The surprising complexity of the transcriptional regulation of the spdri gene reveals the existence of new linkages inside sea urchin's PMC and Oral Ectoderm Gene Regulatory Networks

Developmental Biology

Volumn 322, Issue 2, 2008, Pages 425-434

  Al Mahmud, Abdullah ^a   Amore, Gabriele ^a  

^a STAZIONE ZOOLOGICA ANTON DOHRN   (Italy)

Author keywords

cis regulation; Endomesoderm; Gene Regulatory Networks; Oral Ectoderm; PMCs; Sea urchin embryo; Spdeadringer; spdri

Indexed keywords

GENOMIC DNA; PROTEIN SPDRI; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; ECTODERM; GENE EXPRESSION; GENE REGULATORY NETWORK; IN SITU HYBRIDIZATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA EXTRACTION; SEA URCHIN; TRANSGENICS;

ECHINOIDEA;

EID: 54849373600     PISSN: 00121606     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ydbio.2008.07.036     Document Type: Article

References (37)

1. Amore G., and Davidson E. cis-Regulatory control of cyclophilin, a member of the ETS-DRI skeletogenic gene battery in the sea urchin embryo. Dev. Biol. 293 (2006) 555-564
2. Amore G., Yavrouian R., Peterson K., Ransick A., McClay D., and Davidson E. Spdeadringer, a sea urchin embryo gene required separately in skeletogenic and oral ectoderm gene regulatory networks. Dev. Biol. 261 (2003) 55-81
3. Angerer L., Oleksyn D., Levine A., Li X., Klein W., and Angerer R. Sea urchin goosecoid function links fate specification along the animal-vegetal and oral-aboral embryonic axes. Development 128 (2001) 4393-4404
4. Bradham C., and McClay D. p38 MAPK is essential for secondary axis specification and patterning in sea urchin embryos. Development 133 (2006) 21-32
5. Brown C., Rust A., Clarke P., Pan Z., Schilstra M., De Buysscher T., Griffin G., Wold B., Cameron R., Davidson E., and Bolouri H. New computational approaches for analysis of cis-regulatory networks. Dev. Biol. 246 (2002) 86-102
6. Cai R. Human CART1, a paired-class homeodomain protein, activates transcription through palindromic binding sites. Biochem. Biophys. Res. Commun. 250 (1998) 305-311
7. Cameron R., Oliveri P., Wyllie J., and Davidson E. cis-Regulatory activity of randomly chosen genomic fragments from the sea urchin. Gene. Expr. Patterns 4 (2004) 205-213
8. Coffman J., and Denegre J. Mitochondria, redox signaling and axis specification in metazoan embryos. Dev. Biol. 308 (2007) 266-280
9. Coffman J., McCarthy J., Dickey-Sims C., and Robertson A. Oral-aboral axis specification in the sea urchin embryo II. Mitochondrial distribution and redox state contribute to establishing polarity in Strongylocentrotus purpuratus. Dev. Biol. 273 (2004) 160-171
10. Consales C., and Arnone M. Functional characterization of Ets-binding sites in the sea urchin embryo: three base pair conversions redirect expression from mesoderm to ectoderm and endoderm. Gene 287 (2002) 75-81
11. Cowell I., and Hurst H. Transcriptional repression by the human bZIP factor E4BP4: definition of a minimal repression domain. Nucleic Acids Res. 22 (1994) 59-65
12. Davidson E. The regulatory genome. Gene Regulatory Networks in Development and Evolution (2006), Elsevier-Academic Press
13. Duboc V., and Lepage T. A conserved role for the nodal signaling pathway in the establishment of dorso-ventral and left-right axes in deuterostomes. J. Exp. Zoolog. B. Mol. Dev. Evol. (2006)
14. Duboc V., Röttinger E., Besnardeau L., and Lepage T. Nodal and BMP2/4 signaling organizes the oral-aboral axis of the sea urchin embryo. Dev Cell 6 (2004) 397-410
15. Ettensohn C., Illies M., Oliveri P., and De Jong D. Alx1, a member of the Cart1/Alx3/Alx4 subfamily of Paired-class homeodomain proteins, is an essential component of the gene network controlling skeletogenic fate specification in the sea urchin embryo. Development 130 (2003) 2917-2928
16. Goldberg Y., Treier M., Ghysdael J., and Bohmann D. Repression of AP-1-stimulated transcription by c-Ets-1. J. Biol. Chem. 269 (1994) 16566-16573
17. Hobert O. PCR fusion-based approach to create reporter gene constructs for expression analysis in transgenic C. elegans. Biotechniques 32 (2002) 728-730
18. Istrail S., De-Leon S., and Davidson E. The regulatory genome and the computer. Dev. Biol. 310 (2007) 187-195
19. Martin E., Consales C., Davidson E., and Arnone M. Evidence for a mesodermal embryonic regulator of the sea urchin CyIIa gene. Dev. Biol. 236 (2001) 46-63
20. McMahon A., Flytzanis C., Hough-Evans B., Katula K., Britten R., and Davidson E. Introduction of cloned DNA into sea urchin egg cytoplasm: replication and persistence during embryogenesis. Dev. Biol. 108 (1985) 420-430
21. Minokawa T., Wikramanayake A., and Davidson E. cis-Regulatory inputs of the wnt8 gene in the sea urchin endomesoderm network. Dev. Biol. 288 (2005) 545-558
22. Nam J., Su Y., Lee P., Robertson A., Coffman J., and Davidson E. Cis-regulatory control of the nodal gene, initiator of the sea urchin oral ectoderm gene network. Dev. Biol. 306 (2007) 860-869
23. Oliveri P., and Davidson E. Gene regulatory network analysis in sea urchin embryos. Methods Cell Biol. 74 (2004) 775-794
24. Oliveri P., Carrick D., and Davidson E. A regulatory gene network that directs micromere specification in the sea urchin embryo. Dev. Biol. 246 (2002) 209-228
25. Oliveri P., Davidson E., and McClay D. Activation of pmar1 controls specification of micromeres in the sea urchin embryo. Dev. Biol. 258 (2003) 32-43
26. Oliveri P., Tu Q., and Davidson E. Global regulatory logic for specification of an embryonic cell lineage. Proc. Natl. Acad. Sci. U. S. A. 105 (2008) 5955-5962
27. Otim O., Amore G., Minokawa T., McClay D., and Davidson E. SpHnf6, a transcription factor that executes multiple functions in sea urchin embryogenesis. Dev. Biol. 273 (2004) 226-243
28. Revilla-i-Domingo R., Minokawa T., and Davidson E. R11: a cis-regulatory node of the sea urchin embryo gene network that controls early expression of SpDelta in micromeres. Dev. Biol. 274 (2004) 438-451
29. Revilla-i-Domingo R., Oliveri P., and Davidson E. A missing link in the sea urchin embryo gene regulatory network: hesC and the double-negative specification of micromeres. Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 12383-12388
30. Rizzo F., Fernandez-Serra M., Squarzoni P., Archimandritis A., and Arnone M. Identification and developmental expression of the ets gene family in the sea urchin (Strongylocentrotus purpuratus). Dev. Biol. 300 (2006) 35-48
31. Sodergren E., Weinstock G., Davidson E., Cameron R., Gibbs R., Angerer R., Angerer L., Arnone M., Burgess D., Burke R., Coffman J., Dean M., Elphick M., Ettensohn C., Foltz K., Hamdoun A., Hynes R., Klein W., Marzluff W., McClay D., Morris R., Mushegian A., Rast J., Smith L., Thorndyke M., Vacquier V., GM W., G W., Zhang L., Elsik C., Ermolaeva O., Hlavina W., Hofmann G., Kitts P., Landrum M., Mackey A., Maglott D., Panopoulou G., Poustka A., Pruitt K., Sapojnikov V., Song X., Souvorov A., Solovyev V., Wei Z., Whittaker C., Worley K., Durbin K., Shen Y., Fedrigo O., Garfield D., Haygood R., Primus A., Satija R., Severson T., Gonzalez-Garay M., Jackson A., Milosavljevic A., Tong M., Killian C., Livingston B., Wilt F., Adams N., Belle R., Carbonneau S., Cheung R., Cormier P., Cosson B., Croce J., Fernandez-Guerra A., Geneviere A., Goel M., Kelkar H., Morales J., Mulner-Lorillon O., Robertson A., Goldstone J., Cole B., Epel D., Gold B., Hahn M., Howard-Ashby M., Scally M., Stegeman J., Allgood E., Cool J., Judkins K., McCafferty S., Musante A., Obar R., Rawson A., Rossetti B., Gibbons I., Hoffman M., Leone A., Istrail S., Materna S., Samanta M., Stolc V., Tongprasit W., Tu Q., Bergeron K., Brandhorst B., Whittle J., Berney K., Bottjer D., Calestani C., Peterson K., Chow E., Yuan Q., Elhaik E., Graur D., Reese J., Bosdet I., Heesun S., Marra M., Schein J., Anderson M., Brockton V., Buckley K., Cohen A., Fugmann S., Hibino T., Loza-Coll M., Majeske A., Messier C., Nair S., Pancer Z., Terwilliger D., Agca C., Arboleda E., Chen N., Churcher A., Hallbook F., Humphrey G., Idris M., Kiyama T., Liang S., Mellott D., Mu X., Murray G., Olinski R., Raible F., Rowe M., Taylor J., Tessmar-Raible K., Wang D., Wilson K., Yaguchi S., Gaasterland T., Galindo B., Gunaratne H., Juliano C., Kinukawa M., Moy G., Neill A., Nomura M., Raisch M., Reade A., Roux M., Song J., Su Y., Townley I., Voronina E., Wong J., Amore G., Branno M., Brown E., Cavalieri V., Duboc V., Duloquin L., Flytzanis C., Gache C., Lapraz F., Lepage T., Locascio A., Martinez P., Matassi G., Matranga V., Range R., Rizzo F., Rottinger E., Beane W., Bradham C., Byrum C., Glenn T., Hussain S., Manning F., Miranda E., Thomason R., Walton K., Wikramanayke A., Wu S., Xu R., Brown C., Chen L., Gray R., Lee P., Nam J., Oliveri P., Smith J., Muzny D., Bell S., Chacko J., Cree A., Curry S., Davis C., Dinh H., Dugan-Rocha S., Fowler J., Gill R., Hamilton C., Hernandez J., Hines S., Hume J., Jackson L., Jolivet A., Kovar C., Lee S., Lewis L., Miner G., Morgan M., Nazareth L., Okwuonu G., Parker D., Pu L., Thorn R., and Wright R. The genome of the sea urchin Strongylocentrotus purpuratus. Science 314 (2006) 941-952
32. Tu Q., Brown C., Davidson E., and Oliveri P. Sea urchin Forkhead gene family: phylogeny and embryonic expression. Dev. Biol. 300 (2006) 49-62
33. Wilsker D., Patsialou A., Dallas P., and Moran E. ARID proteins: a diverse family of DNA binding proteins implicated in the control of cell growth, differentiation, and development. Cell Growth Differ. 13 (2002) 95-106
34. Wilsker D., Probst L., Wain H., Maltais L., Tucker P., and Moran E. Nomenclature of the ARID family of DNA-binding proteins. Genomics 86 (2005) 242-251
35. Wilt F. Matrix and mineral in the sea urchin larval skeleton. J. Struct. Biol. 126 (1999) 216-226
36. Yon J., and Fried M. Precise gene fusion by PCR. Nucleic Acids Res. 17 (1989) 4895
37. Yuh C., Brown C., Livi C., Rowen L., Clarke P., and Davidson E. Patchy interspecific sequence similarities efficiently identify positive cis-regulatory elements in the sea urchin. Dev. Biol. 246 (2002) 148-161