Acquisition of lineage specific fate depends on the well orchestrated performance of master transcription factors and on dynamic changes in chromatin structure that account for epigenetic regulation. Epigenetic mechanisms regulate transcription at the promoter level and involve the recruitment of numerous chromatin modifiers in order to permit tissue-selective gene transcription. The dynamics of chromatin structural changes are achieved by the actions of two classes of enzymes: ATP-dependent chromatin remodelers, and histone modifying enzymes. The enzymes are partners in multi-protein complexes that activate or repress transcription depending on the composition of the protein complex. It is fully appreciated now that mechanisms triggering changes in chromatin structure are an integral in determining the stem cell fate. Elucidating the nature of cross talk between chromatin remodelers and master genes is important for identifying pathways that govern stem cell fate and lineage decision.