title: A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo.
abstract: We present the current form of a provisional DNA sequence-based regulatory gene network that explains in outline how endomesodermal specification in the sea urchin embryo is controlled. The model of the network is in a continuous process of revision and growth as new genes are added and new experimental results become available; see http://www.its.caltech.edu/~mirsky/endomeso.htm (End-mes Gene Network Update) for the latest version. The network contains over 40 genes at present, many newly uncovered in the course of this work, and most encoding DNA-binding transcriptional regulatory factors. The architecture of the network was approached initially by construction of a logic model that integrated the extensive experimental evidence now available on endomesoderm specification. The internal linkages between genes in the network have been determined functionally, by measurement of the effects of regulatory perturbations on the expression of all relevant genes in the network. Five kinds of perturbation have been applied: (1) use of morpholino antisense oligonucleotides targeted to many of the key regulatory genes in the network; (2) transformation of other regulatory factors into dominant repressors by construction of Engrailed repressor domain fusions; (3) ectopic expression of given regulatory factors, from genetic expression constructs and from injected mRNAs; (4) blockade of the beta-catenin/Tcf pathway by introduction of mRNA encoding the intracellular domain of cadherin; and (5) blockade of the Notch signaling pathway by introduction of mRNA encoding the extracellular domain of the Notch receptor. The network model predicts the cis-regulatory inputs that link each gene into the network. Therefore, its architecture is testable by cis-regulatory analysis. Strongylocentrotus purpuratus and Lytechinus variegatus genomic BAC recombinants that include a large number of the genes in the network have been sequenced and annotated. Tests of the cis-regulatory predictions of the model are greatly facilitated by interspecific computational sequence comparison, which affords a rapid identification of likely cis-regulatory elements in advance of experimental analysis. The network specifies genomically encoded regulatory processes between early cleavage and gastrula stages. These control the specification of the micromere lineage and of the initial veg(2) endomesodermal domain; the blastula-stage separation of the central veg(2) mesodermal domain (i.e., the secondary mesenchyme progenitor field) from the peripheral veg(2) endodermal domain; the stabilization of specification state within these domains; and activation of some downstream differentiation genes. Each of the temporal-spatial phases of specification is represented in a subelement of the network model, that treats regulatory events within the relevant embryonic nuclei at particular stages.
authors.affiliation: Division of Biology, California Institute of Technology, Pasadena 91125, USA. davidson@caltech.edu
authors.forename: Eric H
authors.initials: EH
authors.lastname: Davidson
authors.forename: Jonathan P
authors.initials: JP
authors.lastname: Rast
authors.forename: Paola
authors.initials: P
authors.lastname: Oliveri
authors.forename: Andrew
authors.initials: A
authors.lastname: Ransick
authors.forename: Cristina
authors.initials: C
authors.lastname: Calestani
authors.forename: Chiou-Hwa
authors.initials: CH
authors.lastname: Yuh
authors.forename: Takuya
authors.initials: T
authors.lastname: Minokawa
authors.forename: Gabriele
authors.initials: G
authors.lastname: Amore
authors.forename: Veronica
authors.initials: V
authors.lastname: Hinman
authors.forename: César
authors.initials: C
authors.lastname: Arenas-Mena
authors.forename: Ochan
authors.initials: O
authors.lastname: Otim
authors.forename: C Titus
authors.initials: CT
authors.lastname: Brown
authors.forename: Carolina B
authors.initials: CB
authors.lastname: Livi
authors.forename: Pei Yun
authors.initials: PY
authors.lastname: Lee
authors.forename: Roger
authors.initials: R
authors.lastname: Revilla
authors.forename: Maria J
authors.initials: MJ
authors.lastname: Schilstra
authors.forename: Peter J C
authors.initials: PJ
authors.lastname: Clarke
authors.forename: Alistair G
authors.initials: AG
authors.lastname: Rust
authors.forename: Zhengjun
authors.initials: Z
authors.lastname: Pan
authors.forename: Maria I
authors.initials: MI
authors.lastname: Arnone
authors.forename: Lee
authors.initials: L
authors.lastname: Rowen
authors.forename: R Andrew
authors.initials: RA
authors.lastname: Cameron
authors.forename: David R
authors.initials: DR
authors.lastname: McClay
authors.forename: Leroy
authors.initials: L
authors.lastname: Hood
authors.forename: Hamid
authors.initials: H
authors.lastname: Bolouri
mesh_terms: D000818:Animals; D004707:Endoderm; D005809:Genes, Regulator; D008648:Mesoderm; D008954:Models, Biological; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012617:Sea Urchins / Q000196:embryology*
chemical_list: D012333:RNA, Messenger