Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene.
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.
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Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.
Bolouri
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Davidson
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D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D015815:Cell Adhesion Molecules / Q000235:genetics* / Q000502:physiology; D003198:Computer Simulation; D004268:DNA-Binding Proteins / Q000378:metabolism; D004625:Embryo, Nonmammalian / Q000378:metabolism; D004707:Endoderm / Q000378:metabolism; D005775:Gastrula / Q000378:metabolism; D018507:Gene Expression Regulation, Developmental; D018021:Lithium Chloride / Q000494:pharmacology; D008957:Models, Genetic; D008969:Molecular Sequence Data; D016296:Mutagenesis; D011401:Promoter Regions, Genetic / Q000235:genetics / Q000502:physiology*; D011506:Proteins / Q000235:genetics* / Q000502:physiology; D012617:Sea Urchins / Q000196:embryology / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic / Q000187:drug effects
D015815:Cell Adhesion Molecules; D004268:DNA-Binding Proteins; D011506:Proteins; C061515:endo16 protein, sea urchin; D018021:Lithium Chloride