Modeling DNA sequence-based cis-regulatory gene networks - PubMed (original) (raw)
Review
. 2002 Jun 1;246(1):2-13.
doi: 10.1006/dbio.2002.0617.
Affiliations
- PMID: 12027430
- DOI: 10.1006/dbio.2002.0617
Free article
Review
Modeling DNA sequence-based cis-regulatory gene networks
Hamid Bolouri et al. Dev Biol. 2002.
Free article
Abstract
Gene network analysis requires computationally based models which represent the functional architecture of regulatory interactions, and which provide directly testable predictions. The type of model that is useful is constrained by the particular features of developmentally active cis-regulatory systems. These systems function by processing diverse regulatory inputs, generating novel regulatory outputs. A computational model which explicitly accommodates this basic concept was developed earlier for the cis-regulatory system of the endo16 gene of the sea urchin. This model represents the genetically mandated logic functions that the system executes, but also shows how time-varying kinetic inputs are processed in different circumstances into particular kinetic outputs. The same basic design features can be utilized to construct models that connect the large number of cis-regulatory elements constituting developmental gene networks. The ultimate aim of the network models discussed here is to represent the regulatory relationships among the genomic control systems of the genes in the network, and to state their functional meaning. The target site sequences of the cis-regulatory elements of these genes constitute the physical basis of the network architecture. Useful models for developmental regulatory networks must represent the genetic logic by which the system operates, but must also be capable of explaining the real time dynamics of cis-regulatory response as kinetic input and output data become available. Most importantly, however, such models must display in a direct and transparent manner fundamental network design features such as intra- and intercellular feedback circuitry; the sources of parallel inputs into each cis-regulatory element; gene battery organization; and use of repressive spatial inputs in specification and boundary formation. Successful network models lead to direct tests of key architectural features by targeted cis-regulatory analysis.
(c) 2002 Elsevier Science (USA).
Similar articles
- A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo.
Davidson EH, Rast JP, Oliveri P, Ransick A, Calestani C, Yuh CH, Minokawa T, Amore G, Hinman V, Arenas-Mena C, Otim O, Brown CT, Livi CB, Lee PY, Revilla R, Schilstra MJ, Clarke PJ, Rust AG, Pan Z, Arnone MI, Rowen L, Cameron RA, McClay DR, Hood L, Bolouri H. Davidson EH, et al. Dev Biol. 2002 Jun 1;246(1):162-90. doi: 10.1006/dbio.2002.0635. Dev Biol. 2002. PMID: 12027441 - An otx cis-regulatory module: a key node in the sea urchin endomesoderm gene regulatory network.
Yuh CH, Dorman ER, Howard ML, Davidson EH. Yuh CH, et al. Dev Biol. 2004 May 15;269(2):536-51. doi: 10.1016/j.ydbio.2004.02.025. Dev Biol. 2004. PMID: 15110718 - New computational approaches for analysis of cis-regulatory networks.
Brown CT, Rust AG, Clarke PJ, Pan Z, Schilstra MJ, De Buysscher T, Griffin G, Wold BJ, Cameron RA, Davidson EH, Bolouri H. Brown CT, et al. Dev Biol. 2002 Jun 1;246(1):86-102. doi: 10.1006/dbio.2002.0619. Dev Biol. 2002. PMID: 12027436 - Developmental gene network analysis.
Revilla-i-Domingo R, Davidson EH. Revilla-i-Domingo R, et al. Int J Dev Biol. 2003;47(7-8):695-703. Int J Dev Biol. 2003. PMID: 14756345 Review. - Computational representation of developmental genetic regulatory networks.
Longabaugh WJ, Davidson EH, Bolouri H. Longabaugh WJ, et al. Dev Biol. 2005 Jul 1;283(1):1-16. doi: 10.1016/j.ydbio.2005.04.023. Dev Biol. 2005. PMID: 15907831 Review.
Cited by
- Towards a physical understanding of developmental patterning.
Negrete J Jr, Oates AC. Negrete J Jr, et al. Nat Rev Genet. 2021 Aug;22(8):518-531. doi: 10.1038/s41576-021-00355-7. Epub 2021 May 10. Nat Rev Genet. 2021. PMID: 33972772 Review. - Developmental gene regulatory networks in sea urchins and what we can learn from them.
Martik ML, Lyons DC, McClay DR. Martik ML, et al. F1000Res. 2016 Feb 22;5:F1000 Faculty Rev-203. doi: 10.12688/f1000research.7381.1. eCollection 2016. F1000Res. 2016. PMID: 26962438 Free PMC article. Review. - Eric Davidson: Steps to a gene regulatory network for development.
Rothenberg EV. Rothenberg EV. Dev Biol. 2016 Apr 15;412(2 Suppl):S7-19. doi: 10.1016/j.ydbio.2016.01.020. Epub 2016 Jan 26. Dev Biol. 2016. PMID: 26825392 Free PMC article. - A framework for the establishment of a cnidarian gene regulatory network for "endomesoderm" specification: the inputs of ß-catenin/TCF signaling.
Röttinger E, Dahlin P, Martindale MQ. Röttinger E, et al. PLoS Genet. 2012;8(12):e1003164. doi: 10.1371/journal.pgen.1003164. Epub 2012 Dec 27. PLoS Genet. 2012. PMID: 23300467 Free PMC article. - Population-specific regulation of Chmp2b by Lbx1 during onset of synaptogenesis in lateral association interneurons.
Xu J, Nonogaki M, Madhira R, Ma HY, Hermanson O, Kioussi C, Gross MK. Xu J, et al. PLoS One. 2012;7(12):e48573. doi: 10.1371/journal.pone.0048573. Epub 2012 Dec 21. PLoS One. 2012. PMID: 23284619 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Miscellaneous