Expression-independent gene trap vectors for random and targeted mutagenesis in embryonic stem cells

Nucleic Acids Research

Volumn 37, Issue 19, 2009, Pages

  Tsakiridis, Anestis ^a,b   Tzouanacou, Elena ^a,c   Rahman, Afifah ^a   Colby, Douglas ^a   Axton, Richard ^b   Chambers, Ian ^a   Wilson, Valerie ^a   Forrester, Lesley ^b   Brickman, Joshua M ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

^c INSTITUT PASTEUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BETA ACTIN; MICRORNA; ACTIN;

ANIMAL CELL; ARTICLE; CONTROLLED STUDY; EMBRYONIC STEM CELL; GENE EXPRESSION; GENE INSERTION; GENE TARGETING; INTRON; MUTAGENESIS; NONHUMAN; NONSENSE MUTATION; NUCLEOTIDE SEQUENCE; POLYADENYLATION; PRIORITY JOURNAL; PROMOTER REGION; RNA SEQUENCE; RNA SPLICING; RNA STABILITY; TRANSCRIPTION INITIATION; CELL LINE; GENE VECTOR; GENETICS; HUMAN; METABOLISM; METHODOLOGY;

ACTINS; CELL LINE; EMBRYONIC STEM CELLS; GENE EXPRESSION; GENE TARGETING; GENETIC VECTORS; HUMANS; MUTAGENESIS; PROMOTER REGIONS, GENETIC;

EID: 71049145214     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp640     Document Type: Article

References (54)

1. Skarnes,W.C., von Melchner,H., Wurst,W., Hicks,G., Nord,A.S., Cox,T., Young,S.G., Ruiz,P., Soriano,P., Tessier-Lavigne,M. et al. (2004) A public gene trap resource for mouse functional genomics. Nat. Genet., 36, 543-544.
2. Gossler,A., Joyner,A.L., Rossant,J. and Skarnes,W.C. (1989) Mouse embryonic stem cells and reporter constructs to detect developmentally regulated genes. Science, 244, 463-465.
3. Friedrich,G. and Soriano,P. (1991) Promoter traps in embryonic stem cells: A genetic screen to identify and mutate developmental genes in mice. Genes Dev., 5, 1513-1523.
4. Skarnes,W.C., Moss,J.E., Hurtley,S.M. and Beddington,R.S. (1995) Capturing genes encoding membrane and secreted proteins important for mouse development. Proc. Natl Acad. Sci. USA, 92, 6592-6596.
5. Friedel,R.H., Plump,A., Lu,X., Spilker,K., Jolicoeur,C., Wong,K., Venkatesh,T.R., Yaron,A., Hynes,M., Chen,B. et al. (2005) From The Cover: Gene targeting using a promoterless gene trap vector ('targeted trapping') is an efficient method to mutate a large fraction of genes. Proc. Natl Acad. Sci. USA, 102, 13188-13193.
6. Niwa,H., Araki,K., Kimura,S., Taniguchi,S., Wakasugi,S. and Yamamura,K. (1993) An efficient gene-trap method using poly A trap vectors and characterization of gene-trap events. J. Biochem., 113, 343-349.
7. Zambrowicz,B.P., Friedrich,G.A., Buxton,E.C., Lilleberg,S.L., Person,C. and Sands,A.T. (1998) Disruption and sequence identification of 2,000 genes in mouse embryonic stem cells. Nature, 392, 608-611.
8. Salminen,M., Meyer,B.I. and Gruss,P. (1998) Efficient poly A trap approach allows the capture of genes specifically active in differentiated embryonic stem cells and in mouse embryos. Dev. Dyn. 212, 326-333.
9. Skarnes,W.C. (2005) Two ways to trap a gene in mice. Proc. Natl Acad. Sci. USA, 102, 13001-13002.
10. Zambrowicz,B.P., Abuin,A., Ramirez-Solis,R., Richter,L.J., Piggott,J., BeltrandelRio,H., Buxton,E.C., Edwards,J., Finch,R.A., Friddle,C.J. et al. (2003) Wnk1 kinase deficiency lowers blood pressure in mice: A gene-trap screen to identify potential targets for therapeutic intervention. Proc. Natl Acad. Sci. USA, 100, 14109-14114.
11. Schnutgen,F., De-Zolt,S., Van Sloun,P., Hollatz,M., Floss,T., Hansen,J., Altschmied,J., Seisenberger,C., Ghyselinck,N.B., Ruiz,P. et al. (2005) Genomewide production of multipurpose alleles for the functional analysis of the mouse genome. Proc. Natl Acad. Sci. USA, 102 7221-7226.
12. Nord,A.S., Vranizan,K., Tingley,W., Zambon,A.C., Hanspers,K., Fong,L.G., Hu,Y., Bacchetti,P., Ferrin,T.E., Babbitt,P.C. et al. (2007) Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells. PLoS ONE, 2, e617.
13. Friedel,R.H., Seisenberger,C., Kaloff,C. and Wurst,W. (2007) EUCOMM-the European conditional mouse mutagenesis program. Brief Funct. Genomic Proteomic, 6, 180-185.
14. Floss,T. and Schnutgen,F. (2008) Conditional gene trapping using the FLEx system. Methods Mol. Biol., 435, 127-138.
15. Hirashima,M., Bernstein,A., Stanford,W.L. and Rossant,J. (2004) Gene-trap expression screening to identify endothelial-specific genes. Blood, 104, 711-718.
16. Matsuda,E., Shigeoka,T., Iida,R., Yamanaka,S., Kawaichi,M. and Ishida,Y. (2004) Expression profiling with arrays of randomly disrupted genes in mouse embryonic stem cells leads to in vivo functional analysis. Proc. Natl Acad. Sci. USA, 101, 4170-4174.
17. Shigeoka,T., Kawaichi,M. and Ishida,Y. (2005) Suppression of nonsense-mediated mRNA decay permits unbiased gene trapping in mouse embryonic stem cells. Nucleic Acids Res., 33, e20.
18. Osipovich,A.B., Singh,A. and Ruley,H.E. (2005) Post-entrapment genome engineering: First exon size does not affect the expression of fusion transcripts generated by gene entrapment. Genome Res., 15, 428-435.
19. Lin,Q., Donahue,S.L., Moore-Jarrett,T., Cao,S., Osipovich,A.B. and Ruley,H.E. (2006) Mutagenesis of diploid mammalian genes by gene entrapment. Nucleic Acids Res., 34, e139.
20. Maquat,L.E. (2004) Nonsense-mediated mRNA decay: Splicing, translation and mRNP dynamics. Nature Rev., 5, 89-99.
21. Xu,N., Chen,C.Y. and Shyu,A.B. (1997) Modulation of the fate of cytoplasmic mRNA by AU-rich elements: Key sequence features controlling mRNA deadenylation and decay. Mol. Cell Biol., 17, 4611-4621.
22. Tsakiridis,A., Tzouanacou,E., Larralde,O., Watts,T.M., Wilson,V., Forrester,L. and Brickman,J.M. (2007) A novel triple fusion reporter system for use in gene trap mutagenesis. Genesis, 45, 353-360.
23. Chen,W.V., Delrow,J., Corrin,P.D., Frazier,J.P. and Soriano,P. (2004) Identification and validation of PDGF transcriptional targets by microarray-coupled gene-trap mutagenesis. Nat. Genet., 36, 304-312.
24. Pear,W.S., Nolan,G.P., Scott,M.L. and Baltimore,D. (1993) Production of high-titer helper-free retroviruses by transient transfection. Proc. Natl Acad. Sci. USA, 90, 8392-8396.
25. Yao,S., Osborne,C.S., Bharadwaj,R.R., Pasceri,P., Sukonnik,T., Pannell,D., Recillas-Targa,F., West,A.G. and Ellis,J. (2003) Retrovirus silencer blocking by the cHS4 insulator is CTCF independent. Nucleic Acids Res., 31, 5317-5323.
26. Morrison,G.M. and Brickman,J.M. (2006) Conserved roles for Oct4 homologues in maintaining multipotency during early vertebrate development. Development, 133, 2011-2022.
27. Morrison,G.M., Oikonomopoulou,I., Migueles,R.P., Soneji,S., Livigni,A., Enver,T. and Brickman,J.M. (2008) Anterior definitive endoderm from ES cells reveals a novel role for FGF signaling. Cell Stem Cell, 3 402-415.
28. Zamparini,A.L., Watts,T., Gardner,C.E., Tomlinson,S.R., Johnston,G.I. and Brickman,J.M. (2006) Hex acts with beta-catenin to regulate anteroposterior patterning via a Groucho-related co-repressor and Nodal. Development, 133, 3709-3722.
29. Chambers,I., Silva,J., Colby,D., Nichols,J., Nijmeijer,B., Robertson,M., Vrana,J., Jones,K., Grotewold,L. and Smith,A. (2007) Nanog safeguards pluripotency and mediates germline development. Nature, 450, 1230-1234.
30. Ashfield,R., Patel,A.J., Bossone,S.A., Brown,H., Campbell,R.D., Marcu,K.B. and Proudfoot,N.J. (1994) MAZ-dependent termination between closely spaced human complement genes. EMBO J., 13, 5656-5667.
31. Sambrook,J. and Russell,D.W. (2001) Molecular Cloning: A Laboratory Manual, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
32. Tanaka,T.S., Davey,R.E., Lan,Q., Zandstra,P.W. and Stanford,W.L. (2008) Development of a gene-trap vector with a highly sensitive fluorescent protein reporter system for expression profiling. Genesis, 46 347-356.
33. Chappell,S.A., Edelman,G.M. and Mauro,V.P. (2000) A 9-nt segment of a cellular mRNA can function as an internal ribosome entry site (IRES) and when present in linked multiple copies greatly enhances IRES activity. Proc. Natl Acad. Sci. USA, 97, 1536-1541.
34. Nagai,T., Ibata,K., Park,E.S., Kubota,M., Mikoshiba,K. and Miyawaki,A. (2002) A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications. Nat. Biotechnol., 20, 87-90.
35. Ishida,Y. and Leder,P. (1999) RET: A poly A-trap retrovirus vector for reversible disruption and expression monitoring of genes in living cells. Nucleic Acids Res., 27, e35.
36. Hansen,G.M., Markesich,D.C., Burnett,M.B., Zhu,Q., Dionne,K.M., Richter,L.J., Finnell,R.H., Sands,A.T., Zambrowicz,B.P. and Abuin,A. (2008) Large-scale gene trapping in C57BL/6N mouse embryonic stem cells. Genome Res., 18, 1670-1679.
37. Oda,T., Kujovich,J., Reis,M., Newman,B. and Druker,B.J. (1997) Identification and characterization of two novel SH2 domain-containing proteins from a yeast two hybrid screen with the ABL tyrosine kinase. Oncogene, 15, 1255-1262.
38. Sasner,M. and Buonanno,A. (1996) Distinct N-methyl-D-aspartate receptor 2B subunit gene sequences confer neural and developmental specific expression. J. Biol. Chem., 271, 21316-21322.
39. Sato,A., Sekine,Y., Saruta,C., Nishibe,H., Morita,N., Sato,Y., Sadakata,T., Shinoda,Y., Kojima,T. and Furuichi,T. (2008) Cerebellar development transcriptome database (CDT-DB): Profiling of spatio-temporal gene expression during the postnatal development of mouse cerebellum. Neural Netw., 21, 1056-1069.
40. Nagy,E. and Maquat,L.E. (1998) A rule for termination-codon position within intron-containing genes: When nonsense affects RNA abundance. Trends Biochem. Sci., 23, 198-199.
41. Nichols,J., Zevnik,B., Anastassiadis,K., Niwa,H., Klewe-Nebenius,D., Chambers,I., Scholer,H. and Smith,A. (1998) Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4. Cell, 95, 379-391.
42. Enssle,J., Kugler,W., Hentze,M.W. and Kulozik,A.E. (1993) Determination of mRNA fate by different RNA polymerase II promoters. Proc. Natl Acad. Sci. USA, 90, 10091-10095.
43. Zetoune,A.B., Fontaniere,S., Magnin,D., Anczukow,O., Buisson,M., Zhang,C.X. and Mazoyer,S. (2008) Comparison of nonsense-mediated mRNA decay efficiency in various murine tissues. BMC Genet., 9, 83.
44. Viegas,M.H., Gehring,N.H., Breit,S., Hentze,M.W. and Kulozik,A.E. (2007) The abundance of RNPS1, a protein component of the exon junction complex, can determine the variability in efficiency of the nonsense mediated decay pathway. Nucleic Acids Res., 35, 4542-4551.
45. Mohn,F., Buhler,M. and Muhlemann,O. (2005) Nonsense-associated alternative splicing of T-cell receptor beta genes: No evidence for frame dependence. RNA, 11, 147-156.
46. Paillusson,A., Hirschi,N., Vallan,C., Azzalin,C.M. and Muhlemann,O. (2005) A GFP-based reporter system to monitor nonsense-mediated mRNA decay. Nucleic Acids Res., 33, e54.
47. Gatfield,D. and Izaurralde,E. (2004) Nonsense-mediated messenger RNA decay is initiated by endonucleolytic cleavage in Drosophila. Nature 429, 575-578.
48. Buhler,M., Paillusson,A. and Muhlemann,O. (2004) Efficient downregulation of immunoglobulin mu mRNA with premature translation-termination codons requires the 5′-half of the VDJ exon. Nucleic Acids Res., 32, 3304-3315.
49. Carter,M.S., Doskow,J., Morris,P., Li,S., Nhim,R.P., Sandstedt,S. and Wilkinson,M.F. (1995) A regulatory mechanism that detects premature nonsense codons in T-cell receptor transcripts in vivo is reversed by protein synthesis inhibitors in vitro. J. Biol. Chem., 270, 28995-29003.
50. Chambers,I., Colby,D., Robertson,M., Nichols,J., Lee,S., Tweedie,S. and Smith,A. (2003) Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells. Cell, 113, 643-655.
51. Roma,G., Cobellis,G., Claudiani,P., Maione,F., Cruz,P., Tripoli,G., Sardiello,M., Peluso,I. and Stupka,E. (2007) A novel view of the transcriptome revealed from gene trapping in mouse embryonic stem cells. Genome Res., 17, 1051-1060.
52. Hansen,J., Floss,T., Van Sloun,P., Fuchtbauer,E.M., Vauti,F., Arnold,H.H., Schnutgen,F., Wurst,W., von Melchner,H. and Ruiz,P. (2003) A large-scale, gene-driven mutagenesis approach for the functional analysis of the mouse genome. Proc. Natl Acad. Sci. USA, 100 9918-9922.
53. Cooper,L.J., Topp,M.S., Pinzon,C., Plavec,I., Jensen,M.C., Riddell,S.R. and Greenberg,P.D. (2004) Enhanced transgene expression in quiescent and activated human CD8+ T cells. Hum. Gene Ther., 15, 648-658.
54. Yenofsky,R.L., Fine,M. and Pellow,J.W. (1990) A mutant neomycin phosphotransferase II gene reduces the resistance of transformants to antibiotic selection pressure. Proc. Natl Acad. Sci. USA, 87 3435-3439.