P transposable elements in drosophila melanogaster

Mobile DNA II

Volumn , Issue , 2022, Pages 484-518

  Rio, Donald C ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Affinity chromotography; DNA repair; Drosophila genetics; Mutagenesis; Transposable elements

Indexed keywords

EID: 85158065940     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1128/9781555817954.ch21     Document Type: Chapter

References (223)

1. Adams, M. D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F., George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N., Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X., Brandon R.C., Rogers Y.H., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C., Baxter E.G., Helt G., Nelson C.R., Gabor Miklos G.L., Abril J.F., Agbayani A., An H.J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A., Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V., Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J., Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E., Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B., Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I., Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C., Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S., Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M., Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M., Harris N.L., Harvey D., Heiman T.J., Hernandez J.R., Houck J., Hostin D., Houston K.A., Howland T.J., Wei M.H., Ibegwam C., Jalali M., Kalush F., Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D., Kraft C., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A., Li J., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C., McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C., Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L., Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R., Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V., Reese M.G., Reinert K., Remington K., Saunders R.D., Scheeler F., Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T., Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R., Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.Y., Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T., Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.F., Zaveri J.S., Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W., Zhou X., Zhu S., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M., Venter J.C. 2000. The genome sequence of Drosophila melanogaster. Science 287: 2185-2195.
2. Adams, M. D., Tarng R.S., Rio D.C. 1997. The alternative splicing factor PSI regulates P-element third intron splicing in vivo. Genes Dev. 11:129-138.
3. Andrews, J. D., Gloor G.B. 1995. A role for the KP leucine zipper in regulating P element transposition in Drosophila melanogaster. Genetics 141:587-594.
4. Ashburner, M., Misra S., Roote J., Lewis S.E., Blazej R., Davis T., Doyle C., Galle R., Harris N. 1999. An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster. Genetics 153:179-219.
5. Ballinger, D. G., Benzer S. 1989. Targeted gene mutations in Drosophila. Proc. Natl. Acad. Sci. USA 86: 9402-9406.
6. Banga, S. S., Velazquez A., Boyd J.B. 1991. P transposition in Drosophila provides a new tool for analyzing postreplication repair and double-strand break repair. Mutat. Res. 255:79-88.
7. Basler, K., Struhl G. 1994. Compartment boundaries and the control of Drosophila limb pattern by hedgehog protein. Nature 368:208-214.
8. Beall, E. L., Admon A., Rio D.C. 1994. A Drosophila protein homologous to the human p70 Ku autoimmune antigen interacts with the P transposable element inverted repeats. Proc. Natl. Acad. Sci. USA 91:12681-12685.
9. Beall, E. L., Rio D.C. 1996. Drosophila IRBP/Ku p70 corresponds to the mutagen-sensitive mus309 gene and is involved in P-element excision in vivo. Genes Dev. 10: 921-933.
10. Beall, E. L., Rio D.C. 1997. Drosophila P-element transposase is a novel site-specific endonuclease. Genes Dev. 11: 2137-2151.
11. Beall, E. L., Rio D.C. 1998. Transposase makes critical contacts with, is stimulated by, single-stranded DNA at the P element termini in vitro. EMBO J. 17:2122-2136.
12. Bellaiche, Y., Mogila V., Perrimon N. 1999. I-Scel endonuclease, a new tool for studying DNA double-strand break repair mechanisms in Drosophila. Genetics 152:1037-1044.
13. Bellen, H. J., O'Kane C.J., Wilson C., Grossniklaus U., Pearson R.K., Gehring W.J. 1989. P-element-mediated enhancer detection: a vesatile method to study development in Drosophila. Genes Dev. 3:1288-1300.
14. Berg, C. A., Spradling A.C. 1991. Studies on the rate and site-specificity of P element transposition. Genetics 127: 515-524.
15. Bier, E., Vaessin H., Shepherd S., Lee K., McCall K., Barbel S., Ackerman L., Carretto R., Uemura T., Grell E., et al. 1989. Searching for pattern and mutation in the Drosophila genome with a P-lacZ vector. Genes Dev. 3:1273-1287.
16. Bingham, P. M., Kidwell M.G., Rubin G.M. 1982. The molecular basis of P-M hybrid dysgenesis: the role of the P element, a P strain-specific transposon family. Cell 29: 995-1004.
17. Bingham, P. M., Levis R., Rubin G.M. 1981. Cloning of DNA sequences from the white locus of D. melanogaster by a novel and general method. Cell 25:693-704.
18. 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.
19. Bourne, H. R., Sanders D.A., McCormick F. 1990. The GTPase superfamily: a conserved switch for diverse cell functions. Nature 348:125-132.
20. Bourne, H. R., Sanders D.A., McCormick F. 1991. The GTPase superfamily: conserved structure and molecular mechanism. Nature 349:117-127.
21. Boyd, J. B., Golino M.D., Shaw K.E., Osgood C.J., Green M.M. 1981. Third-chromosome mutagen-sensitive mutants of Drosophila melanogaster. Genetics 97:607-623.
22. Boyd, J. B., Setlow R.B. 1976. Characterization of postreplication repair in mutagen-sensitive strains of Drosophila melanogaster. Genetics 84:507-526.
23. Brand, A. H., Manoukian A.S., Perrimon N. 1994. Ectopic expression in Drosophila. Methods Cell Biol. 44: 635-654.
24. Brand, A. H., Perrimon N. 1993. Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 118:401-415.
25. Brautigam, C. A., Steitz T.A. 1998. Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes. Curr. Opin. Struct. Biol. 8:54-63.
26. Burd, C. G., Dreyfuss G. 1994. RNA binding specificity of hnRNP A1: significance of hnRNP A1 high-affinity binding sites in pre-mRNA splicing. EMBO J. 13:1197-1204.
27. Burd, C. G., Dreyfuss G. 1994. Conserved structures and diversity of functions of RNA-binding proteins. Science 265:615-621.
28. Cech, T. R. 1990. Self-splicing of group I introns. Annu. Rev. Biochem. 59:543-568.
29. Chabot, B. 1996. Directing alternative splicing: cast and scenarios. Trends Genet. 12:472-478.
30. Chain, A. C., Zollman S., Tseng J.C., Laski F.A. 1991. Identification of a cis-acting sequence required for germ line- specific splicing of the P element ORF2-ORF3 intron. Mol. Cell. Biol. 11:1538-1546.
31. Chen, B., Chu T., Harms E., Gergen J.P., Strickland S. 1998. Mapping of Drosophila mutations using site-specific male recombination. Genetics 149:157-163.
32. Chou, T. B., Noll E., Perrimon N. 1993. Autosomal P[ovoD1] dominant female-sterile insertions in Drosophila and their use in generating germ-line chimeras. Development 119:1359-1369.
33. Chou, T. B., Perrimon N. 1992. Use of a yeast site- specific recombinase to produce female germline chimeras in Drosophila. Genetics 131:643-653.
34. Chou, T. B., Perrimon N. 1996. The autosomal FLP- DFS technique for generating germline mosaics in Drosophila melanogaster. Genetics 144:1673-1679.
35. Chow, S. A., Vincent K.A., Ellison V., Brown P.O. 1992. Reversal of integration and DNA splicing mediated by integrase of human immunodeficiency virus. Science 255: 723-726.
36. Chu, G. 1997. Double strand break repair. Biol J. Chem. 272:24097-24100.
37. Coen, D. 1990. P element regulatory products enhance zeste repression of a P[white duplicated] transgene in Drosophila melanogaster. Genetics 126:949-960.
38. Cooley, L., Kelley R., Spradling A. 1988. Insertional mutagenesis of the Drosophila genome with single P elements. Science 239:1121-1128.
39. Cooley, L., Thompson D., Spradling A.C. 1990. Constructing deletions with defined endpoints in Drosophila. Proc. Natl. Acad. Sci. USA 87:3170-3173.
40. Craig, N. L. 1995. Unity in transposition reactions. Science 270:253-254.
41. Critchlow, S. E., Jackson S.P. 1998. DNA end-joining: from yeast to man. Trends Biochem. Sci. 23:394-398.
42. Curcio, M. J., Garfinkel D.J. 1999. New lines of host defense: inhibition of Ty1 retrotransposition by Fus3p and NER/Trends Genet TFIIH. 15:43-45.
43. Dalby, B., Pereira A.J., Goldstein L.S. 1995. An inverse PCR screen for the detection of P element insertions in cloned genomic intervals in Drosophila melanogaster. Genetics 139: 757-766.
44. Dang, D. T., Perrimon N. 1992. Use of a yeast site- specific recombinase to generate embryonic mosaics in Drosophila. Dev. Genet 13:367-375.
45. Desai, A., Mitchison T.J. 1997. Microtubule polymerization dynamics. Annu. Rev. Cell. Dev. Biol. 13:83-117.
46. Dray, T., Gloor G.B. 1997. Homology requirements for targeting heterologous sequences during P-induced gap repair in Drosophila melanogaster. Genetics 147:689-699.
47. Dynan, W. S., Yoo S. 1998. Interaction of Ku protein and DNA-dependent protein kinase catalytic subunit with nucleic acids. Nucleic Acids Res. 26:1551-1559.
48. Engels, W.R. 1979. Hybrid dysgenesis in Drosophila melano- gaster: rules of inheritance of female sterility. Genet. Res. 33: 219-236.
49. Engels, W.R. 1979. Extrachromosomalcontrolofmutability in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 76: 4011-4015.
50. Engels, W. R. 1983. The P family of transposable elements in Drosophila. Annu. Rev. Genet. 17:315-344.
51. Engels, W. R. 1984. A trans-acting product needed for P factor transposition in Drosophila. Science 226:1194-1196.
52. Engels, W.R. 1989. P elements in Drosophila melanogaster, P. 437-484. In D.E. Berg and M.M. Howe (ed.), Mobile DNA. American Society for Microbiology, Washington, D.C.
53. Engels, W. R. 1992. The origin of P elements in Drosophila melanogaster. Bioessays 14:681-686.
54. Engels, W. R. 1996. P elements in Drosophila. Curr. Top. Microbiol. Immunol. 204:103-123.
55. Engels, W. R. 1997. Invasions of P elements. Genetics 145: 11-15.
56. Engels, W. R., Benz W.K., Preston C.R., Graham P.L., Phillis R.W., Robertson H.M. 1987. Somatic effects of P element activity in Drosophila melanogaster: pupal lethality. Genetics 117:745-757.
57. Engels, W. R., Johnson-Schlitz D.M., Eggleston W.B., Sved J. 1990. High-frequency P element loss in Drosophila is homolog-dependent. Cell 62:515-525.
58. Engels, W. R., Preston C.R., Johnson-Schlitz D.M. 1994. Long-range cis preference in DNA homology search over the length of a Drosophila chromosome. Science 263: 1623-1625.
59. Esposito, D., Craigie R. 1999. HIV integrase structure and function. Adv. Virus Res. 52:319-333.
60. Fire, A. 1999. RNA-triggered gene silencing. Trends Genet. 15:358-363.
61. Formosa, T., Alberts B.M. 1986. DNA synthesis dependent on genetic recombination: characterization of a reaction catalyzed by purified bacteriophage T4 proteins. Cell 47: 793-806.
62. Fugmann, S. D., Villey I.J., Ptaszek L.M., Schatz D.G. 2000. Identification of two catalytic residues in RAG1 that define a single active site within the RAG1/RAG2 protein complex. Mol. Cell 5:97-107.
63. Gell, D., Jackson S.P. 1999. Mapping of protein-protein interactions within the DNA-dependent protein kinase complex. Nucleic Acids Res. 27:3494-3502.
64. Gloor, G. B., Lankenau D.H. 1998. Gene conversion in mitotically dividing cells: a view from Drosophila. Trends Genet. 14:43-46.
65. Gloor, G. B., Moretti J., Mouyal J., Keeler K.J. 2000. Distinct P element excision products in somatic and germline cells of Drosophila. Genetics 155:1821-1830.
66. Gloor, G. B., Nassif N.A., Johnson-Schlitz D.M., Preston C.R., Engels W.R. 1991. Targeted gene replacement in Drosophila via P element-induced gap repair. Science 253: 1110-1117.
67. Gloor, G. B., Preston C.R., Johnson-Schlitz D.M., Nassif N.A., Phillis R.W., Benz W.K., Robertson H.M., Engels W.R. 1993. Type I repressors of P element mobility. Genetics 135:81-95.
68. Golic, K. G. 1991. Site-specific recombination between homologous chromosomes in Drosophila. Science 252: 958-961.
69. Golic, K. G., Golic M.M. 1996. Engineering the Drosophila genome: chromosome rearrangements by design. Genetics 144:1693-1711.
70. Golic, K. G., Lindquist S. 1989. The FLP recombinase of yeast catalyzes site-specific recombination in the Drosophila genome. Cell 59:499-509.
71. Gray, Y. H. M., Tanaka M.M., Sved J.A. 1996. P element-induced recombination in Drosophila melanogaster: hybrid element insertion. Genetics 144:1601-1610.
72. Grindley, N. D., Leschziner A.E. 1995. DNA transposition: from a black box to a color monitor. Cell 83: 1063-1066.
73. Grossniklaus, U., Bellen H.J., Wilson C., Gehring W.J. 1989. P-element-mediated enhancer detection applied to the study of oogenesis in Drosophila. Genes Dev. 107:189-200.
74. Hamilton, B. A., Palazzolo M.J., Chang J.H., Vijay Raghavan K., Mayeda C.A., Whitney M.A., Meyerowitz E.M. 1991. Large scale screen for transposon insertions into cloned genes. Proc. Natl. Acad. Sci. USA 88:2731-2735.
75. Hamilton, B. A., Zinn K. 1994. From clone to mutant gene. Methods Cell Biol. 44:81-94.
76. Hammond, L. E., Rudner D.Z., Kanaar R., Rio D.C. 1997. Mutations in the hrp48 gene, which encodes a Drosophila heterogeneous nuclear ribonucleoprotein particle protein, cause lethality and developmental defects and affect P- element third-intron splicing in vivo. Mol. Cell Biol. 17: 7260-7267.
77. Hay, B. A., Maile R., Rubin G.M. 1997. P element insertion-dependent gene activation in the Drosophila eye. Proc. Natl. Acad. Sci. USA 94:5195-5200.
78. Hazelrigg, T., Levis R., Rubin G.M. 1984. Transforma- tion of white locus DNA in drosophila: dosage compensation, zeste interaction, position effects. Cell 36:469-481.
79. Heath, E. M., Simmons M.J. 1991. Genetic and molecular analysis of repression in the P-M system of hybrid dysgenesis in Drosophila melanogaster. Genet. Res. 57:213-226.
80. Hesse, J. E., Lieber M.R., Gellert M., Mizuuchi K. 1987. Extrachromosomal DNA substrates in pre-B cells undergo inversion or deletion at immunoglobulin V-(D)-J joining signals. Cell 49:775-783.
81. Hickman, A. B., Li Y., Mathew S.V., May E.W., Craig N.L., Dyda F. 2000. Unexpected structural diversity in DNA recombination: the restriction endonuclease connection. Mol. Cell 5:10025-11034.
82. Hiraizumi, Y. 1971. Spontaneous recombination in Drosophila melanogaster males. Proc. Natl. Acad. Sci. USA 68: 268-270.
83. Hirose, Y., Manley J.L. 2000. RNA polymerase II and the integration of nuclear events. Genes Dev. 14:1415-1429.
84. Horowitz, D. S., Krainer A.R. 1994. Mechanisms for selecting 5' splice sites in mammalian pre-mRNA splicing. Trends Genet. 10:100-106.
85. Hoskins, R. A., Nelson C.R., Berman B.P., Laverty T.R., George R.A., Ciesiolka L., Naeemuddin M., Arenson A.D., Durbin J., David R.G., Tabor P.E., Bailey M.R., DeShazo D.R., Catanese J., Mammoser A., Osoegawa K., de Jong P.J., Celniker S.E., Gibbs R.A., Rubin G.M., Scherer S.E. 2000. A BAC-based physical map of the major autosomes of Drosophila melanogaster. Science 287:2271-2274.
86. Houck, M. A., Clark J.B., Peterson K.R., Kidwell M.G. 1991. Possible horizontal transfer of Drosophila genes by the mite Proctolaelaps regalis. Science 253:1125-1128.
87. Jackson, M. S., Black D.M., Dover G.A. 1988. Amplifi- cation of KP elements associated with the repression of hybrid dysgenesis in Drosophila melanogaster. Genetics 120: 1003-1013.
88. Jacoby, D. B., Wensink P.C. 1994. Yolk protein factor 1 is a Drosophila homolog of Ku, the DNA-binding subunit of a DNA-dependent protein kinase from humans. Biol J. Chem. 269:11484-11491.
89. Jasin, M. 1996. Genetic manipulation of genomes with rare- cutting endonucleases. Trends Genet. 12:224-228.
90. Johnson-Schlitz, D. M., Engels W.R. 1993. P-element- induced interallelic gene conversion of insertions and deletions in Drosophila melanogaster. Mol. Cell. Biol. 13: 7006-7018.
91. Joyce, C. M., Steitz T.A. 1995. Polymerase structures and function: variations on a theme? Bacteriol J. 177: 6321-6329.
92. Kaiser, K., Goodwin S.F. 1990. "Site-selected" transpo- son mutagenesis of Drosophila. Proc. Natl. Acad. Sci. USA 87:1686-1690.
93. Kanaar, R., Hoeijmakers J.H., van Gent D.C. 1998. Molecular mechanisms of DNA double strand break repair. Trends Cell. Biol. 8:483-489.
94. Karess, R. E., Rubin G.M. 1984. Analysis ofPtranspos- able element function in Drosophila. Cell 38:135-146.
95. Karpen, G. H., Spradling A.C. 1992. Analysis of subtel- omeric heterochromatin in the Drosophila minichromosome Dp1187 by single P element insertional mutagenesis. Genetics 132:737-753.
96. Kassis, J. A., Noll E., VanSickle E.P., Odenwald W.F., Perrimon N. 1992. Altering the insertional specificity of a Drosophila transposable element. Proc. Natl. Acad. Sci. USA 89:1919-1923.
97. Kaufman, P. D., Doll R.F., Rio D.C. 1989. Drosophila P element transposase requires internal P element DNA sequences. Cell 38:135-146.
98. Kaufman, P. D., Rio D.C. 1991. Drosophila P-element transposase is a transcriptional repressor in vitro. Proc. Natl. Acad. Sci. USA 88:2613-2617.
99. Kaufman, P. D., Rio D.C. 1992. P element transposition in vitro proceeds by a cut-and-paste mechanism and uses GTP as a cofactor. Cell 69:27-39.
100. Keeler, K. J., Dray T., Penney J.E., Gloor G.B. 1996. Gene targeting of a plasmid-borne sequence to a doublestrand DNA break in Drosophila melanogaster. Mol. Cell. Biol. 16:522-528.
101. Keeler, K. J., Gloor G.B. 1997. Efficient gap repair in Drosophila melanogaster requires a maximum of 31 nucleotides of homologous sequence at the searching ends. Mol. Cell. Biol. 17:627-634.
102. Ketting, R. F., Haverkamp T.H., van Luenen H.G., 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.
103. Kidwell, M. G. 1981. Hybrid dysgenesis in Drosphila melanogaster: the genetics of cytotype determination in a neutral strain. Genetics 98:275-290.
104. Kidwell, M. G. 1983. Evolution of hybrid dysgenesis determinants in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 80:1655-1659.
105. Kidwell, M. G. 1985. Hybrid dysgenesis in Drosophila mela- nogaster: nature and inheritance of P element regulation. Genetics 111:337-350.
106. Kidwell, M. G. 1992. Horizontal transfer of P elements and other short inverted repeat transposons. Genetica 86: 275-286.
107. Kidwell, M. G. 1992. Horizontal transfer. Curr. Opin. Genet. Dev. 2:868-873.
108. Kidwell, M. G., Kidwell J.F. 1975. Cytoplasm-chromosome interactions in Drosophila melanogaster. Nature 253: 755-756.
109. Kidwell, M. G., Kidwell J.F., Nei M. 1973. A case of high rate of spontaneous mutation affecting viability in Drosophila melanogaster. Genetics 75:133-153.
110. Kidwell, M. G., Kidwell J.F., Sved J.A. 1977. Hybrid dysgenesis in Drosophila melanogaster: a syndrome of aberrant traits including mutation, sterility and male recombination. Genetics 86:813-833.
111. Kidwell, M. G., Novy J.B. 1979. Hybrid dysgenesis in Drosophila melanogaster: sterility resulting from gonadal dysgenesis in the P-M system. Genetics 92:1127-1140.
112. Kim, D. R., Dai Y., Mundy C.L., Yang W., Oettinger M.A. 1999. Mutations of acidic residues in RAG1 define the active site of the V(D)J recombinase. Genes Dev. 13: 3070-3080.
113. Kim, S. T., Lim D.S., Canman C.E., Kastan M.B. 1999. Substrate specifications and identification of putative substrates of ATM kinase family members. Biol J. Chem. 274:37538-37543.
114. Kooistra, R., Pastink A., Zonneveld J.B., Lohman P.H., Eeken J.C. 1999. The Drosophila melanogaster DmRAD54 gene plays a crucial role in double- strand break repair after P-element excision and acts synergistically with Ku70 in the repair of X-ray damage. Mol. Cell. Biol. 19:6269-6275.
115. Krasnow, M. A., Cumberledge S., Manning G., Herzenberg L.A., Nolan G.P. 1991. Whole animal cell sorting of Drosophila embryos. Science 251:81-85.
116. Kusano, K., Johnson-Schiltz D.M., Engels W.R. 2001. Sterility of Drosophila with mutations in the Bloom syndrome gene-complementation by Ku70. Science 291:2600-2602.
117. Labourier, E., Adams M.D., Rio D.C. 2001. Modulation of P element pre-mRNA splicing by a direct interaction between PSI and U1 snRNP 70K protein. Mol. Cell 8: 363-373.
118. Landree, M. A., Wibbenmeyer J.A., Roth D.B. 1999. Mutational analysis of RAG1 and RAG2 identifies three catalytic amino acids in RAG1 critical for both cleavage steps of V(D)J recombination. Genes Dev. 13:3059-3069.
119. Lankenau, D. H., Corces V.G., Engels W.R. 1996. Comparison of targeted-gene replacement frequencies in Drosophila melanogaster at the forked and white loci. Mol. Cell. Biol. 16:3535-3544.
120. Lankenau, D. H., Gloor G.B. 1998. In vivo gap repair in Drosophila: a one-way street with many destinations. Bioessays 20:317-327.
121. Laski, F. A., Rio D.C., Rubin G.M. 1986. Tissue specificity of Drosophila P element transposition is regulated at the level of mRNA splicing. Cell 44:7-19.
122. Laski, F. A., Rubin G.M. 1989. Analysis of the cis- acting requirements for germ-line-specific splicing of the P- element ORF2-ORF3 intron. Genes Dev. 3:720-728.
123. Lee, C. C., Beall E.L., Rio D.C. 1998. DNA binding by the KP repressor protein inhibits P element transposase activity in vitro. EMBO J. 17:4166-4174.
124. 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.
125. Lemaitre, B., Coen D. 1991. P regulatory products repress in vivo the P promoter activity in P-lacZ fusion genes. Proc. Natl. Acad. Sci. USA 88:4419-4423.
126. Lemaitre, B., Ronsseray S., Coen D. 1993. Maternal repression of the P element promoter in the germline of Drosophila melanogaster: a model for the P cytotype. Genetics 135:149-160.
127. 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.
128. Lopez, A. J. 1998. Alternative splicing of pre-mRNA: developmental consequences and mechanisms of regulation. Annu. Rev. Genet. 32:279-305.
129. Matunis, E. L., Matunis M.J., Dreyfuss G. 1992. Characterization of the major hnRNP proteins from Drosophila melanogaster. Cell Biol J. 116:257-269.
130. Mayeda, A., Krainer A.R. 1992. Regulation of alternative pre-mRNA splicing by hnRNP A1 and splicing factor SF2. Cell 68:365-375.
131. McClintock, B. 1984. The significance of responses of the genome to challenge. Science 226:792-801.
132. Melek, M., Gellert M. 2000. RAG1/2-mediated resolution of transposition intermediates: two pathways and possible consequences. Cell 101:625-633.
133. Miklos, G. L., Rubin G.M. 1996. The role of the genome project in determining gene function: insights from model organisms. Cell 86:521-529.
134. Miller, W. J., Paricio N., Hagemann S., Martinez-Sebastian M.J., Pinsker W., de Frutos R. 1995. Structure and expression of clustered P element homologues in Drosophila subobscura and Drosophila guanche. Gene 156:167-174.
135. Min, H., Turck C.W., Nikolic J.M., Black D.L. 1997. A new regulatory protein, KSRP, mediates exon inclusion through an intronic splicing enhancer. Genes Dev. 11: 1023-1036.
136. Misra, S., Buratowski R.M., Ohkawa T., Rio D.C. 1993. Cytotype control of Drosophila melanogaster P element transposition: genomic position determines maternal repression. Genetics 135:785-800.
137. 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.
138. Moore, M. J., Query C.C., Sharp P.A. 1993. Splicing of precursors to messenger RNAs by the spliceosome. In RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
139. Mul, Y. M., Rio D.C. 1997. Reprogramming the purine nucleotide cofactor requirement of Drosophila P element transposase in vivo. EMBO J. 16:4441-4447.
140. Mullins, M. C., Rio D.C., Rubin G.M. 1989. Cis-acting DNA sequence requirements for P-element transposition. Genes Dev. 3:729-738.
141. Myers, E. W., Sutton G.G., Delcher A.L., Dew I.M., Fasulo D.P., Flanigan M.J., Kravitz S.A., Mobarry C.M., Reinert K.H., Remington K.A., Anson E.L., Bolanos R.A., Chou H.H., Jordan C.M., Halpern A.L., Lonardi S., Beasley E.M., Brandon R.C., Chen L., Dunn P.J., Lai Z., Liang Y., Nusskern D.R., Zhan M., Zhang Q., Zheng X., Rubin G.M., Adams M.D., Venter J.C. 2000. A whole-genome assembly of Drosophila. Science 287:2196-2204.
142. Nassif, N., Penney J., Pal S., Engels W.R., Gloor G.B. 1994. Efficient copying of nonhomologous sequences from ectopic sites via P-element-induced gap repair. Mol. Cell. Biol. 14:1613-1625.
143. Nitasaka, E., Mukai T., Yamazaki T. 1987. Repressor of P elements in Drosophila melanogaster: Cytotype determination by a defective P element carrying only open reading frames 0 through 2. Proc. Natl. Acad. Sci. USA 84: 7605-7608.
144. O'Brochta, D. A., Gomez S.P., Handler A.M. 1991. P element excision in Drosophila melanogaster and related drosophilids. Mol. Gen. Genet. 225:387-394.
145. O'Hare, K., Driver A., McGrath S., D. Johnson-Schiltz M. 1992. Distribution and structure of cloned P elements from the Drosophila melanogaster P strain pi 2. Genet. Res. 60:33-41.
146. O'Hare, K., Rubin G.M. 1983. Structures ofPtranspos- able elements and their sites of insertion and excision in the Drosophila melanogaster genome. Cell 34:25-35.
147. O'Kane, C. J., Gehring W.J. 1987. Detection in situ of genomic regulatory elements in Drosophila. Proc. Natl. Acad. Sci. USA 84:9123-9127.
148. Paques, F., Haber J.E. 1999. Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 63:349-404.
149. Paterson, J., O'Hare K. 1991. Structure and transcription of the singed locus of Drosophila melanogaster. Genetics 129:1073-1084.
150. Polard, P., Chandler M. 1995. Bacterial transposases and retroviral integrases. Mol. Microbiol. 15:13-23.
151. Powers, T., Walter P. 1995. Reciprocal stimulation of GTP hydrolysis by two directly interacting GTPases. Science 269:1422-1424.
152. Preston, C. R., Engels W.R. 1996. P-element-induced male recombination and gene conversion in Drosophila. Genetics 144:1611-1622.
153. Preston, C. R., Sved J.A., Engels W.R. 1996. Flanking duplications and deletions associated with P-induced male recombination in Drosophila. Genetics 144:1623-1638.
154. Ramsden, D. A., van Gent D.C., Gellert M. 1997. Specificity inV(D)J recombination: new lessons from biochemistry and genetics. Curr. Opin. Immunol. 9:114-120.
155. Rasmusson, K. E., Raymond J.D., Simmons M.J. 1993. Repression of hybrid dysgenesis in Drosophila melanogaster by individual naturally occurring P elements. Genetics 133: 605-622.
156. Rasmusson, K. E., Simmons M.J., Raymond J.D., McLarnon C.F. 1990. Quantitative effects of P elements on hybrid dysgenesis in Drosophila melanogaster. Genetics 124: 647-662.
157. Reed, R. 1996. Initial splice-site recognition and pairing during pre-mRNA splicing. Curr. Opin. Genet. Dev. 6:215-220.
158. Rice, P., Craigie R., Davies D.R. 1996. Retroviral integrases and their cousins. Curr. Opin. Struct. Biol. 6:76-83.
159. Rio, D. C. 1990. Molecular mechanisms regulating Drosophila P element transposition. Annu. Rev. Genet. 24: 543-578.
160. Rio, D. C. 1991. Regulation of Drosophila P element transposition. Trends Genet. 7:282-287.
161. Rio, D. C., Laski F.A., Rubin G.M. 1986. Identification and immunochemical analysis of biologically active Drosophila P element transposase. Cell 44:21-32.
162. Rio, D. C., Rubin G.M. 1988. Identification and purification of a Drosophila protein that binds to the terminal 31- base-pair inverted repeats of the P transposable element. Proc. Natl. Acad. Sci. USA 85:8929-8933.
163. Robertson, H. M., Engels W.R. 1989. Modified P elements that mimic the P cytotype in Drosophila melanogaster. Genetics 123:815-824.
164. Robertson, H. M., Preston C.R., Phillis R.W., Johnson-Schlitz D.M., Benz W.K., Engels W.R. 1988. A stable genomic source of P element transposase in Drosophila mela- nogaster. Genetics 118:461-470.
165. Roche, S. E., Rio D.C. 1998. Trans-silencing by P elements inserted in subtelomeric heterochromatin involves the Drosophila Polycomb group gene, Enhancer of zeste. Genetics 149:1839-1855.
166. Roche, S. E., Schiff M., Rio D.C. 1995. P-element repressor autoregulation involves germ-line transcriptional repression and reduction of third intron splicing. Genes Dev. 9:1278-1288.
167. Roiha, H., Rubin G.M., O'Hare K. 1988. P element insertions and rearrangements at the singed locus of Drosophila melanogaster. Genetics 119:75-83.
168. Rong, Y. S., Golic K.G. 2000. Gene targeting by homologous recombination in drosophila. Science 228:2013-2018.
169. Ronsseray, S., Lehmann M., Anxolabehere D. 1991. The maternally inherited regulation of P elements in Drosophila melanogaster can be elicited by two P copies at cytological site 1A on the X chromosome. Genetics 129:501-512.
170. Ronsseray, S., Lehmann M., Nouaud D., Anxolabehere D. 1996. The regulatory properties of autonomous subtel- omeric P elements are sensitive to a suppressor of variegation in Drosophila melanogaster. Genetics 143:1663-1674.
171. Ronsseray, S., Lemaitre B., Coen D. 1993. Maternal inheritance ofP cytotype in Drosophila melanogaster: a ''preP cytotype'' is strictly extra-chromosomally transmitted. Mol. Gen. Genet. 241:115-123.
172. Ronsseray, S., Marin L., Lehmann M., Anxolabehere D. 1998. Repression of hybrid dysgenesis in Drosophila melano- gaster by combinations of telomeric P-element reporters and naturally occurring P elements. Genetics 149:1857-1866.
173. Rorth, P. 1996. A modular misexpression screen in Drosophila detecting tissue-specific phenotypes. Proc. Natl. Acad. Sci. USA 93:12418-12422.
174. Rorth, P. 1998. Gal4 in the Drosophila female germline. Mech. Dev. 78:113-118.
175. Rorth, P., Szabo K., Bailey A., Laverty T., Rehm J., Rubin G.M., Weigmann K., Milan M., Benes V., Ansorge W. 1998. Systematic gain-of-function genetics in Drosophila. Development 125:1049-1057.
176. Roth, D. B., Gellert M. 2000. New guardians of the genome. Nature 404:823-825.
177. Rubin, G. M., Hong L., Brokstein P., Evans-Holm M., Frise E., Stapleton M., Harvey D.A. 2000. A Drosophila complementary DNA resource. Science 287:2222-2224.
178. 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.
179. Rubin, G. M., Lewis E.B. 2000. A brief history of Drosophila's contributions to genome research. Science 287: 2216-2218.
180. Rubin, G. M., Spradling A.C. 1982. Genetic transformation of Drosophila with transposable element vectors. Science 218:348-353.
181. Rubin, G. M., Yandell M.D., Wortman J.R., Gabor Miklos G.L., Nelson C.R., Hariharan I.K., Fortini M.E., Li P.W., Apweiler R., Fleischmann W., Cherry J.M., Henikoff S., Skupski M.P., Misra S., Ashburner M., Birney E., Boguski M.S., Brody T., Brokstein P., Celniker S.E., Chervitz S.A., Coates D., Cravchik A., Gabrielian A., Galle R.F., W.Gelbart M., George R.A., Goldstein L.S., Gong F., Guan P., Harris N.L., Hay B.A., Hoskins R.A., Li J., Li Z., Hynes R.O., Jones S.J., Kuehl P.M., Lemaitre B., Littleton J.T., Morrison D.K., Mungall C., O'Farrell P.H., Pickeral O.K., Shue C., Vosshall L.B., Zhang J., Zhao Q., Zheng X.H., Zhong F., Zhong W., Gibbs R., Venter J.C., Adams M.D., Lewis S. 2000. Comparative genomics of the eukaryotes. Science 287:2204-2215.
182. Savilahti, H., Rice P.A., Mizuuchi K. 1995. The phage Mu transpososome core: DNA requirements for assembly and function. EMBO J. 14:4893-4903.
183. Schmid, S. L., McNiven M.A., De Camilli P. 1998. Dynamin and its partners: a progress report. Curr. Opin. Cell. Biol. 10:504-512.
184. Scottoline, B. P., Chow S., Ellison V., Brown P.O. 1997. Disruption of the terminal base pairs of retroviral DNA during integration. Genes Dev. 11:371-382.
185. Sentry, J. W., Kaiser K. 1994. Application of inverse PCR to site-selected mutagenesis of Drosophila. Nucleic Acids Res. 22:3429-3430.
186. Sepp, K. J., Auld V.J. 1999. Conversion of lacZ enhancer trap lines to GAL4 lines using targeted transposition in Drosophila melanogaster. Genetics 151:1093-1101.
187. Sharp, P. A. 1999. RNAi and double-strand Genes Dev RNA. 13:139-141.
188. 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.
189. 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. 6:1386-1401.
190. Siebel, C. W., Kanaar R., Rio D.C. 1994. Regulation of tissue-specific P-element pre-mRNA splicing requires the RNA-binding protein Genes Dev PSI. 8:1713-1725.
191. Siebel, C. W., Rio D.C. 1990. Regulated splicing of the Drosophila P transposable element third intron in vitro: somatic repression. Science 248:1200-1208.
192. Simmons, M. J., Bucholz L.M. 1985. Transposase titration in Drosophila melanogaster: a model of cytotype in the P-M system of hybrid dysgenesis. Proc. Natl. Acad. Sci. USA 82:8119-8123.
193. Simmons, M. J., Raymond J.D., Grimes C.D., Belinco C., Haake B.C., Jordan M., Lund C., Ojala T.A., Papermaster D. 1996. Repression of hybrid dysgenesis in Drosophila melanogaster by heat- shock-inducible sense and antisense P-element constructs. Genetics 144:1529-1544.
194. Simmons, M. J., Raymond J.D., Rasmusson K.E., Miller L.M., McLarnon C.F., Zunt J.R. 1990. Repression of P element-mediated hybrid dysgenesis in Drosophila mela- nogaster. Genetics 124:663-676.
195. Smith, C. W., Valcarcel J. 2000. Alternative pre-mRNA splicing: the logic of combinational control. Trends Biochem. Sci. 25:381-388.
196. Smith, G. C., Cary R.B., Lakin N.D., Hann B.C., Teo S.H., Chen D.J., Jackson S.P. 1999. Purification and DNA binding properties of the ataxia-telangiectasia gene product Proc ATM. Natl. Acad. Sci. USA 96:11134-11139.
197. Smith, G. C., Jackson S.P. 1999. The DNA-dependent protein kinase. Genes Dev. 13:916-934.
198. Spradling, A. C. 1986. P element-mediated transformation, P. 175-197. In Drosophila: A Practical Approach. RL Press, Oxford, England.
199. Spradling, A. C., Rubin G.M. 1982. Transposition of cloned P elements into Drosophila germ line chromosomes. Science 218:341-347.
200. Spradling, A. C., Stern D., Rhem E.J., Laverty T., Mozden N., Misra S., Rubin G.M. 1999. The Berkeley Drosophila Genome Project gene disruption project: Single P-element insertions mutating 25% of vital Drosophila genes. Genetics 153:135-177.
201. 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.
202. Staveley, B. E., Heslip T.R., Hodgetts R.B., Bell J.B. 1995. Protected P-element termini suggest a role for inverted- repeat-binding protein in transposase-induced gap repair in Drosophila melanogaster. Genetics 139:1321-1329.
203. Stellwagen, A. E., Craig N.L. 1997. Gain-of-function mutations in TnsC, an ATP-dependent transposition protein that activates the bacterial transposon Tn7. Genetics 145: 573-585.
204. Stellwagen, A. E., Craig N.L. 1998. Mobile DNA elements: controlling transposition with ATP-dependent molecular switches. Trends Biochem. Sci. 23:486-490.
205. Struhl, G., Basler K. 1993. Organizing activity of wingless protein in Drosophila. Cell 72:527-540.
206. Sved, J. A., Blackman L.M., Gilchrist A.S., Engels W.R. 1991. High levels of recombination induced by homologous P elements in Drosophila melanogaster. Mol. Gen. Genet. 225:443-447.
207. Sved, J. A., Blackman L.M., Svoboda Y., Colless R. 1995. Male recombination with single and homologous P elements in Drosophila melanogaster. Mol. Gen. Genet. 246: 381-386.
208. Sved, J. A., Eggleston W.B., Engels W.R. 1990. Germline and somatic recombination induced by in vitro modified P elements in Drosophila melanogaster. Genetics 124: 331-337.
209. Svoboda, Y. H., Robson M.K., Sved J.A. 1995. P- element-induced male recombination can be produced in Drosophila melanogaster by combining end-deficient elements in trans. Genetics 139:1601-1610.
210. Tanaka, M. M., Liang X.M., Gray Y.H., Sved J.A. 1997. The accumulation of P-element-induced recombinants in the germline of male Drosophila melanogaster. Genetics 147:1769-1782.
211. Theodosiou, N. A., Xu T. 1998. Use of FLP/FRT system to study Drosophila development. Methods 14:355-365.
212. Thompson-Stewart, D., Karpen G.H., Spradling A.C. 1994. A transposable element can drive the concerted evolution of tandemly repetitious Proc DNA. Natl. Acad. Sci. USA 91:9042-9046.
213. Tower, J., Karpen G.H., Craig N., Spradling A.C. 1993. Preferential transposition of Drosophila P elements to nearby chromosomal sites. Genetics 133:347-359.
214. Tseng, J. C., Zollman S., Chain A.C., Laski F.A. 1991. Splicing of the Drosophila P element ORF2-ORF3 intron is inhibited in a human cell extract. Mech. Dev. 35:65-72.
215. Vos, J. C., De Baere I., Plasterk R.H. 1996. Transposase is the only nematode protein required for in vitro transposition of Tc1. Genes Dev. 10:755-761.
216. Wang, J. C. 1996. DNA topoisomerases. Annu. Rev. Bio- chem. 65:635-692.
217. Weaver, D. T. 1995. What to do at an end: DNA doublestrand-break repair. Trends Genet. 11:388-392.
218. Wilson, C., Pearson R.K., Bellen H.J., O'Kane C.J., Grossniklaus U., Gehring W.J. 1989. P-element-mediated enhancer detection: an efficient method for isolating and characterizing developmentally regulated genes in Drosophila. Genes Dev. 3:1301-1313.
219. Wittinghofer, A., Pai E.F. 1991. The structure of Ras protein: a model for a universal molecular switch. Trends Biochem. Sci. 16:382-387.
220. Xu, T., Harrison S.D. 1994. Mosaic analysis using FLP recombinase. Methods Cell Biol. 44:655-681.
221. Xu, T., Rubin G.M. 1993. Analysis of genetic mosaics in developing and adult Drosophila tissues. Development 117: 1223-1237.
222. Yamauchi, M., Baker T.A. 1998. An ATP-ADP switch in MuB controls progression of the Mu transposition pathway. EMBO J. 17:5509-5518.
223. Zhang, P., Spradling A.C. 1993. Efficient and dispersed local P element transposition from Drosophila females. Genetics 133:361-373.