title: Genomic analysis of Xenopus organizer function.
abstract: BACKGROUND
  Studies of the Xenopus organizer have laid the foundation for our understanding of the conserved signaling pathways that pattern vertebrate embryos during gastrulation. The two primary activities of the organizer, BMP and Wnt inhibition, can regulate a spectrum of genes that pattern essentially all aspects of the embryo during gastrulation. As our knowledge of organizer signaling grows, it is imperative that we begin knitting together our gene-level knowledge into genome-level signaling models. The goal of this paper was to identify complete lists of genes regulated by different aspects of organizer signaling, thereby providing a deeper understanding of the genomic mechanisms that underlie these complex and fundamental signaling events.
  
  
  RESULTS
  To this end, we ectopically overexpress Noggin and Dkk-1, inhibitors of the BMP and Wnt pathways, respectively, within ventral tissues. After isolating embryonic ventral halves at early and late gastrulation, we analyze the transcriptional response to these molecules within the generated ectopic organizers using oligonucleotide microarrays. An efficient statistical analysis scheme, combined with a new Gene Ontology biological process annotation of the Xenopus genome, allows reliable and faithful clustering of molecules based upon their roles during gastrulation. From this data, we identify new organizer-related expression patterns for 19 genes. Moreover, our data sub-divides organizer genes into separate head and trunk organizing groups, which each show distinct responses to Noggin and Dkk-1 activity during gastrulation.
  
  
  CONCLUSIONS
  Our data provides a genomic view of the cohorts of genes that respond to Noggin and Dkk-1 activity, allowing us to separate the role of each in organizer function. These patterns demonstrate a model where BMP inhibition plays a largely inductive role during early developmental stages, thereby initiating the suites of genes needed to pattern dorsal tissues. Meanwhile, Wnt inhibition acts later during gastrulation, and is essential for maintenance of organizer gene expression throughout gastrulation, a role which may depend on its ability to block the expression of a host of ventral, posterior, and lateral fate-specifying factors.
authors.affiliation: Department of Genetics, Stanford University, Stanford, California, USA. alhufton@stanford.edu
authors.forename: Andrew L
authors.initials: AL
authors.lastname: Hufton
authors.forename: Arunachalam
authors.initials: A
authors.lastname: Vinayagam
authors.forename: Sándor
authors.initials: S
authors.lastname: Suhai
authors.forename: Julie C
authors.initials: JC
authors.lastname: Baker
mesh_terms: D000818:Animals; D001368:Axis, Cervical Vertebra / Q000196:embryology / Q000378:metabolism; D019521:Body Patterning / Q000235:genetics*; D002352:Carrier Proteins / Q000235:genetics / Q000378:metabolism; D004625:Embryo, Nonmammalian / Q000196:embryology / Q000378:metabolism; D005260:Female; D018507:Gene Expression Regulation, Developmental / Q000235:genetics*; D016678:Genome / Q000235:genetics*; D023281:Genomics; D036341:Intercellular Signaling Peptides and Proteins / Q000235:genetics / Q000378:metabolism; D005810:Multigene Family / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D014158:Transcription, Genetic / Q000235:genetics; D029867:Xenopus Proteins / Q000235:genetics / Q000378:metabolism; D014982:Xenopus laevis / Q000196:embryology* / Q000235:genetics*; D000099176:Noggin Protein
chemical_list: D002352:Carrier Proteins; D036341:Intercellular Signaling Peptides and Proteins; D029867:Xenopus Proteins; D000099176:Noggin Protein; C110182:dkk1 protein, Xenopus