XB-ART-402Development. May 1, 2006; 133 (10): 1955-66.
Global analysis of the transcriptional network controlling Xenopus endoderm formation.
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 HHS , Wellcome 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 , R01 HD042572-04 NICHD NIH HHS , HD33002 NICHD NIH HHS , R01 HD042572-01 NICHD NIH HHS , HD42572 NICHD NIH HHS , R01 HD042572-03S1 NICHD NIH HHS , DK064403 NIDDK NIH HHS , R01 HD042572-02 NICHD NIH HHS , R01 HD042572-03 NICHD NIH HHS , Wellcome Trust , R01 HD042572 NICHD NIH HHS
Genes referenced: bix1.1 bix1.3 bix2 cdc42ep2 cxcr4 fbln1 foxa4 gata4 gjb1 gjb2 grip2 hao1 kirrel2 mixer nodal odc1 pnhd rnf38 slc12a3.2 sox17a t tmem150b unnamed wnt11 xk81a1
Morpholinos referenced: mixer MO1 mixer MO2 mixer MO3 sox17a MO1 sox17a MO2 sox17a MO3 sox17a MO4 sox17b.1 MO1
Article Images: [+] show captions
|Fig. 2. Validation of endoderm-enriched transcripts. (A) At stage 11, RNA was isolated from animal cap ectoderm (An), endoderm-enriched vegetal tissue (Veg) and mesendoderm enriched equatorial tissue (Eq), and assayed by RT-PCR to validate the expression profile of endoderm-enriched transcripts. The black histogram shows relative normalized expression from the array and the grey histograms show the relative expression levels in RT-PCR normalized to the loading control, ODC. Sox17α, Xbra and Epidermal keratin (Epi-K) are positive controls for the dissections. Fifty-one out of 54 genes were confirmed to have vegetal expression that was three times greater than animal cap expression (see Table S4 in the supplementary material) and 12 representative genes are shown [Xl.10408, Xl.13381, Xl.14891, Xl.15171, Xl.16410, Xl.16875 (Mixer-b), Xl.2410, Xl.2554, Xl.4709, Xl.4935, Xl.5999, Xl.8924 (gap junction subunit 6)]. (B) In situ hybridization to bisected gastrula with probes to the indicated genes validates their endoderm-enriched expression. Xl.1191 and Xl.15054 are not detected until neurula stage (st15).|