XB-ART-35766Dev Dyn June 1, 2007; 236 (6): 1633-49.
Xenopus cDNA microarray identification of genes with endodermal organ expression.
The endoderm is classically defined as the innermost layer of three Metazoan germ layers. During organogenesis, the endoderm gives rise to the digestive and respiratory tracts as well as associated organs such as the liver, pancreas, and lung. At present, however, how the endoderm forms the variety of cell types of digestive and respiratory tracts as well as the budding organs is not well understood. In order to investigate the molecular basis and mechanism of organogenesis and to identify the endodermal organ-related marker genes, we carried out microarray analysis using Xenopus cDNA chips. To achieve this goal, we isolated the Xenopus gut endoderm from three different stages of Xenopus organogenesis, and separated each stage of gut endoderm into anterior and posterior regions. Competitive hybridization of cDNA between the anterior and posterior endoderm regions, to screen genes that specifically expressed in the major organs, revealed 915 candidates. We then selected 104 clones for in situ hybridization analysis. Here, we report the identification and expression patterns of the 104 Xenopus endodermal genes, which would serve as useful markers for studying endodermal organ development.
PubMed ID: 17474120
Article link: Dev Dyn
Genes referenced: a2m a2ml1 ag1 anxa1.1 apoe atp1b3 bmpr1a btf3 c8b ca2 cd82 cers2 cers3 cfap52 cldn4 cnfn.1 col4a5 crebrf ddx3x desi2 dstn entpd2 epcam etv1 fetub fst fzd7 gata6 gpd2 hdac1 hes4 hmgn1 hmgn2 hrg hspd1 iars1 id4 ids ift88 impdh2 jund kng1 mafb meis1 msn myc ndufaf3 nom1 nr2f2 odc1 oxct1 pfkm rab3d rfx3 rpl6 sec61b sema6d sephs1 serbp1 serpinb10 sfrp1 slc6a14.2 sox2 stard10 tbx2 tspan1 tubb usf1 xbp1 zbtb46
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|Figure 3. Genes expressed in the oesophagus and stomach of Xenopus gut endoderm from stages 42-45. In situ hybridization was performed with each antisense probe. The nomenclature is base on NIBB database ID numbers.|
|Figure 4. Genes expressed in the lung of Xenopus gut endoderm from stages 41-42.|
|Figure 5. Genes expressed in the pancreas and other organs of Xenopus gut endoderm from stages 42-45.|
|Figure 6. Genes expressed in the liver of Xenopus gut endoderm from stages 41-44.|
|Figure 7. Genes expressed in the liver and other organs of Xenopus gut endoderm from stages 41-44. [curators notes: gene IDs used here are based on geneome annoations for X laevis as of August 2019: XL060d04/Lass2 = cers3; XL074b17/XBP-1=xbp1; XL078a19/Fetuin-like = fetub; XL084k13/Btbd4 = zbtb46; ; XL087p03/transposase= gene ID uncertain, not curated; XL109f17/A2M = a2ml1]|
|Figure 8. Genes expressed in the gall bladder and other organs of Xenopus gut endoderm from stages 42-44.|
|Figure 9. Genes expressed in the foregut region of Xenopus gut endoderm from stages 41-45.|
|rfx3 (regulatory factor X, 3) gene expression in Xenopus laevis embryo, NF stage 42-45, dissected whole gut tube, as assayed by in situ hybridization.|
|Figure 1. A: Experimental approach. The Xenopus gut endoderms is isolated from three different stages of embryos during Xenopus organogenesis (St. 30, 39, and 46), and separated into anterior and posterior regions. Then, three independent microarray experiments were performed, and the transcriptional difference between anterior and posterior endoderm was analyzed. Anterior endoderm samples were labeled with Cy5 and posterior endoderm samples were labeled with Cy3, and hybridized to the same slide simultaneously. B: Illustrated anatomy of Xenopus gut endoderm. The drawings are adapted from Zorn and Mason (2001).Download figure to PowerPoint|
|Fig. 10. Genes expressed in the intestine of Xenopus gut endoderm from NF stages 41-44.|