A new strategy for gene targeting and functional proteomics using the DT40 cell line

Nucleic Acids Research

Volumn 41, Issue 17, 2013, Pages

  Orlowska, Kinga P ^a,b   Klosowska, Kamila ^a,b   Szczesny, Roman J ^a,b   Cysewski, Dominik ^a,b   Krawczyk, Pawel S ^a,b   Dziembowski, Andrzej ^a,b  

^a UNIVERSITY OF WARSAW   (Poland)

^b INSTITUTE OF BIOCHEMISTRY AND BIOPHYSICS   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

CELL PROTEIN; PROTEIN CNOT7; PROTEIN EXOSC8; PROTEIN EXOSC9; PROTEIN UPF1; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; ARTICLE; CELL LINE; CELL TYPE; CONTROLLED STUDY; DT40 CELL LINE; FLOW CYTOMETRY; FLUORESCENCE MICROSCOPY; FUNCTIONAL PROTEOMICS; GENE TARGETING; HOMOLOGOUS RECOMBINATION; MASS SPECTROMETRY; MOLECULAR CLONING; MULTIGENE SCALE; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; RNA ANALYSIS; SCORING SYSTEM; SEQUENCE AND LIGATION INDEPENDENT CLONING; STABLE EXPRESSION;

ANIMALS; CELL LINE; CHICKENS; CLONING, MOLECULAR; FLOW CYTOMETRY; GENE TARGETING; GENETIC VECTORS; MICROSCOPY, FLUORESCENCE; POLYRIBOSOMES; PROTEIN INTERACTION MAPPING; PROTEINS; PROTEOMICS; RECOMBINANT FUSION PROTEINS; RNA STABILITY;

EID: 84884963386     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt650     Document Type: Article

References (46)

1. Gavin,A.C., Bosche,M., Krause,R., Grandi,P., Marzioch,M., Bauer,A., Schultz,J., Rick,J.M., Michon,A.M., Cruciat,C.M. et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415, 141-147. (Pubitemid 34059510)
2. Ho,Y., Gruhler,A., Heilbut,A., Bader,G.D., Moore,L., Adams,S.L., Millar,A., Taylor,P., Bennett,K., Boutilier,K. et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature, 415, 180-183. (Pubitemid 34059520)
3. Gavin,A.C., Aloy,P., Grandi,P., Krause,R., Boesche,M., Marzioch,M., Rau,C., Jensen,L.J., Bastuck,S., Dumpelfeld,B. et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature, 440, 631-636.
4. Huh,W.K., Falvo,J.V., Gerke,L.C., Carroll,A.S., Howson,R.W., Weissman,J.S. and O'Shea,E.K. (2003) Global analysis of protein localization in budding yeast. Nature, 425, 686-691. (Pubitemid 37314307)
5. Krogan,N.J., Cagney,G., Yu,H., Zhong,G., Guo,X., Ignatchenko,A., Li,J., Pu,S., Datta,N., Tikuisis,A.P. et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature, 440, 637-643.
6. Ghaemmaghami,S., Huh,W.K., Bower,K., Howson,R.W., Belle,A., Dephoure,N., O'Shea,E.K. and Weissman,J.S. (2003) Global analysis of protein expression in yeast. Nature, 425, 737-741. (Pubitemid 37314318)
7. Sander,J.D., Dahlborg,E.J., Goodwin,M.J., Cade,L., Zhang,F., Cifuentes,D., Curtin,S.J., Blackburn,J.S., Thibodeau-Beganny,S., Qi,Y. et al. (2011) Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat. Methods, 8, 67-69.
8. Doyon,Y., Vo,T.D., Mendel,M.C., Greenberg,S.G., Wang,J., Xia,D.F., Miller,J.C., Urnov,F.D., Gregory,P.D. and Holmes,M.C. (2011) Enhancing zinc-finger-nuclease activity with improved obligate heterodimeric architectures. Nat. Methods, 8, 74-79.
9. Gupta,A., Christensen,R.G., Rayla,A.L., Lakshmanan,A., Stormo,G.D. and Wolfe,S.A. (2012) An optimized two-finger archive for ZFN-mediated gene targeting. Nat. Methods, 9, 588-590.
10. Sarov,M., Murray,J.I., Schanze,K., Pozniakovski,A., Niu,W., Angermann,K., Hasse,S., Rupprecht,M., Vinis,E., Tinney,M. et al. (2012) A genome-scale resource for in vivo tag-based protein function exploration in C. elegans. Cell, 150, 855-866.
11. Baba,T.W., Giroir,B.P. and Humphries,E.H. (1985) Cell lines derived from avian lymphomas exhibit two distinct phenotypes. Virology, 144, 139-151. (Pubitemid 15226177)
12. Buerstedde,J.M. and Takeda,S. (1991) Increased ratio of targeted to random integration after transfection of chicken B cell lines. Cell, 67, 179-188. (Pubitemid 121001434)
13. Buerstedde,J.M., Reynaud,C.A., Humphries,E.H., Olson,W., Ewert,D.L. and Weill,J.C. (1990) Light chain gene conversion continues at high rate in an ALV-induced cell line. EMBO J., 9, 921-927.
14. Arakawa,H., Hauschild,J. and Buerstedde,J.M. (2002) Requirement of the activation-induced deaminase (AID) gene for immunoglobulin gene conversion. Science, 295, 1301-1306. (Pubitemid 34157623)
15. Yamaguchi-Iwai,Y., Sonoda,E., Buerstedde,J.M., Bezzubova,O., Morrison,C., Takata,M., Shinohara,A. and Takeda,S. (1998) Homologous recombination, but not DNA repair, is reduced in vertebrate cells deficient in RAD52. Mol. Cell. Biol., 18, 6430-6435. (Pubitemid 28500533)
16. Niedzwiedz,W., Mosedale,G., Johnson,M., Ong,C.Y., Pace,P. and Patel,K.J. (2004) The Fanconi anaemia gene FANCC promotes homologous recombination and error-prone DNA repair. Mol. Cell, 15, 607-620. (Pubitemid 39141787)
17. Mikami,Y., Hori,T., Kimura,H. and Fukagawa,T. (2005) The functional region of CENP-H interacts with the Nuf2 complex that localizes to centromere during mitosis. Mol. Cell. Biol., 25, 1958-1970. (Pubitemid 40280158)
18. Takami,Y. and Nakayama,T. (2000) N-terminal region, C-terminal region, nuclear export signal, and deacetylation activity of histone deacetylase-3 are essential for the viability of the DT40 chicken B cell line. J. Biol. Chem., 275, 16191-16201. (Pubitemid 30366931)
19. Mosedale,G., Niedzwiedz,W., Alpi,A., Perrina,F., Pereira-Leal,J.B., Johnson,M., Langevin,F., Pace,P. and Patel,K.J. (2005) The vertebrate Hef ortholog is a component of the Fanconi anemia tumor-suppressor pathway. Nat. Struct. Mol. Biol., 12, 763-771. (Pubitemid 43086250)
20. Li,M.Z. and Elledge,S.J. (2007) Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nat. Methods, 4, 251-256. (Pubitemid 46358876)
21. Arakawa,H., Lodygin,D. and Buerstedde,J.M. (2001) Mutant loxP vectors for selectable marker recycle and conditional knock-outs. BMC Biotechnol., 1, 7.
22. International Chicken Genome Sequencing Consortium. (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432, 695-716.
23. Saribasak,H. and Arakawa,H. (2006) Targeted transfection of DT40 cells. Subcell. Biochem., 40, 419-421.
24. Esposito,A.M., Mateyak,M., He,D., Lewis,M., Sasikumar,A.N., Hutton,J., Copeland,P.R. and Kinzy,T.G. (2010) Eukaryotic polyribosome profile analysis. J. Vis. Exp., pii: 1948.
25. Aguilar,R.M., Bustamante,J.J., Hernandez,P.G., Martinez,A.O. and Haro,L.S. (1999) Precipitation of dilute chromatographic samples (ng/ml) containing interfering substances for SDS-PAGE. Anal. Biochem., 267, 344-350. (Pubitemid 29095882)
26. Kim,S.C., Chen,Y., Mirza,S., Xu,Y., Lee,J., Liu,P. and Zhao,Y. (2006) A clean, more efficient method for in-solution digestion of protein mixtures without detergent or urea. J. Proteome Res., 5, 3446-3452. (Pubitemid 44904337)
27. Cox,J., Neuhauser,N., Michalski,A., Scheltema,R.A., Olsen,J.V. and Mann,M. (2011) Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res., 10, 1794-1805.
28. Cox,J. and Mann,M. (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol., 26, 1367-1372.
29. Grabherr,M.G., Haas,B.J., Yassour,M., Levin,J.Z., Thompson,D.A., Amit,I., Adiconis,X., Fan,L., Raychowdhury,R., Zeng,Q. et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol., 29, 644-652.
30. Wepf,A., Glatter,T., Schmidt,A., Aebersold,R. and Gstaiger,M. (2009) Quantitative interaction proteomics using mass spectrometry. Nat. Methods, 6, 203-205.
31. Caldwell,R.B., Fiedler,P., Schoetz,U. and Buerstedde,J.M. (2007) Gene function analysis using the chicken B-cell line DT40. Methods Mol. Biol., 408, 193-210.
32. Gallant,P. and Nigg,E.A. (1994) Identification of a novel vertebrate cyclin: cyclin B3 shares properties with both A-and B-type cyclins. EMBO J., 13, 595-605. (Pubitemid 24050673)
33. Tomecki,R., Kristiansen,M.S., Lykke-Andersen,S., Chlebowski,A., Larsen,K.M., Szczesny,R.J., Drazkowska,K., Pastula,A., Andersen,J.S., Stepien,P.P. et al. (2010) The human core exosome interacts with differentially localized processive RNases: hDIS3 and hDIS3L. EMBO J., 29, 2342-2357.
34. Liu,H.Y., Badarinarayana,V., Audino,D.C., Rappsilber,J., Mann,M. and Denis,C.L. (1998) The NOT proteins are part of the CCR4 transcriptional complex and affect gene expression both positively and negatively. EMBO J., 17, 1096-1106. (Pubitemid 28077663)
35. Yamashita,A., Chang,T.C., Yamashita,Y., Zhu,W., Zhong,Z., Chen,C.Y. and Shyu,A.B. (2005) Concerted action of poly(A) nucleases and decapping enzyme in mammalian mRNA turnover. Nat. Struct. Mol. Biol., 12, 1054-1063. (Pubitemid 41746775)
36. Applequist,S.E., Selg,M., Raman,C. and Jack,H.M. (1997) Cloning and characterization of HUPF1, a human homolog of the Saccharomyces cerevisiae nonsense mRNA-reducing UPF1 protein. Nucleic Acids Res., 25, 814-821. (Pubitemid 27299838)
37. Lykke-Andersen,J., Shu,M.D. and Steitz,J.A. (2000) Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon. Cell, 103, 1121-1131. (Pubitemid 32037398)
38. Mendell,J.T., ap Rhys,C.M. and Dietz,H.C. (2002) Separable roles for rent1/hUpf1 in altered splicing and decay of nonsense transcripts. Science, 298, 419-422. (Pubitemid 35176351)
39. Atkin,A.L., Altamura,N., Leeds,P. and Culbertson,M.R. (1995) The majority of yeast UPF1 co-localizes with polyribosomes in the cytoplasm. Mol. Biol. Cell., 6, 611-625.
40. Lubas,M., Christensen,M.S., Kristiansen,M.S., Domanski,M., Falkenby,L.G., Lykke-Andersen,S., Andersen,J.S., Dziembowski,A. and Jensen,T.H. (2011) Interaction profiling identifies the human nuclear exosome targeting complex. Mol. Cell, 43, 624-637.
41. Bawankar,P., Loh,B., Wohlbold,L., Schmidt,S. and Izaurralde,E. (2013) NOT10 and C2orf29/NOT11 form a conserved module of the CCR4-NOT complex that docks onto the NOT1 N-terminal domain. RNA Biol., 10, 228-244.
42. Mendell,J.T., Medghalchi,S.M., Lake,R.G., Noensie,E.N. and Dietz,H.C. (2000) Novel Upf2p orthologues suggest a functional link between translation initiation and nonsense surveillance complexes. Mol. Cell. Biol., 20, 8944-8957. (Pubitemid 32245925)
43. Schell,T., Kocher,T., Wilm,M., Seraphin,B., Kulozik,A.E. and Hentze,M.W. (2003) Complexes between the nonsense-mediated mRNA decay pathway factor human upf1 (up-frameshift protein 1) and essential nonsense-mediated mRNA decay factors in HeLa cells. Biochem. J., 373, 775-783. (Pubitemid 36981087)
44. Kashima,I., Yamashita,A., Izumi,N., Kataoka,N., Morishita,R., Hoshino,S., Ohno,M., Dreyfuss,G. and Ohno,S. (2006) Binding of a novel SMG-1-Upf1-eRF1-eRF3 complex (SURF) to the exon junction complex triggers Upf1 phosphorylation and nonsensemediated mRNA decay. Genes Dev., 20, 355-367. (Pubitemid 43200289)
45. Zhang,Y., Werling,U. and Edelmann,W. (2012) SLiCE: a novel bacterial cell extract-based DNA cloning method. Nucleic Acids Res., 40, e55.
46. Stadler,C., Rexhepaj,E., Singan,V.R., Murphy,R.F., Pepperkok,R., Uhlen,M., Simpson,J.C. and Lundberg,E. (2013) Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells. Nat. Methods, 10, 315-323.