Caenorhabditis elegans reporter fusion genes generated by seamless modification of large genomic DNA clones

Nucleic Acids Research

Volumn 34, Issue 9, 2006, Pages

  Dolphin, Colin T ^b   Hope, Ian A ^a  

^a UNIVERSITY OF LEEDS   (United Kingdom)

^b KING'S COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; CAENORHABDITIS ELEGANS PROTEIN; DNA; GREEN FLUORESCENT PROTEIN; HYBRID PROTEIN; LUMINESCENT AGENT;

ARTICLE; CAENORHABDITIS ELEGANS; CARBOXY TERMINAL SEQUENCE; CELLULAR DISTRIBUTION; CONTROLLED STUDY; DNA FLANKING REGION; DNA MODIFICATION; FUNCTIONAL GENOMICS; FUSION GENE; GENE EXPRESSION; GENE INSERTION; GENE LOCATION; GENE LOCUS; GENE SEQUENCE; GENE TARGETING; GENETIC CODE; GENOME; MOLECULAR CLONING; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REPORTER GENE; RNA TRANSLATION; ANIMAL; BACTERIOPHAGE LAMBDA; GENE; GENETIC RECOMBINATION; GENETICS; GENOMICS; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; TRANSGENIC ANIMAL;

CAENORHABDITIS ELEGANS;

3' FLANKING REGION; 5' FLANKING REGION; ANIMALS; ANIMALS, GENETICALLY MODIFIED; BACTERIOPHAGE LAMBDA; BASE SEQUENCE; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; CLONING, MOLECULAR; DNA; GENE EXPRESSION; GENE TARGETING; GENES, HELMINTH; GENES, REPORTER; GENOME, HELMINTH; GENOMICS; GREEN FLUORESCENT PROTEINS; LUMINESCENT AGENTS; MOLECULAR SEQUENCE DATA; RECOMBINANT FUSION PROTEINS; RECOMBINATION, GENETIC;

EID: 33744820844     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl352     Document Type: Article

References (45)

1. C.elegans Sequencing Consortium (1998) Genome sequence of the nematode C.elegans: A platform for investigating biology. Science, 282, 2012-2018.
2. Kamath,R.S., Fraser,A.G., Dong,Y., Poulin,G., Durbin,R., Gotta,M., Kanapin,A., Le Bot,N., Moreno,S., Sohrmann,M. et al. (2003) Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature, 421, 231-237.
3. Sugimoto,A. (2004) High-throughput RNAi in Caenorhabditis elegans: genome-wide screens and functional genomics. Differentiation, 72, 81-91.
4. Ashrafi,K., Chang,F.Y., Watts,J.L., Fraser,A.G., Kamath,R.S., Ahringer,J. and Ruvkun,G. (2003) Genome-wide RNAi analysis of Caenorhabditis elegans fat regulatory genes. Nature, 421, 268-272.
5. Poulin,G., Nandakumar,R. and Ahringer,J. (2004) Genome-wide RNAi screens in Caenorhabditis elegans: Impact on cancer research. Oncogene, 23, 8340-8345.
6. Kim,S.K., Lund,J., Kiraly,M., Duke,K., Jiang,M., Stuart,J.M., Eizinger,A., Wylie,B.N. and Davidson,G.S. (2001) A gene expression map for Caenorhabditis elegans. Science, 293, 2087-2092.
7. Jones,S.J., Riddle,D.L., Pouzyrev,A.T., Velculescu,V.E., Hillier,L., Eddy,S.R., Stricklin,S.L., Baillie,D.L., Waterston,R. and Marra,M.A. (2001) Changes in gene expression associated with developmental arrest and longevity in Caenorhabditis elegans. Genome Res., 11, 1346-1352.
8. Holt,S.J. and Riddle,D.L. (2003) SAGE surveys C.elegans carbohydrate metabolism: Evidence for an anaerobic shift in the long-lived dauer larva. Mech. Ageing. Dev., 124, 779-800.
9. Zhang,Y., Ma,C., Delohery,T., Nasipak,B., Foat,B.C., Bounoutas,A., Bussemaker,H.J., Kim,S.K. and Chalfie,M. (2002) Identification of genes expressed in C.elegans touch receptor neurons. Nature, 418, 331-335.
10. Roy,P.J., Stuart,J.M., Lund,J. and Kim,S.K. (2002) Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature, 418, 975-979.
11. Tabara,H., Motohashi,T. and Kohara,Y. (1996) A multi-well version of in situ hybridization on whole mount embryos of Caenorhabditis elegans. Nucleic Acids Res., 24, 2119-2124.
12. Fire,A., Harrison,S.W. and Dixon,D. (1990) A modular set of lacZ fusion vectors for studying gene expression in Caenorhabditis elegans. Gene, 93, 189-198.
13. Hope,I.A., Stevens,J., Garner,A., Hayes,J., Cheo,D.L., Brasch,M.A. and Vidal,M. (2004) Feasibility of genome-scale construction of promoter: Reporter gene fusions for expression in Caenorhabditis elegans using a multisite gateway recombination system. Genome Res., 14, 2070-2075.
14. Dupuy,D., Li,Q.R., Deplancke,B., Boxem,M., Hao,T., Lamesch,P., Sequerra,R., Bosak,S., Doucette-Stamm,L., Hope,I.A. et al. (2004) A first version of the Caenorhabditis elegans Promoterome. Genome Res., 10B, 2169-2175.
15. Copeland,N.G., Jenkins,N.A. and Court,D.L. (2001) Recombineering: A powerful new tool for mouse functional genomics. Nature Rev. Genet., 2, 769-779.
16. Sambrook,J., Fritsch,E.F. and Maniatis,T. (1989) Molecular Cloning: A Laboratory Manual. 2nd Edn, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, Plainview, NY.
17. Lee,E.C., Yu,D., Martinez de Velasco,J., Tessarollo,L., Swing,D.A., Court,D.L., Jenkins,N.A. and Copeland,N.G. (2001) A highly efficient Escherichia coli-based chromosome engineering system adapted for recombinogenic targeting and subcloning of BAC DNA. Genomics, 73, 56-65.
18. Stavropoulos,T.A. and Strathdee,C.A. (2001) Synergy between tetA and rpsL provides high stringency positive and negative selection in bacterial artificial chromosome vectors. Genomics, 72, 99-104.
19. Yu,D., Ellis,H.M., Lee,E.C., Jenkins,N.A., Copeland,N.G. and Court,D.L. (2000) An efficient recombination system for chromosome engineering in Escherichia coli. Proc. Natl Acad. Sci. USA, 97, 5978-5983.
20. Sulston,J. and Hodgkin,J. (1988) Methods. In Wood,W.B. (ed.), The Nematode Caenorhabditis elegans. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, pp. 587-606.
21. Brenner,S. (1974) The genetics of Caenorhabditis elegans. Genetics, 77, 71-94.
22. Mello,C.C., Kramer,J.M., Stinchcomb,D. and Ambros,V. (1991) Efficient gene transfer in C.elegans: Extrachromosomal maintenance and integration of transforming sequences. EMBO J., 10, 3959-3970.
23. Hope,I.A. (1991) 'Promoter trapping' in Caenorhabditis elegans. Development, 113, 399-408.
24. Coulson,A., Sulston,A., Brenner,S. and Karn,J. (1986) Towards a physical map of the genome of the nematode Caenorhabditis elegans. Proc. Natl Acad. Sci. USA, 83, 7821-7825.
25. Datsenko,K.A. and Wanner,B.L. (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA, 97, 6640-6645.
26. Court,D.L., Swaminathan,S., Yu,D., Wilson,H., Baker,T., Bubunenko,M., Sawitzke,J. and Sharan,S.K. (2003) Mini-lambda: A tractable system for chromosome and BAC engineering. Gene, 315, 63-69.
27. Lederberg,J. (1951) Streptomycin resistance; a genetically recessive mutation. J. Bacteriol., 61, 549-550.
28. Kim,U.-J., Shizuya,H., de Jong,P.J., Birren,B. and Simon,M. (1992) Stable propagation of cosmid sized human DNA inserts in an F factor based vector. Nucleic Acids Res., 20, 1083-1085.
29. Petalcorin,M.I., Joshua,G.W., Agapow,P.M. and Dolphin,C.T. (2005) The fmo genes of Caenorhabditis elegans and C. briggsae: Characterisation, gene expression and comparative genomic analysis. Gene, 346, 83-96.
30. Garofalo,A., Rowlinson,M.C., Amambua,N.A., Hughes,J.M., Kelly,S.M., Price,N.C., Cooper,A., Watson,D.G., Kennedy,M.W. and Bradley,J.E. (2003) The FAR protein family of the nematode Caenorhabditis elegans. Differential lipid binding properties, structural characteristics, and developmental regulation. J. Biol. Chem., 278, 8065-8074.
31. Paupard,M.C., Miller,A., Grant,B., Hirsh,D. and Hall,D.H. (2001) Immuno-EM localization of GFP-tagged yolk proteins in C. elegans using microwave fixation. J. Histochem. Cytochem., 49, 949-956.
32. Hartley,J.L., Temple,G.F. and Brasch,M.A. (2000) DNA cloning using in vitro site-specific recombination. Genome Res., 10, 1788-1795.
33. Muyrers,J.P., Zhang,Y. and Stewart,A.F. (2001) Techniques: recombinogenic engineering - new options for cloning and manipulating DNA. Trends Biochem. Sci., 26, 325-331.
34. Court,D.L., Sawitzke,J.A. and Thomason,L.C. (2002) Genetic engineering using homologous recombination. Annu. Rev. Genet., 36, 361-388.
35. Zhang,Y., Buchholz,F., Muyrers,J.P. and Stewart,A.F. (1998) A new logic for DNA engineering using recombination in Escherichia coli. Nature Genet., 20, 123-128.
36. Polanowska,J., Martin,J.S., Fisher,R., Scopa,T., Rae,I. and Boulton,S.J. (2004) Tandem immunoaffinity purification of protein complexes from Caenorhabditis elegans. Biotechniques, 36, 778-782.
37. Cheeseman,I.M. and Desai,A. (2005) A combined approach for the localization and tandem affinity purification of protein complexes from metazoans. Sci. STKE., 266, 1.
38. Hobert,O. (2002) PCR fusion-based approach to create reporter gene constructs for expression analysis in transgenic C. elegans. Biotechniques, 32, 728-730.
39. Sassi,H.E., Renihan,S., Spence,A.M. and Cooperstock,R.L. (2005) Gene CATCHR-gene cloning and tagging for Caenorhabditis elegans using yeast homologous recombination: A novel approach for the analysis of gene expression. Nucleic Acids Res., 33, e163.
40. Reyrat,J.M., Pelicic,V., Gicquel,B. and Rappuoli,R. (1998) Counterselectable markers: Untapped tools for bacterial genetics and pathogenesis. Infect. Immun., 66, 4011-4017.
41. Jamsai,D., Orford,M., Nefedov,M., Fucharoen,S., Williamson,R. and Ioannou,P.A. (2003) Targeted modification of a human beta-globin locus BAC clone using GET recombination and an I-SceI counterselection cassette. Genomics, 82, 68-77.
42. Warming,S., Costantino,N., Court,D.L., Jenkins,N.A. and Copeland,N.G. (2005) Simple and highly efficient BAC recombineering using galK selection. Nucleic Acids Res., 33, e36.
43. Wong,Q.N., Ng,V.C., Lin,M.C., Kung,H.F., Chan,D. and Huang,J.D. (2005) Efficient and seamless DNA recombineering using a thymidylate synthase A selection system in Escherichia coli. Nucleic Acids Res., 33, e59.
44. Dunn,W., Chou,C., Li,H., Hai,R., Patterson,D., Stolc,V., Zhu,H. and Liu,F. (2003) Functional profiling of a human cytomegalovirus genome. Proc. Natl Acad. Sci. USA, 100, 14223-14228.
45. Praitis,V., Casey,E., Collar,D. and Austin,J. (2001) Creation of low-copy integrated transgenic lines in Caenorhabditis elegans. Genetics, 157, 1217-1226.