Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of Xenopus laevis early embryos to investigate the roles of Nodal, Mixer and Sox17 in endoderm formation

ABSTRACT: 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. While a linear epistatic pathway has been proposed, the precise hierarchical relationships between these factors and their downstream targets are largely unresolved. Here we 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 as well as over a hundred uncharacterized genes. Surprisingly only 10% of the endoderm transcriptome is regulated as predicted by the current linear model. We find that Nodals, 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, Sox17 and Bix1, 2, 4 and between Sox17 and Xnr4. We find that Mixer does not function primarily via Sox17 as previously proposed. This data provides a new insight into the complexity of endoderm formation and will serve as valuable resource for establishing a complete endoderm gene regulatory network. Experiment Overall Design: Define a set of transcripts with enriched expression in the gastrula endoderm of the Xenopus laevis embryo and determine how these are regulated by nodal signaling, Mixer and Sox17 using loss-of-function experiments. For more specific details see Sinner et al., (2006) Global analysis of the transcriptional network controlling Xenopus endoderm formation.

ORGANISM(S): Xenopus laevis

SUBMITTER: Aaron Zorn

PROVIDER: E-GEOD-4448 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Global analysis of the transcriptional network controlling Xenopus endoderm formation.

Sinner Débora D Kirilenko Pavel P Rankin Scott S Wei Eric E Howard Laura L Kofron Matthew M Heasman Janet J Woodland Hugh R HR Zorn Aaron M AM

Development (Cambridge, England) 20060501 10

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 analy ...[more]

PMID: 16651540

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Dataset Information

Transcription profiling of Xenopus laevis early embryos to investigate the roles of Nodal, Mixer and Sox17 in endoderm formation

Publications

Global analysis of the transcriptional network controlling Xenopus endoderm formation.

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