Mutagenesis of diploid mammalian genes by gene entrapment

Nucleic Acids Research

Volumn 34, Issue 20, 2006, Pages

  Lin, Qing ^a   Donahue, Sarah L ^a   Moore Jarrett, Tracy ^a   Cao, Shang ^a   Osipovich, Anna B ^a   Ruley, H Earl ^a  

^a VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; NEOMYCIN; POLYADENYLIC ACID;

ANIMAL CELL; ARTICLE; CARCINOGENESIS; CELL CULTURE; CENTROMERE; CHROMOSOMAL INSTABILITY; CONTROLLED STUDY; DIPLOIDY; EMBRYONIC STEM CELL; GENE EXPRESSION; GENE FUNCTION; GENE LIBRARY; GENE LOCUS; GENE MUTATION; GENE VECTOR; GENETIC ENGINEERING; GENOME; GERM LINE; HETEROZYGOSITY LOSS; HOMOZYGOSITY; MAMMAL CELL; MITOTIC RECOMBINATION; MOLECULAR CLONING; MOUSE; MUTAGENESIS; MUTANT; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; ANIMAL; CELL LINE; GENE TARGETING; GENOMICS; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; SEQUENCE TAGGED SITE;

MAMMALIA; MUS;

ANIMALS; BASE SEQUENCE; CELL LINE; DIPLOIDY; EMBRYONIC STEM CELLS; GENE TARGETING; GENETIC VECTORS; GENOMICS; LOSS OF HETEROZYGOSITY; MICE; MOLECULAR SEQUENCE DATA; MUTAGENESIS; SEQUENCE TAGGED SITES;

EID: 33845388943     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl728     Document Type: Article

References (50)

1. Stryke,D., Kawamoto,M., Huang,C.C., Johns,S.J., King,L.A., Harper,C.A., Meng,E.C., Lee,R.E., Yee,A., L'Italien,L. et al. (2003) BayGenomics: A resource of insertional mutations in mouse embryonic stem cells. Nucleic Acids Res., 31, 278-281.
2. 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. Gen., 36, 543-544.
3. Austin,C.P., Battey,J.F., Bradley,A., Bucan,M., Capecchi,M., Collins,F.S., Dove,W.F., Duyk,G., Dymecki,S., Eppig,J.T. et al. (2004) The knockout mouse project. Nat. Genet., 36, 921-924.
4. Li,L. and Cohen,S.N. (1996) Tsg101: A novel tumor susceptibility gene isolated by controlled homozygous functional knockout of allelic loci in mammalian cells. Cell, 85, 319-329.
5. Hubbard,S.C., Walls,L., Ruley,H.E. and Muchmore,E.A. (1994) Generation of Chinese hamster ovary cell glycosylation mutants by retroviral insertional mutagenesis: Integration into a discrete locus generates mutants expressing high levels of N-glycolyneuraminic acid. J. Biol. Chem., 269, 3717-3724.
6. Organ,E.L., Sheng,J., Ruley,H.E. and Rubin,D.H. (2004) Discovery of mammalian genes that participate in virus infection. BMC Cell Biol., 5, 41.
7. Guo,G., Wang,W. and Bradley,A. (2004) Mismatch repair genes identified using genetic screens in Blm-deficient embryonic stem cells. Nature, 429, 891-895.
8. Sheng,J., Organ,E.L., Hao,C., Wells,K.S., Ruley,H.E. and Rubin,D.H. (2004) Mutations in the IGF-II pathway that confer resistance to lytic reovirus infection. BMC Cell Biol., 5, 32.
9. Murray,J.L., Mavrakis,M., McDonald,N.J., Yilla,M., Sheng,J., Bellini,W.J., Zhao,L., Le Doux,J.M., Shaw,M.W., Luo,C.C. et al. (2005) Rab9 GTPase is required for replication of human immunodeficiency virus type 1, filoviruses, and measles virus. J. Virol., 79, 11742-11751.
10. Koike,H., Horie,K., Fukuyama,H., Kondoh,G., Nagata,S. and Takeda,J. (2002) Efficient biallelic mutagenesis with Cre/loxP-mediated inter-chromosomal recombination. EMBO Rep., 3, 433-437.
11. Liu,P., Jenkins,N.A. and Copeland,N.G. (2002) Efficient Cre-loxP-induced mitotic recombination in mouse embryonic stem cells. Nat. Genet., 30, 66-72.
12. Morley,A.A. (1991) Mitotic recombination in mammalian cells in vivo. Mutat. Res., 250, 345-349.
13. Shao,C., Deng,L., Henegariu,O., Liang,L., Raikwar,N., Sahota,A., Stambrook,P.J. and Tischfield,J.A. (1999) Mitotic recombination produces the majority of recessive fibroblast variants in heterozygous mice. Proc. Natl Acad. Sci. USA, 96, 9230-9235.
14. Gupta,P.K., Sahota,A., Boyadjiev,S.A., Bye,S., Shao,C., O'Neill,J.P., Hunter,T.C., Albertini,R.J., Stambrook,P.J. and Tischfield,J.A. (1997) High frequency in vivo loss of heterozygosity is primarily a consequence of mitotic recombination. Cancer Res., 57, 1188-1193.
15. Wijnhoven,S.W., Kool,H.J., van Teijlingen,C.M., van Zeeland,A.A. and Vrieling,H. (2001) Loss of heterozygosity in somatic cells of the mouse. An important step in cancer initiation? Mutat. Res., 473, 23-36.
16. Mortensen,R.M., Conner,D.A., Chao,S., Geisterfer-Lowrance,A.A. and Seidman,J.G. (1992) Production of homozygous mutant ES cells with a single targeting construct. Mol. Cell Biol., 12, 2391-2395.
17. Paludan,K., Duch,M., Jorgensen,P., Kjeldgaard,N.O. and Pedersen,F.S. (1989) Graduated resistance to G418 leads to differential selection of cultured mammalian cells expressing the neo gene. Gene, 85, 421-426.
18. Van Sloun,P.P., Wijnhoven,S.W., Kool,H.J., Slater,R., Weeda,G., van Zeeland,A.A., Lohman,P.H. and Vrieling,H. (1998) Determination of spontaneous loss of heterozygosity mutations in Aprt heterozygous mice. Nucleic Acids Res., 26, 4888-4894.
19. Lefebvre,L., Dionne,N., Karaskova,J., Squire,J.A. and Nagy,A. (2001) Selection for transgene homozygosity in embryonic stem cells results in extensive loss of heterozygosity. Nat. Genet., 27, 257-258.
20. 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.
21. 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.
22. Mortensen,R.M. (2000) Production of a homozygous mutant embryonic stem cell line (Double Knockout). In Ausubel,F.M., Kingston,R.E., Brent,R., Moore,D.D., Seidman,J.G., Smith,J.A. and Struhl,K. (eds), Current Protocols in Molecular Biology. John Wiley and Sons Inc., New York, p. Supplement 52.
23. 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.
24. Yoshida,M., Yagi,T., Furuta,Y., Takayanagi,K., Kominami,R., Takeda,N., Tokunaga,T., Chiba,J., Ikawa,Y. and Aizawa,S. (1995) A new strategy of gene trapping in ES cells using 3′RACE. Transgenic Res., 4, 277-287.
25. Zambrowicz,B., Friedrich,G.A., Buxton,E.C., Lilleberg,S.L., Person,C. and Sands,A.T. (1998) Disruption and sequence identification of 2000 genes in mouse embryonic stem cells. Nature, 392, 608-611.
26. Hardouin,N. and Nagy,A. (2000) Gene-trap-based target site for cre-mediated transgenic insertion. Genesis, 26, 245-252.
27. Araki,K., Imaizumi,T., Sekimoto,T., Yoshinobu,K., Yoshimuta,J., Akizuki,M., Miura,K., Araki,M. and Yamamura,K. (1999) Exchangeable gene trap using the Cre/mutated lox system. Cell Mol. Biol. (Noisy-le-grand), 45, 737-750.
28. Osipovich,A.B., Singh,A. and Ruley,H.E. (2005) Post-entrapment genome engineering: Fast exon size does not affect the expression of fusion transcripts generated by gene entrapment. Genome Res., 15, 428-435.
29. Cobellis,G., Nicolaus,G., Iovino,M., Romito,A., Marra,E., Barbarisi,M., Sardiello,M., Di Giorgio,F.P., Iovino,N., Zollo,M. et al. (2005) Tagging genes with cassette-exchange sites. Nucleic Acids Res., 33, e44.
30. Zheng,B., Sage,M., Cai,W.W., Thompson,D.M., Tavsanli,B.C., Cheah,Y.C. and Bradley,A. (1999) Engineering a mouse balancer chromosome. Nat. Genet., 22, 375-378.
31. Ramirez-Solis,R., Liu,P. and Bradley,A. (1995) Chromosome engineering in mice. Nature, 378, 720-724.
32. 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.
33. 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.
34. Adra,C.N., Boer,P.H. and McBurney,M.W. (1987) Cloning and expression of the mouse pgk-1 gene and the nucleotide sequence of its promoter. Gene, 60, 65-74.
35. Lee,G. and Saito,I. (1998) Role of nucleotide sequences of loxP spacer region in Cre-mediated recombination. Gene, 216, 55-65.
36. Osipovich,A.B., White-Grindley,E.K., Hicks,G.G., Roshon,M.J., Shaffer,C., Moore,J.H. and Ruley,H.E. (2004) Activation of cryptic 3′ splice sites within introns of cellular genes following gene entrapment. Nucleic Acids Res., 32, 2912-2924.
37. Cheng,J., Kapranov,P., Drenkow,J., Dike,S., Brubaker,S., Patel,S., Long,J., Stern,D., Tammana,H., Helt,G. et al. (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science, 308, 1149-1154.
38. 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.
39. 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.
40. 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.
41. Dattani,M.T., Martinez-Barbera,J.P., Thomas,P.Q., Brickman,J.M., Gupta,R., Martensson,I.L., Toresson,H., Fox,M., Wales,J.K., Hindmarsh,P.C. et al. (1998) Mutations in the homeobox gene HESX1/Hesx1 associated with septo-optic dysplasia in human and mouse. Nat. Genet., 19, 125-133.
42. Paupe,V., Gilbert,T., Le Merrer,M., Munnich,A., Cormier-Daire,V. and El Ghouzzi,V. (2004) Recent advances in Dyggve-Melchior-Clausen syndrome. Mol. Genet. Metab., 83, 51-59.
43. Vainberg,I.E., Lewis,S.A., Rommelaere,H., Ampe,C., Vandekerckhove,J., Klein,H.L. and Cowan,N.J. (1998) Prefoldin, a chaperone that delivers unfolded proteins to cytosolic chaperonin. Cell, 93, 863-873.
44. Cao,S., Bendall,H., Hicks,G.G., Nashabi,A., Sakano,H., Shinkai,Y., Gariglio,M., Oltz,E.M. and Ruley,H.E. (2003) The high-mobility-group box protein SSRP1/T160 is essential for cell viability in day 3.5 mouse embryos. Mol. Cell Biol., 23, 5301-5307.
45. Stoler,D.L., Chen,N., Basik,M., Kahlenberg,M.S., Rodriguez-Bigas,M.A., Petrelli,N.J. and Anderson,G.R. (1999) The onset and extent of genomic instability in sporadic colorectal tumor progression. Proc. Natl Acad. Sci. USA, 96, 15121-15126.
46. Donahue,S.L., Lin,Q., Cao,S. and Ruley,H.E. (2006) Carcinogens induce genome-wide loss of heterozygosity in normal stem cells without persistent chromosomal instability. Proc. Natl Acad. Sci. USA, 103, 11642-11646.
47. Yusa,K., Horie,K., Kondoh,G., Kouno,M., Maeda,Y., Kinoshita,T. and Takeda,J. (2004) Genome-wide phenotype analysis in ES cells by regulated disruption of Bloom's syndrome gene. Nature, 429, 896-899.
48. Hicks,G.G., Shi,E.G., Li,X.M., Li,C.H., Pawlak,M. and Ruley,H.E. (1997) Functional genomics in mice by tagged sequence mutagenesis. Nat. Genet., 16, 338-344.
49. von Melchner,H., DeGregori,J.V., Rayburn,H., Reddy,S., Friedel,C. and Ruley,H.E. (1992) Selective disruption of genes expressed in totipotent embryonal stem cells. Genes Dev., 6, 919-927.
50. Wu,X., Li,Y., Crise,B. and Burgess,S.M. (2003) Transcription start regions in the human genome are favored targets for MLV integration. Science, 300, 1749-1751.