Literature DB >> 12578984

Regulatory gene networks and the properties of the developmental process.

Eric H Davidson1, David R McClay, Leroy Hood.   

Abstract

Genomic instructions for development are encoded in arrays of regulatory DNA. These specify large networks of interactions among genes producing transcription factors and signaling components. The architecture of such networks both explains and predicts developmental phenomenology. Although network analysis is yet in its early stages, some fundamental commonalities are already emerging. Two such are the use of multigenic feedback loops to ensure the progressivity of developmental regulatory states and the prevalence of repressive regulatory interactions in spatial control processes. Gene regulatory networks make it possible to explain the process of development in causal terms and eventually will enable the redesign of developmental regulatory circuitry to achieve different outcomes.

Keywords:  NASA Discipline Evolutionary Biology; Non-NASA Center

Mesh:

Substances:

Year:  2003        PMID: 12578984      PMCID: PMC149855          DOI: 10.1073/pnas.0437746100

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


  34 in total

1.  Requirement of SpOtx in cell fate decisions in the sea urchin embryo and possible role as a mediator of beta-catenin signaling.

Authors:  X Li; A H Wikramanayake; W H Klein
Journal:  Dev Biol       Date:  1999-08-15       Impact factor: 3.582

Review 2.  Animal-vegetal axis patterning mechanisms in the early sea urchin embryo.

Authors:  L M Angerer; R C Angerer
Journal:  Dev Biol       Date:  2000-02-01       Impact factor: 3.582

3.  Regulation of Wnt signaling by Sox proteins: XSox17 alpha/beta and XSox3 physically interact with beta-catenin.

Authors:  A M Zorn; G D Barish; B O Williams; P Lavender; M W Klymkowsky; H E Varmus
Journal:  Mol Cell       Date:  1999-10       Impact factor: 17.970

4.  Recovery of developmentally defined gene sets from high-density cDNA macroarrays.

Authors:  J P Rast; G Amore; C Calestani; C B Livi; A Ransick; E H Davidson
Journal:  Dev Biol       Date:  2000-12-15       Impact factor: 3.582

5.  The role of Brachyury (T) during gastrulation movements in the sea urchin Lytechinus variegatus.

Authors:  J M Gross; D R McClay
Journal:  Dev Biol       Date:  2001-11-01       Impact factor: 3.582

Review 6.  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

7.  Interaction between the bHLH-PAS protein Trachealess and the POU-domain protein Drifter, specifies tracheal cell fates.

Authors:  E Zelzer; B Z Shilo
Journal:  Mech Dev       Date:  2000-03-01       Impact factor: 1.882

8.  Roles of Hoxa1 and Hoxa2 in patterning the early hindbrain of the mouse.

Authors:  J R Barrow; H S Stadler; M R Capecchi
Journal:  Development       Date:  2000-03       Impact factor: 6.868

9.  Cis-regulatory logic in the endo16 gene: switching from a specification to a differentiation mode of control.

Authors:  C H Yuh; H Bolouri; E H Davidson
Journal:  Development       Date:  2001-03       Impact factor: 6.868

10.  SpKrl: a direct target of beta-catenin regulation required for endoderm differentiation in sea urchin embryos.

Authors:  E W Howard; L A Newman; D W Oleksyn; R C Angerer; L M Angerer
Journal:  Development       Date:  2001-02       Impact factor: 6.868

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  70 in total

Review 1.  Lineage programming: navigating through transient regulatory states via binary decisions.

Authors:  Vincent Bertrand; Oliver Hobert
Journal:  Curr Opin Genet Dev       Date:  2010-05-27       Impact factor: 5.578

Review 2.  Triple-negative breast cancer: present challenges and new perspectives.

Authors:  Franca Podo; Lutgarde M C Buydens; Hadassa Degani; Riet Hilhorst; Edda Klipp; Ingrid S Gribbestad; Sabine Van Huffel; Hanneke W M van Laarhoven; Jan Luts; Daniel Monleon; Geert J Postma; Nicole Schneiderhan-Marra; Filippo Santoro; Hans Wouters; Hege G Russnes; Therese Sørlie; Elda Tagliabue; Anne-Lise Børresen-Dale
Journal:  Mol Oncol       Date:  2010-04-24       Impact factor: 6.603

3.  Transcriptional regulatory cascades in development: initial rates, not steady state, determine network kinetics.

Authors:  Hamid Bolouri; Eric H Davidson
Journal:  Proc Natl Acad Sci U S A       Date:  2003-07-25       Impact factor: 11.205

4.  Developmental gene regulatory network architecture across 500 million years of echinoderm evolution.

Authors:  Veronica F Hinman; Albert T Nguyen; R Andrew Cameron; Eric H Davidson
Journal:  Proc Natl Acad Sci U S A       Date:  2003-10-31       Impact factor: 11.205

5.  Evolution of the yeast protein interaction network.

Authors:  Hong Qin; Henry H S Lu; Wei B Wu; Wen-Hsiung Li
Journal:  Proc Natl Acad Sci U S A       Date:  2003-10-13       Impact factor: 11.205

6.  Notch signaling, wt1 and foxc2 are key regulators of the podocyte gene regulatory network in Xenopus.

Authors:  Jeffrey T White; Bo Zhang; Débora M Cerqueira; Uyen Tran; Oliver Wessely
Journal:  Development       Date:  2010-04-28       Impact factor: 6.868

7.  Phylogenetic analysis of 5'-noncoding regions from the ABA-responsive rab16/17 gene family of sorghum, maize and rice provides insight into the composition, organization and function of cis-regulatory modules.

Authors:  Christina D Buchanan; Patricia E Klein; John E Mullet
Journal:  Genetics       Date:  2004-11       Impact factor: 4.562

Review 8.  Logic functions of the genomic cis-regulatory code.

Authors:  Sorin Istrail; Eric H Davidson
Journal:  Proc Natl Acad Sci U S A       Date:  2005-03-23       Impact factor: 11.205

Review 9.  Gene regulatory networks for development.

Authors:  Michael Levine; Eric H Davidson
Journal:  Proc Natl Acad Sci U S A       Date:  2005-03-23       Impact factor: 11.205

10.  Delayed, asynchronous, and reversible T-lineage specification induced by Notch/Delta signaling.

Authors:  Tom N Taghon; Elizabeth-Sharon David; Juan Carlos Zúñiga-Pflücker; Ellen V Rothenberg
Journal:  Genes Dev       Date:  2005-04-15       Impact factor: 11.361

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