Random-clone Strategy for Genomic Restriction Mapping in Yeast

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1986 Oct 1

PMID 3463999

Citations 133

Authors

M V Olson

J E Dutchik

M Y Graham

G M Brodeur

C Helms

M Frank

M Maccollin

R Scheinman

T Frank

Affiliations

Soon will be listed here.

Abstract

An approach to global restriction mapping is described that is applicable to any complex source DNA. By analyzing a single restriction digest for each member of a redundant set of lambda clones, a data base is constructed that contains fragment-size lists for all the clones. The clones are then grouped into subsets, each member of which is related to at least one other member by a significant overlap. Finally, a tree-searching algorithm seeks restriction maps that are consistent with the fragment-size lists for all the clones in each subset. The feasibility of the approach has been demonstrated by collecting data on 5000 lambda clones containing random 15-kilobase inserts of yeast DNA. It is shown that these data can be analyzed to produce regional maps of the yeast genome, extending in some cases for over 100 kilobases. In combination with hybridization probes to previously cloned genes, these local maps are already useful for defining the physical arrangement of closely linked genes. They may in the future serve as building blocks for the construction of a continuous global map.

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References

Struhl K, Stinchcomb D, Scherer S, Davis R . High-frequency transformation of yeast: autonomous replication of hybrid DNA molecules. Proc Natl Acad Sci U S A. 1979; 76(3):1035-9. PMC: 383183. DOI: 10.1073/pnas.76.3.1035. View

Hinnebusch A, Fink G . Positive regulation in the general amino acid control of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1983; 80(17):5374-8. PMC: 384258. DOI: 10.1073/pnas.80.17.5374. View

Rimm D, Horness D, Kucera J, Blattner F . Construction of coliphage lambda Charon vectors with BamHI cloning sites. Gene. 1980; 12(3-4):301-9. DOI: 10.1016/0378-1119(80)90113-4. View

Carle G, Olson M . An electrophoretic karyotype for yeast. Proc Natl Acad Sci U S A. 1985; 82(11):3756-60. PMC: 397866. DOI: 10.1073/pnas.82.11.3756. View

Coulson A, Sulston J, Brenner S, Karn J . Toward a physical map of the genome of the nematode Caenorhabditis elegans. Proc Natl Acad Sci U S A. 1986; 83(20):7821-5. PMC: 386814. DOI: 10.1073/pnas.83.20.7821. View

Karn J, Brenner S, Barnett L, Cesareni G . Novel bacteriophage lambda cloning vector. Proc Natl Acad Sci U S A. 1980; 77(9):5172-6. PMC: 350019. DOI: 10.1073/pnas.77.9.5172. View

Montgomery D, Boss J, McAndrew S, Marr L, Walthall D, Zitomer R . The molecular characterization of three transcriptional mutations in the yeast iso-2-cytochrome c gene. J Biol Chem. 1982; 257(13):7756-61. View

MORTIMER R, JOHNSTON J . Genealogy of principal strains of the yeast genetic stock center. Genetics. 1986; 113(1):35-43. PMC: 1202798. DOI: 10.1093/genetics/113.1.35. View

MORTIMER R, Schild D . Genetic map of Saccharomyces cerevisiae, edition 9. Microbiol Rev. 1985; 49(3):181-213. PMC: 373033. DOI: 10.1128/mr.49.3.181-213.1985. View

10.

Rose M, GRISAFI P, Botstein D . Structure and function of the yeast URA3 gene: expression in Escherichia coli. Gene. 1984; 29(1-2):113-24. DOI: 10.1016/0378-1119(84)90172-0. View

11.

Loenen W, Brammar W . A bacteriophage lambda vector for cloning large DNA fragments made with several restriction enzymes. Gene. 1980; 10(3):249-59. DOI: 10.1016/0378-1119(80)90054-2. View

12.

Gray A, Beecher D, Olson M . Computer-based image analysis of one-dimensional electrophoretic gels used for the separation of DNA restriction fragments. Nucleic Acids Res. 1984; 12(1 Pt 2):473-91. PMC: 321064. DOI: 10.1093/nar/12.1part2.473. View

13.

Maine G, Surosky R, Tye B . Isolation and characterization of the centromere from chromosome V (CEN5) of Saccharomyces cerevisiae. Mol Cell Biol. 1984; 4(1):86-91. PMC: 368661. DOI: 10.1128/mcb.4.1.86-91.1984. View

14.

Lauer G, Roberts T, Klotz L . Determination of the nuclear DNA content of Saccharomyces cerevisiae and implications for the organization of DNA in yeast chromosomes. J Mol Biol. 1977; 114(4):507-26. DOI: 10.1016/0022-2836(77)90175-9. View

15.

Steinmetz M, Stephan D, Fischer Lindahl K . Gene organization and recombinational hotspots in the murine major histocompatibility complex. Cell. 1986; 44(6):895-904. DOI: 10.1016/0092-8674(86)90012-7. View

16.

Bouche J, Gelugne J, Louarn J, Louarn J, Kaiser K . Relationships between the physical and genetic maps of a 470 x 10(3) base-pair region around the terminus of Escherichia coli K12 DNA replication. J Mol Biol. 1982; 154(1):21-32. DOI: 10.1016/0022-2836(82)90414-4. View

17.

Bender W, Spierer P, Hogness D . Chromosomal walking and jumping to isolate DNA from the Ace and rosy loci and the bithorax complex in Drosophila melanogaster. J Mol Biol. 1983; 168(1):17-33. DOI: 10.1016/s0022-2836(83)80320-9. View

18.

Helms C, Graham M, Dutchik J, Olson M . A new method for purifying lambda DNA from phage lysates. DNA. 1985; 4(1):39-49. DOI: 10.1089/dna.1985.4.39. View

19.

Hinnebusch A . Evidence for translational regulation of the activator of general amino acid control in yeast. Proc Natl Acad Sci U S A. 1984; 81(20):6442-6. PMC: 391940. DOI: 10.1073/pnas.81.20.6442. View