Enhancer trapping in zebrafish using the Sleeping Beauty transposon

BMC Genomics

Volumn 5, Issue , 2004, Pages

  Balciunas, Darius ^a   Davidson, Ann E ^a,b   Sivasubbu, Sridhar ^a   Hermanson, Spencer B ^a   Welle, Zachary ^a   Ekker, Stephen C ^a  

^a Minnesota Medical School Minneapolis   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FIBROBLAST GROWTH FACTOR 8; GLYCOSIDASE; GREEN FLUORESCENT PROTEIN; MESSENGER RNA; POLY(ADENOSINE DIPHOSPHATE RIBOSE); TRANSPOSASE; ZEBRAFISH PROTEIN; POLY ADP RIBOSE GLYCOHYDROLASE; POLY ADP-RIBOSE GLYCOHYDROLASE;

ANIMAL CELL; ANIMAL TISSUE; ANTIBODY SPECIFICITY; BRAIN VENTRICLE; CONTROLLED STUDY; EMBRYO; EMBRYO DEVELOPMENT; ENHANCER REGION; FOREBRAIN; GENE CASSETTE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE INSERTION; GENE LOCUS; GENE REPLICATION; GENETIC IDENTIFICATION; GENETIC LINKAGE; GENETIC MODEL; GENETIC SCREENING; GENOMIC IN SITU HYBRIDIZATION; GERM LINE; INTRON; MESENCEPHALON; MOTONEURON; NONHUMAN; PREDICTION; PROGENY; PROTEIN DOMAIN; PROTEIN LOCALIZATION; REVIEW; RHOMBENCEPHALON; TISSUE SPECIFICITY; TRANSGENICS; TRANSPOSON; ZEBRA FISH; ANIMAL; ARTICLE; BIOSYNTHESIS; DNA SEQUENCE; GENE TRANSFER; GENETICS; GENOMICS; GERM CELL; IN SITU HYBRIDIZATION; METABOLISM; METHODOLOGY; PILOT STUDY; POLYMERASE CHAIN REACTION; PRENATAL DEVELOPMENT; PROMOTER REGION;

DANIO RERIO; INVERTEBRATA; METAZOA; VERTEBRATA;

ANIMALS; DNA TRANSPOSABLE ELEMENTS; EMBRYONIC DEVELOPMENT; ENHANCER ELEMENTS, GENETIC; GENE TRANSFER TECHNIQUES; GENOMICS; GERM CELLS; GLYCOSIDE HYDROLASES; GREEN FLUORESCENT PROTEINS; IN SITU HYBRIDIZATION; MOTOR NEURONS; PILOT PROJECTS; POLYMERASE CHAIN REACTION; PROMOTER REGIONS, GENETIC; SEQUENCE ANALYSIS, DNA; ZEBRAFISH;

EID: 9144251784     PISSN: 14712164     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2164-5-62     Document Type: Review

References (64)

1. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, et al: Initial sequencing and analysis of the human genome. [see comment][erratum appears in Nature 2001 Aug 2; 412(6846): 565 Note: Szustakowki J [corrected to Szustakowski J]. Nature 2001, 409(6822):860-921.
2. Venter JC, Adams MD, Myers EWLiPW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, et al.: The sequence of the human genome. [see comment][erratum appears in Science 2001 Jun 5;292(5523):1838]. Science 2001, 291(5507):1304-1351.
3. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigo R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, et al, Mouse Genome Sequencing C: Initial sequencing and comparative analysis of the mouse genome. [see comment]. Nature 2002, 420(6915):520-562.
4. Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera , Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, et al: Rat Genome Sequencing Project C: Genome sequence of the Brown Norway rat yields insights into mammalian evolution. [see comment]. Nature 2004, 428(6982):493-521.
5. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG: Life with 6000 genes. Science 1996, 274(546):563-547.
6. Genome sequence of the nematode C. elegans: a platform for investigating biology. The C. elegans Sequencing Consortium. Science 1998, 282(5396):2012-2018.
7. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, Gabor GL, Abril JF, Agbayani A, An HJ, Andrews-Pfannkoch C, Baldwin D, Ballew RM, Basu A, Baxendale J, Bayraktaroglu L, Beasley EM, Beeson KY, Benos PV, Berman BP, Bhandari D, Bolshakov S, Borkova D, Botchan MR, Bouck J, Brokstein P, Brottier P, Burtis KC, Busam DA, Butler H, Cadieu E, Center A, Chandra I, Cherry JM, Cawley S, Dahlke C, Davenport LB, Davies P, de Pablos B, Delcher A, Deng Z, Mays AD, Dew I, Dietz SM, Dodson K, Doup LE, Downes M, Dugan-Rocha S, Dunkov BC, Dunn P, Durbin KJ, Evangelista CC, Ferraz C, Ferriera S, Fleischmann W, Fosler C, Gabrielian AE, Garg NS, Gelbart WM, Glasser K, Glodek A, Gong F, Gorrell JH, Gu Z, Guan P, Harris M, Harris NL, Harvey D, Heiman TJ, Hernandez JR, Houck J, Hostin D, Houston KA, Howland TJ, Wei MH, et al: The genome sequence of Drosophila melanogaster. Science 2000, 287(5461): 185-2195.
8. Nobrega MA, Ovcharenko I, Afzal V, Rubin EM: Scanning human gene deserts for long-range enhancers. Science 2003, 302(5644):413.
9. Ruvinsky I, Ruvkun G: Functional tests of enhancer conservation between distantly related species. Development 2003, 130(21):5133-5142.
10. O'Kane CJ, Gehring WJ: Detection in situ of genomic regulatory elements in Drosophila. Proc Natl Acad Sci U S A 1987, 84(24):9123-9127.
11. Bellen HJ, O'Kane CJ, Wilson C, Grossniklaus U, Pearson RK, Gehring WJ: P-element-mediated enhancer detection: a versatile method to study development in Drosophila. Genes Dev 1989, 3(9 : 288-1300.
12. Bier E, Vaessin H, Shepherd S, Lee K, McCall K, Barbel S, Ackerman L, Carretto R, Uemura T, Grell E, et al.: Searching for pattern and mutation in the Drosophila genome with a P-lacZ vector. Genes Dev 1989, 3(9):1273-1287.
13. Wilson C, Pearson RK, Bellen HJ, O'Kane CJ, Grossniklaus U, Gehring WJ: P-element-mediated enhancer detection: an efficient method for isolating and characterizing developmentally regulated genes in Drosophila. Genes Dev 1989, [3(9):1301-1313.
14. Hama C, Ali Z, Kornberg TB: Region-specific recombination and expression are directed by portions of the Drosophila engrailed promoter. Genes Dev 1990, 4(7):1079-1093.
15. Kassis JA, Noll E, VanSickle EP, Odenwald WF, Perrimon N: Altering the insertional specificity of a Drosophila transposable element. Proc Natl Acad Sci U S A 1992, 89(5 ):1919-1923.
16. Mlodzik M, Hiromi Y: Enhancer Trap Method in Drosophila: Its Application to Neurobiology. Methods in Neurosciences 1992, 9:397-414.
17. Brand AH, Perrimon N: Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 1993, 118(2):401-415.
18. Phelps CB, Brand AH: Ectopic gene expression in Drosophila using GAL4 system. Methods 1998, 14(4):367-379.
19. Timmons L, Becker J, Barthmaier P, Fyrberg C, Shearn A, Fyrberg E: Green fluorescent protein/beta-galactosidase double reporters for visualizing Drosophila gene expression patterns. Dev Genet 1997, 20(4):338-347.
20. Smith D, Wohlgemuth J, Calvi BR, Franklin I, Gelbart WM: hobo enhancer trapping mutagenesis in Drosophila reveals an insertion specificity different from P elements. Genetics 1993, 135(4): 063-1076.
21. Horn C, Offen N, Nystedt S, Hacker U, Wimmer EA: piggyBacbased insertional mutagenesis and enhancer detection as a tool for functional insect genomics. Genetics 2003, 163(2): 47-661.
22. Bellen HJ: Ten years of enhancer detection: lessons from the fly. Plant Cell 1999, 11(12):2271-2281.
23. Robertson HM, Preston CR, Phillis RW, Johnson-Schlitz DM, Benz WK, Engels WR: A stable genomic source of P element transposase in Drosophila melanogaster. Genetics 1988, 118(3 ):461-470.
24. Allen ND, Cran DG, Barton SC, Hettle S, Reik W, Surani MA: Transgenes as probes for active chromosomal domains in mouse development. Nature 1988, 333(6176):852-855.
25. Kothary R, Clapoff S, Brown A, Campbell R, Peterson A, Rossant J: A transgene containing lacZ inserted into the dystonia locus is expressed in neural tube. Nature 1988, 335(6189 : 35-437.
26. Gossler A, Joyner AL, Rossant J, Skarnes WC: Mouse embryonic stem cells and reporter constructs to detect developmentally regulated genes. Science 1989, 244(4903):463-465.
27. Bonnerot C, Grimber G, Briand P, Nicolas JF: Patterns of expression of position-dependent integrated transgenes in mouse embryo. Proc Natl Acad Sci U S A 1990, 87(16 ):6331-6335.
28. Korn R, Schoor M, Neuhaus H, Henseling U, Soininen R, Zachgo J, Gossler A: Enhancer trap integrations in mouse embryonic stem cells give rise to staining patterns in chimaeric embryos with a high frequency and detect endogenous genes. Mech Dev 1992, 39(1-2): 5-109.
29. Stanford WL, Cohn JB, Cordes SP: Gene-trap mutagenesis: past, present and beyond. Nat Rev Genet 2001, 2(10): 56-768.
30. Brown A, Copeland NG, Gilbert DJ, Jenkins NA, Rossant J, Kothary R: The genomic structure of an insertional mutation in the dystonia musculorum locus. Genomics 1994, 20(3 ):371-376.
31. Ivics Z, Hackett PB, Plasterk RH, Izsvak Z: Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells. Cell 1997, 91(4): 01-510.
32. Davidson AE, Balciunas D, Mohn D, Shaffer J, Hermanson S, Sivasubbu S, Cliff MP, Hackett PB, Ekker SC: Efficient gene delivery and gene expression in zebrafish using the Sleeping Beauty transposon. Developmental Biology 2003, 263(2):191-202.
33. Gaiano N, Amsterdam A, Kawakami K, Allende M, Becker T, Hopkins N: Insertional mutagenesis and rapid cloning of essential genes in zebrafish. Nature 1996, 383(6603):829-832.
34. Chen W, Burgess S, Golling G, Amsterdam A, Hopkins N: Highthroughput selection of retrovirus producer cell lines leads to markedly improved efficiency of germ line-transmissible insertions in zebra fish. [erratum appears in J Virol 2002 May;76(10):5300]. Journal of Virology 2002, 76(5):2192-2198.
35. Jaenisch R, Jahner D, Nobis P, Simon I, Lohler J, Harbers K, Grotkopp D: Chromosomal position and activation of retroviral genomes inserted into the germ line of mice. Cell 1981, 24(2): 19-529.
36. Lacy E, Roberts S, Evans EP, Burtenshaw MD, Costantini FD: A foreign beta-globin gene in transgenic mice: integration at abnormal chromosomal positions and expression in inappropriate tissues. Cell 1983, 34(2):343-358.
37. Bayer TA, Campos-Ortega JA: A transgene containing lacZ is expressed in primary sensory neurons in zebrafish. Development 1992, 115(2):421-426.
38. Lin S, Yang S, Hopkins N: lacZ expression in germline transgenic zebrafish can be detected in living embryos. Developmental Biology 1994, 161(1):77-83.
39. Field HA, Ober EA, Roeser T, Stainier DY: Formation of the digestive system in zebrafish. I. Liver morphogenesis. Dev Biol 2003, 253(2):279-290.
40. Grabher C, Henrich T, Sasado T, Arenz A, Wittbrodt J, Furutani-Seiki M: Transposon-mediated enhancer trapping in medaka. Gene 2003, 322:57-66.
41. Johnson AD, Krieg PA: A Xenopus laevis gene encoding EF-1 alpha S, the somatic form of elongation factor 1 alpha: sequence, structure, and identification of regulatory elements required for embryonic transcription. Dev Genet 1995, 17(3):280-290.
42. Offield MF, Hirsch N, Grainger RM: The development of Xenopus tropicalis transgenic lines and their use in studying lens developmental timing in living embryos. Development 2000, 127(9):1789-1797.
43. Dupuy AJ, Clark K, Carlson CM, Fritz S, Davidson AE, Markley KM, Finley K, Fletcher CF, Ekker SC, Hackett PB, Horn S, Largaespada DA: Mammalian germ-line transgenesis by transposition. Proc Natl Acad Sci U S A 2002, 99(7):4495-4499.
44. Plasterk RH, Izsvak Z, Ivics Z: Resident aliens: the Tc1/mariner superfamily of transposable elements. Trends Genet 1999, 15(8):326-332.
45. Liu G, Aronovich EL, Cui Z, Whitley CB, Hackett PB: Excision of Sleeping Beauty transposons: parameters and applications to gene therapy. J Gene Med 2004, 6(5):574-583.
46. Lewis KE, Eisen JS: Paraxial mesoderm specifies zebrafish primary motoneuron subtype identity. Development 2004, 131(4):891-902.
47. Chambon P, Weill JD, Mandel P: Nicotinamide mononucleotide activation of new DNA-dependent polyadenylic acid synthesizing nuclear enzyme. Biochem Biophys Res Commun 1963, 11:39-43.
48. Masutani M, Nakagama H, Sugimura T: Poly(ADP-ribose) and carcinogenesis. Genes, Chromosomes & Cancer 2003, 38(4 : 39-348.
49. Cohen-Armon M, Visochek L, Katzoff A, Levitan D, Susswein AJ, Klein R, Valburn M, Schwartz JH: Long-term memory requires poluADP-ribosylation. Science 2004, 304(5678 ):1820-1822.
50. Ying W, Swanson RA: The poly(ADP-ribose) glycohydrolase inhibitor gallotannin blocks oxidative astrocyte death. Neuroreport 2000, 11(7):1385-1388.
51. Ohashi S, Kanai M, Hanai S, Uchiumi F, Maruta H, Tanuma S, Miwa M: Subcellular localization of poly(ADP-ribose) glycohydrolase in mammalian cells. Biochem Biophys Res Commun 2003, 307(4 : 15-921.
52. Sevigny MB, Silva JM, Lan WC, Alano CC, Swanson RA: Expression and activity of poly(ADP-ribose) glycohydrolase in cultured astrocytes, neurons, and C6 glioma cells. Brain Res Mol Brain Res 2003, 117(2):213-220.
53. Uchiumi F, Ikeda D, Tanuma S: Changes in the activities and gene expressions of poly(ADP-ribose) glycohydrolases during the differentiation of human promyelocytic leukemia cell line HL-60. Biochim Biophys Acta 2004, 1676(1):1-11.
54. Fukuyama K, Yoshida M, Yamashita A, Deyama T, Baba M, Suzuki A, Mohri H, Ikezawa Z, Nakajima H, Hirai S, Ohno S: MAPK upstream kinase (MUK)-binding inhibitory protein, a negative regulator of MUK/dual leucine zipper-bearing kinase/leucine zipper protein kinase. J Biol Chem 2000, 275(28):21247-21254.
55. Kohfeldt E, Sasaki T, Gohring W, Timpl R: Nidogen-2: a new basement membrane protein with diverse binding properties. J Mol Biol 1998, 282(1):99-109.
56. Kawakami Y, Rodriguez-Leon J, Koth CM, Buscher D, Itoh T, Raya A, Ng JK, Esteban CR, Takahashi S, Henrique D, Schwarz MF, Asahara H, Izpisua Belmonte JC: MKP3 mediates the cellular response to FGF8 signalling in the vertebrate limb. Nat Cell Biol 2003, 5(6 : 13-519.
57. Tsang M, Maegawa S, Kiang A, Habas R, Weinberg E, Dawid IB: A role for MKP3 in axial patterning of the zebrafish embryo. Development 2004, 131(12):2769-2779.
58. Reifers F, Walsh EC, Leger S, Stainier DY, Brand M: Induction and differentiation of the zebrafish heart requires fibroblast growth factor 8 (fgf8/acerebellar). Development 2000, 127(2): 25-235.
59. Nasevicius A, Ekker SC: Effective targeted gene 'knockdown' in zebrafish.[see comment]. Nature Genetics 2000, 26(2):216-220.
60. Gritsman K, Zhang J, Cheng S, Heckscher E, Talbot WS, Schier AF: The EGF-CFC protein one-eyed pinhead is essential for nodal signaling. Cell 1999, 97(1):121-132.
61. Klee EW, Ekker SC, Ellis LB: Target selection for Danio rerio functional genomics. Genesis 2001, 30(3):123-125.
62. Yant SR, Kay MA: Nonhomologous-end-joining factors regulate DNA repair fidelity during Sleeping Beauty element transposition in mammalian cells. Molecular & Cellular Biology 2003, 23(23):8505-8518.
63. Izsvak Z, Stuwe EE, Fiedler D, Katzer A, Jeggo PA, Ivics Z: Healing the wounds inflicted by sleeping beauty transposition by double-strand break repair in mammalian somatic cells. Molecular Cell 2004, 13(2):279-290.
64. Hermanson S, Davidson AE, Sivasubbu S, Balciunas D, Ekker SC: Sleeping Beauty Transposon for Efficient Gene Delivery. Methods in Cell Biology 2004, 77:351-364.