-276.
237. Spradling, A. C., Stern D.M., Kiss I., Roote J., Laverty T., Rubin G.M. 1995. Gene disruptions using P transposable elements: an integral component of the Drosophila genome project. Proc. Natl. Acad. Sci. USA 92:10824-10830.
238. Stavenhagen, J. B., Robins D.M. 1988. An ancient provirus has imposed androgen regulation on the adjacent mouse sex-limited protein gene. Cell 55:247-254.
239. Steinemann, M., Steinemann S. 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.
240. Sun, X., Wahlstrom J., Karpen G. 1997. Molecular structure of a functional Drosophila centromere. Cell 91: 1007-1019.
241. Surzycki, S. A., Belknap W.R. 2000. Repetitive-DNA elements are similarly distributed on Caenorhabditis elegans autosomes. Proc. Natl. Acad. Sci. USA 97:245-949.
242. Tabara, H., Sarkissian M., Kelly W.G., Fleenor J., A. Gris- hok, Timmons L., Fire A., Mello C.C. 1999. The rde- 1 gene, RNA interference, transposon silencing in C. ele- gans. Cell 99:123-132.
243. Takahashi, H., Okazaki S., Fujiwara H. 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.
244. Takahashi, S., Inagaki Y., Satoh H., Hoshino A., Iida S. 1999. Capture of a genomic HMG domain sequence by the En/Spm-related transposable element Tpnl in the Japanese morning glory. Mol. Gen. Genet. 261:447-451.
245. Talbert, L. E., Chandler V.L. 1988. Characterization of a highly conserved sequence related to mutator transposable elements in maize. Mol. Biol. Evol. 5:519-529.
246. Tarchini, R., Biddle P., Wineland R., Tingey S., 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.
247. Taruscio, D., Manuelidis L. 1991. Integration site preferences of endogenous retroviruses. Chromosoma 101: 141-156.
248. Tate, P. H., Bird A.P. 1993. Effects of DNA methylation on DNA-binding proteins and gene expression. Curr. Opin. Genet. Dev. 3:226-231.
249. Terrinoni, A., Franco C.D., Dimitri P., Junakovic N. 1997. Intragenomic distribution and stability of transposable elements in euchromatin and heterochromatin of Drosophila melanogaster: non-LTR retrotransposon. Mol J. Evol. 45: 145-153.
250. Timmons, L., Fire A. 1998. Specific interference by ingested dsRNA. Nature 395:854.
251. Torti, C., Gomulski L.M., Moralli D., Raimondi E., Robertson H.M., Capy P., Gasperi G., Malacrida A.R. 2000. Evolution of different subfamilies of mariner elements within the medfly genome inferred from abundance and chromosomal distribution. Chromosoma 108:523-532.
252. Trelogan, S. A., Martin S.L. 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.
253. Tschiersch, B., Hofmann A., Krauss V., Dorn R., Korge G., Reuter G. 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.
254. 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.
255. 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.
256. Tyler-Smith, C., Oakey R.J., Larin Z., Fisher R.B., Crocker M., Affara N.A., M. A. Ferguson-Smith, Muenke M., Zuffardi O., Jobling M.A. 1993. Localization of DNA sequences required for human centromere function through an analysis of rearranged Y chromosomes. Nat. Genet. 5: 368-375.
257. van der Krol, A. R., Mur L.A., Beld M., Mol J.N., Stuitje A.R. 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.
258. Venables, P. J., Brookes S.M., Griffiths D., Weiss R.A., Boyd M.T. 1995. Abundance of an endogenous retroviral envelope protein in placental trophoblasts suggests a biological function. Virology 211:589-592.
259. Vicient, C. M., Suoniemi A., K. Anamthawat-Jonsson, J. Tan- skanen, Beharav A., Nevo E., Schulman A.H. 1999. Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum. Plant Cell 11:1769-1784.
260. Vielle-Calzada, J. P., Thomas J., Spillane C., Coluccio A., Hoeppner M.A., Grossniklaus U. 1999. Maintenance of genomic imprinting at the Arabidopsis medea locus requires zygotic DDM1 activity. Genes Dev. 13:2971-2982.
261. Walker, E. L. 1998. Paramutation of the r1 locus of maize is associated with increased cytosine methylation. Genetics 148:1973-1981.
262. Walsh, C. P., Chaillet J.R., Bestor T.H. 1998. Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat. Genet. 20:116-117.
263. Wargelius, A., Ellingsen S., Fjose A. 1999. Doublestranded RNA induces specific developmental defects in ze- brafish embryos. Biochem. Biophys. Res. Commun. 263: 156-161.
264. Waterhouse, P. M., Graham M.W., Wang M.B. 1998. Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense Proc RNA. Natl. Acad. Sci. USA 95:13959-13964.
265. Waterston, R., Sulston J. 1995. The genome of Caeno- rhabditis elegans. Proc. Natl. Acad. Sci. USA 92: 10836-10840.
266. Weiler, K. S., Wakimoto B.T. 1995. Heterochromatin and gene expression in Drosophila. Annu. Rev. Genet. 29: 577-605.
267. Wendel, J. F., Wessler S.R. 2000. Retrotransposon- mediated genome evolution on a local ecological scale. Proc. Natl. Acad. Sci. USA 97:6250-6252.
268. Wessler, S. R. 1988. Phenotypic diversity mediated by the maize transposable elements Ac and Spm. Science 242: 399-405.
269. Wessler, S. R. 1996. Turned on by stress. Plant retrotranspo- sons. Curr. Biol. 6:959-961.
270. Wessler, S. R., Bureau T.E., White S.E. 1995. LTR- retrotransposons and MITEs: important players in the evolution of plant genomes. Curr. Opin. Genet. Dev. 5:814-821.
271. Wichman, H. A., R. A. Van den Bussche, Hamilton M.J., Baker R.J. 1992. Transposable elements and the evolution of genome organization in mammals. Genetica 86:287-293.
272. Wilke, C. M., Adams J. 1992. Fitness effects of Ty transposition in Saccharomyces cerevisiae. Genetics 131:31-42.
273. Wolffe, A. P., Matzke M.A. 1999. Epigenetics: regulation through repression. Science 286:481-486.
274. Wu, Y. H., Wilks A.V., Gibson J.B. 1998. A KP element inserted between the two promoters of the alcohol dehydrogenase gene of Drosophila melanogaster differentially affects expression in larvae and adults. Biochem. Genet. 36: 363-379.
275. Xiong, Y., Eickbush T.H. 1988. The site-specific ribo- somal DNA insertion element R1Bm belongs to a class of non-long-terminal-repeat retrotransposons. Mol. Cell. Biol. 8:114-123.
276. Yang, Z., Boffelli D., Boonmark N., Schwartz K., Lawn R. 1998. Apolipoprotein(a) gene enhancer resides within a LINE element. Biol J. Chem. 273:891-897.
277. Yoder, J. A., Walsh C.P., Bestor T.H. 1997. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 13:335-340.
278. Zhang, P., Stankiewicz R.L. 1998. Y-Linked male sterile mutations induced by P element in Drosophila melanogaster. Genetics 150:735-744.
279. Zhang, Q., Arbuckle J., Wessler S.R. 2000. Recent, extensive, preferential insertion of members of the miniature inverted-repeat transposable element family Heart- breaker into genic regions of maize. Proc. Natl. Acad. Sci. USA 97:1160-1165.
280. Zou, S., Ke N., Kim J.M., Voytas D.F. 1996. The Saccharomyces retrotransposon Ty5 integrates preferentially into regions of silent chromatin at the telomeres and mating loci. Genes Dev. 10:634-645.