title: Genomic targets of Brachyury (T) in differentiating mouse embryonic stem cells.
abstract: BACKGROUND
  The T-box transcription factor Brachyury (T) is essential for formation of the posterior mesoderm and the notochord in vertebrate embryos. Work in the frog and the zebrafish has identified some direct genomic targets of Brachyury, but little is known about Brachyury targets in the mouse.
  
  
  RESULTS
  Here we use chromatin immunoprecipitation and mouse promoter microarrays to identify targets of Brachyury in embryoid bodies formed from differentiating mouse ES cells. The targets we identify are enriched for sequence-specific DNA binding proteins and include components of signal transduction pathways that direct cell fate in the primitive streak and tailbud of the early embryo. Expression of some of these targets, such as Axin2, Fgf8 and Wnt3a, is down regulated in Brachyury mutant embryos and we demonstrate that they are also Brachyury targets in the human. Surprisingly, we do not observe enrichment of the canonical T-domain DNA binding sequence 5'-TCACACCT-3' in the vicinity of most Brachyury target genes. Rather, we have identified an (AC)(n) repeat sequence, which is conserved in the rat but not in human, zebrafish or Xenopus. We do not understand the significance of this sequence, but speculate that it enhances transcription factor binding in the regulatory regions of Brachyury target genes in rodents.
  
  
  CONCLUSIONS
  Our work identifies the genomic targets of a key regulator of mesoderm formation in the early mouse embryo, thereby providing insights into the Brachyury-driven genetic regulatory network and allowing us to compare the function of Brachyury in different species.
authors.affiliation: Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Amanda L
authors.initials: AL
authors.lastname: Evans
authors.forename: Tiago
authors.initials: T
authors.lastname: Faial
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Gilchrist
authors.forename: Thomas
authors.initials: T
authors.lastname: Down
authors.forename: Ludovic
authors.initials: L
authors.lastname: Vallier
authors.forename: Roger A
authors.initials: RA
authors.lastname: Pedersen
authors.forename: Fiona C
authors.initials: FC
authors.lastname: Wardle
authors.forename: James C
authors.initials: JC
authors.lastname: Smith
mesh_terms: D000818:Animals; D060466:Axin Protein / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D015153:Blotting, Western; D002454:Cell Differentiation; D002460:Cell Line; D002478:Cells, Cultured; D004622:Embryo, Mammalian / Q000166:cytology / Q000196:embryology / Q000378:metabolism; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism*; D005326:Fetal Proteins / Q000235:genetics / Q000378:metabolism*; D051524:Fibroblast Growth Factor 8 / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D006801:Humans; D017403:In Situ Hybridization; D051379:Mice; D057507:Mice, 129 Strain; D018345:Mice, Knockout; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding; D011506:Proteins / Q000235:genetics / Q000378:metabolism*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D020825:T-Box Domain Proteins / Q000235:genetics / Q000378:metabolism*; D013997:Time Factors; D060509:Wnt3A Protein / Q000235:genetics / Q000378:metabolism; D000098908:Brachyury Protein
chemical_list: D060466:Axin Protein; D005326:Fetal Proteins; D051524:Fibroblast Growth Factor 8; D011506:Proteins; D020825:T-Box Domain Proteins; D060509:Wnt3A Protein; D000098908:Brachyury Protein; C111729:Axin2 protein, mouse; C496457:Fgf8 protein, mouse; C555511:Wnt3a protein, mouse