Utilizing adult stem cells for regenerative medicine of skeletal tissues requires the development of molecular and biochemical tools that will allow isolation of these cells and direction of their differentiation towards a desired lineage and tissue formation. Stem cell commitment and fate decision into specialized functional cells involve coordinated activation and silencing of lineage-specific genes. Transcription factors and chromatin-remodeling proteins are key players in the control process of lineage commitment and differentiation during embryogenesis and adulthood. Transcription factors act in cooperation with co-regulator proteins to generate tissue-specific responses that elicits the tissue specific gene expression. Consequently, one of the main challenges of today's research is to characterize molecular pathways that coordinate the lineage-specific differentiation. Epigenetic regulation includes chromatin remodeling that control structural changes of DNA required for the binding of transcription factors to promoter regions. Revealing the mechanisms of action of such factors will provide understanding of how transcription and chromatin regulatory factors function together to regulate stem cell lineage fate decision.