A multicassette gateway vector set for high throughput and comparative analysis in Ciona and vertebrate embryos

PLoS ONE

Volumn 2, Issue 9, 2007, Pages

  Roure, Agnès ^a   Rothbächer, Ute ^a   Robin, François ^a   Kalmar, Eva ^b   Ferone, Giustina ^c   Lamy, Clément ^a   Missero, Caterina ^c   Mueller, Ferenc ^b   Lemaire, Patrick ^a  

^a AIX MARSEILLE UNIVERSITÉ   (France)

^b KARLSRUHE INSTITUTE OF TECHNOLOGY   (Germany)

^c CEINGE BIOTECNOLOGIE AVANZATE   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL CULTURE; ARTICLE; CIONA INTESTINALIS; COMPARATIVE STUDY; CONTROLLED STUDY; ELECTROPORATION; EMBRYO; EMBRYO DEVELOPMENT; GENE CASSETTE; GENE OVEREXPRESSION; GENE VECTOR; HIGH THROUGHPUT SCREENING; MAMMAL CELL; MOLECULAR EVOLUTION; NONHUMAN; PROTEIN FUNCTION; SEQUENCE ANALYSIS; VERTEBRATE; WILD TYPE; ANIMAL; CELL LINE; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRENATAL DEVELOPMENT; REGULATORY SEQUENCE;

ASCIDIA; CIONA; CIONA INTESTINALIS; MAMMALIA; VERTEBRATA;

COMPLEMENTARY DNA; PRIMER DNA;

ANIMALS; BASE SEQUENCE; CELL LINE; CIONA INTESTINALIS; DNA PRIMERS; DNA, COMPLEMENTARY; OPEN READING FRAMES; REGULATORY SEQUENCES, NUCLEIC ACID; VERTEBRATES;

EID: 41249100736     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0000916     Document Type: Article

References (51)

1. Levine M, Tjian R (2003) Transcription regulation and animal diversity. Nature 424: 147-151.
2. Hinman VF, Nguyen AT, Cameron RA, Davidson EH (2003) Developmental gene regulatory network architecture across 500 million years of echinoderm evolution. Proc Natl Acad Sci U S A 100: 13356-13361.
3. Prud'homme B, Gompel N, Rokas A, Kassner VA, Williams TM, et al. (2006) Repeated morphological evolution through Cis-regulatory changes in a pleiotropic gene. Nature 440: 1050-1053.
4. Delsuc F, Brinkmann H, Chourrout D, Philippe H (2006) Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 439: 965-968.
5. Conklin EG (1905) The organization and cell-lineage of the ascidian egg. J Acad Nat Sci 13: 1-119.
6. Marcellini S, Technau U, Smith JC, Lemaire P (2003) Evolution of Brachyury proteins: identification of a novel regulatory domain conserved within Bilateria. Dev Biol 260: 352-361.
7. Oda-Ishii I, Bertrand V, Matsuo I, Lemaire P, Saiga H (2005) Making very similar embryos with divergent genomes: conservation of regulatory mechanisms of Otx between the ascidians Halocynthia roretzi and Ciona intestinalis. Development 132: 1663-1674.
8. Ikuta T, Yoshida N, Satoh N, Saiga H (2004) Ciona intestinalis Hox gene cluster. Its dispersed structure and residual colinear expression in development. Proc Natl Acad Sci U S A 101: 15118-15123.
9. Hartley JL, Temple GF, Brasch MA (2000) DNA cloning using in vitro site-specific recombination. Genome Res 10: 1788-1795.
10. Hope IA, Stevens J, Garner A, Hayes J, Cheo, DL, et al. (2004) Feasibility of genome-scale construction of promoter.:reporter gene fusions for expression in Caenorhabditis elegans using a multisite gateway recombination system. Genome Res 14: 2070-2075.
11. Sasaki Y, Sone T, Yahata K, Kishine H, Hotta J, et al. (2005) Multi-gene gateway clone design for expression of multiple heterologous genes in living cells: Eukaryotic clones containing two and three ORF multi-gene cassettes expressed from a single promotor. J Biotechnol.
12. Yahata K, Kishine H, Sone T, Sasaki Y, Hotta J, et al. (2005) Multi-gene gateway clone design for expression of multiple heterologous genes in living cells: conditional gene expression at near physiological levels. J Biotechnol 1118: 123-134.
13. Cheo DL, Titus SA, Byrd DR, Hartley JL, Temple GF, et al. (2004) Concerted assembly and cloning of multiple DNA segments using in vitro site-specific recombination: functional analysis of multi-segment expression clones. Genome Res 14: 2111-2120.
14. Dupuy D, Li QR, Deplancke B, Boxem M, Hato T, et al. (2004) A first version of the Caenorhabditis elegans Promoterome. Genome Res 14: 2169-2175.
15. Brasch MA, Hartley JL, Vidal M (2004) ORFeome cloning and systems biology: standardized mass production of the parts from the parts-list. Genome Res 14: 2001-2009.
16. Corbo JC, Levine M, Zeller RW (1997) Characterization of a notochord-specific enhancer from the Brachyury promoter region of the ascidian, Ciona intestinalis. Development 124: 589-602.
17. Fire A, Harrison SW, Dixon D (1990) A modular set of lacZ fusion vectors for studying gene expression in Caenorhabditis elegans. Gene 93: 189-198.
18. Pasini A, Amiel A, Rothbacher U, Roure A, Lemaire P, et al. (2006) Formation of the Ascidian Epidermal Sensory Neurons: Insights into the Origin of the Chordate Peripheral Nervous System. PLoS Biol 4: e225.
19. Kim SH, Yamamoto A, Bouwmeester T, Agius E, Robertis EM (1998) The role of paraxial protocadherin in selective adhesion and cell movements of the mesoderm during Xenopus gastrulation. Development 125: 4681-4690.
20. Moriyoshi K, Richards LJ, Akazawa C, O'Leary DD, Nakanishi S (1996) Labeling neural cells using adenoviral gene transfer of membrane-targeted GFP. Neuron 16: 255-260.
21. Carmena M, Earnshaw WC (2003) The cellular geography of aurora kinases. Nat Rev Mol Cell Biol 4: 842-854.
22. Lamy C, Rothbacher U, Caillol D, Lemaire P (2006) Ci-FoxA-a is the earliest zygotic determinant of the ascidian anterior ectoderm and directly activates Ci-sFRPI/5. Development 133: 2835-2844.
23. Sasaki Y, Sone T, Yoshida S, Yahata K, Hotta J, et al. (2004) Evidence for high specificity and efficiency of multiple recombination signals in mixed DNA cloning by the Multisite Gateway system. J Biotechnol 107: 233-243.
24. Erives A, Corbo, JC, Levine M (1998) Lineage-specific regulation of the Ciona snail gene in the embryonic mesoderm and neuroectoderm. Dev Biol 194: 213-225.
25. Bertrand V, Hudson C, Caillol D, Popovici C, Lemaire P (2003) Neural tissue in ascidian embryos is induced by FGF9/16/20, acting via a combination of maternal GATA and Ets transcription factors. Cell 115: 615-627.
26. Fanelli A, Lania G, Spagnuolo A, Di Lauro R (2003) Interplay of negative and positive signals controls endoderm-specific expression of the ascidian Cititfl gene promoter. Dev Biol 263: 12-23.
27. Lemaire P, Garrett N, Gordon JB (1995) Expression cloning of Siamois, a Xenopus homeobox gene expressed in dorsal-vegetal cells of blastulae and able to induce a complete secondary axis. Cell 81: 85-94:
28. Rottinger E, Croce J, Lhomond G, Besnardeau L, Gache C, et al. (2006) Nemo-like kinase (NLK) acts downstream of Notch/Delta signalling to downregulate TCF during mesoderm induction in the sea urchin embryo. Development 133: 4341-4353.
29. Poulain M, Furthauer M, Thisse B, Thisse C, Lepage T (2006) Zebrafish endoderm formation is regulated by combinatorial Nodal, FGF and BMP signalling. Development 133: 2189-2200.
30. Ohno M, Zannini M, Levy O, Carrasco N, di Lauro R (1999) The paired-domain transcription factor Pax8 binds to the upstream enhancer of the rat sodium/iodide symporter gene and participates in both thyroid-specific and cyclic-AMP-dependent transcription. Mol Cell Biol 19: 2051-2060.
31. Antonini D, Rossi B, Han R, Minichiello, A, Di Palma T, et al. (2006) An autoregulatory loop directs the tissue-specific expression of p63 through a long-range evolutionarily conserved enhancer. Mol Cell Biol 26: 3308-3318.
32. Ertzer R, Muller F, Hadzhiev Y, Rathnam S, Fischer N, et al. (2007) Cooperation of sonic hedgehog enhancers in midline expression. Dev Biol 301: 578-589.
33. Muller F, Chang B, Albert S, Fischer N, Tora L, et al. (1999) Intronic enhancers control expression of zebrafish sonic hedgehog in floor plate and notochord. Development 126: 2103-2116.
34. Brand L, Horler M, Nuesch E, Vassalli S, Barrell P, et al. (2006) A versatile and reliable two-component system for tissue-specific gene induction in Arabidopsis. Plant Physiol 141: 1194-1204.
35. Curtis MD, Grossniklaus U (2003) A gateway cloning vector set for high-throughput functional analysis of genes in planta. Plant Physiol 133: 462-469.
36. Walhout AJ, Temple GF, Brasch MA, Hartley JL, Lorson MA, et al. (2000) GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes. Methods Enzymol 328: 575-592.
37. Simpson JC, Wellenreuther R, Poustka A, Pepperkok R, Wiemann S (2000) Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. EMBO Rep 1: 287-292.
38. Oda H, Tsukita S (2001), Real-time imaging of cell-cell adherens junctions reveals that Drosophila mesoderm invagination begins with two phases of apical constriction of cells. Journal of Cell Science 114: 493-501.
39. Tarsitano, M, De Falco S, Colonna V, McGhee JD, Persico MG (2006) The C. elegans pvf-1 gene encodes a PDGF/VEGF-like factor able to bind mammalian VEGF receptors and to induce angiogenesis. Faseb J 20: 227-233.
40. Ruvinsky I, Ruvkun G (2003, Functional tests of enhancer conservation between distantly related species. Development 130: 5133-5142.
41. Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, et al. (2002) The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 298: 2157-2167.
42. Kusakabe T (2005) Decoding Cis-regulatory systems in ascidians. Zoolog Sci 22: 129-146.
43. Woolfe A, Goodson M, Goode DK, Snell P, McEwen GK, et al. (2005) Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol 3: e7.
44. Locascio A, Aniello F, Amoroso A, Manzanares M, Krumlauf R, et al. (1999) Patteming the ascidian nervous system: structure, expression and transgenic analysis of the CiHox3 gene. Development 126: 4737-4748.
45. Muller F, Lele Z, Varadi L, Menczel L, Orban L (1993) Efficient transient expression system based on square pulse electroporation and in vivo luciferase essay of fertilized fish eggs. FEBS Lett 324: 27-32.
46. Ho SN, Hunt HD, Horton RM, Pullen JK, Pease LR (1989) Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77: 51-59.
47. Satou Y, Yamada L, Mochizuki Y, Takatori N, Kawashima T, et al. (2002) A cDNA resource from the basal chordate Ciona intestinalis. Genesis 33: 153-154.
48. Mombaerts P, Wang F, Dulac C, Chao SK, Nemes A, et al. (1996) Visualizing an olfactory sensory map. Cell 87: 675-686.
49. Koster RW, Fraser SE (2001) Tracing transgene expression in living zebrafish embryos. Dev Biol 233: 329-346.
50. Nagai T, Ibata. K, Park ES, Kubota M, Mikoshiba K, et al. (2002) A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications. Nat Biotechnol 20: 87-90.
51. Lenart P, Bacher CP, Daigle N, Hand AR, Eils R, et al. (2005) A contractile nuclear actin network drives chromosome congression in oocytes. Nature 436: 812-818.