A gene regulatory network directed by zebrafish No tail accounts for its roles in mesoderm formation

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 10, 2009, Pages 3829-3834

  Morley, Rosalind H ^a   Lachani, Kim ^b   Keefe, Damian ^c   Gilchrist, Michael J ^b   Flicek, Paul ^c   Smith, James C ^a,b   Wardle, Fiona C ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

Brachyury; Chromatin immunopreciptitation; Microarray

Indexed keywords

T BOX TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; BRACHYURY GENE; CHROMATIN IMMUNOPRECIPITATION; DNA MICROARRAY; FLH GENE; GENE; GENE EXPRESSION REGULATION; GENE TARGETING; IN VITRO STUDY; MESODERM; NONHUMAN; NOTOCHORD; NTL GENE; PRIORITY JOURNAL; ZEBRA FISH;

ANIMALS; BASE SEQUENCE; BINDING SITES; BODY PATTERNING; CELL LINEAGE; CONSERVED SEQUENCE; FETAL PROTEINS; GASTRULATION; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE REGULATORY NETWORKS; HOMEODOMAIN PROTEINS; MESODERM; MOLECULAR SEQUENCE DATA; MUSCLES; PROTEIN BINDING; T-BOX DOMAIN PROTEINS; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC; ZEBRAFISH; ZEBRAFISH PROTEINS;

DANIO RERIO;

EID: 62649158882     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0808382106     Document Type: Article

References (52)

1. Imai KS, Levine M, Satoh N, Satou Y (2006) Regulatory blueprint for a chordate embryo. Science 312:1183-1187.
2. Oliveri P, Tu Q, Davidson EH (2008) Global regulatory logic for specification of an embryonic cell lineage. Proc Natl Acad Sci USA 105:5955-5962.
3. Loose M, Patient R (2004) A genetic regulatory network for Xenopus mesendoderm formation. Dev Biol 271:467-478.
4. Nikitina NV, Bronner-Fraser M (2008) Gene regulatory networks that control the specification of neural-crest cells in the lamprey. Biochim Biophys Acta, 10.1016/ j.bbagrm.2008.03.006.
5. Smith JC, Wardle FC, Loose M, Stanley E, Patient R (2007) in Current Protocols in Stem Cell Biology, eds Bhatia M, Eggan K, Elefanty A, Fisher S, Patient R, Pera M (John Wiley & Sons, New York).
6. Wardle FC, Papaioannou VE (2008) Teasing out T-box targets in early mesoderm. Curr Opin Genet Dev 18:418-425.
7. Showell C, Binder O, Conlon FL (2004) T-box genes in early embryogenesis. Dev Dyn 229:201-218.
8. Martin BL, Kimelman D (2008) Regulation of canonical Wnt signaling by Brachyury is essential for posterior mesoderm formation. Dev Cell 15:121-133.
9. Schulte-Merker S, Ho RK, Herrmann BG, Nusslein-Volhard C (1992) The protein product of the zebrafish homologue of the mouse T gene is expressed in nuclei of the germ ring and the notochord of the early embryo. Development 116:1021-1032.
10. Conlon FL, Sedgwick SG, Weston KM, Smith JC (1996) Inhibition of Xbra transcription activation causes defects in mesodermal patterning and reveals autoregulation of Xbra in dorsal mesoderm. Development 122:2427-2435.
11. Kispert A, Koschorz B, Herrmann BG (1995) The T protein encoded by Brachyury is a tissue-specific transcription factor. EMBO J 14:4763-4772.
12. Amacher SL, Draper BW, Summers BR, Kimmel CB (2002) The zebrafish T-box genes no tail and spadetail are required for development of trunk and tail mesoderm and medial floor plate. Development 129:3311-3323.
13. Draper BW, Stock DW, Kimmel CB (2003) Zebrafish fgf24 functions with fgf8 to promote posterior mesodermal development. Development 130:4639-4654.
14. Essner JJ, Laing JG, Beyer EC, Johnson RG, Hackett PB, Jr (1996) Expression of zebrafish connexin43.4 in the notochord and tail bud of wild-type and mutant no tail embryos. Dev Biol 177:449-462.
15. Goering LM, et al. (2003) An interacting network of T-box genes directs gene expression and fate in the zebrafish mesoderm. Proc Natl Acad Sci USA 100:9410-9415.
16. Griffin KJ, Amacher SL, Kimmel CB, Kimelman D (1998) Molecular identification of spadetail: regulation of zebrafish trunk and tail mesoderm formation by T-box genes. Development 125:3379-3388.
17. Joly JS, Joly C, Schulte-Merker S, Boulekbache H, Condamine H (1993) The ventral and posterior expression of the zebrafish homeobox gene eve1 is perturbed in dorsalized and mutant embryos. Development 119:1261-1275.
18. Makita R, Mizuno T, Koshida S, Kuroiwa A, Takeda H (1998) Zebrafish wnt11: pattern and regulation of the expression by the yolk cell and No tail activity. Mech Dev 71:165-176.
19. Melby AE, Kimelman D, Kimmel CB (1997) Spatial regulation of floating head expression in the developing notochord. Dev Dyn 209:156-165.
20. Thisse C, Thisse B, Schilling TF, Postlethwait JH (1993) Structure of the zebrafish snail1 gene and its expression in wild-type, spadetail and no tail mutant embryos. Development 119:1203-1215.
21. Weinberg ES, et al. (1996) Developmental regulation of zebrafish MyoD in wild-type, no tail and spadetail embryos. Development 122:271-280.
22. Tada M, Smith JC (2001) T-targets: clues to understanding the functions of T-box proteins. Dev Growth Differ 43:1-11.
23. Down TA, Hubbard TJ (2005) Nested MICA: sensitive inference of over-represented motifs in nucleic acid sequence. Nucleic Acids Res 33:1445-1453.
24. Ettwiller L, Paten B, Ramialison M, Birney E, Wittbrodt J (2007) Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation. Nat Methods 4:563-565.
25. Durbin R, Eddy SR, Krogh A, Mitchison G (1998) in Biological Sequence Analysis. (Cambridge Univ Press, Cambridge, UK).
26. Muller CW, Herrmann BG (1997) Crystallographic structure of the T domain-DNA complex of the Brachyury transcription factor. Nature 389:884-888.
27. Miller W, et al. (2007) 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res 17:1797-1808.
28. Siepel A, et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15:1034-1050.
29. Messenger NJ, et al. (2005) Functional specificity of the Xenopus T-domain protein brachyury is conferred by its ability to interact with smad1. Dev Cell 8:599-610.
30. Halpern ME, Ho RK, Walker C, Kimmel CB (1993) Induction of muscle pioneers and floor plate is distinguished by the zebrafish no tail mutation. Cell 75:99-111.
31. Schulte-Merker S, van Eeden FJ, Halpern ME, Kimmel CB, Nusslein-Volhard C (1994) No tail (ntl) is the zebrafish homologue of the mouse T (Brachyury) gene. Development 120:1009-1015.
32. Talbot WS, et al. (1995) A homeobox gene essential for zebrafish notochord development. Nature 378:150-157.
33. Halpern ME, et al. (1997) Genetic interactions in zebrafish midline development. Dev Biol 187:154-170.
34. Bruce AE, et al. (2003) The maternally expressed zebrafish T-box gene eomesodermin regulates organizer formation. Development 130:5503-5517.
35. Zhao J, Cao Y, Zhao C, Postlethwait J, Meng A (2003) An SP1-like transcription factor Spr2 acts downstream of Fgf signaling to mediate mesoderm induction. EMBO J 22:6078-6088.
36. Shimizu T, Bae YK, Muraoka O, Hibi M (2005) Interaction of Wnt and caudal-related genes in zebrafish posterior body formation. Dev Biol 279:125-141.
37. Holley SA (2007) The genetics and embryology of zebrafish metamerism. Dev Dyn 236:1422-1449.
38. Latimer AJ, Appel B (2006) Notch signaling regulates midline cell specification and proliferation in zebrafish. Dev Biol 298:392-402.
39. Lee HC, Huang HY, Lin CY, Chen YH, Tsai HJ (2006) Foxd3 mediates zebrafish myf5 expression during early somitogenesis. Dev Biol 290:359-372.
40. Glickman NS, Kimmel CB, Jones MA, Adams RJ (2003) Shaping the zebrafish notochord. Development 130:873-887.
41. Marlow F, Gonzalez EM, Yin C, Rojo C, Solnica-Krezel L (2004) No tail co-operates with non-canonical Wnt signaling to regulate posterior body morphogenesis in zebrafish. Development 131:203-216.
42. Heisenberg CP, et al. (2000) Silberblick/Wnt11 mediates convergent extension movements during zebrafish gastrulation. Nature 405:76-81.
43. Tada M, Smith JC (2000) Xwnt11 is a target of Xenopus Brachyury: regulation of gastrulation movements via Dishevelled, but not through the canonical Wnt pathway. Development 127:2227-2238.
44. Bisgrove BW, Snarr BS, Emrazian A, Yost HJ (2005) Polaris and Polycystin-2 in dorsal forerunner cells and Kupffer's vesicle are required for specification of the zebrafish left-right axis. Dev Biol 287:274-288.
45. Gourronc F, Ahmad N, Nedza N, Eggleston T, Rebagliati M (2007) Nodal activity around Kupffer's vesicle depends on the T-box transcription factors Notail and Spadetail and on Notch signaling. Dev Dyn 236:2131-2146.
46. Rast JP, Cameron RA, Poustka AJ, Davidson EH (2002) Brachyury target genes in the early sea urchin embryo isolated by differential macroarray screening. Dev Biol 246:191-208.
47. Takahashi H, et al. (1999) Brachyury downstream notochord differentiation in the ascidian embryo. Genes Dev 13:1519-1523.
48. Wardle FC, et al. (2006) Zebrafish promoter microarrays identify actively transcribed embryonic genes. Genome Biol 7:R71.
49. Martin D, et al. (2004) GOToolBox: functional analysis of gene datasets based on Gene Ontology. Genome Biol 5:R101.
50. Nusslien-Volhard C, Dahm R (2002) Zebrafish (Oxford Univ Press, Oxford, UK).
51. Longabaugh WJ, Davidson EH, Bolouri H (2005) Computational representation of developmental genetic regulatory networks. Dev Biol 283:1-16.
52. Garnett AT, et al. (2009) Identification of direct T-box target genes in the developing zebrafish mesoderm. Development 136:749-760.