Transposons as tools for enhancer trap screens in vertebrates

Genome Biology

Volumn 8, Issue SUPPL. 1, 2007, Pages

  Korzh, Vladimir ^a,b  

^a INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Singapore)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIN; BETA GLOBIN; CYTOKERATIN 8; CYTOSKELETON PROTEIN; DNA; ELONGATION FACTOR 1ALPHA; ENHANCED GREEN FLUORESCENT PROTEIN; TRANSCRIPTION FACTOR GATA 2; YELLOW FLUORESCENT PROTEIN;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; CELL SPECIFICITY; COMPARATIVE GENE MAPPING; DNA FLANKING REGION; DNA SEQUENCE; ENHANCER REGION; GENE INSERTION; GENE INTERACTION; GENETIC ANALYSIS; GENETIC SCREENING; NONHUMAN; ORGANOGENESIS; POLYMERASE CHAIN REACTION; PROMOTER REGION; PROTEIN EXPRESSION; REGULATOR GENE; REVIEW; TISSUE SPECIFICITY; TRANSGENICS; TRANSPOSON; VERTEBRATE; ANIMAL; GENETICS; ZEBRA FISH;

DANIO RERIO; ORYZIINAE; VERTEBRATA;

ANIMALS; DNA TRANSPOSABLE ELEMENTS; ENHANCER ELEMENTS (GENETICS); PROMOTER REGIONS (GENETICS); VERTEBRATES; ZEBRAFISH;

EID: 38449119082     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2007-8-s1-s8     Document Type: Review

References (45)

1. Kawakami K Transposon tools and methods in zebrafish. Dev Dyn 2005 234 244-254 16110506
2. Miskey C Izsvak Z Kawakami K Ivics I DNA transposons in vertebrate functional genomics. Cell Mol Life Sci 2005 62 629-641 15770416
3. Wadman S Clark K Hackett PB Fishing for answers with transposons. Mar Biotechnol (NY) 2005 7 135-141 15864468
4. Weiser KC Justice MJ Sleeping Beauty awakens. Nature 2005 436 184-186 16015313
5. Chen WJ Orti G Meyer A Novel evolutionary relationship among four fish model systems. Trends Genet 2004 26 424-431
6. Kawakami K Takeda H Kawakami N Kobayashi M Matsuda N Mishina M A transposon-mediated gene trap approach identifies developmentally regulated genes in zebrafish. Dev Cell 2004 7 133-144 15239961
7. Raz E van Luenen HG Schaerringer B Plasterk RH Driever W Transposition of the nematode Caenorhabditis elegans Tc3 element in the zebrafish Danio rerio. Curr Biol 1998 8 82-88 9427643
8. Kawakami K Shima A Kawakami N Identification of a functional transposase of the Tol2 element, an Ac-like element from the Japanese medaka fish, and its transposition in the zebrafish germ lineage. Proc Natl Acad Sci USA 2000 97 11403-11408 17212 11027340
9. 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. Dev Biol 2003 263 191-202 14597195
10. Parinov S Kondrichin I Korzh V Emelyanov A Tol2 transposon-mediated enhancer trap to identify developmentally regulated zebrafish genes in vivo. Dev Dyn 2004 231 449-459 15366023
11. Fadool JM Hartl DL Dowling JE Transposition of the mariner element from Drosophila mauritiana in zebrafish. Proc Natl Acad Sci USA 1998 95 5182-5186 20235 9560250
12. Szabo M Muller F Kiss J Balduf C Strahle U Olasz F Transposition and targeting of the prokaryotic mobile element IS30 in zebrafish. FEBS Lett 2003 550 46-50 12935884
13. Miskey C Izsvak Z Plasterk RH Ivics Z The Frog Prince: A reconstructed transposon from Rana pipiens with high transpositional activity in vertebrate cells. Nucleic Acids Res 2003 31 6873-6881 290277 14627820
14. Balciunas D Davidson AE Sivasubbu S Hermanson SB Welle Z Ekker SC Enhancer trapping in zebrafish using the Sleeping Beauty transposon. BMC Genomics 2004 5 62 520745 15347431
15. Emelyanov A Gao Y Naqvi NI Parinov S Trans-kingdom transposition of the maize Dissociation element. Genetics 2006 174 1095-1104 1667081 16951067
16. Parinov S Emelyanov A Transposable elements in fish functional genomics: technical challenges and perspectives. Genome Biol 2007 8 Suppl 1 S6
17. 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 91 501-510 9390559
18. Grabher C Henrich T Sasado T Arenz A Wittbrodt J Furutani-Seiki M Transposon-mediated enhancer trapping in medaka. Gene 2003 322 57-66 14644497
19. Kazazian HH Mobile elements: Drivers of genome evolution. Science 2004 303 1626-1632 15016989
20. Ostertag EM DeBerardinis RJ Goodier JL Zhang Y Yang N Gerton GL Kazazian HH Jr A mouse model of human L1 retrotransposition. Nat Genet 2002 32 655-60 12415270
21. Bourc'his D Bestor TH Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 2004 431 96-99 15318244
22. Bestor TH Transposons reanimated in mice. Cell 2005 122 322-325 16096053
23. Ellingsen S Laplante MA Konig M Kikuta H Furmanek T Hoivik EA Becker TS Large-scale enhancer detection in the zebrafish genome. Development 2005 132 3799-3811 16049110
24. Wu X Li Y Crise B Burgess SM Transcription start regions in the human genome are favored targets for MLV integration. Science 2003 300 1749-1751 12805549
25. Bellen HJ Ten years of enhancer detection: Lessons from the fly. Plant Cell 1999 11 2271-2281 144146 10590157
26. Wijgerde M Grosveld F Fraser P Transcription complex stability and chromatin dynamics in vivo. Nature 1995 377 209-213 7675106
27. Grosveld F de Boer E Dillon N Gribnau J McMorrow T Milot E Trimborn T Wijgerde M Fraser P The dynamics of globin gene expression and position effects. Novartis Found Symp 1998 214 67-79 9601012
28. Bulger M Groudine M Lopping versus linking: Toward a model for long-distance gene activation. Genes Dev 1999 13 2465-2477 10521391
29. Carter D Chakalova L Osborne CS Dai Y-F Fraser P Long-range chromatin regulatory interactions in vivo. Nat Genet 2002 32 623-626 12426570
30. Ronshaugen M Levine M Visualization of trans-homolog enhancer-promoter interactions at the Abd-B Hox locus in the Drosophila embryo. Dev Cell 2004 7 925-932 15572134
31. Duncan IW Transvection effects in Drosophila. Annu Rev Genet 2002 36 521-556 12429702
32. Müller F Williams DW Kobolak J Gauvry L Goldspink G Orban L Maclean N Activator effect of coinjected enhancers on the muscle-specific expression of promoters in zebrafish embryos. Mol Reprod Dev 1997 47 404-412 9211424
33. Müller F Chang B Albert S Fischer N Tora L Strähle U Intronic enhancers control expression of zebrafish sonic hedgehog in floor plate and notochord. Development 1999 126 2103-2116 10207136
34. Chong SW Nguyen TT Chu LT Jiang YJ Korzh V Zebrafish id2 developmental expression pattern contains evolutionary conserved and species-specific characteristics. Dev Dynam 2005 234 1055-1063
35. Choo BG Kondrichin I Parinov S Emelyanov A Go W Toh WC Korzh V Zebrafish transgenic Enhancer TRAP line database (ZETRAP). BMC Dev Biol 2006 6 5 1386650 16478534
36. Zebrafish Enhancer TRAP lines database http://plover.imcb.a-star.edu.sg/ ~zetrap/ZETRAP.htm
37. Balciunas D Wangensteen KJ Wilber A Bell J Geurts AM Sivasubbu S Wang X Hackett PB Largaespada DA McIvor RS et al Harnessing a high cargo-capacity transposon for genetic applications in vertebrates. PLoS Genet 2006 2 e169 1635535 17096595
38. Urasaki A Morvan G Kawakami K Functional dissection of the Tol2 transposable element identified the minimal cis-sequence and a highly repetitive sequence in the subterminal region essential for transposition. Genetics 2006 174 639-649 1602067 16959904
39. Gomez-Skarmeta JL Lenhard B Becker TS New technologies, new findings, and new concepts in the study of vertebrate cis-regulatory sequences. Dev Dynam 2006 235 870-885
40. Lee AP Koh EGL Tay A Brenner S Venkatesh B Highly conserved syntenic blocks at the vertebrate Hox loci and conserved regulatory elements within and outside Hox gene clusters. Proc Natl Acad Sci USA 2006 103 69946999 1459007 16636282
41. Müller F Blader P Strähle U Search for enhancers: Teleost models in comparative genomic and transgenic analysis of cis regulatory elements. Bioessays 2002 24 564-572 12111739
42. Plessy C Dickmeis T Chalmel F Strähle U Enhancer sequence conservation between vertebrates is favoured in developmental regulator genes. Trends Genet 2005 21 207-210 15797614
43. Fisher S Grice EA Vinton RM Bessling SL McCallion AS Conservation of RET regulatory function from human to zebrafish without sequence similarity. Science 2006 312 276-279 16556802
44. Fugu rubripes v4.0 http://genome.jgi-psf.org/Takru4/Takru4.home.html
45. Tetraodon Genome Browser http://www.genoscope.cns.fr/externe/tetranew/