ECB-ART-39361
Proc Natl Acad Sci U S A
2005 Apr 05;10214:4936-42. doi: 10.1073/pnas.0408031102.
Show Gene links
Show Anatomy links
Gene regulatory networks for development.
Levine M, Davidson EH.
???displayArticle.abstract???
The genomic program for development operates primarily by the regulated expression of genes encoding transcription factors and components of cell signaling pathways. This program is executed by cis-regulatory DNAs (e.g., enhancers and silencers) that control gene expression. The regulatory inputs and functional outputs of developmental control genes constitute network-like architectures. In this PNAS Special Feature are assembled papers on developmental gene regulatory networks governing the formation of various tissues and organs in nematodes, flies, sea urchins, frogs, and mammals. Here, we survey salient points of these networks, by using as reference those governing specification of the endomesoderm in sea urchin embryos and dorsal-ventral patterning in the Drosophila embryo.
???displayArticle.pubmedLink??? 15788537
???displayArticle.pmcLink??? PMC555974
???displayArticle.link??? Proc Natl Acad Sci U S A
???displayArticle.grants??? [+]
Genes referenced: LOC100887844 LOC115919910
References [+] :
Alberga,
The snail gene required for mesoderm formation in Drosophila is expressed dynamically in derivatives of all three germ layers.
1991, Pubmed
Alberga, The snail gene required for mesoderm formation in Drosophila is expressed dynamically in derivatives of all three germ layers. 1991, Pubmed
Amiri, Dorsoventral patterning: a direct route from ovary to embryo. 2002, Pubmed
Belvin, A conserved signaling pathway: the Drosophila toll-dorsal pathway. 1996, Pubmed
Bolouri, Modeling transcriptional regulatory networks. 2002, Pubmed
Calestani, Isolation of pigment cell specific genes in the sea urchin embryo by differential macroarray screening. 2003, Pubmed , Echinobase
Chang, The CNS midline cells control the spitz class and Egfr signaling genes to establish the proper cell fate of the Drosophila ventral neuroectoderm. 2001, Pubmed
Cornell, Vnd/nkx, ind/gsh, and msh/msx: conserved regulators of dorsoventral neural patterning? 2000, Pubmed
Cowden, The Snail repressor positions Notch signaling in the Drosophila embryo. 2002, Pubmed
Davidson, Regulatory gene networks and the properties of the developmental process. 2003, Pubmed
Davidson, A genomic regulatory network for development. 2002, Pubmed , Echinobase
Davidson, A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo. 2002, Pubmed , Echinobase
Davidson, Specification of cell fate in the sea urchin embryo: summary and some proposed mechanisms. 1998, Pubmed , Echinobase
Emily-Fenouil, GSK3beta/shaggy mediates patterning along the animal-vegetal axis of the sea urchin embryo. 1998, Pubmed , Echinobase
Frank, A group of genes required for maintenance of the amnioserosa tissue in Drosophila. 1996, Pubmed
Gabay, EGF receptor signaling induces pointed P1 transcription and inactivates Yan protein in the Drosophila embryonic ventral ectoderm. 1996, Pubmed
Golembo, The Drosophila embryonic midline is the site of Spitz processing, and induces activation of the EGF receptor in the ventral ectoderm. 1996, Pubmed
Golembo, Vein expression is induced by the EGF receptor pathway to provide a positive feedback loop in patterning the Drosophila embryonic ventral ectoderm. 1999, Pubmed
Gray, Short-range repression permits multiple enhancers to function autonomously within a complex promoter. 1994, Pubmed
Halfon, Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. 2002, Pubmed
Hinman, Developmental gene regulatory network architecture across 500 million years of echinoderm evolution. 2003, Pubmed , Echinobase
Inoue, Transcriptional network underlying Caenorhabditis elegans vulval development. 2005, Pubmed
Istrail, Logic functions of the genomic cis-regulatory code. 2005, Pubmed , Echinobase
Jiang, Binding affinities and cooperative interactions with bHLH activators delimit threshold responses to the dorsal gradient morphogen. 1993, Pubmed
Kasai, Specification of the Drosophila CNS midline cell lineage: direct control of single-minded transcription by dorsal/ventral patterning genes. 1998, Pubmed
Koide, Xenopus as a model system to study transcriptional regulatory networks. 2005, Pubmed , Echinobase
Kosman, Establishment of the mesoderm-neuroectoderm boundary in the Drosophila embryo. 1991, Pubmed
Lee, The CNS midline cells and spitz class genes are required for proper patterning of Drosophila ventral neuroectoderm. 1999, Pubmed
Lee, Regulated intracellular ligand transport and proteolysis control EGF signal activation in Drosophila. 2001, Pubmed
Leptin, twist and snail as positive and negative regulators during Drosophila mesoderm development. 1991, Pubmed
Logan, Nuclear beta-catenin is required to specify vegetal cell fates in the sea urchin embryo. 1999, Pubmed , Echinobase
Markstein, A regulatory code for neurogenic gene expression in the Drosophila embryo. 2004, Pubmed
Minokawa, cis-Regulatory inputs of the wnt8 gene in the sea urchin endomesoderm network. 2005, Pubmed , Echinobase
Morel, Repression by suppressor of hairless and activation by Notch are required to define a single row of single-minded expressing cells in the Drosophila embryo. 2000, Pubmed
Nambu, The Drosophila single-minded gene encodes a helix-loop-helix protein that acts as a master regulator of CNS midline development. 1991, Pubmed
Nilson, EGF receptor signaling in Drosophila oogenesis. 1999, Pubmed
Ochoa-Espinosa, The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila. 2005, Pubmed
Oliveri, Gene regulatory network controlling embryonic specification in the sea urchin. 2004, Pubmed , Echinobase
Oliveri, A regulatory gene network that directs micromere specification in the sea urchin embryo. 2002, Pubmed , Echinobase
Oliveri, Activation of pmar1 controls specification of micromeres in the sea urchin embryo. 2003, Pubmed , Echinobase
Papatsenko, Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo. 2005, Pubmed
Peri, Mechanisms of Gurken-dependent pipe regulation and the robustness of dorsoventral patterning in Drosophila. 2002, Pubmed
Podos, Morphogen gradients: new insights from DPP. 1999, Pubmed
Pyrowolakis, A simple molecular complex mediates widespread BMP-induced repression during Drosophila development. 2004, Pubmed
Raftery, Gradients and thresholds: BMP response gradients unveiled in Drosophila embryos. 2003, Pubmed
Reim, The T-box-encoding Dorsocross genes function in amnioserosa development and the patterning of the dorsolateral germ band downstream of Dpp. 2003, Pubmed
Revilla-i-Domingo, R11: a cis-regulatory node of the sea urchin embryo gene network that controls early expression of SpDelta in micromeres. 2004, Pubmed , Echinobase
Roth, Axis determination. Proteolytic generation of a morphogen. 1994, Pubmed
Rushlow, Transcriptional regulation of the Drosophila gene zen by competing Smad and Brinker inputs. 2001, Pubmed
Sherwood, LvNotch signaling mediates secondary mesenchyme specification in the sea urchin embryo. 1999, Pubmed , Echinobase
Sherwood, Identification and localization of a sea urchin Notch homologue: insights into vegetal plate regionalization and Notch receptor regulation. 1997, Pubmed , Echinobase
Singh, Contingent gene regulatory networks and B cell fate specification. 2005, Pubmed
Small, Regulation of even-skipped stripe 2 in the Drosophila embryo. 1992, Pubmed
Stathopoulos, Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo. 2002, Pubmed
Stathopoulos, Dorsal gradient networks in the Drosophila embryo. 2002, Pubmed
Stathopoulos, pyramus and thisbe: FGF genes that pattern the mesoderm of Drosophila embryos. 2004, Pubmed
Sweet, The role of micromere signaling in Notch activation and mesoderm specification during sea urchin embryogenesis. 1999, Pubmed , Echinobase
von Ohlen, Convergence of dorsal, dpp, and egfr signaling pathways subdivides the drosophila neuroectoderm into three dorsal-ventral columns. 2000, Pubmed
Weiss, Dorsoventral patterning in the Drosophila central nervous system: the intermediate neuroblasts defective homeobox gene specifies intermediate column identity. 1998, Pubmed
Weitzel, Differential stability of beta-catenin along the animal-vegetal axis of the sea urchin embryo mediated by dishevelled. 2004, Pubmed , Echinobase
Wharton, Smad affinity can direct distinct readouts of the embryonic extracellular Dpp gradient in Drosophila. 2004, Pubmed
Wikramanayake, beta-Catenin is essential for patterning the maternally specified animal-vegetal axis in the sea urchin embryo. 1998, Pubmed , Echinobase
Yuh, An otx cis-regulatory module: a key node in the sea urchin endomesoderm gene regulatory network. 2004, Pubmed , Echinobase
Zaffran, Early signals in cardiac development. 2002, Pubmed
Zhang, Brinker is a sequence-specific transcriptional repressor in the Drosophila embryo. 2001, Pubmed
Zinn, Slit branches out: a secreted protein mediates both attractive and repulsive axon guidance. 1999, Pubmed