Using chromatin immunoprecipitation combined with genomic microarrays we have identified targets of No tail (Ntl), a zebrafish Brachyury ortholog that plays a central role in mesoderm formation. We show that Ntl regulates a downstream network of other transcription factors and identify an in vivo Ntl binding site that resembles the consensus T-box binding site (TBS) previously identified by in vitro studies. We show that the notochord-expressed gene floating head ( flh) is a direct transcriptional target of Ntl and that a combination of TBSs in the flh upstream region are required for Ntl-directed expression. Using our genome-scale data we have assembled a preliminary gene regulatory network that begins to describe mesoderm formation and patterning in the early zebrafish embryo.brachyury ͉ chromatin immunopreciptitation ͉ microarray E mbryonic development proceeds through a series of progressively more restricted cell states in which sets of state-specific genes are expressed in a finely controlled temporal and spatial order. This coordination of gene expression is brought about by the integration of signaling inputs and binding of transcription factors at cis-regulatory modules (CRMs) associated with target genes, and can be described by a gene regulatory network (GRN). Such GRNs have been useful in understanding how development proceeds in the early lineages of sea urchins and ascidians (1, 2). However, although GRNs using data from single gene studies have been used to describe aspects of Xenopus mesendoderm and lamprey neural crest development (3, 4) a systematic approach to building a GRN by genome-scale analysis has not yet been used to describe early cell fate commitment in developing vertebrate embryos. Understanding how transcriptional regulation drives cell fate commitment in vertebrates is essential not only in understanding their development, but also for informing future efforts to recapitulate cell restriction to different tissue lineages for stem cell-based replacement therapies (5). We have thus set out to assemble a GRN that can describe vertebrate mesoderm development using zebrafish as a model system to identify targets of a key transcriptional regulator, No tail (Ntl).Ntl is a zebrafish ortholog of Brachyury, a T-domain transcription factor that is expressed as an early response to mesoderm induction and plays a central role in mesoderm development in all vertebrates. For instance, studies in mice, Xenopus, and zebrafish reveal that Brachyury orthologs influence many aspects of mesoderm specification and patterning, being required for formation of the notochord and posterior somites, for normal cell movements during gastrulation and tail outgrowth, and for establishment of left-right asymmetry (reviewed in refs. 6, 7).Here, we use chromatin immunoprecipitation combined with zebrafish genomic microarrays (ChIP-chip) to survey binding of Ntl at promoter regions. We show that Ntl binds the promoters of transcription factors implicated in posterior identity, muscle specification, cell movements, ...