DOI: 10.1126/science.279.5358.1896. Genomic Cis-Regulatory Logic: Experimental and Computational Analysis of a Sea Urchin Gene

Genomic Cis-Regulatory Logic: Experimental and Computational Analysis of a Sea Urchin Gene

10.1126/science.279.5358.1896

Crossref journal-article

American Association for the Advancement of Science (AAAS)

Science (221)

Abstract

The genomic regulatory network that controls gene expression ultimately determines form and function in each species. The operational nature of the regulatory programming specified in cis-regulatory DNA sequence was determined from a detailed functional analysis of a sea urchin control element that directs the expression of a gene in the endoderm during development. Spatial expression and repression, and the changing rate of transcription of this gene, are mediated by a complex and extended cis-regulatory system. The system may be typical of developmental cis-regulatory apparatus. All of its activities are integrated in the proximal element, which contains seven target sites for DNA binding proteins. A quantitative computational model of this regulatory element was constructed that explicitly reveals the logical interrelations hard-wired into the DNA.

Bibliography

Yuh, C.-H., Bolouri, H., & Davidson, E. H. (1998). Genomic Cis-Regulatory Logic: Experimental and Computational Analysis of a Sea Urchin Gene. Science, 279(5358), 1896â1902.

Authors 3

Chiou-Hwa Yuh (first)
Hamid Bolouri (additional)
Eric H. Davidson (additional)

References 22 Referenced 508

10.1242/dev.124.10.1851
10.1006/dbio.1994.1235
Nocente-McGrath C., Brenner C. A., Ernst S. G., ibid. 136, 264 (1989). / ibid. by Nocente-McGrath C. (1989)
10.1016/0925-4773(93)90001-E
Yuh C.-H., Davidson E. H., Development 122, 1069 (1996). (10.1242/dev.122.4.1069) / Development by Yuh C.-H. (1996)
A. Ransick and E. H. Davidson Dev. Biol. in press.
Yuh C.-H., Ransick A., Martinez P., Britten R. J., Davidson E. H., Mech. Dev. 47, 165 (1994). (10.1016/0925-4773(94)90088-4) / Mech. Dev. by Yuh C.-H. (1994)
Yuh C.-H., Moore J. G., Davidson E. H., Development 122, 4045 (1996). (10.1242/dev.122.12.4045) / Development by Yuh C.-H. (1996)
Kirchhamer C. V., Yuh C.-H., Davidson E. H., Proc. Natl. Acad. Sci. U.S.A. 93, 9322 (1996). (10.1073/pnas.93.18.9322) / Proc. Natl. Acad. Sci. U.S.A. by Kirchhamer C. V. (1996)
S. Hörstadius Experimental Embryology of Echinoderms (Clarendon Oxford 1973) Chapter 6.
10.1006/dbio.1997.8615
Gan L., et al., ibid. 167, 517 (1995). / ibid. by Gan L. (1995)
X. Li C. K. Chuang C. A. Mao L. M. Angerer W. H. Klein ibid. 187 253 (1997). (10.1006/dbio.1997.8610)
Zeller R. W., et al., Proc. Natl. Acad. Sci. U.S.A. 92, 2989 (1995). (10.1073/pnas.92.7.2989) / Proc. Natl. Acad. Sci. U.S.A. by Zeller R. W. (1995)
10.1242/dev.122.1.333
Akasaka K., et al., J. Biol. Chem. 269, 20592 (1994). (10.1016/S0021-9258(17)32034-3) / J. Biol. Chem. by Akasaka K. (1994)
Coffman J. A., Kirchhamer C. V., Harrington M. G., Davidson E. H., Development 124, 4717 (1997). (10.1242/dev.124.23.4717) / Development by Coffman J. A. (1997)
C.-H. Yuh and E. H. Davidson unpublished data.
Kirchhamer C. V., Bogarad L. D., Davidson E. H., Proc. Natl. Acad. Sci. U.S.A. 93, 13849 (1996). (10.1073/pnas.93.24.13849) / Proc. Natl. Acad. Sci. U.S.A. by Kirchhamer C. V. (1996)
Michael L. F., Alcorn J. L., Gao E., Mendelson C. R., Mol. Endocrinol. 10, 159 (1996). / Mol. Endocrinol. by Michael L. F. (1996)
C.-H. Yuh E. H. Davidson H. Bolouri data not shown.
We thank R. J. Britten and J. A. Coffman for perspicacious and critical reviews of this manuscript. We also thank many other colleagues who have discussed this work with us. Supported by a grant from the National Institute of Child Health and Human Development and by the Stowers Institute for Medical Research.

Dates

Type	When
Created	23 years, 1 month ago (July 27, 2002, 5:42 a.m.)
Deposited	1 year, 7 months ago (Jan. 13, 2024, 12:53 a.m.)
Indexed	3 weeks, 2 days ago (Aug. 6, 2025, 10:01 a.m.)
Issued	27 years, 5 months ago (March 20, 1998)
Published	27 years, 5 months ago (March 20, 1998)
Published Print	27 years, 5 months ago (March 20, 1998)

Funders 0

None

BibTeX

@article{Yuh_1998, title={Genomic Cis-Regulatory Logic: Experimental and Computational Analysis of a Sea Urchin Gene}, volume={279}, ISSN={1095-9203}, url={http://dx.doi.org/10.1126/science.279.5358.1896}, DOI={10.1126/science.279.5358.1896}, number={5358}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Yuh, Chiou-Hwa and Bolouri, Hamid and Davidson, Eric H.}, year={1998}, month=mar, pages={1896–1902} }

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