Logic of gene regulatory networks

Current Opinion in Biotechnology

Volumn 18, Issue 4, 2007, Pages 351-354

  Materna, Stefan C ^a   Davidson, Eric H ^a  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELLS; GENES; MOLECULES;

IMPLEMENTS LOGIC FUNCTIONS; REGULATORY NETWORKS;

TRANSCRIPTION FACTORS;

CELL MATURATION; EMBRYO DEVELOPMENT; GENE CONTROL; GENETIC REGULATION; GENETIC TRANSCRIPTION; MEMBRANE FORMATION; NONHUMAN; PIGMENT CELL; PRIORITY JOURNAL; REVIEW; TRANSLATION REGULATION;

ANIMALS; CELL LINEAGE; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE REGULATORY NETWORKS; MODELS, BIOLOGICAL; SEA URCHINS;

ECHINOIDEA;

EID: 34548523700     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2007.07.008     Document Type: Review

References (19)

1. Davidson E.H. The Regulatory Genome (2006), Academic Press, San Diego. Extensive treatment of gene regulatory networks in developmental systems covering topics from cis-regulation, structure and function of GRNs, to the implications for evolution.
2. Stathopoulos A., and Levine M. Genomic regulatory networks and animal development. Dev Cell 9 (2005) 449-462
3. Istrail S., and Davidson E.H. Logic functions of the genomic cis-regulatory code. Proc Nat Acad Sci USA 102 (2005) 4954-4959. This paper is an attempt to conceptualize the events at the promotor. It illustrates the repertoire of cis-regulatory logic operations, as an approach toward a functional interpretation of the genomic regulatory code.
4. Ben-Tabou de-Leon S, Davidson EH: Gene regulation: gene control network in development. Annu Rev Biophys Biomol Struct 2007, in print.
5. Ruffins S.W., and Ettensohn C.A. A fate map of the vegetal plate of the sea urchin (Lytechinus variegatus) mesenchyme blastula. Development 122 (1996) 253-263
6. Davidson E.H., Cameron R.A., and Ransick A. Specification of cell fate in the sea urchin embryo: summary and some proposed mechanisms. Development 125 (1998) 3269-3290
7. Lai E. Notch signaling: control of cell communication and cell fate. Development 131 (2004) 965-973
8. Range R.C., Venuti J.M., and McClay D.R. LvGroucho and nuclear beta-catenin functionally compete for Tcf binding to influence activation of the endomesoderm gene regulatory network in the sea urchin embryo. Dev Biol 279 (2005) 252-267
9. Ransick A., and Davidson E.H. cis-regulatory processing of Notch signaling input to the sea urchin glial cells missing gene during mesoderm specification. Dev Biol 297 (2006) 587-602. This paper is a detailed account of gcm regulation by SuH. It teases apart the activating and repressive functions of the SuH binding sites.
10. Sherwood D.R., and McClay D.R. LvNotch signaling mediates secondary mesenchyme specification in the sea urchin embryo. Development 126 (1999) 1703-1713
11. Walton K.D., Croce J.C., Glenn T.D., Wu S.Y., and McClay R.D. Genomics and expression profiles of the Hedgehog and Notch signaling pathways in sea urchin development. Dev Biol 300 (2006) 153-164
12. Davidson E.H., Rast J.P., Oliveri P., Ransick A., Calestani C., Yuh C.H., Minokawa T., Amore G., Hinman V., Arenas-Mena C., et al. A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo. Dev Biol 246 (2002) 162-190. This paper describes the experimental techniques that are used to unravel the architecture of the GRN underlying endomesodermal development in the sea urchin and presents the first version of this network.
13. Calestani C., Rast J.P., and Davidson E.H. Isolation of pigment cell specific genes in the sea urchin embryo by differential macroarray screening. Development 130 (2003) 4587-4596
14. Oliveri P., and Davidson E.H. Development. Built to run, not fail. Science 315 (2007) 1510-1511
15. Oliveri P., Walton K.D., Davidson E.H., and McClay D.R. Repression of mesodermal fate by foxa, a key endoderm regulator of the sea urchin embryo. Development 133 (2006) 4173-4181
16. Howard-Ashby M., Materna S.C., Brown C.T., Tu Q., Oliveri P., Cameron A., and Davidson E.H. High regulatory gene use in sea urchin embryogenesis: implications for bilaterian development and evolution. Dev Biol 300 (2006) 27-34. This paper summarizes a large-scale project to discover and gather expression profiles for all transcription factors in the sea urchin genome. The vast majority of transcription factors is transcribed by late gastrulation underlining the need to act combinatorially for proper regulation of downstream genes to occur.
17. Satou Y., and Satoh N. Cataloging transcription factor and major signaling molecule genes for functional genomic studies in Ciona intestinalis. Dev Biol Evol 215 (2005) 580-596. This paper describes a project aimed at revealing the time and place where transcription factors are expressed during early development in sea squirts. This paper was the first step in establishing a GRN for early Ciona development.
18. Longabaugh W.J.R., Davidson E.H., and Bolouri H. Computational representation of developmental genetic regulatory networks. Dev Biol 283 (2005) 1-16
19. Geier F., Timmer J., and Fleck C. Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge. BMC Syst Biol 1 (2007) 11