Preparation of a set of expression-ready clones of mammalian long cDNAs encoding large proteins by the ORF trap cloning method

DNA Research

Volumn 12, Issue 4, 2005, Pages 257-267

  Nakajima, Daisuke ^a   Saito, Kenji ^b   Yamakawa, Hisashi ^a   Kikuno, Reiko F ^a   Nakayama, Manabu ^a,b   Ohara, Reiko ^a   Okazaki, Noriko ^a   Koga, Hisashi ^a,c   Nagase, Takahiro ^a   Ohara, Osamu ^a,b,d  

^a KAZUSA DNA RESEARCH INSTITUTE   (Japan)

^b CHIBA UNIVERSITY   (Japan)

^c Chiba Industry Advancement Center   (Japan)

^d RIKEN Center for Integrative Medical Sciences   (Japan)

Author keywords

cDNA; Expression clone; Large protein; Proteomics; Subcellular localization

Indexed keywords

COMPLEMENTARY DNA; GENE PRODUCT; GREEN FLUORESCENT PROTEIN; HYBRID PROTEIN; PLASMID DNA;

ANIMAL CELL; ARTICLE; CELL STRAIN HEK293; CONTROLLED STUDY; EMBRYO; GENE; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE MUTATION; GENE SEQUENCE; GENETIC RECOMBINATION; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; IN VITRO STUDY; KIAA GENE; MAMMAL; MOLECULAR CLONING; MOUSE; NONHUMAN; OPEN READING FRAME; PROMOTER REGION; PROTEIN LOCALIZATION; PROTEOMICS; RNA TRANSLATION;

ANIMALS; BASE SEQUENCE; CELL LINE; CLONING, MOLECULAR; DNA, COMPLEMENTARY; ESCHERICHIA COLI; GREEN FLUORESCENT PROTEINS; HUMANS; MICE; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PROMOTER REGIONS (GENETICS); RECOMBINANT FUSION PROTEINS;

ANIMALIA; ESCHERICHIA COLI; MAMMALIA;

EID: 33644851035     PISSN: 13402838     EISSN: 13402838     Source Type: Journal    
DOI: 10.1093/dnares/dsi010     Document Type: Article

References (40)

1. Hudson, R. J. Jr., Dawson, E. P., Rushing, K. L., et al. 1997, The complete set of predicted genes from Saccharomyces cerevisiae in a readily usable form, Genome Res., 7, 1169-1173.
2. Zhu, H., Bilgin, M., Bangham, R., et al. 2001, Global analysis of protein activities using proteome chips, Science, 293, 2101-2105.
3. Ho, Y., Gruhler, A., Heilbut, A., et al. 2002, Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry, Nature, 415, 180-183.
4. Reboul, J., Vaglio, P., Rual, J.-F., et al. 2003, C. elegans ORFeome version 1.1: Experimental verification of the genome annotation and resource for proteome-scale protein expression, Nature Genet., 34, 35-41.
5. Phizicky, E., Bastiaens, P. I. H., Zhu, H., Snyder, M., and Fields, S. 2003, Protein analysis on a proteomic scale, Nature, 422, 208-215.
6. Rual, J.-F., Hirozane-Kishikawa, T., Hao, T., et al. 2004, Human ORFeome version 1.1: A platform for reverse proteomics, Genome Res., 14, 2128-2135.
7. Pearlberg, J. and LaBaer, J. 2004, Protein expression clone repositories for functional proteomics, Curr. Opin. Chem. Biol., 8, 98-102.
8. Simpson, J. C., Wellenreuther, R., Poustka, A., Pepperkok, R., and Wieinann, S. 2000, Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing, EMBO Rep., 3, 287-292.
9. Suzuki, H., Fukunishi, Y., Kagawa, I., et al. 2001, Protein-protein interaction panel using mouse full-length cDNAs, Genome Res., 11, 1758-1765.
10. Wiemann, S., Arlt, D., Huber, W., et al. 2004, From ORFeome to Biology: A functional genomics pipeline, Genome Res., 14, 2136-2144.
11. Nomura, N., Miyajima, N., Sazuka, T., et al. 1994, Prediction of the coding sequences of unidentified human genes. I. The coding sequences of 40 new genes (KIAA0001-KIAA0040) deduced by analysis of randomly sampled cDNA clones from human immature myeloid cell line KG-1, DNA Res., 1, 27-35.
12. Strausberg, R. L., Feingold, E. A., Klausner, R. D., and Collins, F. S. 1999, The mammalian gene collection, Science, 286, 455-457.
13. Wiemann, S., Weil, B., Wellenreuther, R., et al. 2001, Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs, Genome Res., 11, 422-435.
14. Kawai, J., Shinagawa, A., Shibata, K., et al. 2001, Functional annotation of a full-length mouse cDNA collection, Nature, 409, 685-690.
15. Mammalian Gene Collection (MGC) Program Team 2002, Generation and initial analysis of more than 15,000 fulllength human and mouse cDNA sequences, Proc. Natl Acad. Sci. USA, 99, 16899-16903.
16. Okazaki, Y., Furuno, M., Kasukawa, T., et al. 2002, Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs, Nature, 420, 563-573.
17. Okazaki, N., Kikuno, R. F., Ohara, R., et al. 2004, Prediction of the coding sequences of mouse homologues of KIAA gene: IV. The complete nucleotide sequences of 500 mouse KIAA-hoinologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries, DNA Res., 11, 205-218.
18. Ota, T., Suzuki, Y., Nishikawa, T., et al. 2004, Complete sequencing and characterization of 21,243 full-length human cDNAs, Nature Genet., 36, 40-45.
19. Ohara, O., Nagase, T., Ishikawa, K.-I., et al. 1997, Construction and characterization of human brain cDNA libraries suitable for analysis of cDNA clones encoding relatively large proteins, DNA Res., 4, 53-59.
20. Nagase, T., Kikuno, R., and Ohara, O. 2003, The Kazusa cDNA project for identification of unknown human transcripts, C. R. Biol., 326, 959-966.
21. Nakajima, D., Okazaki, N., Yamakawa, H., Kikuno, R., Ohara, O., and Nagase, T. 2002, Construction of expression-ready cDNA clones for KIAA genes: Manual curation of 330 KIAA cDNA clones, DNA Res., 9, 99-106.
22. Okazaki, N., Kikuno, R., Ohara, R., et al. 2002, Prediction of the coding sequences of mouse homologues of KIAA gene: I. The complete nucleotide sequences of 100 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries, DNA Res., 9, 179-188.
23. Hara, Y., Shimada, K., Kohga, H., Ohara, O., and Koga, H. 2003, High-throughput production of recombinant antigens for mouse KIAA proteins in Escherichia coli: computational allocation of plasmids of glutathione-S- transferase-fused antigens by an in vitro recombination-assisted method, DNA Res., 10, 129-136.
24. Koga, H., Shimada, K., Hara, Y., et al. 2004, A comprehensive approach for establishment of the platform to analyze functions of KIAA proteins: Generation and evaluation of anti-mKIAA antibodies, Proteomics, 4, 1412-1416.
25. Kikuno, R., Nagase, T., Nakayama, M., et al. 2004, HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE, Nucleic Acids Res., 32, D502-D504.
26. Camon, E., Magrane, M., Barrell, D., et al. 2003, The Gene Ontology Annotation (GOA) project: Implementation of GO in SWISS-PROT, TrEMBL, and InterPro, Genome Res., 13, 662-672.
27. Gillen, J. R., Willis, D. K., and Clark, A. J. 1981, Genetic analysis of the RecE pathway of genetic recombination in Escherichia coli K-12, J. Bacterial, 145, 521-532.
28. Oliner, J. D., Kinzler, K. W., and Vogelstein, B. 1993, In vivo cloning of PCR products in E. coli,, Nucleic Acids Res., 21, 5192-5197.
29. Zhang, Y., Buchholz, F., Muyrers, J. P., and P., Stewart, A. F 1998, A new logic for DNA engineering using recombination in Escherichia coli, Nature Genet., 20, 123-128.
30. Walhout, A. J. M., Temple, G. F., Brasch, M. A., et al. 2000, GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes, Meth. Enzymol., 328, 575-592.
31. Muyrers, J. P. P., Zhang, Y., and Stewart, F. 2001, Techniques: Recombinogenic engineering - new options for cloning and manipulating DNA, Trends Biochem. Sci., 26, 325-331.
32. Ohara, O. and Teraoka, H. 1987, Anomalous behavior of human leukocyte interferon subtypes on polyacrylamide gel electrophoresis in the presence of dodecyl sulfate, FEBS Lett., 211, 78-82.
33. Thiemann, M., Schrader, M., Volkl, A., Baumgart, E., and Fahimi, H. D 2000, Interaction of peroxisomes with microtubules, Eur. J. Biochem., 267, 6264-6275.
34. Koga, H., Yuasa, S., Nagase, T., et al. 2004,, A comprehensive approach for establishment of the platform to analyze functions of KIAA proteins II: public release of inaugural version of InGaP database containing gene/protein expression profiles for 127 mouse KIAA genes/proteins, DNA Res., 11, 293-304.
35. Brasch, M. A., Hartley, J. L., and Vidal, M. 2004, ORFeome cloning and systems biology: Standardized mass production of the parts from the parts-list, Genome Res., 14, 2001-2009.
36. Maruyama, K. and Sugano, S. 1994, Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides, Gene, 138, 171-174.
37. Carninci, P., Kvam, C., Kitamura, A., et al. 1996, High-efficiency full-length cDNA cloning by biotinylated CAP trapper, Genomics, 37, 327-336.
38. Shiraki, T., Kondo, S., Katayama, S., et al. 2003, Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage, Proc. Natl Acad. Sci. USA., 100, 15776-15781.
39. Hashimoto, S., Suzuki, Y., Kasai, Y., et al. 2004, 5′-end SAGE for the analysis of transcriptional start sites, Nature Biotech., 22, 1146-1149.
40. Wei, C.-L., Ng, P., Chiu, K. P, et al. 2004, 5′ Long serial analysis of gene expression (LongSAGE) and 3′LongSAGE for transcriptome characterization and genome annotation, Proc. Natl Acad. Sci., 101, 11701-11706.