Patching broken chromosomes with extranuclear cellular DNA

Molecular Cell

Volumn 4, Issue 5, 1999, Pages 873-881

  Yu, Xin ^a   Gabriel, Abram ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL DNA; ENDONUCLEASE; MITOCHONDRIAL DNA;

ARTICLE; CELL SURVIVAL; CHROMOSOME BREAKAGE; CHROMOSOME REARRANGEMENT; GENE INSERTION; GENETIC RECOMBINATION; GENOME; INTRON; NONHUMAN; SACCHAROMYCES CEREVISIAE;

EID: 0033231558     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1097-2765(00)80397-4     Document Type: Article

References (55)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
2. Belfort, M., and Roberts, R.J. (1997). Homing endonucleases: keeping the house in order. Nucleic Acids Res. 25, 3379-3388.
3. Berben, G., Dumont, J., Gilliquet, V., Bolle, P.A., and Hilger, F. (1991). The YDp plasmids: a uniform set of vectors bearing versatile gene disruption cassettes for Saccharomyces cerevisiae. Yeast 7, 475-477.
4. Boeke, J.D., Lacroute, F., and Fink, G.R. (1984). A positive selection for mutants lacking orotidine 5′-phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid resistance. Mol. Gen. Genet. 197, 345-346.
5. Critchlow, S.E., and Jackson, S.P. (1998). DNA end-joining: from yeast to man. Trends Biochem. Sci. 23, 394-398.
6. Curcio, M.J., and Garfinkel, D.J. (1991). Single-step selection for Ty1 element retrotransposition. Proc. Natl. Acad. Sci. USA 88, 936-940.
7. Curcio, M.J., and Garfinkel, D.J. (1994). Heterogeneous functional Ty1 elements are abundant in the Saccharomyces cerevisiae genome. Genetics 136, 1245-1259.
8. Curcio, M.J., and Garfinkel, D.J. (1999). New lines of host defense: inhibition of Ty1 retrotransposition by Fus3p and NER/TFIIH. Trends Genet. 15, 43-45.
9. Dombroski, B.A., Feng, Q., Mathias, S.L., Sassaman, D.M., Scott, A.F., Kazazian, H.H., and Boeke, J.D. (1994). An in vivo assay for the reverse transcriptase of human retrotransposon L1 in Saccharomyces cerevisiae. Mol. Cell. Biol. 14, 4485-4492.
10. Dynan, W.S., and Yoo, S. (1998). Interaction of Ku protein and DNA-dependent protein kinase catalytic subunit with nucleic acids. Nucleic Acids Res. 26, 1551-1559.
11. Elder, R.T., Loh, E.Y., and Davis, R.W. (1983). RNA from the yeast transposable element Ty1 has both ends in the direct repeats, a structure similiar to retrovirus RNA. Proc. Natl. Acad. Sci. USA 80, 2432-2436.
12. Farrely, F., and Butow, R.A. (1983). Rearranged mitochondrial genes in the yeast nuclear genome. Nature 301, 296-301.
13. Foury, F., Roganti, T., Lecrenier, N., and Purnelle, B. (1998). The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae. FEBS Lett. 440, 325-331.
14. Gabriel, A., and Boeke, J.D. (1991). Reverse transcriptase encoded by a retrotransposon from the trypanosomatid Crithidia fasciculata. Proc. Natl. Acad. Sci. USA 88, 9794-9798.
15. Gabriel, A., and Boeke, J.D. (1993). Retrotransposon reverse transcription. In Reverse Transcriptase, A.M. Skalka and S.P. Goff, eds. (Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press), pp. 275-328.
16. Gabriel, A., Yen, T.J., Schwartz, D.C., Smith, C.L., Boeke, J.D., Sollner-Webb, B., and Cleveland, D.W. (1990). A rapidly rearranging retrotransposon within the mini-exon gene locus of Crithidia fasciculata. Mol. Cell. Biol. 10, 615-624.
17. Gabriel, A., Willems, M., Mules, E.H., and Boeke, J.D. (1996). Replication infidelity during a single cycle of Ty1 retrotransposition. Proc. Natl. Acad. Sci. USA 93, 7767-7771.
18. Garfinkel, D.J., Boeke, J.D., and Fink, G.R. (1985). Ty element transposition: reverse transcriptase and virus-like particles. Cell 42, 507-517.
19. Heyman, T., Agoutin, B., Friant, S., Wilhelm, F.X., and Wilhelm, M.L. (1995). Plus-strand DNA synthesis of the yeast retrotransposon Ty1 is initiated at two sites, PPT1 next to the 3′ LTR and PPT2 within the pol gene. PPT1 is sufficient for Ty1 transposition. J. Mol. Biol. 253, 291-303.
20. Hoffman, C.S., and Winston, F. (1987). A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene 57, 267-272.
21. Hou, W., Russnak, R., and Platt, T. (1994). Poly(A) site selection in the yeast Ty retroelement requires an upstream region and sequence-specific titratable factor(s) in vitro. EMBO J. 13, 446-452.
22. Hyman, B.C., Cramer, J.H., and Rownd, R.H. (1982). Properties of a Saccharomyces cerevisiae mtDNA segment conferring high-frequency yeast transformation. Proc. Natl. Acad. Sci. USA 79, 1578-1582.
23. Kenna, M.A., Brachmann, C.B., Devine, S.E., and Boeke, J.D. (1998). Invading the yeast nucleus: a nuclear localization signal at the C terminus of Ty1 integrase is required for transposition in vivo. Mol. Cell. Biol. 18, 1115-1124.
24. Kim, J.M., Vanguri, S., Boeke, J.D., Gabriel, A., and Voytas, D.F. (1998). Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the Saccharomyces cerevisiae genome sequence. Genome Res. 8, 464-478.
25. Klinz, F.J., and Gallwitz, D. (1985). Size and position of intervening sequences are critical for the splicing efficiency of pre-mRNA in the yeast Saccharomyces cerevisiae. Nucleic Acids Res. 13, 3791-3804.
26. Lauermann, V., and Boeke, J.D. (1997). Plus strand strong-stop DNA transfer in yeast Ty retrotransposons. EMBO J. 16, 6603-6612.
27. Lauermann, V., Nam, K., Trambley, J., and Boeke, J.D. (1995). Plus-strand strong-stop DNA synthesis in retrotransposon Ty1. J. Virol. 69, 7845-7850.
28. Longo, V.D., Liou, L.L., Valentine, J.S., and Gralla, E.B. (1999). Mitochondrial Superoxide decreases yeast survival in stationary phase. Arch. Biochem. Biophys. 365, 131-142.
29. Louis, E.J., and Haber, J.E. (1991). Evolutionary recent transfer of a group I mitochondrial intron to telomere regions in Saccharomyces cerevisiae. Curr. Genet. 20, 411-415.
30. Moore, J.K., and Haber, J.E. (1996a). Capture of retrotransposon DNA at the sites of chromosomal double-strand breaks. Nature 383, 644-646.
31. Moore, J.K., and Haber, J.E. (1996b). Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double strand breaks in Saccharomyces cerevisiae. Mol. Cell. Biol. 16, 2164-2173.
32. Moore, S.P., Rinckel, L.A., and Garfinkel, D.J. (1998). A Ty1 integrase nuclear localization signal required for retrotransposition. Mol. Cell. Biol. 18, 1105-1114.
33. Mules, E.H., Uzun, O., and Gabriel, A. (1998a). In vivo Ty1 reverse transcription can generate replication intermediates with untidy ends. J. Virol. 72, 6490-6503.
34. Mules, E.H., Uzun, O., and Gabriel, A. (1998b). Replication errors during in vivo Ty1 transposition are linked to heterogeneous RNase H cleavage sites. Mol. Cell. Biol. 18, 1094-1104.
35. Paques, F., and Haber, J.E. (1999). Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 63, 349-404.
36. Paques, F., Leung, W.Y., and Haber, J.E. (1998). Expansions and contractions in a tandem repeat induced by double-strand break repair. Mol. Cell. Biol. 18, 2045-2054.
37. Parikh, V.S., Morgan, M.M., Scott, R., Clements, L.S., and Butow, R.A. (1987). The mitochondrial genotype can influence nuclear gene expression in yeast. Science 235, 576-580.
38. Rothstein, R. (1991). Targeting, disruption, replacement, and allele rescue: integrative DNA transformation in yeast. Methods Enzymol. 194, 281-301.
39. Salomon, S., and Puchta, H. (1998). Capture of genomic and T-DNA sequences during double-strand break repair in somatic plant cells. EMBO J. 17, 6086-6095.
40. Santangelo, G.M., and Tornow, J. (1997). A Saccharomyces cerevisiae mitochondrial DNA fragment activates Reg1p-dependent glucose-repressible transcription in the nucleus. Curr. Genet. 32, 389-398.
41. Sargent, R.G., Brenneman, M.A., and Wilson, J.H. (1997). Repair of site-specific double-strand breaks in a mammalian chromosome by homologous and illegitimate recombination. Mol. Cell. Biol. 17, 267-277.
42. Schiestl, R.H., Dominska, M., and Petes, T.D. (1993). Transformation of Saccharomyces cerevisiae with non-homologous DNA: illegitimate integration of transforming DNA into yeast chromosomes and in vivo ligation of transforming DNA to mitochondrial DNA sequences. Mol. Cell. Biol. 13, 2697-2705.
43. Schmitt, M.E., and Clayton, D.A. (1993). Conserved features of yeast and mammalian mitochondrial DNA replication. Curr. Opin. Genet. Dev. 3, 769-774.
44. Sherman, F., Fink, G.R., and Hicks, J.B. (1986). Methods in Yeast Genetics: A Laboratory Manual (Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press).
45. Sikorski, R.S., and Boeke, J.D. (1991). In vitro mutagenesis and plasmid shuffling: from cloned gene to mutant yeast. Methods Enzymol. 194, 302-329.
46. Sikorski, R.S., and Hieter, P. (1989). A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122, 19-27.
47. Spingola, M., Grate, L., Haussler, D., and Ares, M. (1999). Genomewide bioinformatics and molecular analysisi of introns in Saccharomyces cerevisiae. RNA 5, 221-234.
48. Teng, S.-C., and Gabriel, A. (1997). DNA repair by recycling reverse transcripts. Nature 386, 31-32.
49. Teng, S.-C., Kim, B., and Gabriel, A. (1996). Retrotransposon reverse transcriptase-mediated repair of chromosomal breaks. Nature 383, 641-644.
50. Thorsness, P.E., and Fox, T.D. (1990). Escape of DNA from mitochondria to the nucleus in Saccharomyces cerevisiae. Nature 346, 376-379.
51. Thorsness, P.E., and Fox, T.D. (1993). Nuclear mutations in Saccharomyces cerevisiae that affect the escape of DNA from mitochondria to the nucleus. Genetics 134, 21-28.
52. Thorsness, P.E., and Weber, E.R. (1996). Escape and migration of nucleic acids between chloroplasts, mitochondria, and the nucleus. Int. Rev. Cytology 165, 207-234.
53. Van de Water, N., Williams, R., Ockelford, P., and Browe, P. (1998). A 20.7 kb deletion within the factor VIII gene associated with LINE-1 element insertion. Thromb. Haemost. 79, 938-942.
54. Van Dyck, E., Stasiak, A.Z., Stasiak, A., and West, S.C. (1999). Binding of double-strand breaks in DNA by human Rad52 protein. Nature 398, 728-731.
55. Wilhelm, M., Heyman, T., Friant, S., and Wilhelm, F.-X. (1997). Heterogeneous terminal structure of Ty1 and Ty3 reverse transcripts. Nucleic Acids Res. 25, 2161-2166.