title: Global analysis of the transcriptional network controlling Xenopus 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. 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.
authors.affiliation: Division of Developmental Biology, Cincinnati Children's Hospital Research Foundation and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45299, USA.
authors.forename: Débora
authors.initials: D
authors.lastname: Sinner
authors.forename: Pavel
authors.initials: P
authors.lastname: Kirilenko
authors.forename: Scott
authors.initials: S
authors.lastname: Rankin
authors.forename: Eric
authors.initials: E
authors.lastname: Wei
authors.forename: Laura
authors.initials: L
authors.lastname: Howard
authors.forename: Matthew
authors.initials: M
authors.lastname: Kofron
authors.forename: Janet
authors.initials: J
authors.lastname: Heasman
authors.forename: Hugh R
authors.initials: HR
authors.lastname: Woodland
authors.forename: Aaron M
authors.initials: AM
authors.lastname: Zorn
mesh_terms: D000818:Animals; D004625:Embryo, Nonmammalian; D004707:Endoderm / Q000166:cytology* / Q000378:metabolism; D005775:Gastrula; D018507:Gene Expression Regulation, Developmental; D017403:In Situ Hybridization; D008845:Microinjections; D020411:Oligonucleotide Array Sequence Analysis; D016376:Oligonucleotides, Antisense / Q000494:pharmacology; D009924:Organ Culture Techniques; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic; D014981:Xenopus / Q000196:embryology* / Q000235:genetics / Q000378:metabolism*; D029867:Xenopus Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D016376:Oligonucleotides, Antisense; D014157:Transcription Factors; D029867:Xenopus Proteins