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Dev Biol 2009 May 15;3292:410-21. doi: 10.1016/j.ydbio.2009.02.029.
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A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo.

Su YH , Li E , Geiss GK , Longabaugh WJ , Krämer A , Davidson EH .

The current gene regulatory network (GRN) for the sea urchin embryo pertains to pregastrular specification functions in the endomesodermal territories. Here we extend gene regulatory network analysis to the adjacent oral and aboral ectoderm territories over the same period. A large fraction of the regulatory genes predicted by the sea urchin genome project and shown in ancillary studies to be expressed in either oral or aboral ectoderm by 24 h are included, though universally expressed and pan-ectodermal regulatory genes are in general not. The loci of expression of these genes have been determined by whole mount in situ hybridization. We have carried out a global perturbation analysis in which expression of each gene was interrupted by introduction of morpholino antisense oligonucleotide, and the effects on all other genes were measured quantitatively, both by QPCR and by a new instrumental technology (NanoString Technologies nCounter Analysis System). At its current stage the network model, built in BioTapestry, includes 22 genes encoding transcription factors, 4 genes encoding known signaling ligands, and 3 genes that are yet unknown but are predicted to perform specific roles. Evidence emerged from the analysis pointing to distinctive subcircuit features observed earlier in other parts of the GRN, including a double negative transcriptional regulatory gate, and dynamic state lockdowns by feedback interactions. While much of the regulatory apparatus is downstream of Nodal signaling, as expected from previous observations, there are also cohorts of independently activated oral and aboral ectoderm regulatory genes, and we predict yet unidentified signaling interactions between oral and aboral territories.

PubMed ID: 19268450
PMC ID: PMC2677136
Article link: Dev Biol
Grant support: [+]

Genes referenced: LOC100887844 LOC115925415 LOC575170 nodall
Morpholinos: LOC592057 MO1 arid3a MO3 bmp2 MO1 chrd MO2 dlxl MO1 e2f3 MO1 foxa1 MO1 foxg1 MO2 foxj1 MO1 foxk1 MO1 gemin2 MO2 gscl MO2 hes MO1 hlf MO1 hmxl1 MO1 hoxal MO2 irx4 MO2 lefty1 MO4 lhx1 MO1 lhx9 MO1 nfe2l1 MO1 nkx1 MO1 nkx2-2 MO1 nodall MO3 nr1h3 MO1 nr2c2 MO1 onecut2 MO1 otx2 MO4 sox4 MO1 tbx2 MO1 tbxt MO2 zfhx4 MO1

References [+] :
Amore, Spdeadringer, a sea urchin embryo gene required separately in skeletogenic and oral ectoderm gene regulatory networks. 2003, Pubmed, Echinobase