An efficient DNA sequencing strategy based on the bacteriophage Mu in vitro DNA transposition reaction

Genome Research

Volumn 9, Issue 3, 1999, Pages 308-315

  Haapa, Saija ^a   Suomalainen, Sini ^a   Eerikäinen, Simo ^a   Airaksinen, Matti ^a   Paulin, Lars ^a   Savilahti, Harri ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

CHLORAMPHENICOL ACETYLTRANSFERASE; PLASMID DNA; PRIMER DNA;

ARTICLE; BACTERIOPHAGE MU; CLONE; DNA SEQUENCE; DNA TEMPLATE; DNA TRANSPOSITION; ESCHERICHIA COLI; EXON; GENE INSERTION; GENOME; IN VITRO STUDY; MARKER GENE; METHODOLOGY; MOUSE; NONHUMAN; PLASMID; PRIORITY JOURNAL; SEQUENCE ANALYSIS; TRANSPOSON;

AMINO ACID SEQUENCE; BACTERIOPHAGE MU; DNA TRANSPOSABLE ELEMENTS; MOLECULAR SEQUENCE DATA; PHYSICAL CHROMOSOME MAPPING; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS); ENTEROBACTERIA PHAGE MU; ESCHERICHIA COLI; FELIS CATUS;

EID: 0032897710     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (41)

1. Adachi, T., M. Mizuuchi, E.A. Robinson, E. Appella, M.H. O'Dea, M. Gellert, and K. Mizuuchi. 1987. DNA sequence of the E. coli gyrB gene: Application of a new sequencing strategy. Nucleic Acids Res. 15: 771-784.
2. Adzuma, K. and K. Mizuuchi. 1988. Target immunity of Mu transposition reflects a differential distribution of MuB protein. Cell 53: 257-266.
3. _. 1989. Interaction of proteins located at a distance along DNA: Mechanism of target immunity in the Mu DNA strand-transfer reaction. Cell 57: 41-47.
4. Allet, B. 1979. Mu insertion duplicates a 5 base pair sequence at the host inserted site. Cell 16: 123-129.
5. Ansorge, W., H. Voss, and J. Zimmermann. 1997. DNA sequencing strategies: Automated and advanced approaches. John Wiley & Sons Inc., New York, NY.
6. Ash, C. 1997. Year of the genome. Trends Microbiol. 5: 135-139.
7. Ausubel, F.M., R. Brent, R.E. Kingston, D.D. Moore, J.G. Seidman, J.A. Smith, and K. Struhl. 1989. Curr. Prot. Mol. Biol. 1: 1.8.4.-1.8.10.
8. Baker, T.A. and K. Mizuuchi. 1992. DNA-promoted assembly of the active tetramer of the Mu transposase. Genes & Dev. 6: 2221-2232.
9. Baker, T.A., M. Mizuuchi, H. Savilahti, and K. Mizuuchi. 1993. Division of labor among monomers within the Mu transposase tetramer. Cell 74: 723-733.
10. Beck, S. and P. Sterk. 1998. Genome-scale DNA sequencing: Where are we? Curr. Opin. Biotechnol. 9: 116-120.
11. Berg, C.M., G. Wang, L.D. Straughbaugh, and D.E. Berg. 1993. Transposon-facilitated sequencing of DNAs cloned in plasmids. Methods Enzymol. 218: 279-306.
12. Bonfield, J.K., K.F. Smith, and R. Staden. 1995. A new DNA sequence assembly program. Nucleic Acids Res. 23: 4992-4999.
13. Braiterman, L.T. and J.D. Boeke. 1994. In vitro integration of retrotransposon Ty1: A direct physical assay. Mol. Cell. Biol. 14: 5719-5730.
14. Chaconas, G., B.D. Lavoie, and M.A. Watson. 1996. DNA transposition: Jumping gene machine, some assembly required. Curr. Biol. 6: 817-820.
15. Craigie, R. and K. Mizuuchi. 1986. Role of DNA topology in Mu transposition: Mechanism of sensing the relative orientation of two DNA segments. Cell 45: 793-800.
16. _. 1987. Transposition of Mu DNA: Joining of Mu to target DNA can be uncoupled from cleavage at the ends of Mu. Cell 51: 493-501.
17. Devine, S.E and J.D. Boeke. 1994. Efficient integration of artificial transposons into plasmid targets in vitro: A useful tool for DNA mapping, sequencing and genetic analysis. Nucleic Acids Res. 22: 3765-3772.
18. Devine, S.E., S.L. Chissoe, Y. Eby, R.K. Wilson, and J.D. Boeke. 1997. A Transposon-based strategy for sequencing repetitive DNA in eukaryotic genomes. Genome Res. 7: 551-563.
19. Eichinger, D.J. and J.D. Boeke. 1988. The DNA intermediate in yeast Ty1 element transposition copurifies with virus-like particles: Cell-free Ty1 transposition. Cell 54: 955-966.
20. _. 1990. A specific terminal structure is required for Ty1 transposition. Genes & Dev. 4: 324-330.
21. Fraser, C.M. and R.D. Fleischmann. 1997. Strategies for whole microbial genome sequencing and analysis. Electrophoresis 18: 1207-1216.
22. Holmes, D.S. and M. Quigley. 1981. A rapid boiling method for the preparation of bacterial plasmids. Anal. Biochem. 114: 193-197.
23. Hunkapiller, T., R.J. Kaiser, B.F. Koop, and L. Hood. 1991. Large-scale and automated DNA sequence determination. Science 254: 59-67.
24. Ji, H., D.P. Moore, M.A. Blomberg, L.T. Braiterman, D.F. Voytas, G. Natsoulis, and J.D. Boeke. 1993. Hotspots for unselected Ty1 transposition events on yeast chromosome III are near tRNA genes and LTR sequences. Cell 73: 1007-1018.
25. Kahmann, R. and D. Kamp. 1979. Nucleotide sequences of the attachment sites of bacteriophage Mu DNA. Nature 280: 247-250.
26. Kasai, H., S. Isono, M. Kitakawa, J. Mineno, H. Akiyama, D.M. Kurnit, D.E. Berg, and K. Isono. 1992. Efficient large-scale sequencing of the Escherichia coli genome: Implementation of a transposon- and PCR-based strategy for the analysis of ordered lambda phage clones. Nucleic Acids Res. 20: 6509-6515.
27. Koonin, E.V. 1997. Big time for small genomes. Genome Res. 7: 418-421.
28. Lavoie, B.D. and G. Chaconas. 1996. Transposition of phage Mu. Curr. Top. Microbiol. Immunol. 204: 83-99.
29. Lavoie, B.D., B.S. Chan, R.G. Allison, and G. Chaconas. 1991. Structural aspects of a higher order nucleoprotein complex: Induction of an altered DNA structure at the Mu-host junction of the Mu type 1 transpososome. EMBO J. 10: 3051-3059.
30. Miller, J.H. 1992. A short course in bacterial genetics. A laboratory manual and handbook for Escherichia coli and related bacteria. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
31. Mizuuchi, K. 1992a. Transpositional recombination: Mechanistic insights from studies of Mu and other elements. Annu. Rev. Biochem. 61: 1011-1051.
32. _. 1992b. Polynucleotidyl transfer reactions in transpositional DNA recombination. J. Biol. Chem. 267: 21273-21276.
33. Mizuuchi, M. and K. Mizuuchi. 1989. Efficient Mu transposition requires interaction of transposase with a DNA sequence at the Mu operator: Implications for regulation. Cell 58: 399-408.
34. _. 1993. Target site selection in transposition of phage Mu. Cold Spring Harbor Symp. Quant. Biol. 58: 515-523.
35. Payne, J.A., T.J. Stevenson, and L.F. Donaldson. 1996. Molecular characterization of a putative K-Cl cotransporter in rat brain. A neuronal-specific isoform. J. Biol. Chem. 271: 16245-16252.
36. Phadnis, S.H., H.V. Huang, and D.E. Berg. 1989. Tn5supF, a 264-base-pair transposon derived from Tn5 for insertion mutagenesis and sequencing DNAs cloned in phage λ. Proc. Natl. Acad. Sci. 86: 5908-5912.
37. Sambrook, J., E.F. Fritsch, and T. Maniatis. 1989. Molecular cloning. A laboratory manual. 2nd edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
38. Savilahti, H. and K. Mizuuchi. 1996. Mu transpositional recombination: Donor DNA cleavage and strand transfer in trans by the Mu transposase. Cell 85: 271-280.
39. Savilahti, H., P.A. Rice, and K. Mizuuchi. 1995. The phage Mu transpososome core: DNA requirements for assembly and function. EMBO J. 14: 4893-4903.
40. Strathmann, M., B.A. Hamilton, C.A. Mayeda, M.I. Simon, E.M. Meyerowitz, and M.J. Palazzolo. 1991. Transposon-facilitated DNA sequencing. Proc. Natl. Acad. Sci. 88: 1247-1250.
41. Surette, M.G., S.J. Buch, and G. Chaconas. 1987. Transpososomes: Stable protein-DNA complexes involved in the in vitro transposition of bacteriophage Mu DNA. Cell 49: 253-262.