Journal home
Advance online publication
Current issue
Archive
Press releases
Free Association (blog)
Supplements
Focuses
Guide to authors
Online submissionOnline submission
For referees
Free online issue
Contact the journal
Subscribe
Advertising
work@npg
Reprints and permissions
About this site
For librarians
 
NPG Resources
Nature
Nature Biotechnology
Nature Cell Biology
Nature Medicine
Nature Methods
Nature Reviews Cancer
Nature Reviews Genetics
Nature Reviews Molecular Cell Biology
news@nature.com
Nature Conferences
RNAi Gateway
NPG Subject areas
Biotechnology
Cancer
Chemistry
Clinical Medicine
Dentistry
Development
Drug Discovery
Earth Sciences
Evolution & Ecology
Genetics
Immunology
Materials Science
Medical Research
Microbiology
Molecular Cell Biology
Neuroscience
Pharmacology
Physics
Browse all publications
Article
Nature Genetics  6, 84 - 89 (1994)
doi:10.1038/ng0194-84

A new bacteriophage P1−derived vector for the propagation of large human DNA fragments

Panayiotis A. loannou1, 4, Chris T. Amemiya1, 5, Jeffrey Garnes1, Peter M. Kroisel1, 6, Hiroaki Shizuya2, Chira Chen1, 3, Mark A. Batzer1 & Pieter J. de Jong1, 3, 7

  1Human Genome Center L-452, Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California 94551, USA

  2Division of Biology, 147-75, California Institute of Technology, Pasadena, California 91125, USA

  3Human Genetics Department, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, New York 14263, USA

  4Current address: The Cyprus Institute of Neurology and Genetics, P.O. Box 3462, Nicosia, Cyprus

  5Current address: Center for Human Genetics, Boston University School of Medicine, 80 East Concord St, Boston, Massachusetts 02118, USA

  6Current address: Department of Medical Biology and Human Genetics, Harrachgasse 21/8, A-8010, Graz, Austria

  7Correspondence should be addressed to P.J.d.J. at Roswell Park Cancer Institute

We have designed a P1 vector (pCYPAC−1) for the introduction of recombinant DNA into E. coli using electroporation procedures. The new cloning system, P1−derived arteficial chromosomes (PACs), was used to establish an initial 15,000 clone library with an average insert size of 130−150 kilobase pairs (kb). No chimaerism has been observed in 34 clones, by fluorescence in situ hybridization. Similarly, no insert instability has been observed after extended culturing, for 20 clones. We conclude that the PAC cloning system will be useful in the mapping and detailed analysis of complex genomes.

REFERENCES
  1. Collins, J. & Hohn, B. Cosmids: a type of plasmid gene-cloning vector that is packageable in vitro in bacteriophage lambda heads. Proc. natn. Acad. Sci. U.S.A. 75, 4242−4246 (1978). | ChemPort |
  2. Harrison-Lavoie, K.J., John, R.M., Porteous, D.J. & Little, P.F. A cosmid clone map derived from a small region of human chromosome 11. Genomics 5, 501−509 (1989). | PubMed  | ChemPort |
  3. Craig, A.G., Nizetlc, D., Hoheisel, J.D., Zehetner, G. & Lehrach, H. Ordering of cosmid clones covering the herpes simplex virus type I (HSV-I) genome:a test case for fingerprinting by hybridisation. Nucl. Acids Res. 18, 2653−2660 (1990). | PubMed  | ISI | ChemPort |
  4. Stallings, R.L. et al. Physical mapping of human chromosomes by repetitive sequence fingerprinting. Proc. natn. Acad. .Sci. U.S.A. 87, 6218−6222 (1990). | ChemPort |
  5. Trask, B.J. et al. Fluorescence in situ hybridization mapping of human chromosome 19: cytogenetic band location of 540 cosmids and 70 genes or DNA markers. Genomics 15, 133−145 (1993). | Article | PubMed  | ISI | ChemPort |
  6. Burke, D.T., Carle, G.F. & Olson, M.V. Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors. Science 236, 806−812 (1987). | PubMed  | ISI | ChemPort |
  7. Schlessinger, D. et al. Yeast artificial chromosome-based genome mapping: some lessons from Xq24−q28. Genomics 11, 783−793 (1991). | PubMed  | ISI | ChemPort |
  8. Larin, Z., Monaco, A.P. & Lehrach, H. Yeast artificial chromosome libraries containing large inserts from mouse and human DNA. Proc. natn. Acad. Sci. U.S.A. 88, 4123−4127 (1991). | ChemPort |
  9. Chumakov, I.M. et al. Continuum of overlapping clones spanning the entire human chromosome-21q. Nature 359, 380−387 (1992). | Article | PubMed  | ISI | ChemPort |
  10. Foote, S., Vollrath, D., Hilton, A. & Page, D.C. The human Y-chromosome — overlapping clones spanning the euchromatlc region. Science 258, 60−66 (1992). | PubMed  | ISI | ChemPort |
  11. Maier, E. et al. Complete coverage of the Schizosaccaromyces-pombe genome in yeast artificial chromosomes. Nature Genet. 1, 273−277 (1992). | Article | PubMed  | ISI | ChemPort |
  12. Fuscoe, J.C., MoNinch, J.S., Collins, C.C. & VanDilla, M. Human chromosome-specific DNA libraries: construction and purity analysis. Cytogenet. cell Genet. 50, 211−215 (1989). | PubMed  | ISI | ChemPort |
  13. De Jong, P.J. et al. Human chromosome-specific partial digest libraries in lambda and cosmid vectors. Cytogenet. cell Genet. 51, 985 (1989).
  14. Nizetic, D. et al. Construction, arraying, and high-density screening of large insert libraries of human chromosomes X and 21: their potential use as reference libraries. Proc. natn. Acad.Sci. U.S.A. 88, 3233−3237 (1991). | ChemPort |
  15. Yokobata, K., Trenchak, B. & de Jong, P.J. Rescue of unstable cosmids by in vitro packaging. Nucl. Acids Res. 19, 403−404 (1991). | PubMed  | ISI | ChemPort |
  16. Kim, U.J., Shizuya, H., de Jong, P.J., Birren, B. & Simon, M.I. Stable propagation of cosmid sized human DNA inserts in an F factor based vector. Nucl. Acids Res. 20, 1083−1085 (1992). | PubMed  | ISI | ChemPort |
  17. Burke, D.T. & Olson, M.V. Preparation of clone libraries in yeast artificial chromosome vectors. Meth. Enzymol. 194, 251−270 (1991). | Article | PubMed  | ISI | ChemPort |
  18. Dausset, J. et al. The CEPH YAC library. Behring Institute Mitteilungen Apr., 13−20 (1992). | PubMed  | ChemPort |
  19. Green, E.D., Riethman, H.C., Dutchik, J.E. & Olson, M.V. Detection and characterization of chimeric yeast artificial chromosome clones. Genomics 11, 658−659. | PubMed  | ChemPort |
  20. Bates, G.P. et al. Characterization of a yeast artificial chromosome contig spanning the Huntington's disease gene candidate region. Nature Genet. 1, 180−187 (1992). | Article | PubMed  | ISI | ChemPort |
  21. Baldini, A. et al. Chromosomal assignment of human YAC clones by fluorescence in situ hybridization: use of single-yeast-colony PCR and multiple labeling. Genomics 14, 181−184 (1992). | PubMed  | ISI | ChemPort |
  22. Pierce, J.C., Sternberg, N., SauerB. A mouse genomic library in the bacteriophage P1 cloning system: Organization and characterization. Mamm. Genome 3, 550−558 (1992). | PubMed  | ISI | ChemPort |
  23. Hosoda, F., Nishimura, S., Uchida, H. & Ohki, M., An F-factor based cloning system for large DNA fragments. Nucl. Acids Res. 11, 3863−3869 (1990).
  24. Leonardo, E.D. & Sedivy, J.M. A new vector for cloning large eukaryotic DNA segments in Escherichia coli. Bio/Technology 8, 841−844 (1990). | PubMed  | ISI | ChemPort |
  25. Shizuya, H. et al. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia-coli using an F-factor-based vector. Proc. natn. Acad. Sci. U.S.A. 89, 8794−8797 (1992). | ChemPort |
  26. Rao, V.B., Thaker, V. & Black, L.W. A phage T4 in vitro packaging system for cloning long DNA molecules. Gene 113, 25−33 (1992). | Article | PubMed  | ISI | ChemPort |
  27. Sternberg, N., Ruether, J. & de Riel, K. Generation of a 50, 000-member human DNA library with an average DNA insert size of 75−100 kbp in a bacteriophage P1 cloning vector. New Biologist 2, 151−162 (1990). | PubMed  | ChemPort |
  28. Koppes, L.J.H., F-plasmid replication in Escherichia-coli K-12. J. Bacteriol. 174, 2121−2123 (1992). | PubMed  | ISI | ChemPort |
  29. Pierce, J.C., Sauer, B. & Sternberg, N. A positive selection vector for cloning high molecular weight DNA by the bacteriophage P1 system: improved cloning efficacy. Proc. natn. Acad. Sci. U.S.A. 89, 2056−2060 (1992). | ChemPort |
  30. Hanahan, D., Jessee, J. & Bloom, F.R. Plasmid transformation of Escherichia-coli and other bacteria. Meth. Enzymol. 204, 63−113 (1991). | Article | PubMed  | ISI | ChemPort |
  31. Grant, S.G., Jessee, J., Bloom, F.R. & Hanahan, D. Differential plasmid rescue from transgenic mouse DNAs into Escherichia-coli methylation-restriction mutants. Proc. natn. Acad. Sci. U.S.A. 87, 4645−4649 (1990). | ChemPort |
  32. Neil, D.L. et al. Structural instability of human tandemly repeated DNA sequences cloned in yeast artificial chromosome vectors. Nucl. Acids. Res. 18, 1421−1428 (1991). | ISI |
  33. Aslanidis, C. et al. Cloning of the essential myotonlc dystrophy region and mapping of the putative defect. Nature 355, 548−551 (1992). | ChemPort |
  34. Vilageliu, L. & Tyler-Smith, C. Structural instability of YAC clones and the use of recombinant-deficient yeast host strains. In Techniques for the Analysis of Complex Genomes (ed. Anand, R.) 93−112 (Academic Press, New York, 1992).
  35. Chartier, F.L. et al. Construction of a mouse yeast artificial chromosome library in a recombination-deficient strain of yeast. Nature Genet. 1, 132−136. | PubMed  | ChemPort |
  36. Bellanne-Chantelot, C. et al. Mapping the whole human genome by fingerprinting yeast artificial chromosomes. Cell 70, 1059−1068 (1992). | Article | PubMed  | ISI | ChemPort |
  37. Parimoo, S., Patanjali, S.R., Shukla, H., Chaplin, D.D. & Weissman, S.M. cDNA selection: efficient PCR approach for the selection of cDNAs encoded in large chromosomal DNA fragments. Proc. natn. Acad. Sci. U.S.A. 88, 9623−9627 (1991). | ChemPort |
  38. Morgan, J.G., Dolganov, G.M., Robbins, S.E., Hinton, L.M. & Lovett, M. The selective isolation of novel cDNAs encoded by the regions surrounding the human interleukin 4 and 5 genes. Nucl. Acids Res. 20, 5173−5179 (1992). | PubMed  | ISI | ChemPort |
  39. Duyk, G.M., Kim, S.W., Myers, R.M. & Cox, D.R. Exon trapping: a genetic screen to identify candidate transcribed sequences in cloned mammalian genomic DNA. Proc. natn. Acad. Sci. U.S.A. 87, 8995−8999 (1990). | ChemPort |
  40. Buckler, A.J. et al. Exon amplification: astrategy to isolate mammalian genes based on RNA splicing. Proc. natn. Acad. Sci. U.S.A. 88, 4005−4009 (1991). | ChemPort |
  41. Larin, Z. & Lehrach, H. Yeast artificial chromosomes: an alternative approach to the molecular analysis of mouse developmental mutations. Genetical Research 56, 203−208 (1990). | PubMed  | ISI | ChemPort |
  42. Shedl, A., Montoliu, L., Kelsey, G. & Shultz, G. A yeast artificial chromosome covering the tyrosinase gene confers copy number-dependent expression In transgenic mice. Nature 362, 258−261 (1993). | Article | PubMed  | ISI | ChemPort |
  43. Strauss, W.M. et al. Germ line transmission of a yeast artificial chromosome spanning the murine alpha 1 (l) collagen locus. Science 259, 1904−1907 (1993). | PubMed  | ISI | ChemPort |
  44. Sambrook, J., Fritsch, E.F. & Maniatis, T. Molecular Cloning , a Laboratory Manual 2nd edn. (Cold Spring Harbor Laboratory press, New York 1989).
  45. Birnboim, H.C. & Doly, J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucl. Acids Res. 7, 1513−1523 (1979). | PubMed  | ISI | ChemPort |
  46. Kroisel, P.M., loannou, P.A. & de Jong, P.J. PCR probes for chromosomal in situ hybridization of large-insert bacterial recombinants. Cytogenet. cell Genet. 65, 97−100 (1994). | PubMed  | ISI | ChemPort |
  47. Olsen, A.S. et al. Automated production of high density cosmid and YAC colony filters with a robotic workstation. BioTechniques 14, 116−123 (1993). | PubMed  | ISI | ChemPort |
 Top
 Top
Abstract
Previous | Next
Table of contents
Download PDFDownload PDF
Send to a friendSend to a friend
Save this linkSave this link

Open Innovation Challenges

naturejobs

References
Export citation
Export references
natureproducts

Search buyers guide:

 
ADVERTISEMENT
 
Nature Genetics
ISSN: 1061-4036
EISSN: 1546-1718
Journal home | Advance online publication | Current issue | Archive | Press releases | Supplements | Focuses | For authors | Online submission | Permissions | For referees | Free online issue | About the journal | Contact the journal | Subscribe | Advertising | work@npg | naturereprints | About this site | For librarians
Nature Publishing Group, publisher of Nature, and other science journals and reference works©1994 Nature Publishing Group | Privacy policy