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Isolation of specific clones from nonarrayed BAC libraries through homologous recombination. J Biomed Biotechnol 2010; 2011:560124. [PMID: 20981149 PMCID: PMC2957146 DOI: 10.1155/2011/560124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 09/05/2010] [Indexed: 11/17/2022] Open
Abstract
We have developed a new approach to screen bacterial artificial chromosome (BAC) libraries by recombination selection. To test this method, we constructed an orangutan BAC library using an E. coli strain (DY380) with temperature inducible homologous recombination (HR) capability. We amplified one library segment, induced HR at 42°C to make it recombination proficient, and prepared electrocompetent cells for transformation with a kanamycin cassette to target sequences in the orangutan genome through terminal recombineering homologies. Kanamycin-resistant colonies were tested for the presence of BACs containing the targeted genes by the use of a PCR-assay to confirm the presence of the kanamycin insertion. The results indicate that this is an effective approach for screening clones. The advantage of recombination screening is that it avoids the high costs associated with the preparation, screening, and archival storage of arrayed BAC libraries. In addition, the screening can be conceivably combined with genetic engineering to create knockout and reporter constructs for functional studies.
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2
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Kurnit DM. Recombination-based assay (RBA) for screening bacteriophage lambda libraries. ACTA ACUST UNITED AC 2008; Chapter 6:Unit6.12. [PMID: 18265256 DOI: 10.1002/0471142727.mb0612s27] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The recombination-based assay represents a convenient way to screen a complex library constructed in bacteriophage lambda for homology to a given sequence cloned into a specially designed plasmid. The technique serves to screen a bacteriophage library rapidly and efficiently with a sequence cloned into a plasmid; counterselection then yields the gene product of interest with its plasmid carrier deleted. Because 10(6) to 10(7) plaque-forming units (pfu) may be screened using several petri dishes, and the homology for crossing-over need only be greater than 25 bp, the RBA represents an efficient way to screen complex lambda libraries rapidly for homology to a given sequence. In this procedure, a lambda library is screened using a specially designed plasmid carrying the desired target sequence. Recombinants arising from cross-over events between the plasmid and a bacteriophage carrying a corresponding region of homology are selected by their ability to grow on strain DM21. Growth of lambda on DM21 requires the presence of an allele encoded on the plasmid to suppress an amber mutation in the host strain that prevents lambda propagation. Recovery of the original phage carrying the target sequence requires a reversal of the homologous recombination event. This reversal occurs spontaneously, and is detected by PCR amplification using primers that flank the cloning site in the lambda vector.
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Affiliation(s)
- D M Kurnit
- University of Michigan Medical Center, Ann Arbor, Michigan, USA
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3
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Stewart GD, Kurnit DM. Recombination-based screening for genes on chromosome 21. AMERICAN JOURNAL OF MEDICAL GENETICS. SUPPLEMENT 2005; 7:115-9. [PMID: 2149937 DOI: 10.1002/ajmg.1320370723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In previous work, a reasonably large number of genes was found to be on chromosome 21. This frequency demands the creation of new techniques to investigate the transcription of this small human autosome, and to relate these findings to the phenotype of Down syndrome. Here we describe the elaboration of new vectors and hosts, which in conjunction with flow-sorted cosmid libraries of chromosome 21 and genic (cDNA) libraries of relevant human tissues, will permit us to examine transcription of chromosome 21.
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Affiliation(s)
- G D Stewart
- Howard Hughes Medical Institute, Department of Pediatrics, University of Michigan, Ann Arbor 48109-0650
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4
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Woltjen K, Bain G, Rancourt DE. Retro-recombination screening of a mouse embryonic stem cell genomic library. Nucleic Acids Res 2000; 28:E41. [PMID: 10756208 PMCID: PMC103314 DOI: 10.1093/nar/28.9.e41] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Targeted gene disruption is an important tool in molecular medicine, allowing for the generation of animal models of human disease. Conventional methods of targeting vector (TV) construction are difficult and represent a rate limiting step in any targeting experiment. We previously demonstrated that bacteriophage are capable of acting as TVs directly, obviating the requirement for 'rolling out' plasmids from primary phage clones and thus eliminating an additional, time consuming step. We have also developed methods which facilitate the construction of TVs using recombination. In this approach, modification cassettes and point mutations are shuttled to specific sites in phage TVs using phage-plasmid recombination. Here, we report a further improvement in TV generation using a recombination screening-based approach deemed 'retro-recombination screening' (RRS). We demonstrate that phage vectors containing specific genomic clones can be genetically isolated from a lambdaTK embryonic stem cell genomic library using a cycle of integrative recombination and condensation. By introducing the gam gene of bacteriophage lambda into the probe plasmid it is possible to select for positive clones which have excised the plasmid, thus returning to their native conformation following purification from the library. Rapid clone isolation using the RRS protocol provides another method by which the time required for TV construction may be further reduced.
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Affiliation(s)
- K Woltjen
- Southern Alberta Cancer Research Center, Department of Oncology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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5
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Merkulov GV, Boeke JD. Libraries of green fluorescent protein fusions generated by transposition in vitro. Gene X 1998; 222:213-22. [PMID: 9831655 DOI: 10.1016/s0378-1119(98)00503-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Two artificial transposons have been constructed that carry a gene encoding Green Fluorescent Protein and can be used for generating libraries of GFP fusions in a gene of interest. One such element, AT2GFP, can be used to generate GFP insertions in frame with the amino acid sequence of the protein of interest, with a stop codon at the end of the GFP coding sequence; AT2GFP also contains a selectable marker that confers trimethoprim resistance in bacteria. The second element, GS, can be used to generate tribrid GFP fusions because there is no stop codon in the GFP transposon, and the resulting fusion proteins contain the entire amino acid sequence encoded by the gene. The GS element consists of a gfp open reading frame and a supF amber suppressor tRNA gene; the supF portion of the GS transposon can be utilized as a selectable marker in bacteria. Its sequence contains a fortuitous open reading frame, and thus it can be translated continuously with the gfp amino acid sequence. As a target for GFP insertions, we used a plasmid carrying the native Ty1 retrotransposon of the yeast Sacharomyces cerevisiae. The resulting multiple GFP fusions to Ty1 capsid protein Gag and Ty1 integrase were useful in determining the cellular localization of these proteins. Libraries of GFP fusions generated by transposition in vitro represent a novel and potentially powerful method to study the cell distribution and cellular localization signals of proteins.
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Affiliation(s)
- G V Merkulov
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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6
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Khrebtukova I, Michaud EJ, Foster CM, Stark KL, Garfinkel DJ, Woychik RP. Utilization of microhomologous recombination in yeast to generate targeting constructs for mammalian genes. Mutat Res 1998; 401:11-25. [PMID: 9639665 DOI: 10.1016/s0027-5107(98)00053-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We have developed a new procedure utilizing microhomologous recombination in yeast to generate targeting constructs for producing targeted mutations in mice. This procedure is rapid and efficient, and should be directly applicable to all mammalian genes. Moreover, only minimal information about the locus being targeted is required. The feasibility of this approach was demonstrated by producing another allele of the mouse Tg737 polycystic kidney gene.
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Affiliation(s)
- I Khrebtukova
- Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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7
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Tanaka S, Tanaka Y, Isono K. Systematic mapping of autonomously replicating sequences on chromosome V of Saccharomyces cerevisiae using a novel strategy. Yeast 1996; 12:101-13. [PMID: 8686374 DOI: 10.1002/(sici)1097-0061(199602)12:2<101::aid-yea885>3.0.co;2-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We have developed a new procedure for easy and rapid identification of autonomously replicating sequences (ARSs) and have applied it to the analysis of chromosome V of Saccharomyces cerevisiae. The procedure makes use of the ordered lambda phage clone bank of this chromosome that we have constructed, and includes transposition of a mini-transposon and selection of transposon-containing derivatives, isolation of their DNA and circularization at their cos-ends, transformation of yeast cells with the circularized DNA, and scoring transformation frequency. The transposon used was derived from Tn5supF, contained the yeast LEU2 gene, and was placed, together with the hyperactive transposase gene, on a mini-F plasmid for stable maintenance in Escherichia coli K-12. Sixteen regions of chromosome V showing ARS activity were identified, of which 12 were newly found in this work. Thus, the procedure will be useful for systematic genomic scale analysis of ARSs in yeast and related organisms in which ordered clone banks have been established. The average distance between adjacent ARS-containing regions was approximately 40 kb. Two-dimensional gel electrophoretic analysis of chromosome replication indicated that one of the newly identified ARSs was functional as an actual in situ replication origin, at least under the conditions employed.
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Affiliation(s)
- S Tanaka
- Division of Bioscience, Postgraduate School of Science and Technology, Japan
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Miller AM, Savinelli EA, Couture SM, Hannigan GM, Han Z, Selden RF, Treco DA. Recombination walking: genetic selection of clones from pooled libraries of yeast artificial chromosomes by homologous recombination. Proc Natl Acad Sci U S A 1993; 90:8118-22. [PMID: 8367472 PMCID: PMC47299 DOI: 10.1073/pnas.90.17.8118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Recombination walking is based on the genetic selection of specific human clones from a yeast artificial chromosome (YAC) library by homologous recombination. The desired clone is selected from a pooled (unordered) YAC library, eliminating labor-intensive steps typically used in organizing and maintaining ordered YAC libraries. Recombination walking represents an efficient approach to library screening and is well suited for chromosome-walking approaches to the isolation of genes associated with common diseases.
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Affiliation(s)
- A M Miller
- Transkaryotic Therapies, Inc., Cambridge, MA 02139
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Guo W, Worley K, Adams V, Mason J, Sylvester-Jackson D, Zhang YH, Towbin JA, Fogt DD, Madu S, Wheeler DA. Genomic scanning for expressed sequences in Xp21 identifies the glycerol kinase gene. Nat Genet 1993; 4:367-72. [PMID: 8401584 DOI: 10.1038/ng0893-367] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Rapid genomic scanning methods are required to identify expressed sequences and we report an efficient, sensitive and specific approach which relies upon hybridization of an amplified, labeled cDNA library to digested cosmid DNA. We identified expressed sequences within a cosmid in the glycerol kinase (GK) "critical region" of Xp21 that had impressive similarity to prokaryotic GKs. We used this genomic sequence information to clone the human hepatic GK cDNA. Independent confirmation of the identity of this gene was obtained by functional complementation of GK deficient E. coli mutants with a construct containing the complete human X-linked GK coding sequence.
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Affiliation(s)
- W Guo
- Institute for Molecular Genetics, Baylor College of Medicine, Houston, Texas 77030
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10
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Hanzlik AJ, Osemlak-Hanzlik MM, Hauser MA, Kurnit DM. A recombination-based assay demonstrates that the fragile X sequence is transcribed widely during development. Nat Genet 1993; 3:44-8. [PMID: 8490653 DOI: 10.1038/ng0193-44] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
To identify transcribed sequences rapidly and efficiently, we have developed a recombination-based assay to screen bacteriophage lambda libraries for sequences that share homology with a given probe. This strategy determines analytically whether a given probe is transcribed in a given tissue at a given time of development, and may also be used to isolate preparatively the transcribed sequence free of the screening probe. We illustrate this technology for the fragile X sequence, demonstrating that it is transcribed ubiquitously in an 11 week fetus, in a variety of 20 week human fetal tissues, including brain, spinal cord, eye, liver, kidney and skeletal muscle, and in adult jejunum.
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Affiliation(s)
- A J Hanzlik
- University of Michigan Medical School, Howard Hughes Medical Institute, Ann Arbor 48109-0650
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11
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Kasai H, Isono S, Kitakawa M, Mineno J, Akiyama H, Kurnit DM, Berg DE, Isono K. 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 1992; 20:6509-15. [PMID: 1336178 PMCID: PMC334565 DOI: 10.1093/nar/20.24.6509] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We have developed a strategy for efficient sequence analysis of the genome of E. coli K-12 using insertions of a Tn5-derived mini-transposon into overlapping ordered lambda phage clones to provide universal primer-binding sites, and PCR amplification of DNA segments adjacent to the insertions. Transposon-containing clones were selected by blue plaque formation on a dnaBamber lacZamber E. coli strain. Insertion points every 0.5-1 kb were identified by 'analytical PCR' and segments between the transposon inserts and phage arms were amplified by 'preparative PCR' using one biotinylated and one non-biotinylated primer. Single strands of amplified DNA fragments were coupled to Streptoavidin-coated paramagnetic beads (Dynabeads M280) through their biotin tails, purified magnetically, and used as templates for fluorescence-based automatic nucleotide sequencing.
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Affiliation(s)
- H Kasai
- Postgraduate School, Faculty of Science, Kobe University, Japan
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12
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Neuwald AF, Krishnan BR, Brikun I, Kulakauskas S, Suziedelis K, Tomcsanyi T, Leyh TS, Berg DE. cysQ, a gene needed for cysteine synthesis in Escherichia coli K-12 only during aerobic growth. J Bacteriol 1992; 174:415-25. [PMID: 1729235 PMCID: PMC205732 DOI: 10.1128/jb.174.2.415-425.1992] [Citation(s) in RCA: 105] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The initial steps in assimilation of sulfate during cysteine biosynthesis entail sulfate uptake and sulfate activation by formation of adenosine 5'-phosphosulfate, conversion to 3'-phosphoadenosine 5'-phosphosulfate, and reduction to sulfite. Mutations in a previously uncharacterized Escherichia coli gene, cysQ, which resulted in a requirement for sulfite or cysteine, were obtained by in vivo insertion of transposons Tn5tac1 and Tn5supF and by in vitro insertion of resistance gene cassettes. cysQ is at chromosomal position 95.7 min (kb 4517 to 4518) and is transcribed divergently from the adjacent cpdB gene. A Tn5tac1 insertion just inside the 3' end of cysQ, with its isopropyl-beta-D-thiogalactopyranoside-inducible tac promoter pointed toward the cysQ promoter, resulted in auxotrophy only when isopropyl-beta-D-thiogalactopyranoside was present; this conditional phenotype was ascribed to collision between converging RNA polymerases or interaction between complementary antisense and cysQ mRNAs. The auxotrophy caused by cysQ null mutations was leaky in some but not all E. coli strains and could be compensated by mutations in unlinked genes. cysQ mutants were prototrophic during anaerobic growth. Mutations in cysQ did not affect the rate of sulfate uptake or the activities of ATP sulfurylase and its protein activator, which together catalyze adenosine 5'-phosphosulfate synthesis. Some mutations that compensated for cysQ null alleles resulted in sulfate transport defects. cysQ is identical to a gene called amtA, which had been thought to be needed for ammonium transport. Computer analyses, detailed elsewhere, revealed significant amino acid sequence homology between cysQ and suhB of E. coli and the gene for mammalian inositol monophosphatase. Previous work had suggested that 3'-phosphoadenoside 5'-phosphosulfate is toxic if allowed to accumulate, and we propose that CysQ helps control the pool of 3'-phosphoadenoside 5'-phosphosulfate, or its use in sulfite synthesis.
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Affiliation(s)
- A F Neuwald
- Department of Molecular Microbiology, Washington University Medical School, St. Louis, Missouri 63110-1093
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13
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Krishnan BR, Kersulyte D, Brikun I, Berg CM, Berg DE. Direct and crossover PCR amplification to facilitate Tn5supF-based sequencing of lambda phage clones. Nucleic Acids Res 1991; 19:6177-82. [PMID: 1659687 PMCID: PMC329118 DOI: 10.1093/nar/19.22.6177] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The 264 bp mini-transposon Tn5supF was constructed to sequence DNAs cloned in phage lambda without extensive shotgun subcloning or primer walking. Unique sequences near each transposon end serve as primer binding sites, and a supF gene is used to select transposition to lambda. We describe here PCR methods that facilitate Tn5supF-based sequencing. In a first pass, insertions are mapped relative to the ends of the cloned fragment using pairs of primers specific for vector DNA next to the cloning site and for a Tn5supF end. Most insertions not mapped in this step are near the center of the cloned fragment or in the vector arms, and are then mapped relative to the two innermost insertions by 'crossover' PCR. This involves amplification from primers on different DNA molecules, and generates hybrid DNA products whose lengths correspond to the distances between the two insertions. We routinely amplified more than 6 kb in direct PCR and 3 kb in crossover PCR; at the limit we amplified up to approximately 10 kb in direct PCR and approximately 6 kb in crossover PCR, but not reproducibly. Crossover PCR products were also obtained with insertions separated by only 200 bp, indicating that no rare sites are needed to switch templates. PCR products were purified by adsorption and then elution from glass slurry, and sequenced directly. Ladders of more than 400 bp were obtained from primer sites on each DNA strand; 2 kb was read from crossover PCR products, and showed that they were amplified with fidelity. In conclusion, direct and crossover PCR methods expedite transposon insertion mapping, and yield templates for accurate sequencing of both DNA strands.
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Affiliation(s)
- B R Krishnan
- Department of Molecular Biology, Washington University School of Medicine, St Louis, MO 63110
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14
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Brookes AJ, Porteous DJ. Coincident sequence cloning. Nucleic Acids Res 1991; 19:2609-13. [PMID: 2041738 PMCID: PMC328177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We describe a novel method, Coincident Sequence Cloning (CSC), which permits the selective recovery of common sequences shared between two complex and partially coincident DNA mixtures. We evaluate this method by integrating human DNA with DNA from a mouse-human somatic cell hybrid, and we recover exclusively human DNA products which are all represented in the hybrid genome. CSC strategies should be useful in addressing many highly complex problems in genome analysis.
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Affiliation(s)
- A J Brookes
- MRC Human Genetics Unit, Western General Hospital, Edinburgh, UK
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Hochgeschwender U, Brennan MB. Identifying genes within the genome: new ways for finding the needle in a haystack. Bioessays 1991; 13:139-44. [PMID: 1872824 DOI: 10.1002/bies.950130308] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- U Hochgeschwender
- Unit on Genomics, National Institute of Mental Health, Bethesda, MD 20892
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Phadnis SH, Kulakauskas S, Krishnan BR, Hiemstra J, Berg DE. Transposon Tn5supF-based reverse genetic method for mutational analysis of Escherichia coli with DNAs cloned in lambda phage. J Bacteriol 1991; 173:896-9. [PMID: 1846153 PMCID: PMC207086 DOI: 10.1128/jb.173.2.896-899.1991] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
An efficient method for systematic mutational analysis of the Escherichia coli genome was developed. It entails Tn5supF transposition to lambda-E. coli hybrid phage clones (Kohara library) and then transduction of recipient cells to Sup+. Essential and nonessential genes are distinguished by the ability of insertion mutant phage to form haploid versus only heterozygous partial diploid bacterial recombinants.
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Affiliation(s)
- S H Phadnis
- Department of Molecular Microbiology, Washington University Medical School, St. Louis, Missouri 63110
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