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Development. May 1, 2006; 133 (10): 1955-66.

Global analysis of the transcriptional network controlling Xenopus endoderm formation.

Sinner D , Kirilenko P , Rankin S , Wei E , Howard L , Kofron M , Heasman J , Woodland HR , Zorn AM .

A conserved molecular pathway has emerged controlling endoderm formation in Xenopus zebrafish and mice. Key genes in this pathway include Nodal ligands and transcription factors of the Mix-like paired homeodomain class, Gata4-6 zinc-finger factors and Sox17 HMG domain proteins. Although a linear epistatic pathway has been proposed, the precise hierarchical relationships between these factors and their downstream targets are largely unresolved. Here, we have used a combination of microarray analysis and loss-of-function experiments to examine the global regulatory network controlling Xenopus endoderm formation. We identified over 300 transcripts enriched in the gastrula endoderm, including most of the known endoderm regulators and over a hundred uncharacterized genes. Surprisingly only 10% of the endoderm transcriptome is regulated as predicted by the current linear model. We find that Nodal genes, Mixer and Sox17 have both shared and distinct sets of downstream targets, and that a number of unexpected autoregulatory loops exist between Sox17 and Gata4-6, between Sox17 and Bix1/Bix2/Bix4, and between Sox17 and Xnr4. Furthermore, we find that Mixer does not function primarily via Sox17 as previously proposed. These data provides new insight into the complexity of endoderm formation and will serve as valuable resource for establishing a complete endoderm gene regulatory network.

PubMed ID: 16651540
Article link: Development.
Grant support: DK064403 NIDDK NIH HHS , HD33002 NICHD NIH HHS , HD42572 NICHD NIH HHSWellcome Trust , R01 HD042572-01 NICHD NIH HHS , R01 HD042572-02 NICHD NIH HHS , R01 HD042572-03 NICHD NIH HHS , R01 HD042572-03S1 NICHD NIH HHS , R01 HD042572-04 NICHD NIH HHS , R01 HD042572 NICHD NIH HHS

Genes referenced: bix1.1 bix1.3 bix2 cdc42ep2 cxcr4 fbln1 foxa4 gata4 gjb1 gjb2 grip2 hao1 kirrel2 mixer nodal nodal1 odc1 pisd-like.2 pnhd rnf38 slc12a3.2 sox17a tbxt tmem150b wnt11 xk81a1

Morpholinos referenced: mixer MO1 mixer MO2 mixer MO3 sox17a MO1 sox17a MO2 sox17a MO3 sox17a MO4 sox17b.1 MO1

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