Acquisition of lineage specific fate depends on the well orchestrated performance of 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 dynamic structural changes of chromatin are achieved by the actions of two classes of enzymes: ATP-dependent chromatin remodelers, and histone modifying enzymes. The enzymes are members of multi-protein complexes that operate to activate or repress transcription depending on the composition of proteins in the operating complexes. It is fully appreciated now that mechanisms triggering changes of chromatin structure are an integral part of the developmental program of the stem cells. 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.