The pluripotency of embryonic stem (ES) cells is the result of a highly dynamic equilibrium that is controlled by a complex network of transcription factors that confer unique transcriptional properties to ES cells. Regulation of gene expression appears to correlate with the presence of dual chromatin marks called bivalent domains at the promoters of poised developmental genes. These marks keep differentiation genes silenced but poised and ready to be activated or permanently repressed during differentiation. The process of tissue fate specification is initiated by various signalling molecules that directly impact the dynamic equilibrium of ES cells, particularly on the bivalent domains, inclining and predisposing the balance towards a particular lineage. In here we summarized current knowledge on how different transcription factors and signalling molecules impact on the epigenetic status of ES cells and in turn how this guides the process of mesoderm specification.