A protocol describing the principles of cis-regulatory analysis in the sea urchin

Nature Protocols

Volumn 3, Issue 4, 2008, Pages 710-718

  Smith, Joel ^a  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; DNA FOOTPRINTING; GENE REGULATORY NETWORK; GENE SEQUENCE; GENETIC IDENTIFICATION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; SEA URCHIN; TRANSCRIPTION REGULATION;

ANIMALS; DNA FOOTPRINTING; GENE EXPRESSION REGULATION; GENOMICS; PHYLOGENY; SEA URCHINS; SOFTWARE;

ECHINOIDEA;

EID: 42049091628     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2008.39     Document Type: Article

References (32)

1. Davidson, E.H. The Regulatory Genome: Gene Regulatory Networks in Development and Evolution. (Academic Press, San Diego, California, 2006).
2. Davidson, E.H. et al. A genomic regulatory network for development. Science 295, 1669-1678 (2002).
3. Smith, J., Theodoris, C. & Davidson, E.H. A gene regulatory network subcircuit that drives a dynamic pattern of gene expression. Science 318, 794-797 (2007).
4. Smith, J., Kraemer, E., Liu, H., Theodoris, C. & Davidson, E. A spatially dynamic cohort of regulatory genes in the endomesodermal gene network of the sea urchin embryo. Dev. Biol. 313, 863-875 (2008).
5. Yuh, C.H., Dorman, E.R., Howard, M.L. & Davidson, E.H. An otx cis-regulatory module: A key node in the sea urchin endomesoderm gene regulatory network. Dev. Biol. 269, 536-551 (2004).
6. Minokawa, T., Wikramanayake, A.H. & Davidson, E.H. cis-Regulatory inputs of the wnt8 gene in the sea urchin endomesoderm network. Dev. Biol. 288, 545-558 (2005).
7. Ransick, A. & Davidson, E.H. cis-Regulatory processing of Notch signaling input to the sea urchin glial cells missing gene during mesoderm specification. Dev. Biol. 297, 587-602 (2006).
8. Lee, P.Y., Nam, J. & Davidson, E.H. Exclusive developmental functions of gatae cis-regulatory modules in the Strongylocentrotus purpuratus embryo. Dev. Biol. 307, 434-445 (2007).
9. Revilla-i-Domingo, R., Minokawa, T. & Davidson, E.H. R11: A cis-regulatory node of the sea urchin embryo gene network that controls early expression of SpDelta in micromeres. Dev. Biol. 274, 438-451 (2004).
10. Amore, G. & Davidson, E.H. cis-Regulatory control of cyclophilin, a member of the ETS-DRI skeletogenic gene battery in the sea urchin embryo. Dev. Biol. 293, 555-564 (2006).
11. Alon, U. Network motifs: Theory and experimental approaches. Nat. Rev. Genet. 8, 450-461 (2007).
12. Alan, U. An Introduction to Systems Biology: Design Principles of Biological Circuits (Chapman & Hall/CRC, London, 2006).
13. Davidson, E.H. et al. A genomic regulatory network for development. Science 295, 1669-1678 (2002).
14. Oliveri, P. & Davidson, E.H. Gene regulatory network controlling embryonic specification in the sea urchin. Curr. Opin. Genet. Dev. 14, 351-360 (2004).
15. Clyde, D.E. et al. A self-organizing system of repressor gradients establishes segmental complexity in Drosophila. Nature 426, 849-853 (2003).
16. Stanojevic, D., Small, S. & Levine, M. Regulation of a segmentation stripe by overlapping activators and repressors in the Drosophila embryo. Science 254, 1385-1387 (1991).
17. Stathopoulos, A. & Levine, M. Genomic regulatory networks and animal development. Dev. Cell 9, 449-462 (2005).
18. Nasevicius, A. & Ekker, S.C. Effective targeted gene 'knockdown' in zebrafish. Nat. Genet. 26, 216-220 (2000).
19. Oliveri, P., Carrick, D.M. & Davidson, E.H. A regulatory gene network that directs micromere specification in the sea urchin embryo. Dev. Biol. 246, 209-228 (2002).
20. Revilla-I-Domingo, R., Oliveri, P. & Davidson, E.H. A missing link in the sea urchin embryo gene regulatory network: HesC and the double-negative specification of micromeres. Proc. Natl. Acad. Sci. USA 104, 12383-12388 (2007).
21. Cameron, R.A. et al. A sea urchin genome project: Sequence scan, virtual map, and additional resources. Proc. Natl. Acad. Sci. USA 97, 9514-9518 (2000).
22. Nam, J. et al. cis-regulatory control of the nodal gene, initiator of the sea urchin oral ectoderm gene network. Dev. Biol. 306 860-869 (2007).
23. Yuh, C.H. et al. Patchy interspecific sequence similarities efficiently identify positive cis-regulatory elements in the sea urchin. Dev. Biol. 246, 148-161 (2002).
24. Bolouri, H. & Davidson, E.H. Transcriptional regulatory cascades in development: Initial rates, not steady state, determine network kinetics. Proc. Natl. Acad. Sci. USA 100, 9371-9376 (2003).
25. Cameron, R.A. et al. An evolutionary constraint: Strongly disfavored class of change in DNA sequence during divergence of cis-regulatory modules. Proc. Natl. Acad. Sci. USA 102, 11769-11774 (2005).
26. Johnson, D.S., Mortazavi, A., Myers, R.M. & Wold, B. Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497-1502 (2007).
27. Cameron, R.A. et al. Unusual gene order and organization of the sea urchin hox cluster. J. Exp. Zoolog. B Mol. Dev. Evol. 306 45-58 (2006).
28. Yu, D. et al. An efficient recombination system for chromosome engineering in Escherichia coli. Proc. Natl. Acad. Sci. USA 97 5978-5983 (2000).
29. Rast, J.P. Transgenic manipulation of the sea urchin embryo. In Developmental Biology Protocols Vol. II (eds. Tuan, R.S. & Lo, C.W.) (Humana Press, Totowa, New Jersey, 2000).
30. Range, R.C., Venuti, J.M. & McClay, D.R. LvGroucho and nuclear beta-catenin functionally compete for Tcf binding to influence activation of the endomesoderm gene regulatory network in the sea urchin embryo. Dev. Biol. 279, 252-267 (2005).
31. Castro, B., Barolo, S., Bailey, A.M. & Posakony, J.W. Lateral inhibition in proneural clusters: cis-regulatory logic and default repression by Suppressor of Hairless. Development 132, 3333-3344 (2005).
32. Imai, K.S., Levine, M., Satoh, N. & Satou, Y. Regulatory blueprint for a chordate embryo. Science 312, 1183-1187 (2006).