Rapid identification and isolation of zebrafish cDNA clones

Gene

Volumn 201, Issue 1-2, 1997, Pages 87-98

  Gong, Zhiyuan ^a   Yan, Tie ^a   Liao, Ji ^a   Lee, Sze Ern ^a   He, Jiangyan ^a   Hew, Choy L ^b,c,d  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b HOSPITAL FOR SICK CHILDREN RESEARCH INSTITUTE   (Canada)

^c UNIVERSITY OF TORONTO   (Canada)

^d UNIVERSITY OF TORONTO   (Canada)

Author keywords

Embryo; EST; Gene; Genome; Teleost

Indexed keywords

COMPLEMENTARY DNA; CYTOPLASM PROTEIN; CYTOSKELETON PROTEIN; MEMBRANE PROTEIN; NUCLEAR PROTEIN; POLYADENYLATED RNA; SECRETORY PROTEIN;

ANIMAL TISSUE; ARTICLE; DNA LIBRARY; EMBRYO; GENE ISOLATION; GENE LIBRARY; METHODOLOGY; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; ZEBRA FISH;

ANIMALS; BASE SEQUENCE; DNA, COMPLEMENTARY; MOLECULAR SEQUENCE DATA; ZEBRAFISH;

ANIMALIA; DANIO RERIO; TELEOSTEI;

EID: 0030817790     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(97)00431-9     Document Type: Article

References (40)

1. Adams M.D., Kelley J.M., Gocayne J.D., Dubnick M., Polymeropoulos M.H., Xiao H., Merril C.R., Wu A., Olde B., Moreno R.F., Kerlavage A.R., McCombie W.R., Venter J.C. Complementary DNA sequencing: Expressed sequence tags and human genome project. Science. 252:1991;1651-1656.
2. Adams, M.D. and 84 co-authors, 1995. Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Nature 377, 3-17 (Suppl.).
3. Azam A., Paul J., Sehgal D., Prasad J., Bhattacharya S., Bhattacharya A. Identification of novel genes from Entameoba histolytica by expressed sequence tag analysis. Gene. 181:1996;113-116.
4. Banfield S., Borsani G., Rossi E., Bernard L., Guffanti A., Rubboli F., Marchitiello A., Giglio S., Coluccia E., Zollo M., Zuffard O., Ballabio A. Identification and mapping of human cDNA homologous to Drosophila mutant genes through EST database searching. Nature Genet. 13:1996;167-174.
5. Beier D.R. Single-strand conformation polymorphism (SSCP) analysis as a tool for genetic mapping. Mammal. Genome. 4:1993;627-631.
6. Chomczynski P., Sacchi N. Single-step method of RNA isolation by acid guanidium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162:1987;156-159.
7. Collet C., Joseph R. The identification of nuclear and mitochondrial genes by sequencing randomly chosen clones from a marsupial mammary gland cDNA library. Biochem. Genet. 32:1994;181-188.
8. Cox D.R., Burmeister M., Price E.R., Kim S., Myers R.M. Radiation hybrid mapping: A somatic cell genetic method for constructing high-resolution maps of mammalian chromosomes. Science. 250:1990;245-250.
9. Driever W., Stemple D., Schier A., Solnica-Krezel L. Zebrafish: genetic tools for studying vertebrate development. Trends Genet. 10:1994;152-159.
10. Driever W., Solnica-Krezel L., Schier A.F., Neuhauss S.C.F., Malicki J., Stemple D.L., Stainier D.Y.R., Zwartkruis F., Abdelilah S., Rangini Z., Belak J., Boggs C. A genetic screen for mutations affecting embryogenesis in zebrafish. Development. 123:1996;37-46.
11. Gong Z., Fletcher G.L., Hew C.L. Tissue distribution of fish antifreeze protein mRNAs. Can. J. Zool. 70:1992;810-814.
12. Gong Z., Hu Z., Gong Z.Q., Kitching R., Hew C.L. Bulk isolation and identification of fish genes by cDNA clone tagging. Mol. Mar. Biol. Biotechnol. 3:1994;243-251.
13. Haffter P., Granato M., Brand M., Mullins M.C., Hammerschmidt M., Kane D.A., Odenthal J., van Eeden F.J.M., Jiang Y.-J., Heisenberg C.-P., Kelsh R.N., Furutani-Seiki M., Vogelsang E., Beuchle D., Schach U., Fabian C., Nusslein-Volhard C. The identification of genes with unique and essential functions in the development of the zebrafish, Danio rerio. Development. 123:1996;1-36.
14. Höfte H., Desprez T., Amselem J., Chiapello H., Caboche M., Moisan A., Jourjon M.F., Charpenteau J.L., Berthomieu P., Guerrier D., Giraudat J., Quigley F., Thomas F., Yu D.Y., Mache R., Raynal M., Cooke R., Grellet F., Delseny M., Parmentier Y., Marcillac G., Gigot C., Fleck J., Philipps G., Axelos M., Bardet C., Tremousaygue D., Lescure B. An inventory of 1152 expressed sequence tags obtained by partial sequencing of cDNA from Arabidopsis thaliana. Plant J. 4:1993;1051-1061.
15. Hoog C. Isolation of a large number of novel mammalian genes by a differential cDNA library screening strategy. Nucleic Acids Res. 19:1991;6123-6127.
16. Izsvak Z., Ivics Z., Garcia-Estefania D., Fahrenkrug S.C., Hackett P.B. DANA elements: A family of composite, tRNA-derived short interspersed DNA elements associated with mutational activities in zebrafish (Danio rerio). Proc. Natl. Acad. Sci. USA. 93:1995;1077-1081.
17. Keith C.S., Hoang D.O., Barret B.M., Feigelman B., Nelson M.C., Thai H., Baysdorfer C. Partial sequence analysis of 130 randomly selected maize cDNA clones. Plant Physiol. 101:1993;329-332.
18. Khan A.B., Wilcox A.S., Polymeropoulos M.H., Hopkins J.A., Stevens T.J., Robinson M., Orpana A.K., Sikela J.M. Single pass sequencing and physical and genetic mapping of human brain cDNAs. Nature Genet. 2:1992;180-185.
19. Kim C., Markiewicz P., Lee J., Schierle C., Miller J. Studies of the hyperthermophile Thermotoga maritima by random sequencing of cDNA and genomic libraries. Identification and sequencing of the trpEG (D) operon. J. Mol. Biol. 231:1993;960-981.
20. Kimmel C.B. Genetics and early development of zebrafish. Trends Genet. 5:1988;283-288.
21. Kimmel C.B., Ballard W.W., Kimmel S.R., Ullmann B., Schilling T.F. Stages of embryonic development of the zebrafish. Dev. Dyn. 20:1995;253-310.
22. Knapik E.W., Goodman A., Atkinson O.S., Roberts C.T., Shiozawa M., Sim C.U., Weksler-Zangen S., Trolliet M.R., Futrell C., Innes B.A., Koike G., McLaughlin M.G., Pierre L., Simon J.S., Vilallonga E., Roy M., Chiang P.-W., Fishman M.C., Driever W., Jacob H.J. A reference cross DNA panel for zebrafish (Danio rerio) anchored with simple sequence length polymorphisms. Development. 123:1996;451-460.
23. Lanfranchi G., Muraro T., Caldara F., Pacchioni B., Pallavicini A., Pandolfo D., Toppo S., Trevisan S., Scarso S., Valle G. Identification of 4370 expressed sequence tags from a 3′-end-specific cDNA library of human skeletal muscle by DNA sequencing and filter hybridization. Genome Res. 6:1996;35-42.
24. Liew C.C., Hwang D.M., Fung Y.M., Laurenssen C., Cukerman E., Tsui S., Lee C.Y. A catalogue of genes in the cardiovascular system as identified by expressed sequence tags. Proc. Natl. Acad. Sci. USA. 91:1994;10645-10649.
25. McCombie W.R., Adams M.D., Kelley J.M., FitzGerald M.G., Utterback T.R., Khan M., Dubnick M., Kerlavage A.R., Venter J.C., Fields C. Caenorhabditis elegans expressed sequence tags identify gene families and potential disease gene homologues. Nature Genet. 1:1992;124-131.
26. Newman T., de Bruijn F., Green P., Keegstra K., Kende H., McIntosh L., Ohlrogge J., Raikhel N., Somerville S., Thomashow M., Retzel E.F., Somerville C. Genes galore: A summary of methods for accessing results from large-scale partial sequencing of anonymous Arabidopsis cDNA clones. Plant Physiol. 106:1994;1241-1255.
27. Nusslein-Volhard C. Of flies and fishes. Science. 266:1994;572-574.
28. Okubo K., Hori N., Matoba R., Niiyama T., Fukushima A., Kojima Y., Matsubara K. Large scale cDNA sequencing for analysis of quantitative and qualitative aspects of gene expression. Nature Genetics. 2:1992;173-179.
29. Park Y.S., Kwak J.M., Kim Y.S., Lee D.S., Cho M.J., Lee H.H., Nam H.G. Generation of expressed sequence tags of random root cDNA clones of Brassica napus by single-run partial sequencing. Plant Physiol. 103:1993;359-370.
30. Pearson W.R., Lipman D.J. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA. 85:1988;2444-2448.
31. Postlethwait J.H., Johnson S.L., Midson C.N., Talbot W.S., Gates M., Ballinger E.W., Africa D., Andrews R., Carl T., Eisen J.S., Horne S., Kimmel C.B., Hutchinson M., Johnson M., Rodriguez A. A genetic linkage map for the zebrafish. Science. 264:1994;699-703.
32. Putney S.D., Herlihy W.C., Schimmel P. A new troponin T and cDNA clones for 13 different muscle proteins, found by shotgun sequencing. Nature. 302:1983;718.
33. Rossant J., Hopkins N. Of fin and fur: mutational analysis of vertebrate embryonic development. Genes Dev. 6:1992;1-13.
34. Sambrook, J., Fritsch, E.F., Maniatis, T., 1989. Molecular Cloning: A Laboratory Manual, 2nd ed. Cold Spring Harbour Laboratory Press, Cold Spring Harbor, NY.
35. Smith L.C., Chang L., Britten R.J., Davidson E.H. Sea urchin genes expressed in activated coelomocytes are identified by expressed sequence tags. Complement homologues and other putative immune response genes suggest immune system homology within the deuterostomes. J. Immunol. 156:1996;593-602.
36. Streisinger G., Walker C., Dower N., Knauber D., Singer F. Production of clones of homozygous diploid zebra fish (Brachydanio rerio). Nature. 291:1981;293-296.
37. Tugendreich S., Boguski M.S., Seldin M.S., Hieter P. Linking yeast genetics to mammalian genomes: Identification and mapping of the human homolog of CDC27 via the expressed sequence tag (EST) data base. Proc. Natl. Acad. Sci. USA. 90:1993;10031-10035.
38. Uchimiya H., Kidou S., Shimazaki T., Takamatsu S., Hashimoto H., Nishi R., Aotsuka S., Matsubayashi Y., Kidou N., Umeda M., Kato A. Random sequencing of cDNA libraries reveals a variety of expressed genes in cultured cells of rice (Oryza sativa L.). Plant J. 2:1992;1005-1009.
39. Waterston R., Martin C., Craxton M., Huynh C., Coulson A., Hillier L., Durbin R., Green P., Shownkeen R., Halloran N., Metzstein M., Hawkins T., Wilson R., Berks M., Du Z., Thomas K., Thierry-Mieg J., Sulston J. A survey of expressed genes in Caenorhabditis elegans. Nature Genet. 1:1992;114-131.
40. Westerfield, M., 1994. The Zebrafish Book, ed. 2.1. University of Oregon Press, Eugene, OR.