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PMID: 12578984 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

Regulatory gene networks and the properties of the developmental process.

Davidson EH, McClay DR, Hood L

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 Terms
Animals DNA/genetics Embryonic and Fetal Development/genetics Genome
Chemicals
DNA
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Davidson Eric H
Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA. davidson@caltech.edu
McClay David R
Hood Leroy
Investigators
1 investigators, click to expand
Davidson E H
CIT, Pasadena
References (34)
34 references, click to expand
  1. Regulation of Wnt signaling by Sox proteins: XSox17 alpha/beta and XSox3 physically interact with beta-catenin.
    Mol Cell. 1999 Oct;4(4):487-98 PMID: 10549281
  2. Requirement of SpOtx in cell fate decisions in the sea urchin embryo and possible role as a mediator of beta-catenin signaling.
    Dev Biol. 1999 Aug 15;212(2):425-39 PMID: 10433832
  3. Animal-vegetal axis patterning mechanisms in the early sea urchin embryo.
    Dev Biol. 2000 Feb 1;218(1):1-12 PMID: 10644406
  4. Roles of Hoxa1 and Hoxa2 in patterning the early hindbrain of the mouse.
    Development. 2000 Mar;127(5):933-44 PMID: 10662633
  5. Interaction between the bHLH-PAS protein Trachealess and the POU-domain protein Drifter, specifies tracheal cell fates.
    Mech Dev. 2000 Mar 1;91(1-2):163-73 PMID: 10704841
  6. Recovery of developmentally defined gene sets from high-density cDNA macroarrays.
    Dev Biol. 2000 Dec 15;228(2):270-86 PMID: 11112329
  7. SpKrl: a direct target of beta-catenin regulation required for endoderm differentiation in sea urchin embryos.
    Development. 2001 Feb;128(3):365-75 PMID: 11152635
  8. Cis-regulatory logic in the endo16 gene: switching from a specification to a differentiation mode of control.
    Development. 2001 Mar;128(5):617-29 PMID: 11171388
  9. The role of Brachyury (T) during gastrulation movements in the sea urchin Lytechinus variegatus.
    Dev Biol. 2001 Nov 1;239(1):132-47 PMID: 11784024
  10. A genomic regulatory network for development.
    Science. 2002 Mar 1;295(5560):1669-78 PMID: 11872831
  11. LvDelta is a mesoderm-inducing signal in the sea urchin embryo and can endow blastomeres with organizer-like properties.
    Development. 2002 Apr;129(8):1945-55 PMID: 11934860
  12. Modeling DNA sequence-based cis-regulatory gene networks.
    Dev Biol. 2002 Jun 1;246(1):2-13 PMID: 12027430
  13. Control of cardiac development by an evolutionarily conserved transcriptional network.
    Dev Biol. 2002 Jun 1;246(1):14-28 PMID: 12027431
  14. Elements of transcription factor network design for T-lineage specification.
    Dev Biol. 2002 Jun 1;246(1):29-44 PMID: 12027432
  15. Dorsal gradient networks in the Drosophila embryo.
    Dev Biol. 2002 Jun 1;246(1):57-67 PMID: 12027434
  16. Making worm guts: the gene regulatory network of the Caenorhabditis elegans endoderm.
    Dev Biol. 2002 Jun 1;246(1):68-85 PMID: 12027435
  17. New computational approaches for analysis of cis-regulatory networks.
    Dev Biol. 2002 Jun 1;246(1):86-102 PMID: 12027436
  18. New early zygotic regulators expressed in endomesoderm of sea urchin embryos discovered by differential array hybridization.
    Dev Biol. 2002 Jun 1;246(1):132-47 PMID: 12027439
  19. Patchy interspecific sequence similarities efficiently identify positive cis-regulatory elements in the sea urchin.
    Dev Biol. 2002 Jun 1;246(1):148-61 PMID: 12027440
  20. A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo.
    Dev Biol. 2002 Jun 1;246(1):162-90 PMID: 12027441
  21. brachyury Target genes in the early sea urchin embryo isolated by differential macroarray screening.
    Dev Biol. 2002 Jun 1;246(1):191-208 PMID: 12027442
  22. A regulatory gene network that directs micromere specification in the sea urchin embryo.
    Dev Biol. 2002 Jun 1;246(1):209-28 PMID: 12027443
  23. Modeling transcriptional regulatory networks.
    Bioessays. 2002 Dec;24(12):1118-29 PMID: 12447977
  24. Early inductive interactions are involved in restricting cell fates of mesomeres in sea urchin embryos.
    Dev Biol. 1989 Nov;136(1):140-53 PMID: 2806717
  25. The oral-aboral axis of a sea urchin embryo is specified by first cleavage.
    Development. 1989 Aug;106(4):641-7 PMID: 2562659
  26. A complete second gut induced by transplanted micromeres in the sea urchin embryo.
    Science. 1993 Feb 19;259(5098):1134-8 PMID: 8438164
  27. Micromeres are required for normal vegetal plate specification in sea urchin embryos.
    Development. 1995 Oct;121(10):3215-22 PMID: 7588056
  28. Segmental expression of Hoxa-2 in the hindbrain is directly regulated by Krox-20.
    Development. 1996 Feb;122(2):543-54 PMID: 8625806
  29. Hoxb-2 transcriptional activation in rhombomeres 3 and 5 requires an evolutionarily conserved cis-acting element in addition to the Krox-20 binding site.
    EMBO J. 1996 Oct 1;15(19):5383-96 PMID: 8895582
  30. Transient appearance of Strongylocentrotus purpuratus Otx in micromere nuclei: cytoplasmic retention of SpOtx possibly mediated through an alpha-actinin interaction.
    Dev Genet. 1996;19(3):231-7 PMID: 8952065
  31. Specification of cell fate in the sea urchin embryo: summary and some proposed mechanisms.
    Development. 1998 Sep;125(17):3269-90 PMID: 9693132
  32. Nuclear beta-catenin is required to specify vegetal cell fates in the sea urchin embryo.
    Development. 1999 Jan;126(2):345-57 PMID: 9847248
  33. LvNotch signaling mediates secondary mesenchyme specification in the sea urchin embryo.
    Development. 1999 Apr;126(8):1703-13 PMID: 10079232
  34. SpSoxB1, a maternally encoded transcription factor asymmetrically distributed among early sea urchin blastomeres.
    Development. 1999 Dec;126(23):5473-83 PMID: 10556071
Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
Published
2003-02-18
Epub
2003-00-10
Pages
1475-80
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC149855
Subset
IM
Grants
NICHD NIH HHS · P01 HD037105 · United States
NIGMS NIH HHS · GM-61005 · United States
NIGMS NIH HHS · R01 GM061005 · United States
NCRR NIH HHS · R01 RR006591 · United States
NCRR NIH HHS · RR-15044 · United States
NCRR NIH HHS · P40 RR015044 · United States
NCRR NIH HHS · RR-06591 · United States
NICHD NIH HHS · HD-37105 · United States
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