New strategy for mapping the human genome based on a novel procedure for construction of jumping libraries

Eugene R. Zabarovsky, Ferenc Boldog, Rikard Erlandsson, Vladimir I. Kashuba, Rando L. Allikmets, Zoltan Marcsek, Lev L. Kisselev, Eric Stanbridge, George Klein, Janos Sumegi, Gösta Winberg

Research output: Contribution to journalArticle

36 Citations (Scopus)

Abstract

A novel procedure for construction of jumping libraries is described. The essential features of this procedure are as follows: (1) two diphasmid vectors (λSK17 and λSK22) are simultaneously used in the library construction to improve representativity, (2) a partial filling-in reaction is used to eliminate cloning of artifactual jumping clones and to obviate the need for a selectable marker. The procedure has been used to construct a representative human NotI jumping library (220,000 independent recombinant clones) from the lymphoblastoid cell line CBMI-Ral-STO, which features a low level of methylation of its resident EBV genomes. A human chromosome 3-specific NotI jumping library (500,000 independent recombinant clones) from the human chromosome 3 × mouse hybrid cell line MCH 903.1 has also been constructed. Of these recombinant clones 50-80% represent jumps to the neighboring cleavable NotI site. With our previously published method for construction of linking libraries this procedure makes a new genome mapping strategy feasible. This strategy includes the determination of tagging sequences adjacent to NotI sites in random linking and jumping clones. Special features of the λSK17 and λSK22 vectors facilitate such sequencing. The STS (sequence tagged site) information obtained can be assembled by computer into a map representing the linear order of the NotI sites for a chromosome or for the entire genome. The computerized mapping data can be used to retrieve clones near a region of interest. The corresponding clones can be obtained from the panel of original clones, or necessary probes can be made from genomic DNA by PCR.

Original languageEnglish (US)
Pages (from-to)1030-1039
Number of pages10
JournalGenomics
Volume11
Issue number4
DOIs
StatePublished - Jan 1 1991

Fingerprint

Human Genome
Libraries
Clone Cells
Chromosomes, Human, Pair 3
Human Chromosomes
Sequence Tagged Sites
Genome
Cell Line
Hybrid Cells
Chromosome Mapping
Human Herpesvirus 4
Methylation
Sequence Analysis
Organism Cloning
Chromosomes
Polymerase Chain Reaction
DNA

ASJC Scopus subject areas

  • Genetics

Cite this

Zabarovsky, E. R., Boldog, F., Erlandsson, R., Kashuba, V. I., Allikmets, R. L., Marcsek, Z., ... Winberg, G. (1991). New strategy for mapping the human genome based on a novel procedure for construction of jumping libraries. Genomics, 11(4), 1030-1039. https://doi.org/10.1016/0888-7543(91)90029-E

New strategy for mapping the human genome based on a novel procedure for construction of jumping libraries. / Zabarovsky, Eugene R.; Boldog, Ferenc; Erlandsson, Rikard; Kashuba, Vladimir I.; Allikmets, Rando L.; Marcsek, Zoltan; Kisselev, Lev L.; Stanbridge, Eric; Klein, George; Sumegi, Janos; Winberg, Gösta.

In: Genomics, Vol. 11, No. 4, 01.01.1991, p. 1030-1039.

Research output: Contribution to journalArticle

Zabarovsky, ER, Boldog, F, Erlandsson, R, Kashuba, VI, Allikmets, RL, Marcsek, Z, Kisselev, LL, Stanbridge, E, Klein, G, Sumegi, J & Winberg, G 1991, 'New strategy for mapping the human genome based on a novel procedure for construction of jumping libraries', Genomics, vol. 11, no. 4, pp. 1030-1039. https://doi.org/10.1016/0888-7543(91)90029-E
Zabarovsky ER, Boldog F, Erlandsson R, Kashuba VI, Allikmets RL, Marcsek Z et al. New strategy for mapping the human genome based on a novel procedure for construction of jumping libraries. Genomics. 1991 Jan 1;11(4):1030-1039. https://doi.org/10.1016/0888-7543(91)90029-E
Zabarovsky, Eugene R. ; Boldog, Ferenc ; Erlandsson, Rikard ; Kashuba, Vladimir I. ; Allikmets, Rando L. ; Marcsek, Zoltan ; Kisselev, Lev L. ; Stanbridge, Eric ; Klein, George ; Sumegi, Janos ; Winberg, Gösta. / New strategy for mapping the human genome based on a novel procedure for construction of jumping libraries. In: Genomics. 1991 ; Vol. 11, No. 4. pp. 1030-1039.
@article{5387be01722b4cfab96fae5ff97258b4,
title = "New strategy for mapping the human genome based on a novel procedure for construction of jumping libraries",
abstract = "A novel procedure for construction of jumping libraries is described. The essential features of this procedure are as follows: (1) two diphasmid vectors (λSK17 and λSK22) are simultaneously used in the library construction to improve representativity, (2) a partial filling-in reaction is used to eliminate cloning of artifactual jumping clones and to obviate the need for a selectable marker. The procedure has been used to construct a representative human NotI jumping library (220,000 independent recombinant clones) from the lymphoblastoid cell line CBMI-Ral-STO, which features a low level of methylation of its resident EBV genomes. A human chromosome 3-specific NotI jumping library (500,000 independent recombinant clones) from the human chromosome 3 × mouse hybrid cell line MCH 903.1 has also been constructed. Of these recombinant clones 50-80{\%} represent jumps to the neighboring cleavable NotI site. With our previously published method for construction of linking libraries this procedure makes a new genome mapping strategy feasible. This strategy includes the determination of tagging sequences adjacent to NotI sites in random linking and jumping clones. Special features of the λSK17 and λSK22 vectors facilitate such sequencing. The STS (sequence tagged site) information obtained can be assembled by computer into a map representing the linear order of the NotI sites for a chromosome or for the entire genome. The computerized mapping data can be used to retrieve clones near a region of interest. The corresponding clones can be obtained from the panel of original clones, or necessary probes can be made from genomic DNA by PCR.",
author = "Zabarovsky, {Eugene R.} and Ferenc Boldog and Rikard Erlandsson and Kashuba, {Vladimir I.} and Allikmets, {Rando L.} and Zoltan Marcsek and Kisselev, {Lev L.} and Eric Stanbridge and George Klein and Janos Sumegi and G{\"o}sta Winberg",
year = "1991",
month = "1",
day = "1",
doi = "10.1016/0888-7543(91)90029-E",
language = "English (US)",
volume = "11",
pages = "1030--1039",
journal = "Genomics",
issn = "0888-7543",
publisher = "Academic Press Inc.",
number = "4",

}

TY - JOUR

T1 - New strategy for mapping the human genome based on a novel procedure for construction of jumping libraries

AU - Zabarovsky, Eugene R.

AU - Boldog, Ferenc

AU - Erlandsson, Rikard

AU - Kashuba, Vladimir I.

AU - Allikmets, Rando L.

AU - Marcsek, Zoltan

AU - Kisselev, Lev L.

AU - Stanbridge, Eric

AU - Klein, George

AU - Sumegi, Janos

AU - Winberg, Gösta

PY - 1991/1/1

Y1 - 1991/1/1

N2 - A novel procedure for construction of jumping libraries is described. The essential features of this procedure are as follows: (1) two diphasmid vectors (λSK17 and λSK22) are simultaneously used in the library construction to improve representativity, (2) a partial filling-in reaction is used to eliminate cloning of artifactual jumping clones and to obviate the need for a selectable marker. The procedure has been used to construct a representative human NotI jumping library (220,000 independent recombinant clones) from the lymphoblastoid cell line CBMI-Ral-STO, which features a low level of methylation of its resident EBV genomes. A human chromosome 3-specific NotI jumping library (500,000 independent recombinant clones) from the human chromosome 3 × mouse hybrid cell line MCH 903.1 has also been constructed. Of these recombinant clones 50-80% represent jumps to the neighboring cleavable NotI site. With our previously published method for construction of linking libraries this procedure makes a new genome mapping strategy feasible. This strategy includes the determination of tagging sequences adjacent to NotI sites in random linking and jumping clones. Special features of the λSK17 and λSK22 vectors facilitate such sequencing. The STS (sequence tagged site) information obtained can be assembled by computer into a map representing the linear order of the NotI sites for a chromosome or for the entire genome. The computerized mapping data can be used to retrieve clones near a region of interest. The corresponding clones can be obtained from the panel of original clones, or necessary probes can be made from genomic DNA by PCR.

AB - A novel procedure for construction of jumping libraries is described. The essential features of this procedure are as follows: (1) two diphasmid vectors (λSK17 and λSK22) are simultaneously used in the library construction to improve representativity, (2) a partial filling-in reaction is used to eliminate cloning of artifactual jumping clones and to obviate the need for a selectable marker. The procedure has been used to construct a representative human NotI jumping library (220,000 independent recombinant clones) from the lymphoblastoid cell line CBMI-Ral-STO, which features a low level of methylation of its resident EBV genomes. A human chromosome 3-specific NotI jumping library (500,000 independent recombinant clones) from the human chromosome 3 × mouse hybrid cell line MCH 903.1 has also been constructed. Of these recombinant clones 50-80% represent jumps to the neighboring cleavable NotI site. With our previously published method for construction of linking libraries this procedure makes a new genome mapping strategy feasible. This strategy includes the determination of tagging sequences adjacent to NotI sites in random linking and jumping clones. Special features of the λSK17 and λSK22 vectors facilitate such sequencing. The STS (sequence tagged site) information obtained can be assembled by computer into a map representing the linear order of the NotI sites for a chromosome or for the entire genome. The computerized mapping data can be used to retrieve clones near a region of interest. The corresponding clones can be obtained from the panel of original clones, or necessary probes can be made from genomic DNA by PCR.

UR - http://www.scopus.com/inward/record.url?scp=0026320044&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0026320044&partnerID=8YFLogxK

U2 - 10.1016/0888-7543(91)90029-E

DO - 10.1016/0888-7543(91)90029-E

M3 - Article

VL - 11

SP - 1030

EP - 1039

JO - Genomics

JF - Genomics

SN - 0888-7543

IS - 4

ER -