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Previous studies in Xenopus have shown that forced expression of Nodal signaling can change ectodermal cells to a mesodermal fate by the early gastrula stage, suggesting mesodermal competence in early ectoderm cells. This mesodermal competence in ectodermal cells has been shown to be regulated at the level of nucleocytoplasmic localization of Smad2 in Xenopus. However, the regulation of mesodermal competence through epigenetic mechanisms has not been fully elucidated. Here, we used a constitutively active form of zebrafish Smad2 (Smad2ca) to overcome the inhibition of Nodal signaling via the nuclear exclusion of Smad2. While heat-shock-dependent expression of Smad2ca at 5 h post fertilization (hpf) induced ectopic expression of mesendodermal genes in zebrafish ectodermal cells, responsiveness to Smad2ca was lost by 7 hpf. Chromatin immunoprecipitation-quantitative PCR analyses revealed that in ectodermal cells, levels of H3K27me3, but not H3K9me3, at both transcriptional start site (TSS) and 3'-flanking regions of mesendodermal genes at 9 hpf were markedly higher than those at 5 hpf. In contrast to mesendodermal genes, the levels of H3K27me3 at the TSS, but not 3'-flanking regions, of ectodermal genes remained low in ectodermal cells even at 9 hpf. We also found that chemical inhibition of H3K27me3 modification was able to recover the mesendodermal competence in ectodermal cells at 7 hpf, but not at 10 hpf. Taken together, our results suggest that the mesendodermal competence in zebrafish ectodermal cells is restricted by multiple mechanisms, including upregulation of H3K27me3 levels at the TSS of mesendodermal genes during early gastrulation. [ABSTRACT FROM AUTHOR]