Genome-wide mutant collections: Toolboxes for functional genomics

Current Opinion in Microbiology

Volumn 3, Issue 3, 2000, Pages 309-315

  Coelho, Paulo S R ^a   Kumar, Anuj ^a   Snyder, Michael ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GENETICS; GENE LOCATION; GENOME; NONHUMAN; PHENOTYPE; REVIEW; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS;

BACTERIA (MICROORGANISMS); MYCOPLASMA; SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES;

EID: 0034043381     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1369-5274(00)00095-3     Document Type: Review

References (43)

1. Mewes H.W., Albermann K., Bahr M., Frishman D., Gleissner A., Hani J., Heumann K., Kleine K., Malieri A., Oliver S.G.et al. Overview of the yeast genome. Nature. 387:1997;7-65.
2. Collins F.S., Patrinos A., Jordan E., Chakravarti A., Gesteland R., Walters L. New goals for the US Human Genome Project: 1998-2003. Science. 282:1998;682-689.
3. Johnston M. Towards a complete understanding of how a simple cell works. Trends Genet. 12:1996;242-243.
4. Hieter P., Boguski M. Functional genomics: it's all how you read it. Science. 278:1997;601-602.
5. Miklos G.L., Rubin G.M. The role of the genome project in determining gene function: insights from model organisms. Cell. 86:1996;521-529.
6. Lawrence C.W. Classical mutagenesis techniques. Methods Enzymol. 194:1991;273-280.
7. Winzeler E.A., Davis R.W. Functional analysis of the yeast genome. Curr Opin Genet Dev. 7:1997;771-776.
8. Casabadan M.J., Cohen S.N. Lactose genes fused to exogenous promoters in one step using a Mu-lac bacteriophage: in vivo probe for transcriptional control sequences. Proc Natl Acad Sci. 76:1979;4530-4533.
9. Hensel M., Holden D.W. Molecular genetic approaches for the study of virulence in both pathogenic bacteria and fungi. Microbiology. 142:1996;1049-1058.
10. Burns N., Grimwade B., Ross-Macdonald P.B., Choi E.-Y., Finberg K., Roeder G.S., Snyder M. Large-scale characterization of gene expression, protein localization and gene disruption in Saccharomyces cerevisiae. Genes Dev. 8:1994;1087-1105.
11. Kempken F., Kuck U. Transposons in filamentous fungi - facts and perspectives. Bioessays. 20:1998;652-659.
12. Martienssen R.A. Functional genomics: probing plant gene function and expression with transposons. Proc Natl Acad Sci USA. 95:1998;2021-2026. An informative review of transposon-based approaches to functional genomics in Arabidopsis, maize, and other plant species with particular emphasis placed upon methods to screen mutant libraries by site-selected mutagenesis and systematic insertion site sequencing.
13. Zwaal R.R., Broeks A., Meurs J.V., Groenen J.T., Plasterk R.H. Target-selected gene inactivation in Caenorhabditis elegans by using a frozen transposon insertion mutant bank. Proc Natl Acad Sci USA. 90:1993;7431-7435.
14. Spradling A.C., Stern D., Beaton A., Rhem E.J., Laverty T., Mozden N., Misra S., Rubin G.M. The Berkeley Drosophila Genome Project gene disruption project: single P-element insertions mutating 25% of vital Drosophila genes. Genetics. 153:1999;135-177. An update as to the progress of the BDGP, which currently reports a collection of 1045 mutant strains containing P-element insertions disrupting more than 900 Drosophila genes essential for adult viability.
15. Smith V., Chou K.N., Lashkari D., Botstein D., Brown P.O. Functional analysis of the genes of yeast chromosome V by genetic footprinting. Science. 274:1996;2069-2074.
16. Smith V., Botstein D., Brown P.O. Genetic footprinting: a genomic strategy for determining a gene's function given its sequence. Proc Natl Acad Sci USA. 92:1995;6479-6483.
17. Hoekstra M.F., Burbee D., Singer J., Mull E., Chiao E., Heffron F. A Tn3 derivative that can be used to make short in-frame insertions within genes. Proc Natl Acad Sci USA. 88:1991;5457-5461.
18. Ross-Macdonald P., Sheehan A., Roeder G.S., Snyder M. A multipurpose transposon system for analyzing protein production, localization, and function in Saccharomyces cerevisiae. Proc Natl Acad Sci USA. 94:1997;190-195.
19. Ji H., Moore D.P., Blomberg M.A., Braiterman L.T., Voytas D.F., Natsoulis G., Boeke J.D. Hotspots for unselected Ty1 transposition events on yeast chromosome III are near tRNA genes and LTR sequences. Cell. 73:1993;1007-1018.
20. Tyers M., Tokiwa G., Nash R., Futcher B. The Cln3-Cdc28 kinase complex of S. cerevisiae is regulated by proteolysis and phosphorylation. EMBO J. 11:1992;1773-1784.
21. Ross-MacDonald P., Coehlo P.S.R., Roemer T., Agarwal S., Kumar A., Jansen R., Cheung K-H., Sheehan A., Symoniatis D., Umansky L. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature. 402:1999;413-418. This work represents an extensive application of Tn3-mediated shuttle mutagenesis towards functional genomics in yeast. The approach utilizes a multifunctional minitransposon enabling the genome-wide analysis of disruption phenotypes, gene expression, and protein localization - a data set currently unattainable through any other single genomic approach.
22. Velculescu V.E., Zhang L., Zhou W., Vogelstein J., Basrai M.A., Bassett D.E. Jr., Hieter P., Vogelstein B., Kinzler K.W. Characterization of the yeast transcriptome. Cell. 88:1997;243-251.
23. Kumar A., Cheung K-H., Ross-MacDonald P., Coelho P.S.R., Miller P., Snyder M. TRIPLES: a database of gene function in S. cerevisiae. Nucleic Acids Res. 28:2000;81-84.
24. Baudin A., Ozier-Kalogeropoulos O., Denouel A., Lacroute F., Cullin C. A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. Nucleic Acids Res. 21:1993;3329-3330.
25. Wach A., Brachat A., Pohlmann R., Philippsen P. New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast. 10:1994;1793-1808.
26. Wach A., Brachat A., Alberti-Segui C., Rebischung C., Philippsen P. Heterologous HIS3 marker and GFP reporter modules for PCR-targeting in Saccharomyces cerevisiae. Yeast. 13:1997;1065-1075.
27. Dujon B. European functional analysis network (EUROFAN) and the functional analysis of Saccharomyces cerevisiae. Electrophoresis. 19:1998;617-624.
28. Rieger K.J., El-Alama M., Stein G., Bradshaw C., Slonimski P.P., Maundrell K. Chemotyping of yeast mutants using robotics. Yeast. 15:1999;973-986.
29. Bianchi M.M., Sartori G., Vandenbol M., Uccelletti D., Mazzoni C., DiRago J.P., Carignani G., Slonimski P.P., Frontali L. How to bring orphan genes into functional families. Yeast. 15:1999;513-526.
30. Winzeler E.A., Shoemaker D.D., Astromoff A., Liang H., Anderson K., Andre B., Bangham R., Benito R., Boeke J.D., Bussey H.et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science. 285:1999;901-906. This paper reports the progress of an international consortium of laboratories utilizing targeted PCR-based gene deletions to disrupt each open reading frame (ORF) within the yeast genome. At present, the authors report deletion of 2026 ORFs and subsequent phenotypic analysis of 500 deletion strains.
31. Shoemaker D.D., Lashkari D.A., Morris D., Mittmann M., Davis R.W. Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Nat Genet. 14:1996;450-456.
32. Giaever G., Shoemaker D.D., Jones T.W., Liang H., Winzeler E.A., Astromoff A., Davis R.W. Genomic profiling of drug sensitivities via induced haploinsufficiency. Nat Genet. 21:1999;278-283. An interesting genomic approach to drug target identification in which diploid yeast strains made heterozygous for a single gene are screened for drug-induced sensitivity (haploinsufficiency) on high-density oligonucleotide arrays.
33. Hutchison C.A., Peterson S.N., Gill S.R., Cline R.T., White O., Fraser C.M., Smith H.O., Venter J.C. Global transposon mutagenesis and a minimal Mycoplasma genome. Science. 286:1999;2165-2169. This paper describes the application of genome-wide mutagenesis by Tn4001 to the genomes of M. genitalium and M. pneumoniae as a means of identifying a minimal set of essential genes under laboratory growth conditions.
34. Meyerowitz E.M. Today we have naming of parts. Nature. 402:1999;731-732.
35. Beetham P.R., Kipp P.B., Sawycky X.L., Arntzen C.J., May G.D. A tool for functional plant genomics: Chimeric RNA/DNA oligonucleotides cause in vivo gene-specific mutations. Proc Natl Acad Sci USA. 96:1999;8774-8778. A newly developed technique with genomic potential - self-complementary DNA/RNA chimeric oligonucleotides are used to induce stable, site-specific base substitutions and frameshift mutations in plant cells in vivo.
36. Baulcombe D.C. Fast forward genetics based on virus-induced gene silencing. Curr Opin Plant Biol. 2:1999;109-113. An interesting review of virus-induced gene silencing - a promising technique for plant functional genomics in which a target gene cloned into tobacco mosaic virus induces the silencing of corresponding endogenous mRNA.
37. Rubin G.M. The Drosophila genome project: a progress report. Trends Genet. 14:1998;340-343.
38. Spradling A.C., Stern D.M., Kiss I., Roote J., Laverty T., Rubin G.M. Gene disruptions using P transposable elements: An integral component of the Drosophila genome project. Proc Natl Acad Sci USA. 92:1995;10824-10830.
39. Rorth P. A modular misexpression screen in Drosophila detecting tissue-specific phenotypes. Proc Natl Acad Sci USA. 93:1996;12418-12422.
40. Liu L.X., Spoerke J.M., Mulligan E.L., Chen J., Reardon B., Westlund B., Sun L., Abel K., Armstrong B., Hardiman G.et al. High-throughput isolation of Caenorhabditis elegans deletion mutants. Genome Res. 9:1999;859-867. An application of random chemical mutagenesis to high-throughput genome-wide functional analysis. Chemically mutagenized nematode populations are screened by PCR for deletion mutants in microtiter plate arrays; manipulation of whole animals and genomic DNA in these arrays may provide a blueprint for similar mutagenic approaches in microbial genomes as well.
41. Montgomery M.K., Fire A. Double-stranded RNA as a mediator in sequence-specific genetic silencing and co-suppression. Trends Genet. 14:1998;255-258.
42. Zambrowicz B.P., Friedrich G.A., Buxton E.C., Lilleberg S.L., Person C., Sands A.T. Disruption and sequence identification of 2,000 genes in mouse embryonic stem cells. Nature. 392:1998;608-611. An extensive application of expression-independent gene trapping allowing for the automated identification of sequence tags from insertionally mutagenized genes.
43. Evans M.J., Carlton M.B.L., Russ A.P. Gene trapping and functional genomics. Trends Genet. 13:1997;370-374.