Literature DB >> 15788537

Gene regulatory networks for development.

Michael Levine1, Eric H Davidson.   

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.

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Year:  2005        PMID: 15788537      PMCID: PMC555974          DOI: 10.1073/pnas.0408031102

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  63 in total

Review 1.  A genomic regulatory network for development.

Authors:  Eric H Davidson; Jonathan P Rast; Paola Oliveri; Andrew Ransick; Cristina Calestani; Chiou-Hwa Yuh; Takuya Minokawa; Gabriele Amore; Veronica Hinman; Cesar Arenas-Mena; Ochan Otim; C Titus Brown; Carolina B Livi; Pei Yun Lee; Roger Revilla; Alistair G Rust; Zheng jun Pan; Maria J Schilstra; Peter J C Clarke; Maria I Arnone; Lee Rowen; R Andrew Cameron; David R McClay; Leroy Hood; Hamid Bolouri
Journal:  Science       Date:  2002-03-01       Impact factor: 47.728

2.  A regulatory gene network that directs micromere specification in the sea urchin embryo.

Authors:  Paola Oliveri; Deanna M Carrick; Eric H Davidson
Journal:  Dev Biol       Date:  2002-06-01       Impact factor: 3.582

3.  A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo.

Authors:  Eric H Davidson; Jonathan P Rast; Paola Oliveri; Andrew Ransick; Cristina Calestani; Chiou-Hwa Yuh; Takuya Minokawa; Gabriele Amore; Veronica Hinman; César Arenas-Mena; Ochan Otim; C Titus Brown; Carolina B Livi; Pei Yun Lee; Roger Revilla; Maria J Schilstra; Peter J C Clarke; Alistair G Rust; Zhengjun Pan; Maria I Arnone; Lee Rowen; R Andrew Cameron; David R McClay; Leroy Hood; Hamid Bolouri
Journal:  Dev Biol       Date:  2002-06-01       Impact factor: 3.582

Review 4.  Dorsal gradient networks in the Drosophila embryo.

Authors:  Angelike Stathopoulos; Michael Levine
Journal:  Dev Biol       Date:  2002-06-01       Impact factor: 3.582

5.  Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model.

Authors:  Marc S Halfon; Yonatan Grad; George M Church; Alan M Michelson
Journal:  Genome Res       Date:  2002-07       Impact factor: 9.043

6.  Dorsoventral patterning: a direct route from ovary to embryo.

Authors:  Anahita Amiri; David Stein
Journal:  Curr Biol       Date:  2002-08-06       Impact factor: 10.834

7.  R11: a cis-regulatory node of the sea urchin embryo gene network that controls early expression of SpDelta in micromeres.

Authors:  Roger Revilla-i-Domingo; Takuya Minokawa; Eric H Davidson
Journal:  Dev Biol       Date:  2004-10-15       Impact factor: 3.582

8.  The CNS midline cells control the spitz class and Egfr signaling genes to establish the proper cell fate of the Drosophila ventral neuroectoderm.

Authors:  J Chang; I O Kim; J S Ahn; S H Kim
Journal:  Int J Dev Biol       Date:  2001-09       Impact factor: 2.203

9.  The Snail repressor positions Notch signaling in the Drosophila embryo.

Authors:  John Cowden; Michael Levine
Journal:  Development       Date:  2002-04       Impact factor: 6.868

10.  Mechanisms of Gurken-dependent pipe regulation and the robustness of dorsoventral patterning in Drosophila.

Authors:  Francesca Peri; Martin Technau; Siegfried Roth
Journal:  Development       Date:  2002-06       Impact factor: 6.868

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  238 in total

1.  Zebrafish retinoic acid receptors function as context-dependent transcriptional activators.

Authors:  Joshua S Waxman; Deborah Yelon
Journal:  Dev Biol       Date:  2011-01-27       Impact factor: 3.582

2.  Integration of an abdominal Hox complex with Pax2 yields cell-specific EGF secretion from Drosophila sensory precursor cells.

Authors:  David Li-Kroeger; Tiffany A Cook; Brian Gebelein
Journal:  Development       Date:  2012-03-21       Impact factor: 6.868

3.  On Buckling Morphogenesis.

Authors:  Celeste M Nelson
Journal:  J Biomech Eng       Date:  2016-02       Impact factor: 2.097

4.  RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo.

Authors:  Julia Zeitlinger; Alexander Stark; Manolis Kellis; Joung-Woo Hong; Sergei Nechaev; Karen Adelman; Michael Levine; Richard A Young
Journal:  Nat Genet       Date:  2007-11-11       Impact factor: 38.330

5.  Adaptation of the length scale and amplitude of the Bicoid gradient profile to achieve robust patterning in abnormally large Drosophila melanogaster embryos.

Authors:  David Cheung; Cecelia Miles; Martin Kreitman; Jun Ma
Journal:  Development       Date:  2013-11-27       Impact factor: 6.868

6.  SpGataE, a Strongylocentrotus purpuratus ortholog of mammalian Gata4/5/6: protein expression, interaction with putative target gene spec2a, and identification of friend of Gata factor SpFog1.

Authors:  Takae Kiyama; William H Klein
Journal:  Dev Genes Evol       Date:  2007-08-21       Impact factor: 0.900

7.  The Hox transcription factor Ubx stabilizes lineage commitment by suppressing cellular plasticity in Drosophila.

Authors:  Katrin Domsch; Julie Carnesecchi; Vanessa Disela; Jana Friedrich; Nils Trost; Olga Ermakova; Maria Polychronidou; Ingrid Lohmann
Journal:  Elife       Date:  2019-05-03       Impact factor: 8.140

8.  Systems biology of embryogenesis.

Authors:  Lucas B Edelman; Sriram Chandrasekaran; Nathan D Price
Journal:  Reprod Fertil Dev       Date:  2010       Impact factor: 2.311

9.  Spatiotemporal distribution patterns of oligosaccharides during early embryogenesis in the starfish Patiria pectinifera.

Authors:  Takuya Doihara; Yuji Miguchi; Kyojy Miyawaki; Tetsuya Shimokawa; Fumihiko Hamada; Naoto Kobayashi; Seiji Matsuda
Journal:  Dev Genes Evol       Date:  2009-03-17       Impact factor: 0.900

10.  Maps of cis-Regulatory Nodes in Megabase Long Genome Segments are an Inevitable Intermediate Step Toward Whole Genome Functional Mapping.

Authors:  Lev G Nikolaev; Sergey B Akopov; Igor P Chernov; Eugene D Sverdlov
Journal:  Curr Genomics       Date:  2007-04       Impact factor: 2.236

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